[2025-07-28 19:56:49.280 UTC] Starting pipeline: WGSA2, Current time: 2025-07-28 19:56
[2025-07-28 19:56:49.280 UTC] Pipeline version: 0.1.8, nephele_pipeline_utils version: 0.1.55
[2025-07-28 19:56:49.283 UTC] Pipeline arguments:
	--decontaminate_db_path /dbs/wgsa2/decontam_db/decontam_human+mouse_db
 	--classification_db_name plusPFV
 	--classification_db_path /dbs/wgsa2/classification_db/plusPFV_Mar2023
 	--eggnog_db_path /dbs/wgsa2/eggnog_data
 	--annotations_type ko
 	--annotations_map_db_path /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt
 	--annotations_hrr_db_path /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt
 	--krona_tax_db_path /dbs/wgsa2/KronaTools_taxonomy
 	--amrfind True
 	--tax_genes True
 	--tax_scaffolds True
 	--mag True
 	--include_ted_files False
 	--trim_filter False
 	--average_read_quality 10
 	--min_read_length 60
 	--trim_of_5 20
 	--trim_of_3 15
 	--mapping_file_path /inputs/mapping_file.csv
 	--outputs_dir_path /outputs
[2025-07-28 19:56:49.283 UTC] Pipeline initialized with 4 samples
[2025-07-28 19:56:49.283 UTC] Samples ids: S1_GItract_HiSeq_cami, S28_Skin_HiSeq_cami, S9_Air_HiSeq_cami, S6_Oral_HiSeq_cami
[2025-07-28 19:56:49.283 UTC] Samples info:
[2025-07-28 19:56:49.283 UTC] {'#SampleID': 'S1_GItract_HiSeq_cami', 'TreatmentGroup': 'Gitract', 'ForwardFastqFile': '/inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz', 'ReverseFastqFile': '/inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz'}
[2025-07-28 19:56:49.283 UTC] {'#SampleID': 'S28_Skin_HiSeq_cami', 'TreatmentGroup': 'Skin', 'ForwardFastqFile': '/inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz', 'ReverseFastqFile': '/inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz'}
[2025-07-28 19:56:49.283 UTC] {'#SampleID': 'S9_Air_HiSeq_cami', 'TreatmentGroup': 'Air', 'ForwardFastqFile': '/inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz', 'ReverseFastqFile': '/inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz'}
[2025-07-28 19:56:49.283 UTC] {'#SampleID': 'S6_Oral_HiSeq_cami', 'TreatmentGroup': 'Oral', 'ForwardFastqFile': '/inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz', 'ReverseFastqFile': '/inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz'}
[2025-07-28 19:56:49.289 UTC] Starting WGSA pipeline...
[2025-07-28 19:56:49.289 UTC] snakemake -p --cores --nocolor --use-conda --resources mem_gb=184 --directory /outputs/tmp --config num_cpus=48 map_file=/inputs/mapping_file.csv output_dir=/outputs total_mem_gb=184 tmp_dir=/outputs/tmp trim_filter=False include_ted_files=False ted_file_name=TED.tar biom_file_name=for_analyze_with_microbiomedb.biom decontaminate=/dbs/wgsa2/decontam_db/decontam_human+mouse_db classification_db_name=plusPFV classification_db=/dbs/wgsa2/classification_db/plusPFV_Mar2023 amrfind=True eggnog_db=/dbs/wgsa2/eggnog_data annotations_type=ko annotations_map=/dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt annotations_hrr=/dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt tax_genes=True krona_tax_db=/dbs/wgsa2/KronaTools_taxonomy tax_scaffolds=True mag=True samples='{"S1_GItract_HiSeq_cami": {"f": "/inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz", "r": "/inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz"}, "S28_Skin_HiSeq_cami": {"f": "/inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz", "r": "/inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz"}, "S9_Air_HiSeq_cami": {"f": "/inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz", "r": "/inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz"}, "S6_Oral_HiSeq_cami": {"f": "/inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz", "r": "/inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz"}}'
Dependencies:
SPAdes genome assembler v4.0.0 [metaSPAdes mode]
bowtie2 version 2.5.4
samtools 1.21
MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2:2.17 (Bioconda); 2024-06-20T09:50:37)
Prodigal V2.6.3: February, 2016
checkm-genome 1.2.2
KronaTools 2.8.1  ktImportText 
# MinPath (current version: 1.6)
VERSE v0.1.5
Kraken version 2.1.3
AMRFinder version 3.12.8
emapper-2.1.6
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Snakemake version 7.32.4
Command line: /opt/conda/bin/metaspades.py	-1	/outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz	-2	/outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz	--memory	184	--tmp-dir	/outputs/tmp	-o	/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb	-t	16	--only-assembler	

System information:
  SPAdes version: 4.0.0
  Python version: 3.10.12
  OS: Linux-6.8.0-1021-aws-x86_64-with-glibc2.31

Output dir: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz']
      right reads: ['/outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /outputs/tmp
  Threads: 16
  Memory limit (in Gb): 184


======= SPAdes pipeline started. Log can be found here: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/spades.log

/outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz: max reads length: 150
/outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz: max reads length: 150

Reads length: 150


===== Before start started. 


===== Assembling started. 


===== K21 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/config.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/mda_mode.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/meta_mode.info

  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/config.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/mda_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/configs/meta_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.001     1M / 17M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/dataset.info") with K=21
  0:00:00.001     1M / 17M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     1M / 17M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.001     1M / 17M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.001     1M / 17M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.001     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.001     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.001     1M / 17M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 17M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 17M   INFO    General                 (read_converter.cpp        :  78)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     1M / 17M   INFO    General                 (read_converter.cpp        :  99)   Converting paired reads
  0:00:00.122    82M / 82M   INFO    General                 (binary_converter.cpp      : 127)   16384 reads processed
  0:00:00.197    82M / 82M   INFO    General                 (binary_converter.cpp      : 143)   24829 reads written
  0:00:00.201    46M / 49M   INFO    General                 (read_converter.cpp        : 113)   Converting single reads
  0:00:00.211    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.211    46M / 49M   INFO    General                 (read_converter.cpp        : 119)   Converting merged reads
  0:00:00.217    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.219     1M / 49M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.220     1M / 49M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.220     1M / 49M   INFO    General                 (construction.cpp          : 156)   Average read length 143.041
  0:00:00.220     1M / 49M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.221     1M / 49M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.221     1M / 49M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.221     1M / 49M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.221     1M / 49M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
mimalloc: warning: thread 0x74af2a000700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74af24400000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x74af2aa00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74af1a400000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x74af2e600700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74af16400000, alignment: 67108864, commit: 1)
  0:00:00.319  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 99316 reads
  0:00:00.321     1M / 87M   INFO    General                 (kmer_splitters.hpp        : 134)   Used 99316 reads
  0:00:00.323     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.550     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5504414 kmers in total.
  0:00:00.551     1M / 87M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.552     1M / 87M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.552     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.553     1M / 87M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.553     1M / 87M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.553     1M / 87M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
  0:00:00.710  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5504414 kmers
  0:00:00.710  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5504414 kmers.
  0:00:00.712     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.727     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5524518 kmers in total.
  0:00:00.727     2M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.772     6M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5524518 kmers, 4112656 bytes occupied (5.9555 bits per kmer).
  0:00:00.773     6M / 176M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.836    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.964    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.969    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.969    11M / 176M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.969    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:01.057    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 17740
  0:00:01.058    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 17787
  0:00:01.063    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   413625 22-mers were removed by early tip clipper
  0:00:01.063    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.064    12M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:01.204    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 62011 sequences extracted
  0:00:01.301    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.334    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 15 loops collected
  0:00:01.343    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.344    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.344    15M / 176M  INFO    General                 (debruijn_graph_constructor: 516)   Total 124052 edges to create
  0:00:01.344    20M / 176M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.415    22M / 176M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.417    22M / 176M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.418    23M / 176M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.418    23M / 176M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.418    23M / 176M  INFO    General                 (debruijn_graph_constructor: 542)   Total 82130 vertices to create
  0:00:01.418    31M / 176M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.519    27M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.519    27M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.564    31M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5504414 kmers, 4098312 bytes occupied (5.9564 bits per kmer).
  0:00:01.577    52M / 176M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.671    52M / 176M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.780    53M / 176M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 124021 edges
  0:00:01.807    16M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.807    16M / 176M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.807    16M / 176M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.807    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.810    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.810    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.815    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 239 times
  0:00:01.815    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.867    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 7091 times
  0:00:01.868    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.890    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 22714 times
  0:00:01.891    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.891    14M / 176M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.891    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.891    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.891    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.893    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 210 times
  0:00:01.893    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.943    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 3089 times
  0:00:01.943    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.945    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.945    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.945    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 57 times
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 38 times
  0:00:01.947    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.947    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 3 times
  0:00:01.948    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.948    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 6 times
  0:00:01.948    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.948    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 16 times
  0:00:01.948    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.948    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.950    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 3 times
  0:00:01.950    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.951    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.951    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.953    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.953    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 6
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.953    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.954    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.954    14M / 176M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.954    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.954    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.956    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 12 times
  0:00:01.956    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.957    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.957    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.959    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.959    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.000    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.000    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.001    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.001    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.003    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 9 times
  0:00:02.003    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.004    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:02.004    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.006    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.006    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.007    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:02.007    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.009    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.009    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.011    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.011    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.051    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.051    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.053    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.053    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.054    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:02.054    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.056    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.056    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.057    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.057    14M / 176M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:02.058    14M / 176M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:02.062    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:02.063    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 331 times
  0:00:02.064    14M / 176M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:02.064    14M / 176M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.32478
  0:00:02.065    14M / 176M  INFO    General                 (simplification.cpp        : 510)     Total length = 1946343
  0:00:02.066    14M / 176M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 242
  0:00:02.066    14M / 176M  INFO    General                 (simplification.cpp        : 512)     Edges: 15529
  0:00:02.066    14M / 176M  INFO    General                 (simplification.cpp        : 513)     Vertices: 30202
  0:00:02.066    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:02.066    14M / 176M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/simplified_contigs"
  0:00:02.074    18M / 176M  INFO    General                 (binary_converter.cpp      : 143)   7766 reads written
  0:00:02.077    14M / 176M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:02.082     1M / 176M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 2 seconds

===== K21 finished. 


===== K33 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/config.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/mda_mode.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/meta_mode.info

  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/config.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/mda_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/configs/meta_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/dataset.info") with K=33
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.000     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 17M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.000     1M / 17M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 17M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 17M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 17M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21/simplified_contigs
  0:00:00.263     1M / 17M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.263     1M / 17M   INFO    General                 (construction.cpp          : 156)   Average read length 143.041
  0:00:00.263     1M / 17M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.263     1M / 17M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.263     1M / 17M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.263     1M / 17M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.263     1M / 17M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x736e17800700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x736e0c200000, alignment: 67108864, commit: 1)
  0:00:00.390  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 114848 reads
  0:00:00.392     1M / 147M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 114848 reads
  0:00:00.397     1M / 147M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.410     1M / 147M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5213761 kmers in total.
  0:00:00.411     1M / 147M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.412     1M / 147M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.412     1M / 147M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.413     2M / 147M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.413     2M / 147M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.413     2M / 147M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.584  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5213761 kmers
  0:00:00.585  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5213761 kmers.
  0:00:00.586     2M / 291M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.606     2M / 291M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5240739 kmers in total.
  0:00:00.606     2M / 291M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.654     6M / 291M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5240739 kmers, 3905432 bytes occupied (5.96165 bits per kmer).
  0:00:00.654     6M / 291M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.769    11M / 291M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.899    11M / 291M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.905    11M / 291M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.905    11M / 291M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.905    11M / 291M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:00.993    12M / 291M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 18332
  0:00:00.994    12M / 291M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 18371
  0:00:01.000    11M / 291M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   526761 34-mers were removed by early tip clipper
  0:00:01.000    11M / 291M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.001    11M / 291M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:01.128    14M / 291M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 45357 sequences extracted
  0:00:01.223    14M / 291M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.254    14M / 291M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 8 loops collected
  0:00:01.264    14M / 291M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.265    14M / 291M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.265    14M / 291M  INFO    General                 (debruijn_graph_constructor: 516)   Total 90730 edges to create
  0:00:01.265    17M / 291M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.316    19M / 291M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.317    19M / 291M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.318    20M / 291M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.319    20M / 291M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.319    20M / 291M  INFO    General                 (debruijn_graph_constructor: 542)   Total 72343 vertices to create
  0:00:01.319    26M / 291M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.404    23M / 291M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.404    23M / 291M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.449    27M / 291M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5213761 kmers, 3885984 bytes occupied (5.96266 bits per kmer).
  0:00:01.463    47M / 291M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.533    47M / 291M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.638    47M / 291M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 90723 edges
  0:00:01.675    13M / 291M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.675    13M / 291M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.675    13M / 291M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.675    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.677    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 1 times
  0:00:01.677    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.685    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 243 times
  0:00:01.685    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.708    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 2946 times
  0:00:01.709    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.728    13M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 24075 times
  0:00:01.728    12M / 291M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.728    12M / 291M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.728    12M / 291M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.728    12M / 291M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.728    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.729    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 118 times
  0:00:01.729    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.744    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1423 times
  0:00:01.744    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.745    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.745    12M / 291M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.745    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.745    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 12 times
  0:00:01.745    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 8 times
  0:00:01.746    12M / 291M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 7 times
  0:00:01.746    12M / 291M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.746    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.747    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.747    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.748    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:01.748    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.749    12M / 291M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.749    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.750    12M / 291M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.750    12M / 291M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.750    12M / 291M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.750    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.751    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 4 times
  0:00:01.751    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.752    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.752    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.753    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.753    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.792    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 11 times
  0:00:01.792    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.793    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.793    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.793    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 1 times
  0:00:01.793    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.794    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.794    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.795    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.795    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.796    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.796    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.797    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.797    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.798    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.798    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.837    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.837    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.837    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.837    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.838    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.838    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.839    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.839    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.840    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.840    12M / 291M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:01.841    12M / 291M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:01.843    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:01.844    12M / 291M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 140 times
  0:00:01.844    12M / 291M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:01.844    12M / 291M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.16874
  0:00:01.844    12M / 291M  INFO    General                 (simplification.cpp        : 510)     Total length = 1825081
  0:00:01.845    12M / 291M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 233
  0:00:01.845    12M / 291M  INFO    General                 (simplification.cpp        : 512)     Edges: 14638
  0:00:01.845    12M / 291M  INFO    General                 (simplification.cpp        : 513)     Vertices: 28974
  0:00:01.845    12M / 291M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:01.845    12M / 291M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/simplified_contigs"
  0:00:01.851    15M / 291M  INFO    General                 (binary_converter.cpp      : 143)   7319 reads written
  0:00:01.853    12M / 291M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:01.856     1M / 291M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 1 seconds

===== K33 finished. 


===== K55 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/config.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/mda_mode.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/meta_mode.info

  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/config.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/mda_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/configs/meta_mode.info"
  0:00:00.000     1M / 17M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/dataset.info") with K=55
  0:00:00.000     1M / 17M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution enabled
  0:00:00.000     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 17M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 17M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.000     1M / 17M   INFO    General                 (pipeline.cpp              : 245)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     1M / 17M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 17M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 17M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 17M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/simplified_contigs
  0:00:00.018     1M / 17M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.018     1M / 17M   INFO    General                 (construction.cpp          : 156)   Average read length 143.041
  0:00:00.018     1M / 17M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.018     1M / 17M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.018     1M / 17M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.018     1M / 17M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.018     1M / 17M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x74e466000700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74e45be00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x74e460600700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74e45be00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x74e461a00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x74e45be00000, alignment: 67108864, commit: 1)
  0:00:00.128  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 113954 reads
  0:00:00.130     2M / 127M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 113954 reads
  0:00:00.134     2M / 127M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.146     1M / 127M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4502970 kmers in total.
  0:00:00.146     1M / 127M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.148     1M / 127M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.148     1M / 127M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.148     2M / 127M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.149     2M / 127M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.149     2M / 127M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.318  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 4502970 kmers
  0:00:00.318  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 4502970 kmers.
  0:00:00.320     2M / 246M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.342     2M / 246M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4536734 kmers in total.
  0:00:00.342     2M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.390     5M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4536734 kmers, 3397432 bytes occupied (5.99097 bits per kmer).
  0:00:00.390     5M / 246M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.502    10M / 246M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.633    10M / 246M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.641     9M / 246M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.643    10M / 246M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.802    14M / 246M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 67793 sequences extracted
Command line: /opt/conda/bin/metaspades.py	-1	/outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz	-2	/outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz	--memory	184	--tmp-dir	/outputs/tmp	-o	/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb	-t	16	--only-assembler	

System information:
  SPAdes version: 4.0.0
  Python version: 3.10.12
  OS: Linux-6.8.0-1021-aws-x86_64-with-glibc2.31

Output dir: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz']
      right reads: ['/outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /outputs/tmp
  Threads: 16
  Memory limit (in Gb): 184


======= SPAdes pipeline started. Log can be found here: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/spades.log

  0:00:00.919    13M / 246M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:00.947    14M / 246M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 0 loops collected
  0:00:00.957    13M / 246M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:00.958    13M / 246M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:00.958    13M / 246M  INFO    General                 (debruijn_graph_constructor: 516)   Total 135586 edges to create
  0:00:00.958    19M / 246M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.033    21M / 246M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.034    21M / 246M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.036    22M / 246M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.037    22M / 246M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.037    22M / 246M  INFO    General                 (debruijn_graph_constructor: 542)   Total 101557 vertices to create
  0:00:01.037    32M / 246M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
/outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz: max reads length: 150
  0:00:01.156    28M / 246M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.156    28M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.197    31M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4502970 kmers, 3372592 bytes occupied (5.99176 bits per kmer).
  0:00:01.208    49M / 246M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.262    49M / 246M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
/outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz: max reads length: 150

Reads length: 150


===== Before start started. 


===== Assembling started. 


===== K21 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/config.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/mda_mode.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/dataset.info") with K=21
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.001     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.001     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.001     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  78)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  99)   Converting paired reads
  0:00:01.354    49M / 246M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 135586 edges
  0:00:01.389    19M / 246M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: early_gapcloser)
  0:00:01.393    32M / 246M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.407    34M / 246M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 103125 out of 135586, length: 7484477
  0:00:01.413    35M / 246M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 136266)
  0:00:01.435    35M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.150    82M / 82M   INFO    General                 (binary_converter.cpp      : 127)   16384 reads processed
  0:00:00.229    82M / 82M   INFO    General                 (binary_converter.cpp      : 143)   24832 reads written
  0:00:00.234    46M / 49M   INFO    General                 (read_converter.cpp        : 113)   Converting single reads
  0:00:01.568    38M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4287338 kmers, 3097312 bytes occupied (5.77946 bits per kmer).
  0:00:00.245    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.246    46M / 49M   INFO    General                 (read_converter.cpp        : 119)   Converting merged reads
  0:00:00.252    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.255     1M / 49M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.257     1M / 49M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.257     1M / 49M   INFO    General                 (construction.cpp          : 156)   Average read length 143.069
  0:00:00.257     1M / 49M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.257     1M / 49M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.257     1M / 49M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.257     1M / 49M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.257     1M / 49M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
  0:00:01.594    74M / 246M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
mimalloc: warning: thread 0x768d73a00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x768d6b600000, alignment: 67108864, commit: 1)
  0:00:01.654    74M / 246M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.673    76M / 246M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:00.362  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 99328 reads
  0:00:00.364     1M / 87M   INFO    General                 (kmer_splitters.hpp        : 134)   Used 99328 reads
  0:00:00.367     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:01.712    39M / 246M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.712    39M / 246M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.718    40M / 246M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 3990 tips collected, total 4036 connection candidates
  0:00:01.727    40M / 246M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 32 gaps after checking 4004 candidates
  0:00:01.730    39M / 246M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.735    19M / 246M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.735    19M / 246M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.735    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.738    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.738    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.795    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 11037 times
  0:00:01.795    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.802    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 574 times
  0:00:01.802    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with low flanking coverage
  0:00:01.822    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with low flanking coverage triggered 2559 times
  0:00:01.822    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.849    19M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 29685 times
  0:00:01.849    17M / 246M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Simplification (id: simplification_preliminary)
  0:00:01.849    17M / 246M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.849    17M / 246M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.849    17M / 246M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.849    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.860    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 2117 times
  0:00:01.860    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.862    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 9 times
  0:00:01.862    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.863    17M / 246M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.863    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 106 times
  0:00:01.864    17M / 246M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 2 times
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 1 times
  0:00:01.864    17M / 246M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.864    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.865    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.866    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.867    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.867    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.868    17M / 246M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.868    17M / 246M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.869    17M / 246M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: prelim_gapcloser)
  0:00:01.872    30M / 246M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.874    30M / 246M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 14623 out of 14646, length: 3078035
  0:00:01.875    30M / 246M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 136266)
  0:00:01.879    30M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.922    32M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1539619 kmers, 1112752 bytes occupied (5.78196 bits per kmer).
  0:00:01.926    44M / 246M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.944    44M / 246M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.992    44M / 246M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:02.001    32M / 246M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:02.002    32M / 246M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:02.003    32M / 246M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 593 tips collected, total 594 connection candidates
  0:00:02.004    32M / 246M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 2 gaps after checking 592 candidates
  0:00:02.006    32M / 246M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:00.676     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5470626 kmers in total.
  0:00:00.676     1M / 87M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:02.008    17M / 246M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Paired Information Counting (id: late_pair_info_count_preliminary)
  0:00:00.678     1M / 87M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.678     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.678     1M / 87M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.678     1M / 87M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.678     1M / 87M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
  0:00:02.021    22M / 246M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:02.021    22M / 246M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 136266)
  0:00:02.027    22M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.085    23M / 246M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1540454 kmers, 1113344 bytes occupied (5.7819 bits per kmer).
  0:00:02.088    35M / 246M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:02.108    35M / 246M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 1080 kmers to process
  0:00:02.108    35M / 246M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:02.108    35M / 246M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:02.108    35M / 246M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:02.109    35M / 246M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.109    35M / 246M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:00.854  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5470626 kmers
  0:00:00.855  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5470626 kmers.
  0:00:00.857     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.875     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5489156 kmers in total.
  0:00:00.875     2M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.935     6M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5489156 kmers, 4087488 bytes occupied (5.95718 bits per kmer).
  0:00:00.935     6M / 176M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:02.310   308M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.001    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:01.154    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:01.159    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:01.160    11M / 176M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:01.160    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:01.278    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 19368
  0:00:01.278    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 19401
  0:00:01.283    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   451159 22-mers were removed by early tip clipper
  0:00:01.283    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.285    11M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:01.422    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 62139 sequences extracted
  0:00:02.774   308M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:01.519    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:02.880   308M / 349M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6348
  0:00:02.881   308M / 349M  INFO    General                 (paired_info_utils.cpp     : 106)   11 paired reads (0.044303% of all) aligned to long edges
  0:00:01.551    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 9 loops collected
  0:00:02.881    35M / 349M  INFO    General                 (pair_info_count.cpp       : 188)     Insert size = 260.909, deviation = 33.6842, left quantile = 216, right quantile = 304, read length = 150
  0:00:02.887    35M / 349M  INFO    General                 (pair_info_count.cpp       : 203)   Filtering data for library #0
  0:00:02.887    35M / 349M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.888    36M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.560    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.561    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.561    15M / 176M  INFO    General                 (debruijn_graph_constructor: 516)   Total 124296 edges to create
  0:00:01.562    20M / 176M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:02.957    36M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:02.958    35M / 349M  INFO    General                 (pair_info_count.cpp       : 207)   Mapping library #0
  0:00:02.958    35M / 349M  INFO    General                 (pair_info_count.cpp       : 209)   Mapping paired reads (takes a while)
  0:00:02.958    35M / 349M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.958    35M / 349M  INFO    General                 (paired_info_utils.cpp     : 138)   Left insert size quantile 216, right insert size quantile 304, filtering threshold 1, rounding threshold 0
  0:00:02.961    49M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.631    22M / 176M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.632    22M / 176M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.634    23M / 176M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.635    23M / 176M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.635    23M / 176M  INFO    General                 (debruijn_graph_constructor: 542)   Total 80678 vertices to create
  0:00:01.635    30M / 176M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:03.032    49M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:03.036    36M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Distance Estimation (id: distance_estimation_preliminary)
  0:00:03.036    36M / 349M  INFO    General                 (distance_estimation.cpp   :  42)   Processing library #0
  0:00:03.036    36M / 349M  INFO    General                 (distance_estimation_utils.: 133)   Weight Filter Done
  0:00:03.036    36M / 349M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:03.039    36M / 349M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:03.039    36M / 349M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 14666
  0:00:03.043    34M / 349M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 436
  0:00:03.043    34M / 349M  INFO    General                 (distance_estimation_utils.: 139)   Refining clustered pair information
  0:00:03.044    34M / 349M  INFO    General                 (distance_estimation_utils.: 141)   The refining of clustered pair information has been finished
  0:00:03.044    34M / 349M  INFO    General                 (distance_estimation_utils.: 143)   Improving paired information
  0:00:03.046    34M / 349M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.048    34M / 349M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.048    34M / 349M  INFO    General                 (distance_estimation_utils.:  86)   Filling scaffolding index
  0:00:03.048    34M / 349M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:00:03.050    34M / 349M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:03.051    34M / 349M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 14690
  0:00:03.052    34M / 349M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 14690
  0:00:03.052    34M / 349M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:03.052    34M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Repeat Resolving (id: repeat_resolving_preliminary)
  0:00:03.052    34M / 349M  INFO    General                 (repeat_resolving.cpp      :  75)   Setting up preliminary path extend settings
  0:00:03.052    34M / 349M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:03.052    34M / 349M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:01.731    26M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.731    26M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:03.063    64M / 349M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:03.063    64M / 349M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 436
  0:00:03.064    65M / 349M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 436
  0:00:03.065    68M / 349M  INFO    General                 (extenders_logic.cpp       : 550)   Using 1 paired-end library
  0:00:03.065    68M / 349M  INFO    General                 (extenders_logic.cpp       : 551)   Using 1 paired-end scaffolding library
  0:00:03.065    68M / 349M  INFO    General                 (extenders_logic.cpp       : 552)   Using 0 single read libraries
  0:00:03.065    68M / 349M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 3
  0:00:03.065    68M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 7315 (0%)
  0:00:03.067    69M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 7315 (1%)
  0:00:03.069    69M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 7315 (3%)
  0:00:03.072    70M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 7315 (6%)
  0:00:03.074    71M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 732 paths from 7315 (10%)
  0:00:03.075    72M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 7315 (13%)
  0:00:03.078    74M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1464 paths from 7315 (20%)
  0:00:03.081    76M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 7315 (27%)
  0:00:03.082    77M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2196 paths from 7315 (30%)
  0:00:03.086    80M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2928 paths from 7315 (40%)
  0:00:03.090    83M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3660 paths from 7315 (50%)
  0:00:03.093    84M / 349M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 7315 (55%)
  0:00:03.094    85M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4392 paths from 7315 (60%)
  0:00:03.098    88M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5124 paths from 7315 (70%)
  0:00:03.102    91M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5856 paths from 7315 (80%)
  0:00:03.106    94M / 349M  INFO    General                 (path_extenders.cpp        :  36)   Processed 6588 paths from 7315 (90%)
  0:00:01.777    31M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5470626 kmers, 4074008 bytes occupied (5.95765 bits per kmer).
  0:00:03.117    68M / 349M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:03.117    68M / 349M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:03.120    68M / 349M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:03.121    68M / 349M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:01.791    52M / 176M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:03.124    68M / 349M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:03.124    68M / 349M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:03.138    97M / 349M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:03.146    64M / 349M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:01.871    52M / 176M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:03.255    64M / 349M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:03.255    64M / 349M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:03.255    64M / 349M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:03.259    64M / 349M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:03.259    64M / 349M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:03.262    64M / 349M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:03.262    64M / 349M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:03.263    63M / 349M  INFO    General                 (repeat_resolving.cpp      :  94)   Restoring initial path extend settings
  0:00:03.263    63M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.263    63M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/strain_graph.gfa"
  0:00:03.277    63M / 349M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:01.977    52M / 176M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 124277 edges
  0:00:03.311    96M / 349M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:03.323    63M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Second Phase Setup (id: second_phase_setup)
  0:00:03.323    63M / 349M  INFO    General                 (second_phase_setup.cpp    :  18)   Preparing second phase
  0:00:03.330    30M / 349M  INFO    General                 (second_phase_setup.cpp    :  25)   Moving preliminary contigs from "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.fasta" to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/first_pe_contigs.fasta"
  0:00:03.330    30M / 349M  INFO    General                 (second_phase_setup.cpp    :  37)   Ready to run second phase
  0:00:03.330    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:03.330    17M / 349M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:03.330    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.330    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:03.330    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.331    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.331    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.002    16M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:02.002    16M / 176M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:03.333    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 5 times
  0:00:02.002    16M / 176M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:03.333    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.002    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.334    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.334    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.334    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:03.334    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.335    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.335    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.005    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:02.005    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:03.336    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.336    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.337    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.338    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: late_gapcloser)
  0:00:02.009    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 202 times
  0:00:02.009    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:03.341    30M / 349M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:03.344    30M / 349M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 14599 out of 14612, length: 3077927
  0:00:03.344    31M / 349M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 136266)
  0:00:03.351    31M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.063    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 7416 times
  0:00:02.064    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:03.402    32M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1539096 kmers, 1112368 bytes occupied (5.78193 bits per kmer).
  0:00:03.407    44M / 349M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:02.083    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 21288 times
  0:00:02.083    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:02.083    14M / 176M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:02.083    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.083    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:02.083    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.085    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 179 times
  0:00:02.085    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.429    44M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.118    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 3316 times
  0:00:02.119    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.120    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.120    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:02.120    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 38 times
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 12 times
  0:00:02.121    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 4 times
  0:00:02.121    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:02.121    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.123    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.123    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.124    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.124    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.125    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.126    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:02.126    14M / 176M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:02.126    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.126    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.127    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 1 times
  0:00:02.127    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.128    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.128    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.130    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.130    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.490    44M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:03.499    32M / 349M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:03.499    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:02.169    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.169    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.170    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.170    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.501    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 583 tips collected, total 584 connection candidates
  0:00:02.172    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 1 times
  0:00:02.172    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.502    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 0 gaps after checking 584 candidates
  0:00:02.173    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.173    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.503    32M / 349M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:02.174    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.174    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:03.505    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:03.505    17M / 349M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:03.505    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.505    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.505    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.175    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:02.175    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:03.506    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:03.506    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.176    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.176    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:03.507    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:03.507    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.178    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.178    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.510    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:03.510    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.219    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.219    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.549    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.549    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.220    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.220    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.551    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.551    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.221    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:02.221    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.552    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.552    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.222    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.222    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.553    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.553    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:02.223    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.223    14M / 176M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:03.554    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.554    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.224    14M / 176M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:03.555    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.555    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:03.556    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:03.556    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.226    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:03.557    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:03.557    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.228    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 324 times
  0:00:02.228    14M / 176M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:02.228    14M / 176M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.33381
  0:00:02.229    14M / 176M  INFO    General                 (simplification.cpp        : 510)     Total length = 2044021
  0:00:03.559    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:03.559    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.230    14M / 176M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 246
  0:00:02.230    14M / 176M  INFO    General                 (simplification.cpp        : 512)     Edges: 15782
  0:00:02.230    14M / 176M  INFO    General                 (simplification.cpp        : 513)     Vertices: 31150
  0:00:02.230    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:02.230    14M / 176M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/simplified_contigs"
  0:00:02.238    18M / 176M  INFO    General                 (binary_converter.cpp      : 143)   7891 reads written
  0:00:02.240    14M / 176M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:02.244     1M / 176M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 2 seconds

===== K21 finished. 


===== K33 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/config.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/mda_mode.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/dataset.info") with K=33
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.001     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.003     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.003     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21/simplified_contigs
  0:00:03.598    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.598    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.599    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.599    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.600    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.600    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.601    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.601    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:03.602    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.602    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.603    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.603    17M / 349M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:03.604    17M / 349M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:03.606    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:03.608    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 495 times
  0:00:03.608    17M / 349M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:03.608    17M / 349M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 0.931955
  0:00:03.609    17M / 349M  INFO    General                 (simplification.cpp        : 510)     Total length = 1482768
  0:00:03.610    17M / 349M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 205
  0:00:03.610    17M / 349M  INFO    General                 (simplification.cpp        : 512)     Edges: 13622
  0:00:03.610    17M / 349M  INFO    General                 (simplification.cpp        : 513)     Vertices: 27230
  0:00:03.610    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Mismatch Correction (id: mismatch_correction)
  0:00:03.610    17M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:03.610    17M / 349M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 136266)
  0:00:03.615    17M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:03.656    18M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1482768 kmers, 1071680 bytes occupied (5.78205 bits per kmer).
  0:00:03.658    30M / 349M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:03.678    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 2236 kmers to process
  0:00:03.678    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.678    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 392)   Collect potential mismatches
  0:00:03.678    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 193)   Total 24 edges (out of 13622) with 62 potential mismatch positions (2.58333 positions per edge)
  0:00:03.678    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 394)   Potential mismatches collected
  0:00:03.679    30M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.777    30M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 99316 reads processed
  0:00:03.778    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 387)   All edges processed
  0:00:03.778    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 442)   Corrected 0 nucleotides
  0:00:03.778    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.778    30M / 349M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:03.799    30M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa"
  0:00:03.812    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:03.821    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 2236 kmers to process
  0:00:03.821    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.821    35M / 349M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:03.822    35M / 349M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:03.822    35M / 349M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.822    35M / 349M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:00.292     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.292     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.069
  0:00:00.292     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.292     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.292     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.292     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.292     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x709ec2800700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x709eaec00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x709ec8c00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x709ebcc00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x709ec3200700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x709eb2c00000, alignment: 67108864, commit: 1)
  0:00:03.998   307M / 370M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:00.437  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 115110 reads
  0:00:00.439     1M / 149M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 115110 reads
  0:00:00.445     1M / 149M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.462     1M / 149M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5196005 kmers in total.
  0:00:00.462     1M / 149M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.465     1M / 149M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.465     1M / 149M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.465     2M / 149M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.465     2M / 149M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.465     2M / 149M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.664  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5196005 kmers
  0:00:00.665  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5196005 kmers.
  0:00:00.667     2M / 284M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.688     2M / 284M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5221713 kmers in total.
  0:00:00.688     2M / 284M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.744     6M / 284M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5221713 kmers, 3891696 bytes occupied (5.96233 bits per kmer).
  0:00:00.744     6M / 284M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:04.365   307M / 370M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:00.860    11M / 284M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:04.471   307M / 370M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6041
  0:00:04.472   307M / 370M  INFO    General                 (paired_info_utils.cpp     : 106)   11 paired reads (0.044303% of all) aligned to long edges
  0:00:04.472    35M / 370M  INFO    General                 (pair_info_count.cpp       : 188)     Insert size = 260.909, deviation = 33.6842, left quantile = 216, right quantile = 304, read length = 150
  0:00:04.479    35M / 370M  INFO    General                 (pair_info_count.cpp       : 203)   Filtering data for library #0
  0:00:04.479    35M / 370M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.479    35M / 370M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:04.561    35M / 370M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:04.561    35M / 370M  INFO    General                 (pair_info_count.cpp       : 207)   Mapping library #0
  0:00:04.561    35M / 370M  INFO    General                 (pair_info_count.cpp       : 209)   Mapping paired reads (takes a while)
  0:00:04.561    35M / 370M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.561    35M / 370M  INFO    General                 (paired_info_utils.cpp     : 138)   Left insert size quantile 216, right insert size quantile 304, filtering threshold 1, rounding threshold 0
  0:00:04.565    49M / 370M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.013    11M / 284M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:01.022    11M / 284M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:01.022    11M / 284M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:01.022    11M / 284M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:04.647    49M / 370M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24829 reads processed
  0:00:04.652    35M / 370M  INFO    General                 (pair_info_count.cpp       : 164)   Mapping contigs library #1
  0:00:04.652    35M / 370M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.652    36M / 370M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.131    12M / 284M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 20164
  0:00:01.132    12M / 284M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 20194
  0:00:01.137    11M / 284M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   575629 34-mers were removed by early tip clipper
  0:00:01.138    11M / 284M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.139    11M / 284M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:04.729    37M / 370M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 7300 reads processed
  0:00:04.729    36M / 370M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:04.729    36M / 370M  INFO    General                 (distance_estimation.cpp   :  42)   Processing library #0
  0:00:04.729    36M / 370M  INFO    General                 (distance_estimation_utils.: 133)   Weight Filter Done
  0:00:04.729    36M / 370M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:04.732    36M / 370M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:04.732    36M / 370M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 13632
  0:00:04.736    35M / 370M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 432
  0:00:04.736    35M / 370M  INFO    General                 (distance_estimation_utils.: 139)   Refining clustered pair information
  0:00:04.736    35M / 370M  INFO    General                 (distance_estimation_utils.: 141)   The refining of clustered pair information has been finished
  0:00:04.736    35M / 370M  INFO    General                 (distance_estimation_utils.: 143)   Improving paired information
  0:00:04.738    35M / 370M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:04.740    35M / 370M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:04.740    35M / 370M  INFO    General                 (distance_estimation_utils.:  86)   Filling scaffolding index
  0:00:04.740    35M / 370M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:00:04.743    35M / 370M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:04.743    35M / 370M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 13664
  0:00:04.744    35M / 370M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 13664
  0:00:04.744    35M / 370M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:04.744    35M / 370M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:04.744    35M / 370M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:04.744    35M / 370M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:04.753    62M / 370M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:04.753    63M / 370M  INFO    General                 (launcher.cpp              : 344)   filling path container
  0:00:04.754    63M / 370M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 432
  0:00:04.754    64M / 370M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 432
  0:00:04.756    66M / 370M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 10000
  0:00:04.757    66M / 370M  INFO    General                 (extenders_logic.cpp       : 550)   Using 1 paired-end library
  0:00:04.757    66M / 370M  INFO    General                 (extenders_logic.cpp       : 551)   Using 1 paired-end scaffolding library
  0:00:04.757    66M / 370M  INFO    General                 (extenders_logic.cpp       : 552)   Using 1 single read library
  0:00:04.757    66M / 370M  INFO    General                 (launcher.cpp              : 387)   Filling backbone edges for long reads scaffolding...
  0:00:04.757    66M / 370M  INFO    General                 (launcher.cpp              : 389)    with long reads paths
  0:00:04.757    66M / 370M  INFO    General                 (launcher.cpp              : 398)   Removing fake unique with paired-end libs
  0:00:04.757    66M / 370M  INFO    General                 (launcher.cpp              : 409)   0 unique edges
  0:00:04.757    66M / 370M  INFO    General                 (extenders_logic.cpp       : 453)   Using 0 long reads scaffolding libraries
  0:00:04.757    66M / 370M  INFO    General                 (extenders_logic.cpp       : 463)   Using additional coordinated coverage extender
  0:00:04.757    67M / 370M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 5
  0:00:04.757    67M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 6805 (0%)
  0:00:04.759    68M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 6805 (1%)
  0:00:04.761    68M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 6805 (3%)
  0:00:04.764    69M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 6805 (7%)
  0:00:04.766    70M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 681 paths from 6805 (10%)
  0:00:04.768    71M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 6805 (15%)
  0:00:04.770    72M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1362 paths from 6805 (20%)
  0:00:04.775    75M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2043 paths from 6805 (30%)
  0:00:04.775    75M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 6805 (30%)
  0:00:04.780    78M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2724 paths from 6805 (40%)
  0:00:04.784    80M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3405 paths from 6805 (50%)
  0:00:04.788    83M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4086 paths from 6805 (60%)
  0:00:04.789    83M / 370M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 6805 (60%)
  0:00:04.793    86M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4767 paths from 6805 (70%)
  0:00:04.797    89M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5448 paths from 6805 (80%)
  0:00:04.802    91M / 370M  INFO    General                 (path_extenders.cpp        :  36)   Processed 6129 paths from 6805 (90%)
  0:00:04.812    67M / 370M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.812    67M / 370M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.816    67M / 370M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.816    67M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  60)   Removing overlaps
  0:00:04.816    67M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Marking overlaps
  0:00:04.816    67M / 370M  INFO   OverlapRemover           (overlap_remover.hpp       : 117)   Marking start/end overlaps
  0:00:04.821    67M / 370M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking remaining overlaps
  0:00:04.825    67M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  73)   Splitting paths
  0:00:04.826    67M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  78)   Deduplicating paths
  0:00:04.828    67M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Overlaps removed
  0:00:04.830    68M / 370M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.830    68M / 370M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:04.843    94M / 370M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:04.850    64M / 370M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:01.275    13M / 284M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 44432 sequences extracted
  0:00:04.952    64M / 370M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:04.952    64M / 370M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.952    64M / 370M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:01.369    13M / 284M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:04.955    64M / 370M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.955    64M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  60)   Removing overlaps
  0:00:04.955    64M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Marking overlaps
  0:00:04.955    64M / 370M  INFO   OverlapRemover           (overlap_remover.hpp       : 117)   Marking start/end overlaps
  0:00:04.961    64M / 370M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking remaining overlaps
  0:00:04.965    64M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  73)   Splitting paths
  0:00:04.965    64M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  78)   Deduplicating paths
  0:00:04.967    64M / 370M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Overlaps removed
  0:00:04.970    64M / 370M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.970    64M / 370M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:04.970    61M / 370M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:04.970    61M / 370M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:01.402    14M / 284M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 11 loops collected
  0:00:04.992    61M / 370M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa"
  0:00:01.413    13M / 284M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.414    13M / 284M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.414    13M / 284M  INFO    General                 (debruijn_graph_constructor: 516)   Total 88886 edges to create
  0:00:01.414    17M / 284M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:05.005    61M / 370M  INFO    General                 (contig_output_stage.cpp   : 169)   Outputting FastG graph to "/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph.fastg"
  0:00:01.463    18M / 284M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.465    18M / 284M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:05.050    61M / 370M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:01.466    19M / 284M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.467    19M / 284M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.467    19M / 284M  INFO    General                 (debruijn_graph_constructor: 542)   Total 70151 vertices to create
  0:00:01.467    26M / 284M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:05.079    92M / 370M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:05.087    92M / 370M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.paths
  0:00:05.113    64M / 370M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/scaffolds.fasta
  0:00:05.120    64M / 370M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/scaffolds.paths
  0:00:05.125    64M / 370M  INFO    General                 (contig_output_stage.cpp   : 114)   Populating GFA with scaffold paths
  0:00:05.128    61M / 370M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:01.550    23M / 284M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.550    23M / 284M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:05.138     1M / 370M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 5 seconds

===== K55 finished. 


===== Copy files started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/copy_files.py /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/before_rr.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/contigs.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/first_pe_contigs.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/strain_graph.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/strain_graph.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/scaffolds.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/scaffolds.paths /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.paths /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/assembly_graph.fastg /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph.fastg /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55/final_contigs.paths /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/contigs.paths

  0:00:01.603    27M / 284M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5196005 kmers, 3873144 bytes occupied (5.96326 bits per kmer).

===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta --misc_dir /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/misc --threshold_for_breaking_scaffolds 3

  0:00:01.616    47M / 284M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.

===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled contigs are in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/contigs.fasta
 * Assembled scaffolds are in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.paths
 * Assembly graph is in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph.fastg
 * Assembly graph in GFA format is in /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/spades.log

Thank you for using metaSPAdes! If you use it in your research, please cite:

  Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
  doi.org/10.1101/gr.213959.116

  0:00:01.702    47M / 284M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.823    47M / 284M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 88884 edges
  0:00:01.860    13M / 284M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.860    13M / 284M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.860    13M / 284M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.860    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.862    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.862    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.866    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 233 times
  0:00:01.866    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.890    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 3045 times
  0:00:01.890    13M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.909    12M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 22673 times
  0:00:01.909    11M / 284M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.909    11M / 284M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.909    11M / 284M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.909    11M / 284M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.909    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.910    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 77 times
  0:00:01.910    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.925    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1469 times
  0:00:01.925    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.926    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.926    11M / 284M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.926    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 9 times
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 1 times
  0:00:01.927    11M / 284M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.927    11M / 284M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.927    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.928    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.928    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.929    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.929    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.929    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.930    11M / 284M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.930    11M / 284M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.930    11M / 284M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.930    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.931    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.931    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.932    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.932    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.933    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.933    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.973    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 9 times
  0:00:01.973    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.974    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.974    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.975    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 2 times
  0:00:01.975    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.976    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.976    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.977    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.977    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.977    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.977    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.978    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.978    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.980    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.980    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.019    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.019    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.021    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.021    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.022    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:02.022    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.024    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.024    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.025    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.026    11M / 284M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:02.027    11M / 284M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:02.030    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:02.031    11M / 284M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 116 times
  0:00:02.031    11M / 284M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:02.031    11M / 284M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.17322
  0:00:02.032    11M / 284M  INFO    General                 (simplification.cpp        : 510)     Total length = 1914088
  0:00:02.032    11M / 284M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 238
  0:00:02.032    11M / 284M  INFO    General                 (simplification.cpp        : 512)     Edges: 15050
  0:00:02.032    11M / 284M  INFO    General                 (simplification.cpp        : 513)     Vertices: 29940
  0:00:02.032    11M / 284M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:02.032    11M / 284M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/simplified_contigs"
  0:00:02.038    15M / 284M  INFO    General                 (binary_converter.cpp      : 143)   7525 reads written
  0:00:02.041    11M / 284M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:02.044     1M / 284M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 2 seconds

===== K33 finished. 


===== K55 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/config.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/mda_mode.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/dataset.info") with K=55
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution enabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 245)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/simplified_contigs
  0:00:00.204     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.204     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.069
  0:00:00.204     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.204     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.204     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.204     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.204     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x71d5c4200700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x71d5b7800000, alignment: 67108864, commit: 1)
  0:00:00.348  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 114378 reads
  0:00:00.351     2M / 128M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 114378 reads
  0:00:00.355     2M / 128M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.369     1M / 128M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4511399 kmers in total.
  0:00:00.369     1M / 128M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.371     1M / 128M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.371     1M / 128M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.371     2M / 128M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.371     2M / 128M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.371     2M / 128M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.512  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 4511399 kmers
  0:00:00.513  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 4511399 kmers.
  0:00:00.515     2M / 244M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.533     2M / 244M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4543951 kmers in total.
  0:00:00.533     2M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.575     5M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4543951 kmers, 3402856 bytes occupied (5.99101 bits per kmer).
  0:00:00.575     5M / 244M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.675    10M / 244M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.790    10M / 244M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.797     9M / 244M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.798    10M / 244M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.916    14M / 244M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 70282 sequences extracted
  0:00:01.008    14M / 244M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.035    14M / 244M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 0 loops collected
  0:00:01.044    14M / 244M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.046    14M / 244M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.046    14M / 244M  INFO    General                 (debruijn_graph_constructor: 516)   Total 140564 edges to create
  0:00:01.046    19M / 244M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.124    21M / 244M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.126    21M / 244M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.127    22M / 244M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.128    22M / 244M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.128    22M / 244M  INFO    General                 (debruijn_graph_constructor: 542)   Total 102834 vertices to create
  0:00:01.128    32M / 244M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.249    28M / 244M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.249    28M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.290    32M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4511399 kmers, 3378768 bytes occupied (5.99152 bits per kmer).
  0:00:01.301    50M / 244M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.355    50M / 244M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.450    50M / 244M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 140564 edges
  0:00:01.485    19M / 244M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: early_gapcloser)
  0:00:01.488    32M / 244M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.501    35M / 244M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 104081 out of 140564, length: 7323182
  0:00:01.506    36M / 244M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 141269)
  0:00:01.520    36M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.648    39M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4269991 kmers, 3084792 bytes occupied (5.77948 bits per kmer).
  0:00:01.670    75M / 244M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.725    74M / 244M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.737    76M / 244M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24832 reads processed
  0:00:01.767    40M / 244M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.767    40M / 244M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.774    40M / 244M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 4777 tips collected, total 4832 connection candidates
  0:00:01.783    40M / 244M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 28 gaps after checking 4802 candidates
  0:00:01.786    40M / 244M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.792    19M / 244M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.792    19M / 244M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.792    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.795    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.795    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.859    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 12218 times
  0:00:01.859    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.867    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 668 times
  0:00:01.867    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with low flanking coverage
  0:00:01.888    20M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with low flanking coverage triggered 2863 times
  0:00:01.889    20M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.915    19M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 28602 times
  0:00:01.916    17M / 244M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Simplification (id: simplification_preliminary)
  0:00:01.916    17M / 244M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.916    17M / 244M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.916    17M / 244M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.916    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.927    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 2284 times
  0:00:01.927    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.929    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 6 times
  0:00:01.930    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.931    17M / 244M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.931    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 112 times
  0:00:01.932    17M / 244M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.932    17M / 244M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.932    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.933    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.933    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.934    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.934    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.935    17M / 244M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.936    17M / 244M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: prelim_gapcloser)
  0:00:01.939    30M / 244M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.942    31M / 244M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 15157 out of 15170, length: 3219544
  0:00:01.942    31M / 244M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 141269)
  0:00:01.947    31M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.990    32M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1610297 kmers, 1163792 bytes occupied (5.78175 bits per kmer).
  0:00:01.994    45M / 244M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:02.012    45M / 244M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.065    45M / 244M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24832 reads processed
  0:00:02.075    32M / 244M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:02.075    32M / 244M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:02.076    32M / 244M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 667 tips collected, total 668 connection candidates
  0:00:02.078    32M / 244M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 1 gaps after checking 667 candidates
  0:00:02.079    32M / 244M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:02.080    17M / 244M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Paired Information Counting (id: late_pair_info_count_preliminary)
  0:00:02.091    23M / 244M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:02.091    23M / 244M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 141269)
  0:00:02.097    23M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.141    24M / 244M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1610640 kmers, 1164032 bytes occupied (5.78171 bits per kmer).
  0:00:02.143    37M / 244M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:02.164    37M / 244M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 714 kmers to process
  0:00:02.164    37M / 244M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:02.164    37M / 244M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:02.164    37M / 244M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:02.164    37M / 244M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.164    37M / 244M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:02.333   309M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.685   309M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24832 reads processed
  0:00:02.792   309M / 349M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6541
  0:00:02.792   309M / 349M  INFO    General                 (paired_info_utils.cpp     : 106)   0 paired reads (0% of all) aligned to long edges
  0:00:02.792    37M / 349M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
  0:00:02.798    37M / 349M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
  0:00:02.798    37M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Distance Estimation (id: distance_estimation_preliminary)
  0:00:02.798    37M / 349M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:02.798    37M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Repeat Resolving (id: repeat_resolving_preliminary)
  0:00:02.798    37M / 349M  INFO    General                 (repeat_resolving.cpp      :  75)   Setting up preliminary path extend settings
  0:00:02.798    37M / 349M  WARN    General                 (repeat_resolving.cpp      :  82)   Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
  0:00:02.798    37M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:02.798    37M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/strain_graph.gfa"
  0:00:02.812    37M / 349M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.fasta"
  0:00:02.835    37M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Second Phase Setup (id: second_phase_setup)
  0:00:02.835    37M / 349M  INFO    General                 (second_phase_setup.cpp    :  18)   Preparing second phase
  0:00:02.837    31M / 349M  INFO    General                 (second_phase_setup.cpp    :  25)   Moving preliminary contigs from "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.fasta" to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/first_pe_contigs.fasta"
  0:00:02.837    31M / 349M  INFO    General                 (second_phase_setup.cpp    :  37)   Ready to run second phase
  0:00:02.837    31M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:02.837    17M / 349M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:02.837    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.837    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:02.837    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.838    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.838    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.840    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:02.840    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.841    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.841    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.841    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:02.841    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.842    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.842    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.843    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.843    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.844    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.845    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: late_gapcloser)
  0:00:02.848    30M / 349M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:02.851    31M / 349M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 15147 out of 15156, length: 3220210
  0:00:02.851    31M / 349M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 141269)
  0:00:02.856    31M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.899    32M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1610164 kmers, 1163696 bytes occupied (5.78175 bits per kmer).
  0:00:02.901    45M / 349M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:02.920    45M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.966    45M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24832 reads processed
  0:00:02.975    32M / 349M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:02.975    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:02.977    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 665 tips collected, total 666 connection candidates
  0:00:02.978    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 0 gaps after checking 666 candidates
  0:00:02.979    32M / 349M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:02.981    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:02.981    17M / 349M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:02.981    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.981    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.981    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.982    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:02.982    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.983    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.983    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.985    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.985    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.024    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.024    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.025    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.025    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.026    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.026    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.027    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.027    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:03.028    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.029    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.030    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.030    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:03.031    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:03.031    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:03.032    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:03.032    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:03.034    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:03.034    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.073    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.073    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.074    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.074    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.075    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.075    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.076    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.076    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:03.077    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.077    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.078    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.078    17M / 349M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:03.079    17M / 349M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:03.081    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:03.083    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 568 times
  0:00:03.084    17M / 349M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:03.084    17M / 349M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 0.933077
  0:00:03.084    17M / 349M  INFO    General                 (simplification.cpp        : 510)     Total length = 1544292
  0:00:03.085    17M / 349M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 207
  0:00:03.085    17M / 349M  INFO    General                 (simplification.cpp        : 512)     Edges: 14020
  0:00:03.085    17M / 349M  INFO    General                 (simplification.cpp        : 513)     Vertices: 28028
  0:00:03.085    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Mismatch Correction (id: mismatch_correction)
  0:00:03.085    17M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:03.085    17M / 349M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 141269)
  0:00:03.090    17M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:03.132    18M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1544292 kmers, 1116128 bytes occupied (5.78195 bits per kmer).
  0:00:03.134    30M / 349M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:03.154    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 1070 kmers to process
  0:00:03.154    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.154    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 392)   Collect potential mismatches
  0:00:03.154    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 193)   Total 14 edges (out of 14020) with 20 potential mismatch positions (1.42857 positions per edge)
  0:00:03.154    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 394)   Potential mismatches collected
  0:00:03.155    30M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.240    30M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 99328 reads processed
  0:00:03.241    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 387)   All edges processed
  0:00:03.241    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 442)   Corrected 0 nucleotides
  0:00:03.241    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.241    30M / 349M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:03.262    30M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa"
  0:00:03.275    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:03.284    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 1070 kmers to process
  0:00:03.284    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.285    35M / 349M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:03.285    35M / 349M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:03.285    35M / 349M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.285    35M / 349M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:03.450   308M / 350M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.796   308M / 350M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24832 reads processed
  0:00:03.902   308M / 350M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6215
  0:00:03.902   308M / 350M  INFO    General                 (paired_info_utils.cpp     : 106)   0 paired reads (0% of all) aligned to long edges
  0:00:03.902    35M / 350M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
  0:00:03.907    35M / 350M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
  0:00:03.907    35M / 350M  INFO    General                 (pair_info_count.cpp       : 164)   Mapping contigs library #1
  0:00:03.907    35M / 350M  WARN    General                 (pair_info_count.cpp       :  93)   Single reads are not used in metagenomic mode
  0:00:03.907    35M / 350M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.908    36M / 350M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.984    37M / 350M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 7584 reads processed
  0:00:03.984    36M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:03.984    36M / 350M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:03.984    36M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:03.984    36M / 350M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:03.984    36M / 350M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:03.995    65M / 350M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:03.995    66M / 350M  INFO    General                 (launcher.cpp              : 344)   filling path container
  0:00:03.996    66M / 350M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 10000
  0:00:03.997    66M / 350M  INFO    General                 (extenders_logic.cpp       : 550)   Using 0 paired-end libraries
  0:00:03.997    66M / 350M  INFO    General                 (extenders_logic.cpp       : 551)   Using 0 paired-end scaffolding libraries
  0:00:03.997    66M / 350M  INFO    General                 (extenders_logic.cpp       : 552)   Using 1 single read library
  0:00:03.997    66M / 350M  INFO    General                 (launcher.cpp              : 432)   Will not use new long read scaffolding algorithm in this mode
  0:00:03.997    66M / 350M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 1
  0:00:03.997    66M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 7006 (0%)
  0:00:03.998    67M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 7006 (1%)
  0:00:03.998    67M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 7006 (3%)
  0:00:03.999    68M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 7006 (7%)
  0:00:04.000    69M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 701 paths from 7006 (10%)
  0:00:04.001    71M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 7006 (14%)
  0:00:04.003    72M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1402 paths from 7006 (20%)
  0:00:04.005    75M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 7006 (29%)
  0:00:04.005    75M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2103 paths from 7006 (30%)
  0:00:04.008    78M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2804 paths from 7006 (40%)
  0:00:04.011    80M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3505 paths from 7006 (50%)
  0:00:04.013    83M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 7006 (58%)
  0:00:04.013    83M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4206 paths from 7006 (60%)
  0:00:04.016    86M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4907 paths from 7006 (70%)
  0:00:04.019    89M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5608 paths from 7006 (80%)
  0:00:04.022    91M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 6309 paths from 7006 (90%)
  0:00:04.031    67M / 350M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.031    67M / 350M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.034    67M / 350M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.034    67M / 350M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:04.037    67M / 350M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.037    67M / 350M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:04.049    95M / 350M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:04.055    66M / 350M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:04.159    66M / 350M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:04.159    66M / 350M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.159    66M / 350M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.162    66M / 350M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.162    66M / 350M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:04.165    66M / 350M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.165    66M / 350M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:04.165    64M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:04.165    64M / 350M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:04.187    64M / 350M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa"
  0:00:04.200    64M / 350M  INFO    General                 (contig_output_stage.cpp   : 169)   Outputting FastG graph to "/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph.fastg"
  0:00:04.239    64M / 350M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:04.269    96M / 350M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:04.277    96M / 350M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.paths
  0:00:04.305    67M / 350M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/scaffolds.fasta
  0:00:04.313    67M / 350M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/scaffolds.paths
  0:00:04.319    67M / 350M  INFO    General                 (contig_output_stage.cpp   : 114)   Populating GFA with scaffold paths
  0:00:04.322    64M / 350M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:04.332     1M / 350M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 4 seconds

===== K55 finished. 


===== Copy files started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/copy_files.py /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/before_rr.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/contigs.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/first_pe_contigs.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/strain_graph.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/strain_graph.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/scaffolds.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/scaffolds.paths /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.paths /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/assembly_graph.fastg /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph.fastg /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55/final_contigs.paths /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/contigs.paths


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta --misc_dir /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled contigs are in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/contigs.fasta
 * Assembled scaffolds are in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.paths
 * Assembly graph is in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph.fastg
 * Assembly graph in GFA format is in /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:
 * 0:00:02.792    37M / 349M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
 * 0:00:02.798    37M / 349M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
 * 0:00:02.798    37M / 349M  WARN    General                 (repeat_resolving.cpp      :  82)   Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
 * 0:00:03.907    35M / 350M  WARN    General                 (pair_info_count.cpp       :  93)   Single reads are not used in metagenomic mode
======= Warnings saved to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/warnings.log

SPAdes log can be found here: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/spades.log

Thank you for using metaSPAdes! If you use it in your research, please cite:

  Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
  doi.org/10.1101/gr.213959.116

Running AMRFinder

        ===      ===    %%  %%  %%%%%%  %%   %%  %%       %%%%   %%%%%   
         ==      ==     %% %%     %%    %%% %%%  %%      %%  %%  %%  %%  
          ==    ==      %%%%      %%    %% % %%  %%      %%%%%%  %%%%%   
           ==  ==       %% %%     %%    %%   %%  %%      %%  %%  %%  %%  
            ====        %%  %%  %%%%%%  %%   %%  %%%%%%  %%  %%  %%%%%   
             ==        ................................................. 
	  v0.1.5

//============================== VERSE setting ===============================\\
||            Running mode : Default(featureCounts)                           ||
||            Feature type : CDS                                              ||
||              Input file : 1 BAM file                                       ||
||                           P /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_ ... ||
||             Output file : /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_as ... ||
||         Annotation file : /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_as ... ||
||                                                                            ||
||                 Threads : 4                                                ||
|| Multithreaded BAM unzip : no                                               ||
||                                                                            ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\============= Based on the framework of featureCounts(SUBREAD) =============//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/ge ... ||
||    CDSs : 6890                                                             ||
||    CDSs after merge : 6890                                                 ||
||    Genes : 6890                                                            ||
||    Chromosomes : 6377                                                      ||
||                                                                            ||
|| Process BAM file /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air ... ||
||    Quantifying in paired-end mode.                                         ||
||    Assign read pairs to features...                                        ||
||    Read pairs with missing mates : 11724                                   ||
||    Total read pairs : 16567                                                ||
||    Successfully assigned read pairs : 14206 (85.7%)                        ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\====== VERSE: a Versatile and Efficient Rna-SEq read assignment tool =======//

MetaBAT 2 (2.17 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 250 and minClsSize 200000. with random seed=1753732641
No edges were formed by TNF.
0 bins (0 bases in total) formed.
Command line: /opt/conda/bin/metaspades.py	-1	/outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz	-2	/outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz	--memory	184	--tmp-dir	/outputs/tmp	-o	/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb	-t	16	--only-assembler	

System information:
  SPAdes version: 4.0.0
  Python version: 3.10.12
  OS: Linux-6.8.0-1021-aws-x86_64-with-glibc2.31

Output dir: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz']
      right reads: ['/outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /outputs/tmp
  Threads: 16
  Memory limit (in Gb): 184


======= SPAdes pipeline started. Log can be found here: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/spades.log

/outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz: max reads length: 150
/outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz: max reads length: 150

Reads length: 150


===== Before start started. 


===== Assembling started. 


===== K21 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/config.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/mda_mode.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/dataset.info") with K=21
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.001     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.001     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  78)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  99)   Converting paired reads
  0:00:00.121    82M / 82M   INFO    General                 (binary_converter.cpp      : 127)   16384 reads processed
  0:00:00.195    82M / 82M   INFO    General                 (binary_converter.cpp      : 143)   24822 reads written
  0:00:00.199    46M / 49M   INFO    General                 (read_converter.cpp        : 113)   Converting single reads
  0:00:00.209    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.210    46M / 49M   INFO    General                 (read_converter.cpp        : 119)   Converting merged reads
  0:00:00.215    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.217     1M / 49M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.219     1M / 49M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.219     1M / 49M   INFO    General                 (construction.cpp          : 156)   Average read length 143.073
  0:00:00.219     1M / 49M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.219     1M / 49M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.219     1M / 49M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.219     1M / 49M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.219     1M / 49M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
mimalloc: warning: thread 0x7ca3f8e00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7ca3ee200000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x7ca3f7a00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7ca3e4200000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x7ca3f3e00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7ca3e0200000, alignment: 67108864, commit: 1)
  0:00:00.300  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 99288 reads
  0:00:00.302     1M / 87M   INFO    General                 (kmer_splitters.hpp        : 134)   Used 99288 reads
  0:00:00.304     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.316     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5465917 kmers in total.
  0:00:00.316     1M / 87M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.318     1M / 87M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.318     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.318     1M / 87M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.318     1M / 87M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.318     1M / 87M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
  0:00:00.434  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5465917 kmers
  0:00:00.434  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5465917 kmers.
  0:00:00.435     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.451     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5484264 kmers in total.
  0:00:00.451     2M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.497     6M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5484264 kmers, 4084048 bytes occupied (5.95748 bits per kmer).
  0:00:00.497     6M / 176M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.560    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.684    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.689    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.689    11M / 176M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.689    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:00.780    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 19029
  0:00:00.781    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 19077
  0:00:00.786    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   458946 22-mers were removed by early tip clipper
  0:00:00.786    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.787    11M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.918    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 62924 sequences extracted
  0:00:01.010    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.042    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 21 loops collected
  0:00:01.051    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.052    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.052    15M / 176M  INFO    General                 (debruijn_graph_constructor: 516)   Total 125890 edges to create
  0:00:01.052    20M / 176M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.124    22M / 176M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.125    22M / 176M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.126    23M / 176M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.127    23M / 176M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.127    23M / 176M  INFO    General                 (debruijn_graph_constructor: 542)   Total 81292 vertices to create
  0:00:01.127    30M / 176M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.225    26M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.225    26M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.268    31M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5465917 kmers, 4070416 bytes occupied (5.95752 bits per kmer).
  0:00:01.280    52M / 176M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.352    52M / 176M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.453    52M / 176M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 125863 edges
  0:00:01.477    16M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.477    16M / 176M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.477    16M / 176M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.477    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.480    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.480    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.485    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 245 times
  0:00:01.485    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.550    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 7564 times
  0:00:01.550    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.573    16M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 21819 times
  0:00:01.573    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.573    14M / 176M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.573    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.574    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.574    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.576    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 249 times
  0:00:01.576    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.617    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 3333 times
  0:00:01.617    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.618    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.618    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.618    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 34 times
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 20 times
  0:00:01.619    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 4 times
  0:00:01.619    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.620    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:01.620    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.620    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 14 times
  0:00:01.620    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.620    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.621    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 2 times
  0:00:01.621    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.622    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 3 times
  0:00:01.622    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.623    14M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.623    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.624    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.624    14M / 176M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.624    14M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.624    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.625    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 11 times
  0:00:01.625    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.626    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.626    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.628    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.628    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.667    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.667    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.668    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.668    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.669    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 2 times
  0:00:01.669    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.670    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.670    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.671    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.671    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.672    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.672    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.673    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.673    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.674    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.674    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.713    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.713    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.714    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.714    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.715    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.715    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.716    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.716    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.717    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.717    14M / 176M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:01.718    14M / 176M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:01.720    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:01.721    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 258 times
  0:00:01.722    14M / 176M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:01.722    14M / 176M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.35414
  0:00:01.722    14M / 176M  INFO    General                 (simplification.cpp        : 510)     Total length = 1958351
  0:00:01.723    14M / 176M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 247
  0:00:01.723    14M / 176M  INFO    General                 (simplification.cpp        : 512)     Edges: 15037
  0:00:01.723    14M / 176M  INFO    General                 (simplification.cpp        : 513)     Vertices: 29512
  0:00:01.723    14M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:01.723    14M / 176M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/simplified_contigs"
  0:00:01.730    18M / 176M  INFO    General                 (binary_converter.cpp      : 143)   7519 reads written
  0:00:01.732    14M / 176M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:01.736     1M / 176M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 1 seconds

===== K21 finished. 


===== K33 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/config.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/mda_mode.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/dataset.info") with K=33
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21/simplified_contigs
  0:00:00.015     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.015     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.073
  0:00:00.015     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.015     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.015     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.015     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.015     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x7e6185c00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7e6179c00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x7e6186600700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7e6179c00000, alignment: 67108864, commit: 1)
  0:00:00.144  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 114326 reads
  0:00:00.146     1M / 148M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 114326 reads
  0:00:00.150     1M / 148M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.164     1M / 148M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5192443 kmers in total.
  0:00:00.164     1M / 148M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.166     1M / 148M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.166     1M / 148M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.166     2M / 148M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.166     2M / 148M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.166     2M / 148M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.339  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5192443 kmers
  0:00:00.340  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5192443 kmers.
  0:00:00.341     2M / 288M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.361     2M / 288M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5218143 kmers in total.
  0:00:00.361     2M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.408     6M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5218143 kmers, 3889224 bytes occupied (5.96262 bits per kmer).
  0:00:00.408     6M / 288M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.521    11M / 288M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.650    11M / 288M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.656    11M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.656    11M / 288M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.656    11M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:00.746    12M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 19588
  0:00:00.746    12M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 19631
  0:00:00.752    11M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   568423 34-mers were removed by early tip clipper
  0:00:00.752    11M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.754    11M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.878    14M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 45370 sequences extracted
  0:00:00.971    13M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.002    14M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 17 loops collected
  0:00:01.012    13M / 288M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.013    13M / 288M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.013    13M / 288M  INFO    General                 (debruijn_graph_constructor: 516)   Total 90774 edges to create
  0:00:01.013    17M / 288M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.065    18M / 288M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.066    18M / 288M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.067    19M / 288M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.067    19M / 288M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.068    19M / 288M  INFO    General                 (debruijn_graph_constructor: 542)   Total 71087 vertices to create
  0:00:01.068    26M / 288M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.152    23M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.152    23M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.198    27M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5192443 kmers, 3870480 bytes occupied (5.96325 bits per kmer).
  0:00:01.211    47M / 288M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.275    47M / 288M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.373    47M / 288M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 90768 edges
  0:00:01.410    13M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.410    13M / 288M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.410    13M / 288M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.410    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.412    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.412    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.416    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 252 times
  0:00:01.416    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.442    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 3190 times
  0:00:01.442    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.460    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 23271 times
  0:00:01.461    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.461    12M / 288M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.461    12M / 288M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.461    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.461    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.462    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 107 times
  0:00:01.462    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.478    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1519 times
  0:00:01.478    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.479    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 6 times
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.479    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 3 times
  0:00:01.480    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 3 times
  0:00:01.480    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.480    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.481    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.481    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.482    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.482    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.483    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.483    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.483    12M / 288M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.483    12M / 288M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.483    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.484    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 2 times
  0:00:01.484    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.485    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.485    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.487    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.487    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.525    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 14 times
  0:00:01.525    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.526    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.526    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.527    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 3 times
  0:00:01.527    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.528    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.528    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.529    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.529    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.529    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.530    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.530    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.530    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.532    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.532    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.569    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.569    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.570    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.570    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.571    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.571    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.572    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.572    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.573    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.573    12M / 288M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:01.574    12M / 288M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:01.576    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:01.577    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 99 times
  0:00:01.577    12M / 288M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:01.577    12M / 288M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.18588
  0:00:01.577    12M / 288M  INFO    General                 (simplification.cpp        : 510)     Total length = 1844487
  0:00:01.578    12M / 288M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 238
  0:00:01.578    12M / 288M  INFO    General                 (simplification.cpp        : 512)     Edges: 14370
  0:00:01.578    12M / 288M  INFO    General                 (simplification.cpp        : 513)     Vertices: 28506
  0:00:01.578    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:01.578    12M / 288M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/simplified_contigs"
  0:00:01.584    15M / 288M  INFO    General                 (binary_converter.cpp      : 143)   7185 reads written
  0:00:01.586    12M / 288M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:01.589     1M / 288M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 1 seconds

===== K33 finished. 


===== K55 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/config.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/mda_mode.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/dataset.info") with K=55
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution enabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 245)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/simplified_contigs
  0:00:00.020     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.020     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.073
  0:00:00.020     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.020     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.020     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.020     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.020     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.130  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 113658 reads
  0:00:00.132     2M / 128M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 113658 reads
  0:00:00.136     2M / 128M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.149     1M / 128M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4503380 kmers in total.
  0:00:00.150     1M / 128M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.151     1M / 128M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.151     1M / 128M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.152     2M / 128M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.152     2M / 128M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.152     2M / 128M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.304  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 4503380 kmers
  0:00:00.304  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 4503380 kmers.
  0:00:00.306     2M / 245M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.324     2M / 245M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4536279 kmers in total.
  0:00:00.324     2M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.366     5M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4536279 kmers, 3397152 bytes occupied (5.99108 bits per kmer).
  0:00:00.366     5M / 245M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.468    10M / 245M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.580    10M / 245M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.587     9M / 245M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.589    10M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.710    14M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 69533 sequences extracted
  0:00:00.800    13M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:00.827    14M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 0 loops collected
  0:00:00.836    13M / 245M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:00.838    13M / 245M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:00.838    13M / 245M  INFO    General                 (debruijn_graph_constructor: 516)   Total 139066 edges to create
  0:00:00.838    19M / 245M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:00.916    21M / 245M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:00.918    21M / 245M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:00.920    22M / 245M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:00.921    22M / 245M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:00.921    22M / 245M  INFO    General                 (debruijn_graph_constructor: 542)   Total 102432 vertices to create
  0:00:00.921    32M / 245M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.043    28M / 245M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.043    28M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.083    32M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4503380 kmers, 3372960 bytes occupied (5.99187 bits per kmer).
  0:00:01.095    50M / 245M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.144    50M / 245M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.237    50M / 245M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 139066 edges
  0:00:01.272    19M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: early_gapcloser)
  0:00:01.277    32M / 245M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.290    34M / 245M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 102703 out of 139066, length: 7329470
  0:00:01.295    35M / 245M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 139764)
  0:00:01.309    35M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.434    39M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4245280 kmers, 3066944 bytes occupied (5.77949 bits per kmer).
  0:00:01.457    75M / 245M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.509    74M / 245M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.522    76M / 245M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24822 reads processed
  0:00:01.551    39M / 245M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.551    39M / 245M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.557    40M / 245M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 4282 tips collected, total 4344 connection candidates
  0:00:01.566    40M / 245M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 33 gaps after checking 4310 candidates
  0:00:01.569    39M / 245M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.574    19M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.574    19M / 245M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.574    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.577    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.577    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.635    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 11782 times
  0:00:01.636    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.643    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 681 times
  0:00:01.643    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with low flanking coverage
  0:00:01.664    20M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with low flanking coverage triggered 2669 times
  0:00:01.664    20M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.691    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 29084 times
  0:00:01.691    17M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Simplification (id: simplification_preliminary)
  0:00:01.691    17M / 245M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.691    17M / 245M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.692    17M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.692    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.703    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 2286 times
  0:00:01.703    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.706    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 17 times
  0:00:01.706    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.707    17M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.707    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 127 times
  0:00:01.708    17M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 4 times
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.708    17M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.708    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.709    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.709    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.710    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.710    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.711    17M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.712    17M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: prelim_gapcloser)
  0:00:01.715    30M / 245M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.718    31M / 245M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 14597 out of 14636, length: 3136602
  0:00:01.718    31M / 245M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 139764)
  0:00:01.723    31M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.766    32M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1569201 kmers, 1134104 bytes occupied (5.78182 bits per kmer).
  0:00:01.773    44M / 245M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.791    44M / 245M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.840    44M / 245M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24822 reads processed
  0:00:01.849    32M / 245M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.849    32M / 245M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.851    32M / 245M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 595 tips collected, total 596 connection candidates
  0:00:01.852    32M / 245M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 2 gaps after checking 594 candidates
  0:00:01.853    32M / 245M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.855    17M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Paired Information Counting (id: late_pair_info_count_preliminary)
  0:00:01.865    23M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:01.865    23M / 245M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 139764)
  0:00:01.871    23M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.913    24M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1570383 kmers, 1134952 bytes occupied (5.78178 bits per kmer).
  0:00:01.915    36M / 245M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:01.937    36M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 1980 kmers to process
  0:00:01.937    36M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:01.937    36M / 245M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:01.937    36M / 245M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:01.937    36M / 245M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:01.937    36M / 245M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:02.106   308M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.454   308M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24822 reads processed
  0:00:02.566   308M / 349M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6502
  0:00:02.566   308M / 349M  INFO    General                 (paired_info_utils.cpp     : 106)   0 paired reads (0% of all) aligned to long edges
  0:00:02.566    36M / 349M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
  0:00:02.571    36M / 349M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
  0:00:02.571    36M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Distance Estimation (id: distance_estimation_preliminary)
  0:00:02.571    36M / 349M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:02.571    36M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Repeat Resolving (id: repeat_resolving_preliminary)
  0:00:02.571    36M / 349M  INFO    General                 (repeat_resolving.cpp      :  75)   Setting up preliminary path extend settings
  0:00:02.571    36M / 349M  WARN    General                 (repeat_resolving.cpp      :  82)   Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
  0:00:02.571    36M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:02.572    36M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/strain_graph.gfa"
  0:00:02.586    36M / 349M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.fasta"
  0:00:02.608    36M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Second Phase Setup (id: second_phase_setup)
  0:00:02.608    36M / 349M  INFO    General                 (second_phase_setup.cpp    :  18)   Preparing second phase
  0:00:02.610    30M / 349M  INFO    General                 (second_phase_setup.cpp    :  25)   Moving preliminary contigs from "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.fasta" to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/first_pe_contigs.fasta"
  0:00:02.610    30M / 349M  INFO    General                 (second_phase_setup.cpp    :  37)   Ready to run second phase
  0:00:02.610    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:02.610    17M / 349M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:02.610    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.610    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:02.610    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.611    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.611    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.613    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 7 times
  0:00:02.613    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.614    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.614    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.614    17M / 349M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:02.614    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.615    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.616    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.617    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.617    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:02.618    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:02.618    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: late_gapcloser)
  0:00:02.622    30M / 349M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:02.624    31M / 349M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 14565 out of 14590, length: 3137019
  0:00:02.625    31M / 349M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 139764)
  0:00:02.630    31M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.673    32M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1568574 kmers, 1133648 bytes occupied (5.7818 bits per kmer).
  0:00:02.675    44M / 349M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:02.692    44M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.748    44M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24822 reads processed
  0:00:02.757    32M / 349M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:02.757    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:02.758    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 587 tips collected, total 588 connection candidates
  0:00:02.759    32M / 349M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 0 gaps after checking 588 candidates
  0:00:02.760    32M / 349M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:02.762    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:02.762    17M / 349M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:02.762    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.762    17M / 349M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:02.762    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.763    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:02.763    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.764    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.764    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.766    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.766    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.803    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.803    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.804    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.804    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.805    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:02.805    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.806    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.806    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:02.807    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:02.807    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.808    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.809    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:02.810    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:02.810    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:02.811    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:02.811    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:02.813    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:02.813    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:02.850    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:02.850    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:02.851    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:02.851    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:02.852    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:02.852    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:02.853    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:02.853    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:02.854    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:02.854    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:02.855    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:02.855    17M / 349M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:02.856    17M / 349M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:02.858    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:02.860    17M / 349M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 475 times
  0:00:02.860    17M / 349M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:02.860    17M / 349M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 0.935752
  0:00:02.861    17M / 349M  INFO    General                 (simplification.cpp        : 510)     Total length = 1514624
  0:00:02.862    17M / 349M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 207
  0:00:02.862    17M / 349M  INFO    General                 (simplification.cpp        : 512)     Edges: 13640
  0:00:02.862    17M / 349M  INFO    General                 (simplification.cpp        : 513)     Vertices: 27252
  0:00:02.862    17M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Mismatch Correction (id: mismatch_correction)
  0:00:02.862    17M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:02.862    17M / 349M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 139764)
  0:00:02.867    17M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:02.909    18M / 349M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1514624 kmers, 1094704 bytes occupied (5.78205 bits per kmer).
  0:00:02.911    30M / 349M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:02.931    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 3334 kmers to process
  0:00:02.931    30M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:02.931    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 392)   Collect potential mismatches
  0:00:02.932    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 193)   Total 34 edges (out of 13640) with 90 potential mismatch positions (2.64706 positions per edge)
  0:00:02.932    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 394)   Potential mismatches collected
  0:00:02.932    30M / 349M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.036    30M / 349M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 99288 reads processed
  0:00:03.046    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 387)   All edges processed
  0:00:03.051    30M / 349M  INFO    General                 (mismatch_correction.cpp   : 442)   Corrected 0 nucleotides
  0:00:03.062    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.069    30M / 349M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:03.112    30M / 349M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa"
  0:00:03.148    30M / 349M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:03.158    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 3334 kmers to process
  0:00:03.158    35M / 349M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.158    35M / 349M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:03.158    35M / 349M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:03.158    35M / 349M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.158    35M / 349M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:03.325   308M / 350M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.697   308M / 350M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24822 reads processed
  0:00:03.804   308M / 350M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 6189
  0:00:03.805   308M / 350M  INFO    General                 (paired_info_utils.cpp     : 106)   0 paired reads (0% of all) aligned to long edges
  0:00:03.805    35M / 350M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
  0:00:03.810    35M / 350M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
  0:00:03.810    35M / 350M  INFO    General                 (pair_info_count.cpp       : 164)   Mapping contigs library #1
  0:00:03.810    35M / 350M  WARN    General                 (pair_info_count.cpp       :  93)   Single reads are not used in metagenomic mode
  0:00:03.810    35M / 350M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.810    36M / 350M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.885    37M / 350M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 7316 reads processed
  0:00:03.885    36M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:03.885    36M / 350M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:03.885    36M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:03.885    36M / 350M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:03.885    36M / 350M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:03.897    64M / 350M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:03.897    65M / 350M  INFO    General                 (launcher.cpp              : 344)   filling path container
  0:00:03.897    65M / 350M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 10000
  0:00:03.898    66M / 350M  INFO    General                 (extenders_logic.cpp       : 550)   Using 0 paired-end libraries
  0:00:03.898    66M / 350M  INFO    General                 (extenders_logic.cpp       : 551)   Using 0 paired-end scaffolding libraries
  0:00:03.898    66M / 350M  INFO    General                 (extenders_logic.cpp       : 552)   Using 1 single read library
  0:00:03.898    66M / 350M  INFO    General                 (launcher.cpp              : 432)   Will not use new long read scaffolding algorithm in this mode
  0:00:03.898    66M / 350M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 1
  0:00:03.898    66M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 6808 (0%)
  0:00:03.899    66M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 6808 (1%)
  0:00:03.899    67M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 6808 (3%)
  0:00:03.900    68M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 6808 (7%)
  0:00:03.901    68M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 681 paths from 6808 (10%)
  0:00:03.902    70M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 6808 (15%)
  0:00:03.904    71M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1362 paths from 6808 (20%)
  0:00:03.906    74M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2043 paths from 6808 (30%)
  0:00:03.906    74M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 6808 (30%)
  0:00:03.909    76M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2724 paths from 6808 (40%)
  0:00:03.911    79M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3405 paths from 6808 (50%)
  0:00:03.914    82M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4086 paths from 6808 (60%)
  0:00:03.914    82M / 350M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 6808 (60%)
  0:00:03.917    84M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4767 paths from 6808 (70%)
  0:00:03.919    87M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5448 paths from 6808 (80%)
  0:00:03.922    90M / 350M  INFO    General                 (path_extenders.cpp        :  36)   Processed 6129 paths from 6808 (90%)
  0:00:03.931    66M / 350M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:03.931    66M / 350M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:03.934    66M / 350M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:03.934    66M / 350M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:03.937    66M / 350M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:03.937    66M / 350M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:03.950    93M / 350M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:03.956    65M / 350M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:04.056    65M / 350M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:04.057    65M / 350M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.057    65M / 350M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.059    65M / 350M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.059    65M / 350M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:04.062    65M / 350M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.062    65M / 350M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:04.062    63M / 350M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:04.063    63M / 350M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:04.084    63M / 350M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa"
  0:00:04.097    63M / 350M  INFO    General                 (contig_output_stage.cpp   : 169)   Outputting FastG graph to "/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph.fastg"
  0:00:04.135    63M / 350M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:04.165    94M / 350M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:04.173    94M / 350M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.paths
  0:00:04.199    66M / 350M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/scaffolds.fasta
  0:00:04.207    66M / 350M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/scaffolds.paths
  0:00:04.212    66M / 350M  INFO    General                 (contig_output_stage.cpp   : 114)   Populating GFA with scaffold paths
  0:00:04.215    63M / 350M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:04.225     1M / 350M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 4 seconds

===== K55 finished. 


===== Copy files started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/copy_files.py /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/before_rr.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/contigs.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/first_pe_contigs.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/strain_graph.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/strain_graph.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/scaffolds.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/scaffolds.paths /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.paths /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/assembly_graph.fastg /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph.fastg /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55/final_contigs.paths /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/contigs.paths


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta --misc_dir /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled contigs are in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/contigs.fasta
 * Assembled scaffolds are in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.paths
 * Assembly graph is in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph.fastg
 * Assembly graph in GFA format is in /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:
 * 0:00:02.566    36M / 349M  WARN    General                 (pair_info_count.cpp       : 177)   Unable to estimate insert size for paired library #0
 * 0:00:02.571    36M / 349M  WARN    General                 (pair_info_count.cpp       : 183)   None of paired reads aligned properly. Please, check orientation of your read pairs.
 * 0:00:02.571    36M / 349M  WARN    General                 (repeat_resolving.cpp      :  82)   Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
 * 0:00:03.810    35M / 350M  WARN    General                 (pair_info_count.cpp       :  93)   Single reads are not used in metagenomic mode
======= Warnings saved to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/warnings.log

SPAdes log can be found here: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/spades.log

Thank you for using metaSPAdes! If you use it in your research, please cite:

  Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
  doi.org/10.1101/gr.213959.116

Command line: /opt/conda/bin/metaspades.py	-1	/outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz	-2	/outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz	--memory	184	--tmp-dir	/outputs/tmp	-o	/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb	-t	16	--only-assembler	

System information:
  SPAdes version: 4.0.0
  Python version: 3.10.12
  OS: Linux-6.8.0-1021-aws-x86_64-with-glibc2.31

Output dir: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz']
      right reads: ['/outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [21, 33, 55]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /outputs/tmp
  Threads: 16
  Memory limit (in Gb): 184


======= SPAdes pipeline started. Log can be found here: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/spades.log

/outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz: max reads length: 150
/outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz: max reads length: 150

Reads length: 150


===== Before start started. 


===== Assembling started. 


===== K21 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/config.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/mda_mode.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/dataset.info") with K=21
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.001     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.001     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.001     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.001     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  78)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  99)   Converting paired reads
Running AMRFinder
  0:00:00.122    82M / 82M   INFO    General                 (binary_converter.cpp      : 127)   16384 reads processed
  0:00:00.196    82M / 82M   INFO    General                 (binary_converter.cpp      : 143)   24812 reads written
  0:00:00.201    46M / 49M   INFO    General                 (read_converter.cpp        : 113)   Converting single reads
  0:00:00.210    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.211    46M / 49M   INFO    General                 (read_converter.cpp        : 119)   Converting merged reads
  0:00:00.216    59M / 59M   INFO    General                 (binary_converter.cpp      : 143)   0 reads written
  0:00:00.219     1M / 49M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.220     1M / 49M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.220     1M / 49M   INFO    General                 (construction.cpp          : 156)   Average read length 143.116
  0:00:00.220     1M / 49M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.220     1M / 49M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.220     1M / 49M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.220     1M / 49M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.220     1M / 49M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
mimalloc: warning: thread 0x7f8d4be00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7f8d3b800000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x7f8d50e00700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7f8d45800000, alignment: 67108864, commit: 1)
  0:00:00.320  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 99248 reads
  0:00:00.323     1M / 87M   INFO    General                 (kmer_splitters.hpp        : 134)   Used 99248 reads
  0:00:00.325     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.338     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5717709 kmers in total.
  0:00:00.338     1M / 87M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.340     1M / 87M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.340     1M / 87M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.340     1M / 87M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.340     1M / 87M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.340     1M / 87M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 419430
  0:00:00.528  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5717709 kmers
  0:00:00.528  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5717709 kmers.
  0:00:00.530     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.547     2M / 176M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5748589 kmers in total.
  0:00:00.547     2M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.604     6M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5748589 kmers, 4273456 bytes occupied (5.94714 bits per kmer).
  0:00:00.604     6M / 176M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.673    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.856    12M / 176M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.862    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.862    11M / 176M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.862    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:00.994    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 12568
  0:00:00.995    13M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 12619
  0:00:01.000    11M / 176M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   323313 22-mers were removed by early tip clipper
  0:00:01.000    11M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.002    12M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:01.198    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 51946 sequences extracted
  0:00:01.329    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.373    15M / 176M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 14 loops collected
  0:00:01.382    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.384    15M / 176M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.384    15M / 176M  INFO    General                 (debruijn_graph_constructor: 516)   Total 103920 edges to create
  0:00:01.384    19M / 176M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.443    20M / 176M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.444    20M / 176M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.444    21M / 176M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.445    21M / 176M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.445    21M / 176M  INFO    General                 (debruijn_graph_constructor: 542)   Total 82840 vertices to create
  0:00:01.445    29M / 176M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.545    26M / 176M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.545    26M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.591    30M / 176M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5717709 kmers, 4251168 bytes occupied (5.94807 bits per kmer).
  0:00:01.603    52M / 176M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.680    52M / 176M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.789    52M / 176M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 103881 edges
  0:00:01.815    15M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.816    15M / 176M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.816    15M / 176M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.816    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.818    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.818    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.823    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 207 times
  0:00:01.823    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.848    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 3675 times
  0:00:01.848    15M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.872    14M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 28886 times
  0:00:01.873    13M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.873    13M / 176M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.873    13M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.873    13M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.873    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.875    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 164 times
  0:00:01.875    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.894    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1538 times
  0:00:01.894    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.895    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.895    13M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.895    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 16 times
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 7 times
  0:00:01.896    13M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 4 times
  0:00:01.896    13M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.896    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.897    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1 times
  0:00:01.897    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.898    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.898    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.899    13M / 176M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.899    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.900    13M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.900    13M / 176M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.900    13M / 176M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.900    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.901    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 5 times
  0:00:01.901    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.902    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.902    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.903    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.903    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.941    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.941    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.942    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.942    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.943    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 2 times
  0:00:01.943    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.944    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.944    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.945    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.945    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.946    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.946    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.947    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.947    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.949    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.949    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.987    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.987    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.988    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.988    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.989    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.989    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.990    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.990    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.990    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.990    13M / 176M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:01.991    13M / 176M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:01.993    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:01.995    13M / 176M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 221 times
  0:00:01.995    13M / 176M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:01.995    13M / 176M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.21936
  0:00:01.995    13M / 176M  INFO    General                 (simplification.cpp        : 510)     Total length = 1676841
  0:00:01.996    13M / 176M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 232
  0:00:01.996    13M / 176M  INFO    General                 (simplification.cpp        : 512)     Edges: 14351
  0:00:01.996    13M / 176M  INFO    General                 (simplification.cpp        : 513)     Vertices: 28428
  0:00:01.996    13M / 176M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:01.996    13M / 176M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/simplified_contigs"
  0:00:02.001    17M / 176M  INFO    General                 (binary_converter.cpp      : 143)   7176 reads written
  0:00:02.004    13M / 176M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:02.006     1M / 176M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 2 seconds

===== K21 finished. 


===== K33 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/config.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/mda_mode.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/dataset.info") with K=33
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution disabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21/simplified_contigs
  0:00:00.021     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.022     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.116
  0:00:00.022     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.022     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.022     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.022     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.022     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x7387e8200700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7387dcc00000, alignment: 67108864, commit: 1)
mimalloc: warning: thread 0x7387e7800700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7387dcc00000, alignment: 67108864, commit: 1)
  0:00:00.167  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 113600 reads
  0:00:00.169     1M / 144M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 113600 reads
  0:00:00.173     1M / 144M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.190     1M / 144M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5315981 kmers in total.
  0:00:00.190     1M / 144M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.192     1M / 144M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.192     1M / 144M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.193     2M / 144M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.193     2M / 144M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.193     2M / 144M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.373  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 5315981 kmers
  0:00:00.373  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 5315981 kmers.
  0:00:00.375     2M / 288M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.397     2M / 288M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 5351006 kmers in total.
  0:00:00.398     2M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.451     7M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5351006 kmers, 3984648 bytes occupied (5.95723 bits per kmer).
  0:00:00.451     7M / 288M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.578    12M / 288M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.712    12M / 288M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.718    11M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:00.718    11M / 288M  INFO    General                 (construction.cpp          : 298)   Early tip clipper length bound set as (RL - K)
  0:00:00.718    11M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  48)   Early tip clipping
  0:00:00.809    13M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  83)   #tipped junctions: 11928
  0:00:00.810    13M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  94)   Clipped tips: 11967
  0:00:00.815    11M / 288M  INFO   Early tip clipping       (early_simplification.hpp  :  50)   322339 34-mers were removed by early tip clipper
  0:00:00.815    11M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.817    11M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
  0:00:00.953    14M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 44126 sequences extracted
  0:00:01.052    14M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:01.085    14M / 288M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 8 loops collected
  0:00:01.094    14M / 288M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:01.095    14M / 288M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:01.095    14M / 288M  INFO    General                 (debruijn_graph_constructor: 516)   Total 88268 edges to create
  0:00:01.095    18M / 288M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:01.143    19M / 288M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:01.145    19M / 288M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:01.146    20M / 288M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:01.147    20M / 288M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:01.147    20M / 288M  INFO    General                 (debruijn_graph_constructor: 542)   Total 79159 vertices to create
  0:00:01.147    28M / 288M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.240    24M / 288M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.240    24M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.292    29M / 288M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 5315981 kmers, 3959288 bytes occupied (5.95832 bits per kmer).
  0:00:01.305    50M / 288M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.387    50M / 288M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.507    50M / 288M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 88265 edges
  0:00:01.543    14M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.544    14M / 288M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.544    14M / 288M  INFO    General                 (graph_simplification.hpp  : 674)   Flanking coverage based disconnection disabled
  0:00:01.544    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.546    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.546    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.549    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 144 times
  0:00:01.549    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.565    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 1557 times
  0:00:01.565    14M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.590    13M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 30306 times
  0:00:01.591    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:01.591    12M / 288M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.591    12M / 288M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.591    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.591    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.592    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 49 times
  0:00:01.592    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.601    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 669 times
  0:00:01.601    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.602    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.602    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 7 times
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 1 times
  0:00:01.603    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.603    12M / 288M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.603    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.604    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.604    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.605    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.605    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.606    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.606    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:01.607    12M / 288M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:01.607    12M / 288M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.607    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.608    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 1 times
  0:00:01.608    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.609    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.609    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.610    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.610    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.647    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 2 times
  0:00:01.647    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.648    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.648    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.649    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.649    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.650    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.650    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.651    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.651    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:01.652    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:01.652    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:01.653    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:01.653    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:01.655    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:01.655    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:01.692    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:01.692    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.693    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.694    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:01.695    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:01.695    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.697    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.697    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:01.699    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:01.699    12M / 288M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:01.700    12M / 288M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:01.703    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:01.704    12M / 288M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 63 times
  0:00:01.705    12M / 288M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:01.705    12M / 288M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 1.10853
  0:00:01.706    12M / 288M  INFO    General                 (simplification.cpp        : 510)     Total length = 1569245
  0:00:01.707    12M / 288M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 221
  0:00:01.707    12M / 288M  INFO    General                 (simplification.cpp        : 512)     Edges: 13834
  0:00:01.707    12M / 288M  INFO    General                 (simplification.cpp        : 513)     Vertices: 27612
  0:00:01.707    12M / 288M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:01.707    12M / 288M  INFO    General                 (read_converter.cpp        : 135)   Outputting contigs to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/simplified_contigs"
  0:00:01.714    16M / 288M  INFO    General                 (binary_converter.cpp      : 143)   6917 reads written
  0:00:01.717    12M / 288M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:01.719     1M / 288M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 1 seconds

===== K33 finished. 


===== K55 started. 


== Running: /opt/conda/bin/spades-core /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/config.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/mda_mode.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/meta_mode.info

  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/config.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/mda_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  :  94)   Loaded config from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/configs/meta_mode.info"
  0:00:00.000     1M / 16M   INFO    General                 (memory_limit.cpp          :  55)   Memory limit set to 184 Gb
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 102)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 103)   Maximum k-mer length: 128
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 104)   Assembling dataset ("/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/dataset.info") with K=55
  0:00:00.000     1M / 16M   INFO    General                 (main.cpp                  : 105)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 234)   Two-step repeat resolution enabled
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 689)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.000     1M / 16M   INFO   GraphCore                (graph_core.hpp            : 690)   Vertex size: 48, edge size: 40
  0:00:00.000     1M / 16M   INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:00.000     1M / 16M   INFO    General                 (pipeline.cpp              : 245)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.001     1M / 16M   INFO    General                 (read_converter.cpp        :  57)   Binary reads detected
  0:00:00.002     1M / 16M   INFO   StageManager             (stage.cpp                 : 189)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.002     1M / 16M   INFO    General                 (construction.cpp          : 115)   Contigs from previous K will be used: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/simplified_contigs
  0:00:00.016     1M / 16M   INFO    General                 (construction.cpp          : 150)   Max read length 150
  0:00:00.016     1M / 16M   INFO    General                 (construction.cpp          : 156)   Average read length 143.116
  0:00:00.016     1M / 16M   INFO    General                 (stage.cpp                 : 121)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.016     1M / 16M   INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.016     1M / 16M   INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.016     1M / 16M   INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83332 Gb
  0:00:00.016     1M / 16M   INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
mimalloc: warning: thread 0x7a127f600700: unable to allocate aligned OS memory directly, fall back to over-allocation (67108864 bytes, address: 0x7a1276800000, alignment: 67108864, commit: 1)
  0:00:00.126  9601M / 9601M INFO    General                 (kmer_splitters.hpp        : 128)   Processed 113082 reads
  0:00:00.128     2M / 123M  INFO    General                 (kmer_splitters.hpp        : 134)   Used 113082 reads
  0:00:00.132     2M / 123M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.145     1M / 123M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4483258 kmers in total.
  0:00:00.145     1M / 123M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:00.147     1M / 123M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 453)   Building kmer index
  0:00:00.147     1M / 123M  INFO    General                 (kmer_index_builder.hpp    : 258)   Splitting kmer instances into 160 files using 16 threads. This might take a while.
  0:00:00.147     2M / 123M  INFO    General                 (file_limit.hpp            :  43)   Open file limit set to 1048576
  0:00:00.147     2M / 123M  INFO    General                 (kmer_splitter.hpp         :  94)   Memory available for splitting buffers: 3.83331 Gb
  0:00:00.147     2M / 123M  INFO    General                 (kmer_splitter.hpp         : 102)   Using cell size of 209715
  0:00:00.325  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 197)   Processed 4483258 kmers
  0:00:00.325  9602M / 9602M INFO    General                 (kmer_splitters.hpp        : 202)   Used 4483258 kmers.
  0:00:00.327     2M / 245M  INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:00:00.346     2M / 245M  INFO    General                 (kmer_index_builder.hpp    : 275)   K-mer counting done. There are 4521790 kmers in total.
  0:00:00.346     2M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:00.395     5M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4521790 kmers, 3386472 bytes occupied (5.99138 bits per kmer).
  0:00:00.395     5M / 245M  INFO    General                 (kmer_index_builder.hpp    : 168)   Merging final buckets.
  0:00:00.496    10M / 245M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 101)   Building k-mer extensions from k+1-mers
  0:00:00.611    10M / 245M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 106)   Building k-mer extensions from k+1-mers finished.
  0:00:00.617     9M / 245M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:00.618    10M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 381)   Extracting unbranching paths
MetaBAT 2 (2.17 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 250 and minClsSize 200000. with random seed=1753732656
No edges were formed by TNF.
0 bins (0 bases in total) formed.
  0:00:00.745    13M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 400)   Extracting unbranching paths finished. 60805 sequences extracted
  0:00:00.841    13M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 336)   Collecting perfect loops
  0:00:00.868    13M / 245M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 369)   Collecting perfect loops finished. 0 loops collected
  0:00:00.877    13M / 245M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 586)   Sorting edges...
  0:00:00.878    13M / 245M  INFO   DeBruijnGraphConstructor (debruijn_graph_constructor: 588)   Edges sorted
  0:00:00.878    13M / 245M  INFO    General                 (debruijn_graph_constructor: 516)   Total 121610 edges to create
  0:00:00.879    18M / 245M  INFO    General                 (debruijn_graph_constructor: 519)   Collecting link records
  0:00:00.947    20M / 245M  INFO    General                 (debruijn_graph_constructor: 521)   Ordering link records
  0:00:00.948    20M / 245M  INFO    General                 (debruijn_graph_constructor: 524)   Sorting done
  0:00:00.950    21M / 245M  INFO    General                 (debruijn_graph_constructor: 537)   Sorting LinkRecords...
  0:00:00.951    21M / 245M  INFO    General                 (debruijn_graph_constructor: 540)   LinkRecords sorted
  0:00:00.951    21M / 245M  INFO    General                 (debruijn_graph_constructor: 542)   Total 99337 vertices to create
  0:00:00.951    31M / 245M  INFO    General                 (debruijn_graph_constructor: 545)   Connecting the graph
  0:00:01.068    27M / 245M  INFO    General                 (stage.cpp                 : 121)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.068    27M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.115    31M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4483258 kmers, 3358248 bytes occupied (5.99251 bits per kmer).
  0:00:01.127    49M / 245M  INFO    General                 (coverage_hash_map_builder.:  49)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.193    49M / 245M  INFO    General                 (construction.cpp          : 427)   Filling coverage and flanking coverage from PHM
  0:00:01.285    49M / 245M  INFO    General                 (coverage_filling.hpp      :  83)   Processed 121610 edges
  0:00:01.320    18M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: early_gapcloser)
  0:00:01.323    31M / 245M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.336    34M / 245M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 103137 out of 121610, length: 8042932
  0:00:01.340    35M / 245M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 122221)
  0:00:01.362    35M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.520    38M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 4402039 kmers, 3180176 bytes occupied (5.77946 bits per kmer).
  0:00:01.544    74M / 245M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.600    73M / 245M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.612    75M / 245M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:01.644    39M / 245M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.644    39M / 245M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.650    39M / 245M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 3173 tips collected, total 3194 connection candidates
  0:00:01.656    39M / 245M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 21 gaps after checking 3173 candidates
  0:00:01.659    39M / 245M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.663    18M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:01.663    18M / 245M  INFO    General                 (simplification.cpp        : 129)   PROCEDURE == Initial cleaning
  0:00:01.664    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Self conjugate edge remover
  0:00:01.666    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Self conjugate edge remover triggered 0 times
  0:00:01.666    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial tip clipper
  0:00:01.707    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial tip clipper triggered 7795 times
  0:00:01.707    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial ec remover
  0:00:01.712    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial ec remover triggered 290 times
  0:00:01.712    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with low flanking coverage
  0:00:01.724    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with low flanking coverage triggered 1489 times
  0:00:01.724    19M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Initial isolated edge remover
  0:00:01.753    18M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Initial isolated edge remover triggered 33958 times
  0:00:01.753    16M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Simplification (id: simplification_preliminary)
  0:00:01.753    16M / 245M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:01.753    16M / 245M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:01.753    16M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:01.753    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.759    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 1184 times
  0:00:01.759    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.765    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 57 times
  0:00:01.765    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.766    16M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 3 times
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 31 times
  0:00:01.766    16M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.766    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.767    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.767    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.767    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 1 times
  0:00:01.767    16M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:01.767    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.768    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.768    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.769    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 1 times
  0:00:01.769    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.770    16M / 245M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 5
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:01.770    16M / 245M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:01.771    16M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: prelim_gapcloser)
  0:00:01.774    29M / 245M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:01.776    30M / 245M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 12852 out of 12872, length: 2569950
  0:00:01.776    30M / 245M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 122221)
  0:00:01.782    30M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.826    31M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1285040 kmers, 928880 bytes occupied (5.78273 bits per kmer).
  0:00:01.829    41M / 245M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:01.848    41M / 245M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:01.920    41M / 245M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:01.928    31M / 245M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:01.928    31M / 245M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:01.929    31M / 245M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 215 tips collected, total 216 connection candidates
  0:00:01.930    31M / 245M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 0 gaps after checking 216 candidates
  0:00:01.931    31M / 245M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:01.932    16M / 245M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Paired Information Counting (id: late_pair_info_count_preliminary)
  0:00:01.941    21M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:01.941    21M / 245M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 122221)
  0:00:01.948    21M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:01.994    22M / 245M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1286530 kmers, 929968 bytes occupied (5.7828 bits per kmer).
  0:00:01.996    32M / 245M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:02.012    32M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 6882 kmers to process
  0:00:02.013    32M / 245M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:02.013    32M / 245M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:02.013    32M / 245M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:02.013    32M / 245M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.013    32M / 245M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:02.182   304M / 344M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.567   304M / 344M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:02.676   304M / 344M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 5685
  0:00:02.676   304M / 344M  INFO    General                 (paired_info_utils.cpp     : 106)   140 paired reads (0.564243% of all) aligned to long edges
  0:00:02.677    32M / 344M  INFO    General                 (pair_info_count.cpp       : 188)     Insert size = 266.329, deviation = 26.7254, left quantile = 230, right quantile = 302, read length = 150
  0:00:02.683    32M / 344M  INFO    General                 (pair_info_count.cpp       : 203)   Filtering data for library #0
  0:00:02.683    32M / 344M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.683    32M / 344M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.776    32M / 344M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:02.776    32M / 344M  INFO    General                 (pair_info_count.cpp       : 207)   Mapping library #0
  0:00:02.776    32M / 344M  INFO    General                 (pair_info_count.cpp       : 209)   Mapping paired reads (takes a while)
  0:00:02.776    32M / 344M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:02.776    32M / 344M  INFO    General                 (paired_info_utils.cpp     : 138)   Left insert size quantile 230, right insert size quantile 302, filtering threshold 1, rounding threshold 0
  0:00:02.780    46M / 344M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:02.874    46M / 344M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:02.880    32M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Distance Estimation (id: distance_estimation_preliminary)
  0:00:02.880    32M / 344M  INFO    General                 (distance_estimation.cpp   :  42)   Processing library #0
  0:00:02.880    32M / 344M  INFO    General                 (distance_estimation_utils.: 133)   Weight Filter Done
  0:00:02.880    32M / 344M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:02.883    32M / 344M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:02.883    32M / 344M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 12896
  0:00:02.886    31M / 344M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 256
  0:00:02.886    31M / 344M  INFO    General                 (distance_estimation_utils.: 139)   Refining clustered pair information
  0:00:02.886    31M / 344M  INFO    General                 (distance_estimation_utils.: 141)   The refining of clustered pair information has been finished
  0:00:02.886    31M / 344M  INFO    General                 (distance_estimation_utils.: 143)   Improving paired information
  0:00:02.889    31M / 344M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:02.891    31M / 344M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:02.891    31M / 344M  INFO    General                 (distance_estimation_utils.:  86)   Filling scaffolding index
  0:00:02.891    31M / 344M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:00:02.893    31M / 344M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:02.893    31M / 344M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 12878
  0:00:02.894    31M / 344M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 12878
  0:00:02.894    31M / 344M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:02.895    31M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Preliminary Repeat Resolving (id: repeat_resolving_preliminary)
  0:00:02.895    31M / 344M  INFO    General                 (repeat_resolving.cpp      :  75)   Setting up preliminary path extend settings
  0:00:02.895    31M / 344M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:02.895    31M / 344M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:02.907    57M / 344M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:02.907    57M / 344M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 256
  0:00:02.907    57M / 344M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 256
  0:00:02.909    59M / 344M  INFO    General                 (extenders_logic.cpp       : 550)   Using 1 paired-end library
  0:00:02.909    59M / 344M  INFO    General                 (extenders_logic.cpp       : 551)   Using 1 paired-end scaffolding library
  0:00:02.909    59M / 344M  INFO    General                 (extenders_logic.cpp       : 552)   Using 0 single read libraries
  0:00:02.909    59M / 344M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 3
  0:00:02.909    59M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 6427 (0%)
  0:00:02.911    60M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 6427 (1%)
  0:00:02.913    60M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 6427 (3%)
  0:00:02.915    61M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 6427 (7%)
  0:00:02.915    62M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 643 paths from 6427 (10%)
  0:00:02.918    63M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 6427 (15%)
  0:00:02.919    64M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1286 paths from 6427 (20%)
  0:00:02.923    67M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1929 paths from 6427 (30%)
  0:00:02.924    67M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 6427 (31%)
  0:00:02.927    69M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2572 paths from 6427 (40%)
  0:00:02.931    72M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3215 paths from 6427 (50%)
  0:00:02.934    74M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3858 paths from 6427 (60%)
  0:00:02.936    75M / 344M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 6427 (63%)
  0:00:02.938    77M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4501 paths from 6427 (70%)
  0:00:02.942    79M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5144 paths from 6427 (80%)
  0:00:02.946    82M / 344M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5787 paths from 6427 (90%)
  0:00:02.956    59M / 344M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:02.956    59M / 344M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:02.959    59M / 344M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:02.959    59M / 344M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:02.963    59M / 344M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:02.963    59M / 344M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:02.977    85M / 344M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:02.984    57M / 344M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:03.082    57M / 344M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:03.082    57M / 344M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:03.082    57M / 344M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:03.085    57M / 344M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:03.085    57M / 344M  INFO    General                 (launcher.cpp              : 265)   Overlaps will not be removed
  0:00:03.088    57M / 344M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:03.088    57M / 344M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:03.088    56M / 344M  INFO    General                 (repeat_resolving.cpp      :  94)   Restoring initial path extend settings
  0:00:03.088    56M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.088    56M / 344M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/strain_graph.gfa"
  0:00:03.100    56M / 344M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:03.126    85M / 344M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:03.143    56M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Second Phase Setup (id: second_phase_setup)
  0:00:03.146    56M / 344M  INFO    General                 (second_phase_setup.cpp    :  18)   Preparing second phase
  0:00:03.157    27M / 344M  INFO    General                 (second_phase_setup.cpp    :  25)   Moving preliminary contigs from "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.fasta" to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/first_pe_contigs.fasta"
  0:00:03.157    27M / 344M  INFO    General                 (second_phase_setup.cpp    :  37)   Ready to run second phase
  0:00:03.157    27M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification (id: simplification)
  0:00:03.157    16M / 344M  INFO    General                 (simplification.cpp        : 397)   Graph simplification started
  0:00:03.158    16M / 344M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.158    16M / 344M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 1
  0:00:03.158    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.159    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.159    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.160    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 2 times
  0:00:03.160    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.161    16M / 344M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 2
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.161    16M / 344M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 3
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.161    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.161    16M / 344M  INFO    General                 (simplification.cpp        : 402)   PROCEDURE == Simplification cycle, iteration 4
  0:00:03.162    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.163    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.163    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.164    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.164    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Low coverage edge remover
  0:00:03.165    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Low coverage edge remover triggered 0 times
  0:00:03.165    16M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Gap Closer (id: late_gapcloser)
  0:00:03.169    30M / 344M  INFO    General                 (edge_index.hpp            : 132)   Size of edge index entries: 12/8
  0:00:03.171    30M / 344M  INFO    General                 (gap_closer.cpp            : 102)   Total edges in tip neighborhood: 12848 out of 12862, length: 2569908
  0:00:03.171    30M / 344M  INFO    General                 (edge_index.hpp            : 196)   Using small index (max_id = 122221)
  0:00:03.178    30M / 344M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:03.223    31M / 344M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1284954 kmers, 928824 bytes occupied (5.78277 bits per kmer).
  0:00:03.225    41M / 344M  INFO    General                 (edge_index_builders.hpp   : 266)   Collecting edge information from graph, this takes a while.
  0:00:03.244    41M / 344M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.320    42M / 344M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:03.328    31M / 344M  INFO    General                 (gap_closer.cpp            : 491)   Initializing gap closer
  0:00:03.328    31M / 344M  INFO   GapCloser                (gap_closer.cpp            : 406)   Collecting gap candidates
  0:00:03.330    31M / 344M  INFO   GapCloser                (gap_closer.cpp            : 410)   Total 215 tips collected, total 216 connection candidates
  0:00:03.330    31M / 344M  INFO   GapCloser                (gap_closer.cpp            : 431)   Closing short gaps complete: filled 0 gaps after checking 216 candidates
  0:00:03.331    31M / 344M  INFO    General                 (gap_closer.cpp            : 495)   Gap closer done
  0:00:03.332    16M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Simplification Cleanup (id: simplification_cleanup)
  0:00:03.332    16M / 344M  INFO    General                 (simplification.cpp        : 189)   PROCEDURE == Post simplification
  0:00:03.332    16M / 344M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.332    16M / 344M  INFO    General                 (graph_simplification.hpp  : 646)   Creating parallel br instance
  0:00:03.333    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:03.333    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:03.334    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:03.335    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:03.335    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:03.336    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:03.336    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.369    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.369    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.370    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.370    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.371    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.371    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.372    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.372    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:03.373    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.373    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.374    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.374    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Relative coverage component remover
  0:00:03.375    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Relative coverage component remover triggered 0 times
  0:00:03.375    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Disconnecting edges with relatively low coverage
  0:00:03.376    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Disconnecting edges with relatively low coverage triggered 0 times
  0:00:03.376    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex tip clipper
  0:00:03.378    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex tip clipper triggered 0 times
  0:00:03.378    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Complex bulge remover
  0:00:03.411    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Complex bulge remover triggered 0 times
  0:00:03.411    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Tip clipper
  0:00:03.412    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Tip clipper triggered 0 times
  0:00:03.412    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final tip clipper
  0:00:03.413    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final tip clipper triggered 0 times
  0:00:03.413    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Bulge remover
  0:00:03.414    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Bulge remover triggered 0 times
  0:00:03.414    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Final bulge remover
  0:00:03.415    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Final bulge remover triggered 0 times
  0:00:03.415    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Thorn remover (meta)
  0:00:03.416    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Thorn remover (meta) triggered 0 times
  0:00:03.416    16M / 344M  INFO    General                 (simplification.cpp        : 344)   Running Hidden EC remover (meta)
  0:00:03.417    16M / 344M  INFO    General                 (simplification.cpp        : 348)   Disrupting self-conjugate edges
  0:00:03.419    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 168)   Running Removing isolated edges
  0:00:03.420    16M / 344M  INFO   Simplification           (parallel_processing.hpp   : 171)   Removing isolated edges triggered 260 times
  0:00:03.421    16M / 344M  INFO    General                 (simplification.cpp        : 508)   After simplification:
  0:00:03.421    16M / 344M  INFO    General                 (simplification.cpp        : 509)     Average coverage = 0.931845
  0:00:03.421    16M / 344M  INFO    General                 (simplification.cpp        : 510)     Total length = 1256471
  0:00:03.422    16M / 344M  INFO    General                 (simplification.cpp        : 511)     Median edge length: 199
  0:00:03.422    16M / 344M  INFO    General                 (simplification.cpp        : 512)     Edges: 12342
  0:00:03.424    16M / 344M  INFO    General                 (simplification.cpp        : 513)     Vertices: 24670
  0:00:03.424    16M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Mismatch Correction (id: mismatch_correction)
  0:00:03.424    16M / 344M  INFO    General                 (graph_pack_helpers.cpp    :  44)   Index refill
  0:00:03.424    16M / 344M  INFO    General                 (edge_index.hpp            : 175)   Using small index (max_id = 122221)
  0:00:03.429    16M / 344M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 410)   Building perfect hash indices
  0:00:03.464    17M / 344M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 446)   Index built. Total 1256471 kmers, 908248 bytes occupied (5.78285 bits per kmer).
  0:00:03.466    27M / 344M  INFO    General                 (edge_index_builders.hpp   : 253)   Collecting edge information from graph, this takes a while.
  0:00:03.483    27M / 344M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 7166 kmers to process
  0:00:03.484    27M / 344M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.484    27M / 344M  INFO    General                 (mismatch_correction.cpp   : 392)   Collect potential mismatches
  0:00:03.484    27M / 344M  INFO    General                 (mismatch_correction.cpp   : 193)   Total 6 edges (out of 12342) with 154 potential mismatch positions (25.6667 positions per edge)
  0:00:03.484    27M / 344M  INFO    General                 (mismatch_correction.cpp   : 394)   Potential mismatches collected
  0:00:03.485    28M / 344M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:03.578    28M / 344M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 99248 reads processed
  0:00:03.579    27M / 344M  INFO    General                 (mismatch_correction.cpp   : 387)   All edges processed
  0:00:03.579    27M / 344M  INFO    General                 (mismatch_correction.cpp   : 442)   Corrected 0 nucleotides
  0:00:03.579    27M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:03.579    27M / 344M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:03.598    27M / 344M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa"
  0:00:03.609    27M / 344M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:03.617    32M / 344M  INFO    General                 (graph_pack_helpers.cpp    :  54)   Normalizing k-mer map. Total 7166 kmers to process
  0:00:03.617    32M / 344M  INFO    General                 (graph_pack_helpers.cpp    :  56)   Normalizing done
  0:00:03.617    32M / 344M  INFO    General                 (pair_info_count.cpp       : 157)   Min edge length for estimation: 900
  0:00:03.617    32M / 344M  INFO    General                 (pair_info_count.cpp       : 168)   Estimating insert size for library #0
  0:00:03.617    32M / 344M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:03.617    32M / 344M  INFO    General                 (paired_info_utils.cpp     :  87)   Estimating insert size (takes a while)
  0:00:03.785   304M / 353M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:04.145   304M / 353M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:04.253   304M / 353M  INFO    General                 (paired_info_utils.cpp     : 104)   Edge pairs: 5579
  0:00:04.253   304M / 353M  INFO    General                 (paired_info_utils.cpp     : 106)   149 paired reads (0.600516% of all) aligned to long edges
  0:00:04.253    32M / 353M  INFO    General                 (pair_info_count.cpp       : 188)     Insert size = 266.685, deviation = 26.3023, left quantile = 230, right quantile = 302, read length = 150
  0:00:04.260    32M / 353M  INFO    General                 (pair_info_count.cpp       : 203)   Filtering data for library #0
  0:00:04.260    32M / 353M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.261    32M / 353M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:04.351    32M / 353M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:04.351    32M / 353M  INFO    General                 (pair_info_count.cpp       : 207)   Mapping library #0
  0:00:04.352    32M / 353M  INFO    General                 (pair_info_count.cpp       : 209)   Mapping paired reads (takes a while)
  0:00:04.352    32M / 353M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.352    32M / 353M  INFO    General                 (paired_info_utils.cpp     : 138)   Left insert size quantile 230, right insert size quantile 302, filtering threshold 1, rounding threshold 0
  0:00:04.355    46M / 353M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:04.446    46M / 353M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 24812 reads processed
  0:00:04.450    32M / 353M  INFO    General                 (pair_info_count.cpp       : 164)   Mapping contigs library #1
  0:00:04.450    32M / 353M  INFO    General                 (pair_info_count.cpp       :  41)   Selecting usual mapper
  0:00:04.450    33M / 353M  INFO    General                 (sequence_mapper_notifier.h:  64)   Starting sequence mapping
  0:00:04.508    34M / 353M  INFO    General                 (sequence_mapper_notifier.h: 103)   Total 6434 reads processed
  0:00:04.508    33M / 353M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:04.508    33M / 353M  INFO    General                 (distance_estimation.cpp   :  42)   Processing library #0
  0:00:04.508    33M / 353M  INFO    General                 (distance_estimation_utils.: 133)   Weight Filter Done
  0:00:04.508    33M / 353M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:04.510    33M / 353M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:04.510    33M / 353M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 12360
  0:00:04.513    32M / 353M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 244
  0:00:04.513    32M / 353M  INFO    General                 (distance_estimation_utils.: 139)   Refining clustered pair information
  0:00:04.513    32M / 353M  INFO    General                 (distance_estimation_utils.: 141)   The refining of clustered pair information has been finished
  0:00:04.513    32M / 353M  INFO    General                 (distance_estimation_utils.: 143)   Improving paired information
  0:00:04.515    32M / 353M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:04.517    32M / 353M  INFO   PairInfoImprover         (pair_info_improver.hpp    :  65)   Paired info stats: missing = 0; contradictional = 0
  0:00:04.517    32M / 353M  INFO    General                 (distance_estimation_utils.:  86)   Filling scaffolding index
  0:00:04.518    32M / 353M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:00:04.519    32M / 353M  INFO    General                 (distance_estimation_utils.:  28)   Filtering info
  0:00:04.519    32M / 353M  INFO    General                 (pair_info_filters.hpp     : 243)   Start filtering; library index size: 12346
  0:00:04.521    32M / 353M  INFO    General                 (pair_info_filters.hpp     : 264)   Done filtering; library index size: 12346
  0:00:04.521    32M / 353M  INFO    General                 (distance_estimation.cpp   :  51)   Clearing raw paired index
  0:00:04.521    32M / 353M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:04.521    32M / 353M  INFO    General                 (repeat_resolving.cpp      :  88)   Using Path-Extend repeat resolving
  0:00:04.521    32M / 353M  INFO    General                 (launcher.cpp              : 603)   ExSPAnder repeat resolving tool started
  0:00:04.526    57M / 353M  INFO    General                 (launcher.cpp              : 420)   Creating main extenders, unique edge length = 2000
  0:00:04.526    58M / 353M  INFO    General                 (launcher.cpp              : 344)   filling path container
  0:00:04.527    58M / 353M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 244
  0:00:04.527    59M / 353M  INFO    General                 (extenders_logic.cpp       : 352)   Creating extender; library index size: 244
  0:00:04.528    60M / 353M  INFO    General                 (extenders_logic.cpp       :  54)   resolvable_repeat_length_bound set to 10000
  0:00:04.529    61M / 353M  INFO    General                 (extenders_logic.cpp       : 550)   Using 1 paired-end library
  0:00:04.529    61M / 353M  INFO    General                 (extenders_logic.cpp       : 551)   Using 1 paired-end scaffolding library
  0:00:04.529    61M / 353M  INFO    General                 (extenders_logic.cpp       : 552)   Using 1 single read library
  0:00:04.529    61M / 353M  INFO    General                 (launcher.cpp              : 387)   Filling backbone edges for long reads scaffolding...
  0:00:04.529    61M / 353M  INFO    General                 (launcher.cpp              : 389)    with long reads paths
  0:00:04.529    61M / 353M  INFO    General                 (launcher.cpp              : 398)   Removing fake unique with paired-end libs
  0:00:04.529    61M / 353M  INFO    General                 (launcher.cpp              : 409)   0 unique edges
  0:00:04.529    61M / 353M  INFO    General                 (extenders_logic.cpp       : 453)   Using 0 long reads scaffolding libraries
  0:00:04.529    61M / 353M  INFO    General                 (extenders_logic.cpp       : 463)   Using additional coordinated coverage extender
  0:00:04.529    61M / 353M  INFO    General                 (launcher.cpp              : 449)   Total number of extenders is 5
  0:00:04.529    61M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 0 paths from 6165 (0%)
  0:00:04.531    62M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 128 paths from 6165 (2%)
  0:00:04.532    63M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 256 paths from 6165 (4%)
  0:00:04.534    64M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 512 paths from 6165 (8%)
  0:00:04.534    64M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 617 paths from 6165 (10%)
  0:00:04.537    66M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 1024 paths from 6165 (16%)
  0:00:04.538    66M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1234 paths from 6165 (20%)
  0:00:04.542    69M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 1851 paths from 6165 (30%)
  0:00:04.543    70M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 2048 paths from 6165 (33%)
  0:00:04.546    71M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 2468 paths from 6165 (40%)
  0:00:04.549    74M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3085 paths from 6165 (50%)
  0:00:04.553    76M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 3702 paths from 6165 (60%)
  0:00:04.555    78M / 353M  INFO    General                 (path_extenders.cpp        :  34)   Processed 4096 paths from 6165 (66%)
  0:00:04.557    79M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4319 paths from 6165 (70%)
  0:00:04.561    81M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 4936 paths from 6165 (80%)
  0:00:04.564    83M / 353M  INFO    General                 (path_extenders.cpp        :  36)   Processed 5553 paths from 6165 (90%)
  0:00:04.573    62M / 353M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.573    62M / 353M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.575    62M / 353M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.575    62M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  60)   Removing overlaps
  0:00:04.575    62M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Marking overlaps
  0:00:04.575    62M / 353M  INFO   OverlapRemover           (overlap_remover.hpp       : 117)   Marking start/end overlaps
  0:00:04.579    62M / 353M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking remaining overlaps
  0:00:04.582    62M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  73)   Splitting paths
  0:00:04.582    62M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  78)   Deduplicating paths
  0:00:04.583    62M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Overlaps removed
  0:00:04.585    62M / 353M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.585    62M / 353M  INFO    General                 (launcher.cpp              : 456)   Closing gaps in paths
  0:00:04.596    86M / 353M  INFO    General                 (launcher.cpp              : 486)   Gap closing completed
  0:00:04.600    58M / 353M  INFO    General                 (launcher.cpp              : 304)   Traversing tandem repeats
  0:00:04.691    58M / 353M  INFO    General                 (launcher.cpp              : 314)   Traversed 0 loops
  0:00:04.691    58M / 353M  INFO    General                 (launcher.cpp              : 252)   Finalizing paths
  0:00:04.691    58M / 353M  INFO    General                 (launcher.cpp              : 254)   Deduplicating paths
  0:00:04.693    58M / 353M  INFO    General                 (launcher.cpp              : 258)   Paths deduplicated
  0:00:04.693    58M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  60)   Removing overlaps
  0:00:04.693    58M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  70)   Marking overlaps
  0:00:04.694    58M / 353M  INFO   OverlapRemover           (overlap_remover.hpp       : 117)   Marking start/end overlaps
  0:00:04.698    58M / 353M  INFO   OverlapRemover           (overlap_remover.hpp       : 120)   Marking remaining overlaps
  0:00:04.701    58M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  73)   Splitting paths
  0:00:04.701    58M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  78)   Deduplicating paths
  0:00:04.702    58M / 353M  INFO   PEResolver               (pe_resolver.cpp           :  80)   Overlaps removed
  0:00:04.704    58M / 353M  INFO    General                 (launcher.cpp              : 275)   Paths finalized
  0:00:04.704    58M / 353M  INFO    General                 (launcher.cpp              : 666)   ExSPAnder repeat resolving tool finished
  0:00:04.705    56M / 353M  INFO   StageManager             (stage.cpp                 : 189)   STAGE == Contig Output (id: contig_output)
  0:00:04.705    56M / 353M  INFO    General                 (contig_output.hpp         :  20)   Outputting contigs to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/before_rr.fasta"
  0:00:04.725    56M / 353M  INFO    General                 (contig_output_stage.cpp   : 155)   Writing GFA graph to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa"
  0:00:04.738    56M / 353M  INFO    General                 (contig_output_stage.cpp   : 169)   Outputting FastG graph to "/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph.fastg"
  0:00:04.772    56M / 353M  INFO    General                 (contig_output_stage.cpp   : 200)   Breaking scaffolds
  0:00:04.797    84M / 353M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.fasta
  0:00:04.804    84M / 353M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.paths
  0:00:04.825    59M / 353M  INFO    General                 (contig_output_stage.cpp   : 101)   Outputting contigs to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/scaffolds.fasta
  0:00:04.833    59M / 353M  INFO    General                 (contig_output_stage.cpp   : 107)   Outputting FastG paths to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/scaffolds.paths
  0:00:04.837    59M / 353M  INFO    General                 (contig_output_stage.cpp   : 114)   Populating GFA with scaffold paths
  0:00:04.840    56M / 353M  INFO    General                 (pipeline.cpp              : 292)   SPAdes finished
  0:00:04.848     1M / 353M  INFO    General                 (main.cpp                  : 131)   Assembling time: 0 hours 0 minutes 4 seconds

===== K55 finished. 


===== Copy files started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/copy_files.py /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/before_rr.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph_after_simplification.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/contigs.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/first_pe_contigs.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/strain_graph.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/strain_graph.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/scaffolds.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/scaffolds.paths /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.paths /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/assembly_graph.fastg /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph.fastg /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55/final_contigs.paths /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/contigs.paths


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /opt/conda/bin/python3 /opt/conda/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta --misc_dir /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled contigs are in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/contigs.fasta
 * Assembled scaffolds are in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.paths
 * Assembly graph is in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph.fastg
 * Assembly graph in GFA format is in /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/spades.log

Thank you for using metaSPAdes! If you use it in your research, please cite:

  Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834.
  doi.org/10.1101/gr.213959.116


        ===      ===    %%  %%  %%%%%%  %%   %%  %%       %%%%   %%%%%   
         ==      ==     %% %%     %%    %%% %%%  %%      %%  %%  %%  %%  
          ==    ==      %%%%      %%    %% % %%  %%      %%%%%%  %%%%%   
           ==  ==       %% %%     %%    %%   %%  %%      %%  %%  %%  %%  
            ====        %%  %%  %%%%%%  %%   %%  %%%%%%  %%  %%  %%%%%   
             ==        ................................................. 
	  v0.1.5

//============================== VERSE setting ===============================\\
||            Running mode : Default(featureCounts)                           ||
||            Feature type : CDS                                              ||
||              Input file : 1 BAM file                                       ||
||                           P /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami ... ||
||             Output file : /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_a ... ||
||         Annotation file : /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_a ... ||
||                                                                            ||
||                 Threads : 4                                                ||
|| Multithreaded BAM unzip : no                                               ||
||                                                                            ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\============= Based on the framework of featureCounts(SUBREAD) =============//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/g ... ||
||    CDSs : 7191                                                             ||
||    CDSs after merge : 7191                                                 ||
||    Genes : 7191                                                            ||
||    Chromosomes : 6651                                                      ||
||                                                                            ||
|| Process BAM file /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Or ... ||
||    Quantifying in paired-end mode.                                         ||
||    Assign read pairs to features...                                        ||
||    Read pairs with missing mates : 13036                                   ||
||    Total read pairs : 17794                                                ||
||    Successfully assigned read pairs : 15624 (87.8%)                        ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\====== VERSE: a Versatile and Efficient Rna-SEq read assignment tool =======//

MetaBAT 2 (2.17 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 250 and minClsSize 200000. with random seed=1753732665
No edges were formed by TNF.
0 bins (0 bases in total) formed.
Running AMRFinder
MetaBAT 2 (2.17 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 250 and minClsSize 200000. with random seed=1753732673
No edges were formed by TNF.
0 bins (0 bases in total) formed.

        ===      ===    %%  %%  %%%%%%  %%   %%  %%       %%%%   %%%%%   
         ==      ==     %% %%     %%    %%% %%%  %%      %%  %%  %%  %%  
          ==    ==      %%%%      %%    %% % %%  %%      %%%%%%  %%%%%   
           ==  ==       %% %%     %%    %%   %%  %%      %%  %%  %%  %%  
            ====        %%  %%  %%%%%%  %%   %%  %%%%%%  %%  %%  %%%%%   
             ==        ................................................. 
	  v0.1.5

//============================== VERSE setting ===============================\\
||            Running mode : Default(featureCounts)                           ||
||            Feature type : CDS                                              ||
||              Input file : 1 BAM file                                       ||
||                           P /outputs/asmbMetaSpades/S28_Skin_HiSeq_cam ... ||
||             Output file : /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_ ... ||
||         Annotation file : /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_ ... ||
||                                                                            ||
||                 Threads : 4                                                ||
|| Multithreaded BAM unzip : no                                               ||
||                                                                            ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\============= Based on the framework of featureCounts(SUBREAD) =============//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/ ... ||
||    CDSs : 6886                                                             ||
||    CDSs after merge : 6886                                                 ||
||    Genes : 6886                                                            ||
||    Chromosomes : 6316                                                      ||
||                                                                            ||
|| Process BAM file /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_ ... ||
||    Quantifying in paired-end mode.                                         ||
||    Assign read pairs to features...                                        ||
||    Read pairs with missing mates : 12985                                   ||
||    Total read pairs : 17792                                                ||
||    Successfully assigned read pairs : 14934 (83.9%)                        ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\====== VERSE: a Versatile and Efficient Rna-SEq read assignment tool =======//


        ===      ===    %%  %%  %%%%%%  %%   %%  %%       %%%%   %%%%%   
         ==      ==     %% %%     %%    %%% %%%  %%      %%  %%  %%  %%  
          ==    ==      %%%%      %%    %% % %%  %%      %%%%%%  %%%%%   
           ==  ==       %% %%     %%    %%   %%  %%      %%  %%  %%  %%  
            ====        %%  %%  %%%%%%  %%   %%  %%%%%%  %%  %%  %%%%%   
             ==        ................................................. 
	  v0.1.5

//============================== VERSE setting ===============================\\
||            Running mode : Default(featureCounts)                           ||
||            Feature type : CDS                                              ||
||              Input file : 1 BAM file                                       ||
||                           P /outputs/asmbMetaSpades/S1_GItract_HiSeq_c ... ||
||             Output file : /outputs/asmbMetaSpades/S1_GItract_HiSeq_cam ... ||
||         Annotation file : /outputs/asmbMetaSpades/S1_GItract_HiSeq_cam ... ||
||                                                                            ||
||                 Threads : 4                                                ||
|| Multithreaded BAM unzip : no                                               ||
||                                                                            ||
||              Paired-end : yes                                              ||
||         Strand specific : no                                               ||
||      Multimapping reads : not counted                                      ||
||                                                                            ||
||          Chimeric reads : counted                                          ||
||        Both ends mapped : not required                                     ||
||                                                                            ||
\\============= Based on the framework of featureCounts(SUBREAD) =============//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asm ... ||
||    CDSs : 6474                                                             ||
||    CDSs after merge : 6474                                                 ||
||    Genes : 6474                                                            ||
||    Chromosomes : 5974                                                      ||
||                                                                            ||
|| Process BAM file /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1 ... ||
||    Quantifying in paired-end mode.                                         ||
||    Assign read pairs to features...                                        ||
||    Read pairs with missing mates : 5735                                    ||
||    Total read pairs : 10913                                                ||
||    Successfully assigned read pairs : 10011 (91.7%)                        ||
||    Running time : 0.00 minutes                                             ||
||                                                                            ||
||                         Read assignment finished.                          ||
||                                                                            ||
\\====== VERSE: a Versatile and Efficient Rna-SEq read assignment tool =======//

Running AMRFinder
#  emapper-2.1.6
# emapper.py  -i /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp --scratch_dir /outputs/tmp --dbmem
[1;33m  /opt/conda/bin/diamond blastp -d /dbs/wgsa2/eggnog_data/eggnog_proteins.dmnd -q /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 -o /outputs/tmp/annots.emapper.hits  --sensitive --iterate -e 0.001 --block-size 4.0 -c 2 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp[0m
Loading source DB...
[31mWarning: this can take a few minutes and load up to 45GB to RAM. Using --dbmem is recommended to annotate a large number of sequences.[0m
 Copying result file /outputs/tmp/annots.emapper.hits from scratch to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.seed_orthologs from scratch to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.annotations from scratch to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations
[31mData in /outputs/tmp will be not removed. Please, clear it manually.[0m
[32mDone[0m
   /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits
   /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs
   /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations

================================================================================
CITATION:
If you use this software, please cite:

[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
      prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
      Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernandez-Plaza,
      Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas
      Rattei, Lars J Jensen, Christian von Mering and Peer Bork. Nucleic Acids
      Research, Volume 47, Issue D1, 8 January 2019, Pages D309-D314,
      https://doi.org/10.1093/nar/gky1085 

[3] Sensitive protein alignments at tree-of-life scale using DIAMOND.
       Buchfink B, Reuter K, Drost HG. 2021.
       Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x

e.g. Functional annotation was performed using emapper-2.1.6 [1]
 based on eggNOG orthology data [2]. Sequence searches were performed using [3].


================================================================================

Total hits processed: 6167
Total time: 1158 secs
FINISHED
[2025-07-28 20:16:38] INFO: CheckM v1.2.2
[2025-07-28 20:16:38] INFO: checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:16:38] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:16:38] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-07-28 20:16:38] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:16:38] INFO: Identifying marker genes in 2 bins with 48 threads:
[2025-07-28 20:16:48] INFO: Saving HMM info to file.
[2025-07-28 20:16:48] INFO: Calculating genome statistics for 2 bins with 48 threads:
[2025-07-28 20:16:48] INFO: Extracting marker genes to align.
[2025-07-28 20:16:48] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:16:48] INFO: Extracting 43 HMMs with 48 threads:
[2025-07-28 20:16:48] INFO: Aligning 43 marker genes with 48 threads:
[2025-07-28 20:16:48] INFO: Reading marker alignment files.
[2025-07-28 20:16:48] INFO: Concatenating alignments.
[2025-07-28 20:16:48] INFO: Placing 2 bins into the genome tree with pplacer (be patient).
[2025-07-28 20:17:23] INFO: { Current stage: 0:00:44.706 || Total: 0:00:44.706 }
[2025-07-28 20:17:23] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2025-07-28 20:17:23] INFO: Reading HMM info from file.
[2025-07-28 20:17:23] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:17:23] INFO: Determining marker sets for each genome bin.
[2025-07-28 20:17:24] INFO: Marker set written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
[2025-07-28 20:17:24] INFO: { Current stage: 0:00:00.737 || Total: 0:00:45.444 }
[2025-07-28 20:17:24] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2025-07-28 20:17:24] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:17:24] INFO: Identifying marker genes in 2 bins with 48 threads:
[2025-07-28 20:18:14] INFO: Saving HMM info to file.
[2025-07-28 20:18:14] INFO: { Current stage: 0:00:49.929 || Total: 0:01:35.373 }
[2025-07-28 20:18:14] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:18:14] INFO: Aligning marker genes with multiple hits in a single bin:
[2025-07-28 20:18:14] INFO: { Current stage: 0:00:00.514 || Total: 0:01:35.888 }
[2025-07-28 20:18:14] INFO: Calculating genome statistics for 2 bins with 48 threads:
[2025-07-28 20:18:14] INFO: { Current stage: 0:00:00.148 || Total: 0:01:36.036 }
[2025-07-28 20:18:14] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:18:14] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:18:14] INFO: Reading HMM info from file.
[2025-07-28 20:18:14] INFO: Parsing HMM hits to marker genes:
Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
mag.lowDepth	root (UID1)	5656	56	24	56	0	0	0	0	0	0.00	0.00	0.00
mag.tooShort	o__Burkholderiales (UID4000)	193	427	214	340	73	12	1	1	0	18.63	2.11	9.52
[2025-07-28 20:18:15] INFO: { Current stage: 0:00:00.209 || Total: 0:01:36.246 }
[2025-07-28 20:18:17] INFO: CheckM v1.2.2
[2025-07-28 20:18:17] INFO: checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
[2025-07-28 20:18:17] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:18:17] INFO: [CheckM - coverage] Calculating coverage of sequences.
[2025-07-28 20:18:17] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:18:17] INFO: Determining bin assignment of each sequence.
[2025-07-28 20:18:17] INFO: Processing 1 file(s) with 48 threads.

[2025-07-28 20:18:17] INFO: Processing S1_GItract_HiSeq_cami_assembly.bam (1 of 1):

    # total reads: 16091
      # properly mapped reads: 11091 (68.9%)
      # duplicate reads: 0 (0.0%)
      # secondary reads: 0 (0.0%)
      # reads failing QC: 118 (0.7%)
      # reads failing alignment length: 1858 (11.5%)
      # reads failing edit distance: 1689 (10.5%)
      # reads not properly paired: 1335 (8.3%)

[2025-07-28 20:18:17] INFO: Writing coverage information to file.
[2025-07-28 20:18:18] INFO: Coverage information written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
[2025-07-28 20:18:18] INFO: { Current stage: 0:00:01.488 || Total: 0:00:01.488 }
[2025-07-28 20:18:19] INFO: CheckM v1.2.2
[2025-07-28 20:18:19] INFO: checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:18:19] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:18:19] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-07-28 20:18:19] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:18:19] INFO: Identifying marker genes in 2 bins with 48 threads:
[2025-07-28 20:18:29] INFO: Saving HMM info to file.
[2025-07-28 20:18:29] INFO: Calculating genome statistics for 2 bins with 48 threads:
[2025-07-28 20:18:29] INFO: Extracting marker genes to align.
[2025-07-28 20:18:29] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:18:29] INFO: Extracting 43 HMMs with 48 threads:
[2025-07-28 20:18:29] INFO: Aligning 43 marker genes with 48 threads:
[2025-07-28 20:18:29] INFO: Reading marker alignment files.
[2025-07-28 20:18:29] INFO: Concatenating alignments.
[2025-07-28 20:18:29] INFO: Placing 2 bins into the genome tree with pplacer (be patient).
[2025-07-28 20:19:17] INFO: { Current stage: 0:00:57.772 || Total: 0:00:57.772 }
[2025-07-28 20:19:17] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2025-07-28 20:19:17] INFO: Reading HMM info from file.
[2025-07-28 20:19:17] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:19:17] INFO: Determining marker sets for each genome bin.
[2025-07-28 20:19:18] INFO: Marker set written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
[2025-07-28 20:19:18] INFO: { Current stage: 0:00:00.743 || Total: 0:00:58.515 }
[2025-07-28 20:19:18] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2025-07-28 20:19:18] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:19:18] INFO: Identifying marker genes in 2 bins with 48 threads:
[2025-07-28 20:19:56] INFO: Saving HMM info to file.
[2025-07-28 20:19:56] INFO: { Current stage: 0:00:38.636 || Total: 0:01:37.152 }
[2025-07-28 20:19:56] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:19:56] INFO: Aligning marker genes with multiple hits in a single bin:
[2025-07-28 20:19:58] INFO: { Current stage: 0:00:01.860 || Total: 0:01:39.013 }
[2025-07-28 20:19:58] INFO: Calculating genome statistics for 2 bins with 48 threads:
[2025-07-28 20:19:58] INFO: { Current stage: 0:00:00.166 || Total: 0:01:39.179 }
[2025-07-28 20:19:58] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:19:58] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:19:58] INFO: Reading HMM info from file.
[2025-07-28 20:19:58] INFO: Parsing HMM hits to marker genes:
Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
mag.lowDepth	root (UID1)	5656	56	24	56	0	0	0	0	0	0.00	0.00	0.00
mag.tooShort	o__Lactobacillales (UID544)	293	475	267	263	135	59	14	3	1	39.86	19.81	5.22
[2025-07-28 20:19:58] INFO: { Current stage: 0:00:00.233 || Total: 0:01:39.413 }
[2025-07-28 20:19:59] INFO: CheckM v1.2.2
[2025-07-28 20:19:59] INFO: checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:19:59] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:19:59] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-07-28 20:19:59] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:19:59] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:19:59] INFO: Identifying marker genes in 1 bins with 48 threads:
[2025-07-28 20:20:06] INFO: Saving HMM info to file.
[2025-07-28 20:20:06] INFO: Calculating genome statistics for 1 bins with 48 threads:
[2025-07-28 20:20:06] INFO: Extracting marker genes to align.
[2025-07-28 20:20:06] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:20:06] INFO: Extracting 43 HMMs with 48 threads:
[2025-07-28 20:20:06] INFO: Aligning 43 marker genes with 48 threads:
[2025-07-28 20:20:07] INFO: Reading marker alignment files.
[2025-07-28 20:20:07] INFO: Concatenating alignments.
[2025-07-28 20:20:07] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
[2025-07-28 20:20:58] INFO: { Current stage: 0:00:58.976 || Total: 0:00:58.976 }
[2025-07-28 20:20:58] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2025-07-28 20:20:58] INFO: Reading HMM info from file.
[2025-07-28 20:20:58] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:20:58] INFO: Determining marker sets for each genome bin.
[2025-07-28 20:20:59] INFO: Marker set written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
[2025-07-28 20:20:59] INFO: { Current stage: 0:00:00.718 || Total: 0:00:59.695 }
[2025-07-28 20:20:59] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2025-07-28 20:20:59] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:20:59] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:20:59] INFO: Identifying marker genes in 1 bins with 48 threads:
[2025-07-28 20:22:02] INFO: Saving HMM info to file.
[2025-07-28 20:22:02] INFO: { Current stage: 0:01:02.607 || Total: 0:02:02.302 }
[2025-07-28 20:22:02] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:22:02] INFO: Aligning marker genes with multiple hits in a single bin:
[2025-07-28 20:22:04] INFO: { Current stage: 0:00:02.137 || Total: 0:02:04.440 }
[2025-07-28 20:22:04] INFO: Calculating genome statistics for 1 bins with 48 threads:
[2025-07-28 20:22:04] INFO: { Current stage: 0:00:00.167 || Total: 0:02:04.607 }
[2025-07-28 20:22:04] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:22:04] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:22:04] INFO: Reading HMM info from file.
[2025-07-28 20:22:04] INFO: Parsing HMM hits to marker genes:
Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
mag.tooShort	g__Staphylococcus (UID301)	45	940	178	563	288	76	12	1	0	36.78	9.24	14.41
[2025-07-28 20:22:04] INFO: { Current stage: 0:00:00.246 || Total: 0:02:04.854 }
[2025-07-28 20:22:05] INFO: CheckM v1.2.2
[2025-07-28 20:22:05] INFO: checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:22:05] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:22:05] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-07-28 20:22:05] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:22:05] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:22:05] INFO: Identifying marker genes in 1 bins with 48 threads:
[2025-07-28 20:22:17] INFO: Saving HMM info to file.
[2025-07-28 20:22:17] INFO: Calculating genome statistics for 1 bins with 48 threads:
[2025-07-28 20:22:17] INFO: Extracting marker genes to align.
[2025-07-28 20:22:17] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:22:17] INFO: Extracting 43 HMMs with 48 threads:
[2025-07-28 20:22:17] INFO: Aligning 43 marker genes with 48 threads:
[2025-07-28 20:22:17] INFO: Reading marker alignment files.
[2025-07-28 20:22:17] INFO: Concatenating alignments.
[2025-07-28 20:22:17] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
[2025-07-28 20:23:00] INFO: { Current stage: 0:00:54.373 || Total: 0:00:54.373 }
[2025-07-28 20:23:00] INFO: [CheckM - lineage_set] Inferring lineage-specific marker sets.
[2025-07-28 20:23:00] INFO: Reading HMM info from file.
[2025-07-28 20:23:00] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:23:00] INFO: Determining marker sets for each genome bin.
[2025-07-28 20:23:01] INFO: Marker set written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
[2025-07-28 20:23:01] INFO: { Current stage: 0:00:01.069 || Total: 0:00:55.442 }
[2025-07-28 20:23:01] INFO: [CheckM - analyze] Identifying marker genes in bins.
[2025-07-28 20:23:01] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:23:01] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:23:01] INFO: Identifying marker genes in 1 bins with 48 threads:
[2025-07-28 20:24:01] INFO: Saving HMM info to file.
[2025-07-28 20:24:01] INFO: { Current stage: 0:01:00.232 || Total: 0:01:55.674 }
[2025-07-28 20:24:01] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:01] INFO: Aligning marker genes with multiple hits in a single bin:
[2025-07-28 20:24:02] INFO: { Current stage: 0:00:01.200 || Total: 0:01:56.874 }
[2025-07-28 20:24:02] INFO: Calculating genome statistics for 1 bins with 48 threads:
[2025-07-28 20:24:02] INFO: { Current stage: 0:00:00.169 || Total: 0:01:57.044 }
[2025-07-28 20:24:02] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:24:02] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:24:02] INFO: Reading HMM info from file.
[2025-07-28 20:24:02] INFO: Parsing HMM hits to marker genes:
Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
mag.tooShort	o__Actinomycetales (UID1812)	229	457	227	302	115	31	6	3	0	29.88	7.48	5.97
[2025-07-28 20:24:03] INFO: { Current stage: 0:00:00.345 || Total: 0:01:57.389 }
[2025-07-28 20:24:04] INFO: CheckM v1.2.2
[2025-07-28 20:24:04] INFO: checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
[2025-07-28 20:24:04] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:04] INFO: [CheckM - coverage] Calculating coverage of sequences.
[2025-07-28 20:24:04] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:04] INFO: Determining bin assignment of each sequence.
[2025-07-28 20:24:04] INFO: Processing 1 file(s) with 48 threads.

[2025-07-28 20:24:04] INFO: Processing S9_Air_HiSeq_cami_assembly.bam (1 of 1):

    # total reads: 21410
      # properly mapped reads: 11568 (54.0%)
      # duplicate reads: 0 (0.0%)
      # secondary reads: 0 (0.0%)
      # reads failing QC: 460 (2.1%)
      # reads failing alignment length: 3492 (16.3%)
      # reads failing edit distance: 3365 (15.7%)
      # reads not properly paired: 2525 (11.8%)

[2025-07-28 20:24:04] INFO: Writing coverage information to file.
[2025-07-28 20:24:05] INFO: Coverage information written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
[2025-07-28 20:24:05] INFO: { Current stage: 0:00:01.441 || Total: 0:00:01.441 }
[2025-07-28 20:24:06] INFO: CheckM v1.2.2
[2025-07-28 20:24:06] INFO: checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
[2025-07-28 20:24:06] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:06] INFO: [CheckM - coverage] Calculating coverage of sequences.
[2025-07-28 20:24:06] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:06] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:06] INFO: Determining bin assignment of each sequence.
[2025-07-28 20:24:06] INFO: Processing 1 file(s) with 48 threads.

[2025-07-28 20:24:06] INFO: Processing S6_Oral_HiSeq_cami_assembly.bam (1 of 1):

    # total reads: 22552
      # properly mapped reads: 11730 (52.0%)
      # duplicate reads: 0 (0.0%)
      # secondary reads: 0 (0.0%)
      # reads failing QC: 401 (1.8%)
      # reads failing alignment length: 3888 (17.2%)
      # reads failing edit distance: 3747 (16.6%)
      # reads not properly paired: 2786 (12.4%)

[2025-07-28 20:24:06] INFO: Writing coverage information to file.
[2025-07-28 20:24:07] INFO: Coverage information written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
[2025-07-28 20:24:07] INFO: { Current stage: 0:00:01.360 || Total: 0:00:01.360 }
[2025-07-28 20:24:08] INFO: CheckM v1.2.2
[2025-07-28 20:24:08] INFO: checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
[2025-07-28 20:24:08] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:08] INFO: [CheckM - coverage] Calculating coverage of sequences.
[2025-07-28 20:24:08] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:08] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:08] INFO: Determining bin assignment of each sequence.
[2025-07-28 20:24:08] INFO: Processing 1 file(s) with 48 threads.

[2025-07-28 20:24:08] INFO: Processing S28_Skin_HiSeq_cami_assembly.bam (1 of 1):

    # total reads: 22599
      # properly mapped reads: 11750 (52.0%)
      # duplicate reads: 0 (0.0%)
      # secondary reads: 0 (0.0%)
      # reads failing QC: 439 (1.9%)
      # reads failing alignment length: 3974 (17.6%)
      # reads failing edit distance: 3940 (17.4%)
      # reads not properly paired: 2496 (11.0%)

[2025-07-28 20:24:09] INFO: Writing coverage information to file.
[2025-07-28 20:24:09] INFO: Coverage information written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
[2025-07-28 20:24:09] INFO: { Current stage: 0:00:01.360 || Total: 0:00:01.360 }
[2025-07-28 20:24:10] INFO: CheckM v1.2.2
[2025-07-28 20:24:10] INFO: checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:10] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:10] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:24:10] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:24:10] INFO: Reading HMM info from file.
[2025-07-28 20:24:10] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:11] INFO: QA information written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt
[2025-07-28 20:24:11] INFO: { Current stage: 0:00:00.235 || Total: 0:00:00.235 }
[2025-07-28 20:24:11] INFO: CheckM v1.2.2
[2025-07-28 20:24:11] INFO: checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:11] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:11] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2025-07-28 20:24:11] INFO: Reading HMM info from file.
[2025-07-28 20:24:11] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:13] INFO: QA information written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
[2025-07-28 20:24:13] INFO: { Current stage: 0:00:01.848 || Total: 0:00:01.848 }
[2025-07-28 20:24:14] INFO: CheckM v1.2.2
[2025-07-28 20:24:14] INFO: checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:14] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:14] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:24:14] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:24:14] INFO: Reading HMM info from file.
[2025-07-28 20:24:14] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:14] INFO: QA information written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt
[2025-07-28 20:24:14] INFO: { Current stage: 0:00:00.225 || Total: 0:00:00.225 }
[2025-07-28 20:24:15] INFO: CheckM v1.2.2
[2025-07-28 20:24:15] INFO: checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:15] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:15] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2025-07-28 20:24:15] INFO: Reading HMM info from file.
[2025-07-28 20:24:15] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:17] INFO: QA information written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
[2025-07-28 20:24:17] INFO: { Current stage: 0:00:01.717 || Total: 0:00:01.717 }
[2025-07-28 20:24:17] INFO: CheckM v1.2.2
[2025-07-28 20:24:17] INFO: checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:17] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:17] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:24:17] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:24:17] INFO: Reading HMM info from file.
[2025-07-28 20:24:17] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:18] INFO: QA information written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt
[2025-07-28 20:24:18] INFO: { Current stage: 0:00:00.244 || Total: 0:00:00.244 }
[2025-07-28 20:24:18] INFO: CheckM v1.2.2
[2025-07-28 20:24:18] INFO: checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:18] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:18] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2025-07-28 20:24:18] INFO: Reading HMM info from file.
[2025-07-28 20:24:18] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:20] INFO: QA information written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
[2025-07-28 20:24:20] INFO: { Current stage: 0:00:01.743 || Total: 0:00:01.743 }
[2025-07-28 20:24:21] INFO: CheckM v1.2.2
[2025-07-28 20:24:21] INFO: checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:21] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:21] INFO: [CheckM - qa] Tabulating genome statistics.
[2025-07-28 20:24:21] INFO: Calculating AAI between multi-copy marker genes.
[2025-07-28 20:24:21] INFO: Reading HMM info from file.
[2025-07-28 20:24:21] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:21] INFO: QA information written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt
[2025-07-28 20:24:21] INFO: { Current stage: 0:00:00.212 || Total: 0:00:00.212 }
[2025-07-28 20:24:22] INFO: CheckM v1.2.2
[2025-07-28 20:24:22] INFO: checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/
[2025-07-28 20:24:22] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:22] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2025-07-28 20:24:22] INFO: Reading HMM info from file.
[2025-07-28 20:24:22] INFO: Parsing HMM hits to marker genes:
[2025-07-28 20:24:24] INFO: QA information written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
[2025-07-28 20:24:24] INFO: { Current stage: 0:00:01.804 || Total: 0:00:01.804 }
[2025-07-28 20:24:25] INFO: CheckM v1.2.2
[2025-07-28 20:24:25] INFO: checkm coding_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95
[2025-07-28 20:24:25] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:25] INFO: [CheckM - coding_plot] Creating coding density histogram and delta-CD plot.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] INFO: CheckM v1.2.2
[2025-07-28 20:24:25] INFO: checkm coding_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95
[2025-07-28 20:24:25] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:25] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/mag.lowDepth.fa (1 of 2)
[2025-07-28 20:24:25] INFO: [CheckM - coding_plot] Creating coding density histogram and delta-CD plot.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/mag.lowDepth.fa (1 of 2)
[2025-07-28 20:24:25] INFO: CheckM v1.2.2
[2025-07-28 20:24:25] INFO: checkm coding_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95
[2025-07-28 20:24:25] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:25] INFO: [CheckM - coding_plot] Creating coding density histogram and delta-CD plot.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/mag.tooShort.fa (1 of 1)
[2025-07-28 20:24:25] INFO: CheckM v1.2.2
[2025-07-28 20:24:25] INFO: checkm coding_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95
[2025-07-28 20:24:25] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:25] INFO: [CheckM - coding_plot] Creating coding density histogram and delta-CD plot.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:25] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/mag.tooShort.fa (1 of 1)
Writing /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html...
[2025-07-28 20:24:27] INFO: Plot written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.lowDepth.coding_density_plots.pdf
[2025-07-28 20:24:27] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/mag.tooShort.fa (2 of 2)
[2025-07-28 20:24:27] INFO: Plot written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.lowDepth.coding_density_plots.pdf
[2025-07-28 20:24:27] INFO: Plotting coding density plots for /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/mag.tooShort.fa (2 of 2)
[2025-07-28 20:24:27] INFO: Plot written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.coding_density_plots.pdf
[2025-07-28 20:24:27] INFO: { Current stage: 0:00:02.520 || Total: 0:00:02.520 }
[2025-07-28 20:24:27] INFO: Plot written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.coding_density_plots.pdf
[2025-07-28 20:24:27] INFO: { Current stage: 0:00:02.539 || Total: 0:00:02.539 }
[2025-07-28 20:24:28] INFO: CheckM v1.2.2
[2025-07-28 20:24:28] INFO: checkm marker_plot --image_type pdf -x fa --dpi 400 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:28] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:28] INFO: [CheckM - marker_plot] Creating marker gene position plot.
[2025-07-28 20:24:28] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:28] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:28] INFO: Plotting marker gene position plot for mag.tooShort (1 of 1)
[2025-07-28 20:24:28] INFO: Markers reside on 198 of 7,010 sequences which span 0.06 of 1.93 (3.0%) Mb
[2025-07-28 20:24:28] INFO: CheckM v1.2.2
[2025-07-28 20:24:28] INFO: checkm marker_plot --image_type pdf -x fa --dpi 400 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:28] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:28] INFO: [CheckM - marker_plot] Creating marker gene position plot.
[2025-07-28 20:24:28] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:28] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:28] INFO: Plotting marker gene position plot for mag.tooShort (1 of 1)
[2025-07-28 20:24:28] INFO: Markers reside on 465 of 6,820 sequences which span 0.14 of 1.89 (7.6%) Mb
[2025-07-28 20:24:29] INFO: Plot written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.coding_density_plots.pdf
[2025-07-28 20:24:29] INFO: { Current stage: 0:00:04.668 || Total: 0:00:04.668 }
[2025-07-28 20:24:29] INFO: Plot written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.coding_density_plots.pdf
[2025-07-28 20:24:29] INFO: { Current stage: 0:00:04.755 || Total: 0:00:04.755 }
[2025-07-28 20:24:30] INFO: CheckM v1.2.2
[2025-07-28 20:24:30] INFO: checkm marker_plot --image_type pdf -x fa --dpi 400 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:30] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:30] INFO: [CheckM - marker_plot] Creating marker gene position plot.
[2025-07-28 20:24:30] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:30] INFO: Plotting marker gene position plot for mag.lowDepth (1 of 2)
[2025-07-28 20:24:30] INFO: No marker genes found in bin.
[2025-07-28 20:24:30] INFO: Plotting marker gene position plot for mag.tooShort (2 of 2)
[2025-07-28 20:24:30] INFO: Markers reside on 98 of 6,169 sequences which span 0.03 of 1.59 (1.6%) Mb
[2025-07-28 20:24:30] INFO: CheckM v1.2.2
[2025-07-28 20:24:30] INFO: checkm marker_plot --image_type pdf -x fa --dpi 400 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:30] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:30] INFO: [CheckM - marker_plot] Creating marker gene position plot.
[2025-07-28 20:24:30] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:30] INFO: Plotting marker gene position plot for mag.lowDepth (1 of 2)
[2025-07-28 20:24:30] INFO: No marker genes found in bin.
[2025-07-28 20:24:30] INFO: Plotting marker gene position plot for mag.tooShort (2 of 2)
[2025-07-28 20:24:30] INFO: Markers reside on 303 of 6,795 sequences which span 0.09 of 1.85 (4.9%) Mb
[2025-07-28 20:24:31] INFO: Plot written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.marker_pos_plot.pdf
[2025-07-28 20:24:31] INFO: { Current stage: 0:00:03.348 || Total: 0:00:03.348 }
[2025-07-28 20:24:32] INFO: Plot written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.marker_pos_plot.pdf
[2025-07-28 20:24:32] INFO: { Current stage: 0:00:01.778 || Total: 0:00:01.778 }
[2025-07-28 20:24:32] INFO: CheckM v1.2.2
[2025-07-28 20:24:32] INFO: checkm nx_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:32] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:32] INFO: [CheckM - nx_plot] Creating Nx-plots.
[2025-07-28 20:24:32] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:32] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:32] INFO: Plotting Nx-plot for mag.tooShort (1 of 1)
[2025-07-28 20:24:32] INFO: Plot written to: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.nx_plot.pdf
[2025-07-28 20:24:32] INFO: { Current stage: 0:00:00.337 || Total: 0:00:00.337 }
[2025-07-28 20:24:32] INFO: CheckM v1.2.2
[2025-07-28 20:24:32] INFO: checkm nx_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:32] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:32] INFO: [CheckM - nx_plot] Creating Nx-plots.
[2025-07-28 20:24:32] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:32] INFO: Plotting Nx-plot for mag.lowDepth (1 of 2)
[2025-07-28 20:24:33] INFO: Plot written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.lowDepth.nx_plot.pdf
[2025-07-28 20:24:33] INFO: Plotting Nx-plot for mag.tooShort (2 of 2)
[2025-07-28 20:24:33] INFO: Plot written to: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.nx_plot.pdf
[2025-07-28 20:24:33] INFO: { Current stage: 0:00:00.569 || Total: 0:00:00.569 }
[2025-07-28 20:24:35] INFO: Plot written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.marker_pos_plot.pdf
[2025-07-28 20:24:35] INFO: { Current stage: 0:00:04.948 || Total: 0:00:04.948 }
[2025-07-28 20:24:36] INFO: CheckM v1.2.2
[2025-07-28 20:24:36] INFO: checkm nx_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:36] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:36] INFO: [CheckM - nx_plot] Creating Nx-plots.
[2025-07-28 20:24:36] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:36] INFO: Plotting Nx-plot for mag.lowDepth (1 of 2)
[2025-07-28 20:24:36] INFO: Plot written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.lowDepth.nx_plot.pdf
[2025-07-28 20:24:36] INFO: Plotting Nx-plot for mag.tooShort (2 of 2)
[2025-07-28 20:24:36] INFO: Plot written to: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.nx_plot.pdf
[2025-07-28 20:24:36] INFO: { Current stage: 0:00:00.579 || Total: 0:00:00.579 }
[2025-07-28 20:24:38] INFO: Plot written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.marker_pos_plot.pdf
[2025-07-28 20:24:38] INFO: { Current stage: 0:00:09.645 || Total: 0:00:09.645 }
[2025-07-28 20:24:38] INFO: CheckM v1.2.2
[2025-07-28 20:24:38] INFO: checkm nx_plot --image_type pdf -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/
[2025-07-28 20:24:38] INFO: CheckM data: /opt/conda/envs/checkm/checkm_data
[2025-07-28 20:24:38] INFO: [CheckM - nx_plot] Creating Nx-plots.
[2025-07-28 20:24:38] WARNING: Skipping bin mag.unbinned.fa as it has a size of 0 bytes.
[2025-07-28 20:24:38] WARNING: Skipping bin mag.lowDepth.fa as it has a size of 0 bytes.
[2025-07-28 20:24:38] INFO: Plotting Nx-plot for mag.tooShort (1 of 1)
[2025-07-28 20:24:39] INFO: Plot written to: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/mag.tooShort.nx_plot.pdf
[2025-07-28 20:24:39] INFO: { Current stage: 0:00:00.315 || Total: 0:00:00.315 }
#  emapper-2.1.6
# emapper.py  -i /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp --scratch_dir /outputs/tmp --dbmem
[1;33m  /opt/conda/bin/diamond blastp -d /dbs/wgsa2/eggnog_data/eggnog_proteins.dmnd -q /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 -o /outputs/tmp/annots.emapper.hits  --sensitive --iterate -e 0.001 --block-size 4.0 -c 2 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp[0m
Loading source DB...
[31mWarning: this can take a few minutes and load up to 45GB to RAM. Using --dbmem is recommended to annotate a large number of sequences.[0m
 Copying result file /outputs/tmp/annots.emapper.hits from scratch to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.seed_orthologs from scratch to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.annotations from scratch to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations
[31mData in /outputs/tmp will be not removed. Please, clear it manually.[0m
[32mDone[0m
   /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits
   /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs
   /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations

================================================================================
CITATION:
If you use this software, please cite:

[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
      prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
      Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernandez-Plaza,
      Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas
      Rattei, Lars J Jensen, Christian von Mering and Peer Bork. Nucleic Acids
      Research, Volume 47, Issue D1, 8 January 2019, Pages D309-D314,
      https://doi.org/10.1093/nar/gky1085 

[3] Sensitive protein alignments at tree-of-life scale using DIAMOND.
       Buchfink B, Reuter K, Drost HG. 2021.
       Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x

e.g. Functional annotation was performed using emapper-2.1.6 [1]
 based on eggNOG orthology data [2]. Sequence searches were performed using [3].


================================================================================

Total hits processed: 6295
Total time: 1147 secs
FINISHED
Loading taxonomy...
Importing /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt...
Importing /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt...
Importing /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt...
Importing /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt...
Writing /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html...
#  emapper-2.1.6
# emapper.py  -i /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp --scratch_dir /outputs/tmp --dbmem
[1;33m  /opt/conda/bin/diamond blastp -d /dbs/wgsa2/eggnog_data/eggnog_proteins.dmnd -q /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 -o /outputs/tmp/annots.emapper.hits  --sensitive --iterate -e 0.001 --block-size 4.0 -c 2 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp[0m
Loading source DB...
[31mWarning: this can take a few minutes and load up to 45GB to RAM. Using --dbmem is recommended to annotate a large number of sequences.[0m
 Copying result file /outputs/tmp/annots.emapper.hits from scratch to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.seed_orthologs from scratch to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.annotations from scratch to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations
[31mData in /outputs/tmp will be not removed. Please, clear it manually.[0m
[32mDone[0m
   /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits
   /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs
   /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations

================================================================================
CITATION:
If you use this software, please cite:

[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
      prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
      Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernandez-Plaza,
      Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas
      Rattei, Lars J Jensen, Christian von Mering and Peer Bork. Nucleic Acids
      Research, Volume 47, Issue D1, 8 January 2019, Pages D309-D314,
      https://doi.org/10.1093/nar/gky1085 

[3] Sensitive protein alignments at tree-of-life scale using DIAMOND.
       Buchfink B, Reuter K, Drost HG. 2021.
       Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x

e.g. Functional annotation was performed using emapper-2.1.6 [1]
 based on eggNOG orthology data [2]. Sequence searches were performed using [3].


================================================================================

Total hits processed: 6308
Total time: 1173 secs
FINISHED
Writing /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html...
`summarise()` has grouped output by 'Kingdom', 'Phylum', 'Class', 'Order',
'Family', 'Genus', 'Species'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Kingdom', 'Phylum', 'Class', 'Order',
'Family', 'Genus', 'Species'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Kingdom', 'Phylum', 'Class', 'Order',
'Family', 'Genus', 'Species'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Kingdom', 'Phylum', 'Class', 'Order',
'Family', 'Genus', 'Species'. You can override using the `.groups` argument.
Warning message:
There was 1 warning in `group_by()`.
ℹ In argument: `across(tiers)`.
Caused by warning:
! Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
  # Was:
  data %>% select(tiers)

  # Now:
  data %>% select(all_of(tiers))

See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>. 
Warning message:
In merge.data.frame(x, y, by = c(tiers, "Lineage"), all = T) :
  column names ‘Counts.x’, ‘Counts.y’ are duplicated in the result
Warning message:
In dir.create(output$dir) :
  '/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables' already exists
[1] "-----------> docopt settings---------------------"
[1] "Usage: DiversityPlots_v1.R [options]\n  --help            show this screen.\n  --wdir PATH       give path to working dir /project main dir  [default: pwd ].\n  --indir PATH      give path to input files directory [default: profiles/merged_tables ].\n  --mfile NAME      give name of mapping file [default: mapping.txt ].\n  --outdir NAME     give path & name of output directory to create [default: pwd/profiles/DiversityPlots]."
List of 10
 $ --help  : logi FALSE
 $ --wdir  : chr "/outputs/tmp"
 $ --indir : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ --mfile : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt"
 $ --outdir: chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/"
 $ help    : logi FALSE
 $ wdir    : chr "/outputs/tmp"
 $ indir   : chr "/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/"
 $ mfile   : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt"
 $ outdir  : chr "/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/"
NULL
[1] "-----------> docopt settings------^^^^-----------"
                                   SampleID TreatmentGroup
S1_GItract_HiSeq_cami S1_GItract_HiSeq_cami        Gitract
S28_Skin_HiSeq_cami     S28_Skin_HiSeq_cami           Skin
S6_Oral_HiSeq_cami       S6_Oral_HiSeq_cami           Oral
S9_Air_HiSeq_cami         S9_Air_HiSeq_cami            Air
                                                             ForwardFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz
                                                             ReverseFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz
[1] "-----------> read in mapping file^^^"
         S1_GItract_HiSeq_cami S28_Skin_HiSeq_cami S6_Oral_HiSeq_cami
id544580                     0                   0                  0
id1654                       0                   0                  0
id2049                       0                   1                  0
id1678                      43                   0                  0
id273384                     0                   0                 11
id1703                       0                   0                 15
         S9_Air_HiSeq_cami
id544580                93
id1654                  16
id2049                   0
id1678                   0
id273384                 0
id1703                   0
[1] "-----------> read in Counts file^^^"
          Kingdom         Phylum         Class             Order
id544580 Bacteria Actinomycetota Actinomycetes   Actinomycetales
id1654   Bacteria Actinomycetota Actinomycetes   Actinomycetales
id2049   Bacteria Actinomycetota Actinomycetes   Actinomycetales
id1678   Bacteria Actinomycetota Actinomycetes Bifidobacteriales
id273384 Bacteria Actinomycetota Actinomycetes     Micrococcales
id1703   Bacteria Actinomycetota Actinomycetes     Micrococcales
                     Family           Genus                    Species
id544580   Actinomycetaceae     Actinomyces           Actinomyces_oris
id1654     Actinomycetaceae     Actinomyces             Actinomyces_sp
id2049     Actinomycetaceae                        Actinomycetaceae_sp
id1678   Bifidobacteriaceae Bifidobacterium         Bifidobacterium_sp
id273384  Brevibacteriaceae  Brevibacterium Brevibacterium_aurantiacum
id1703    Brevibacteriaceae  Brevibacterium      Brevibacterium_linens
[1] "-----------> read in TAX file^^^"
[1] "-----------> Calculating alpha diversity indexes"
                      SpRichness  Evenness NumbReads  Shannon InvSimpson
S1_GItract_HiSeq_cami         83 0.6645420     24799 2.936505  10.724059
S28_Skin_HiSeq_cami           81 0.5341040     24491 2.347093   5.437346
S6_Oral_HiSeq_cami           173 0.4762322     24705 2.454163   5.303898
S9_Air_HiSeq_cami            115 0.6124502     24794 2.906035   8.514603
                          chao1
S1_GItract_HiSeq_cami  86.55556
S28_Skin_HiSeq_cami   126.56250
S6_Oral_HiSeq_cami    341.10000
S9_Air_HiSeq_cami     148.13636
[1] "-----------> Adding these apha indices to metadata ^^^"
                   group1  group2   variable  value
                   <char>  <char>     <fctr>  <num>
 1: S1_GItract_HiSeq_cami Gitract SpRichness  83.00
 2:   S28_Skin_HiSeq_cami    Skin SpRichness  81.00
 3:    S6_Oral_HiSeq_cami    Oral SpRichness 173.00
 4:     S9_Air_HiSeq_cami     Air SpRichness 115.00
 5: S1_GItract_HiSeq_cami Gitract   Evenness   0.66
 6:   S28_Skin_HiSeq_cami    Skin   Evenness   0.53
 7:    S6_Oral_HiSeq_cami    Oral   Evenness   0.48
 8:     S9_Air_HiSeq_cami     Air   Evenness   0.61
 9: S1_GItract_HiSeq_cami Gitract    Shannon   2.94
10:   S28_Skin_HiSeq_cami    Skin    Shannon   2.35
11:    S6_Oral_HiSeq_cami    Oral    Shannon   2.45
12:     S9_Air_HiSeq_cami     Air    Shannon   2.91
13: S1_GItract_HiSeq_cami Gitract InvSimpson  10.72
14:   S28_Skin_HiSeq_cami    Skin InvSimpson   5.44
15:    S6_Oral_HiSeq_cami    Oral InvSimpson   5.30
16:     S9_Air_HiSeq_cami     Air InvSimpson   8.51
[1] "-----------> plotting alpha diversity"
null device 
          1 
[1] "-----------> prepping AMPVIS2 object"
[1] "-----------> checking some AMPVIS2 data"
         S1_GItract_HiSeq_cami S28_Skin_HiSeq_cami S6_Oral_HiSeq_cami
id544580                     0                   0                  0
id1654                       0                   0                  0
id2049                       0                   1                  0
id1678                      43                   0                  0
id273384                     0                   0                 11
id1703                       0                   0                 15
         S9_Air_HiSeq_cami
id544580                93
id1654                  16
id2049                   0
id1678                   0
id273384                 0
id1703                   0
          Kingdom         Phylum         Class             Order
id544580 Bacteria Actinomycetota Actinomycetes   Actinomycetales
id1654   Bacteria Actinomycetota Actinomycetes   Actinomycetales
id2049   Bacteria Actinomycetota Actinomycetes   Actinomycetales
id1678   Bacteria Actinomycetota Actinomycetes Bifidobacteriales
                     Family           Genus             Species      OTU
id544580   Actinomycetaceae     Actinomyces    Actinomyces_oris id544580
id1654     Actinomycetaceae     Actinomyces      Actinomyces_sp   id1654
id2049     Actinomycetaceae                 Actinomycetaceae_sp   id2049
id1678   Bifidobacteriaceae Bifidobacterium  Bifidobacterium_sp   id1678
                                   SampleID TreatmentGroup
S1_GItract_HiSeq_cami S1_GItract_HiSeq_cami        Gitract
S28_Skin_HiSeq_cami     S28_Skin_HiSeq_cami           Skin
S6_Oral_HiSeq_cami       S6_Oral_HiSeq_cami           Oral
S9_Air_HiSeq_cami         S9_Air_HiSeq_cami            Air
                                                             ForwardFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz
                                                             ReverseFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz
                      SpRichness Evenness NumbReads Shannon InvSimpson  chao1
S1_GItract_HiSeq_cami         83     0.66     24799    2.94      10.72  86.56
S28_Skin_HiSeq_cami           81     0.53     24491    2.35       5.44 126.56
S6_Oral_HiSeq_cami           173     0.48     24705    2.45       5.30 341.10
S9_Air_HiSeq_cami            115     0.61     24794    2.91       8.51 148.14
[1] "-----------> checking AMPVIS2 data ^^^"
[1] "-----------> making PCOA plot"
null device 
          1 
[1] "-----------> making nMDS plot"
null device 
          1 
[1] "-----------> making heatmap profile graph"
null device 
          1 
[1] "-----------> making rarecurve graph"
null device 
          1 
[1] "-----------> making rank abundance / Whittaker plot"
null device 
          1 
#  emapper-2.1.6
# emapper.py  -i /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp --scratch_dir /outputs/tmp --dbmem
[1;33m  /opt/conda/bin/diamond blastp -d /dbs/wgsa2/eggnog_data/eggnog_proteins.dmnd -q /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 -o /outputs/tmp/annots.emapper.hits  --sensitive --iterate -e 0.001 --block-size 4.0 -c 2 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp[0m
Loading source DB...
[31mWarning: this can take a few minutes and load up to 45GB to RAM. Using --dbmem is recommended to annotate a large number of sequences.[0m
 Copying result file /outputs/tmp/annots.emapper.hits from scratch to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.seed_orthologs from scratch to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations
 Copying result file /outputs/tmp/annots.emapper.annotations from scratch to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations
[31mData in /outputs/tmp will be not removed. Please, clear it manually.[0m
[32mDone[0m
   /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits
   /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs
   /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations

================================================================================
CITATION:
If you use this software, please cite:

[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
      prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
      Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
      Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293

[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
      orthology resource based on 5090 organisms and 2502 viruses. Jaime
      Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernandez-Plaza,
      Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas
      Rattei, Lars J Jensen, Christian von Mering and Peer Bork. Nucleic Acids
      Research, Volume 47, Issue D1, 8 January 2019, Pages D309-D314,
      https://doi.org/10.1093/nar/gky1085 

[3] Sensitive protein alignments at tree-of-life scale using DIAMOND.
       Buchfink B, Reuter K, Drost HG. 2021.
       Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x

e.g. Functional annotation was performed using emapper-2.1.6 [1]
 based on eggNOG orthology data [2]. Sequence searches were performed using [3].


================================================================================

Total hits processed: 5855
Total time: 1161 secs
FINISHED
S1_GItract_HiSeq_cami
S28_Skin_HiSeq_cami
S6_Oral_HiSeq_cami
S9_Air_HiSeq_cami
Writing /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html...
Warning message:
In merge.data.frame(x, y, by = c(tiers, "allTiers"), all = T) :
  column names ‘Counts.x’, ‘Counts.y’ are duplicated in the result
Warning message:
In dir.create(output$dir) :
  '/outputs/PWYprofiles/keggPWYs.MP/merged_tables' already exists
Warning message:
In merge.data.frame(x, y, by = c("annot", "geneNAME"), all = T) :
  column names ‘geneTPM.x’, ‘geneTPM.y’ are duplicated in the result
[1] "------> start of PWY Diversity Plots <------"
[1] "------> docopt settings ------"
[1] "Usage: DiversityPlots_v3.R [options]\n  --help            show this screen.\n  --wdir PATH       give path to working dir /project main dir  [default: pwd ].\n  --indir PATH      give path to input files directory [default: profiles/merged_tables ].\n  --mfile NAME      give name of mapping file [default: mapping.txt ].\n  --outdir NAME     give path & name of output directory to create [default: pwd/profiles/DiversityPlots]."
List of 10
 $ --help  : logi FALSE
 $ --wdir  : chr "/outputs/tmp"
 $ --indir : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ --mfile : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt"
 $ --outdir: chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/"
 $ help    : logi FALSE
 $ wdir    : chr "/outputs/tmp"
 $ indir   : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ mfile   : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt"
 $ outdir  : chr "/outputs/PWYprofiles/keggPWYs.MP/DivPlots/"
NULL
[1] "-----------> docopt settings------^^^^"
[1] "-----------> reading in mapping file:"
                                   SampleID TreatmentGroup
S1_GItract_HiSeq_cami S1_GItract_HiSeq_cami        Gitract
S28_Skin_HiSeq_cami     S28_Skin_HiSeq_cami           Skin
S6_Oral_HiSeq_cami       S6_Oral_HiSeq_cami           Oral
S9_Air_HiSeq_cami         S9_Air_HiSeq_cami            Air
                                                             ForwardFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz
                                                             ReverseFastqFile
S1_GItract_HiSeq_cami /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz
S28_Skin_HiSeq_cami     /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz
S6_Oral_HiSeq_cami       /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz
S9_Air_HiSeq_cami         /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz
[1] "-----------> done importing mapping file^^^"
[1] "-----------> prepping AMPVIS2 object"
                 Phylum                            Order
PWY1 Cellular Processes            Cell growth and death
PWY2 Cellular Processes            Cell growth and death
PWY3 Cellular Processes            Cell growth and death
PWY4 Cellular Processes                    Cell motility
PWY5 Cellular Processes                    Cell motility
PWY6 Cellular Processes Cellular community - prokaryotes
                                  Species S1_GItract_HiSeq_cami
PWY1                      Apoptosis - fly              6.166667
PWY2             Cell cycle - Caulobacter              6.407738
PWY3                      Meiosis - yeast              7.000000
PWY4                 Bacterial chemotaxis              5.591503
PWY5                   Flagellar assembly              5.956790
PWY6 Biofilm formation - Escherichia coli              6.544444
     S28_Skin_HiSeq_cami S6_Oral_HiSeq_cami S9_Air_HiSeq_cami
PWY1            3.250000           6.000000          0.000000
PWY2            8.575000           8.682222          8.615278
PWY3           15.500000           0.000000          0.000000
PWY4            0.000000           0.000000          7.512245
PWY5            6.671429           5.514286          8.522676
PWY6           13.000000           9.727273          7.462222
[1] "-----------> making PCOA plot"
null device 
          1 
[1] "-----------> making nMDS plot"
null device 
          1 
[1] "-----------> making heatmap profile graph"
null device 
          1 
Cleaning output...
---> moving FASTA & BAM files from assembly to /outputs/asmb_files/ 
---> links to create S1_GItract_HiSeq_cami
---> links to create S28_Skin_HiSeq_cami
---> links to create S6_Oral_HiSeq_cami
---> links to create S9_Air_HiSeq_cami
[2025-07-28 21:23:10.110 UTC] Generating outputs report: /outputs/outputs.json
[2025-07-28 21:23:10.111 UTC] Output reported: /outputs/for_analyze_with_microbiomedb.biom
[2025-07-28 21:23:10.111 UTC] Output reported: /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_BetaDiv_PCoA.png
[2025-07-28 21:23:10.112 UTC] Output reported: /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_BetaDiv_PCoA.png
[2025-07-28 21:23:10.112 UTC] Output reported: /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html
[2025-07-28 21:23:10.112 UTC] Output reported: /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html
[2025-07-28 21:23:10.112 UTC] Output reported: /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX.txt
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY+allTiers.txt
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_geneTPMtable.txt
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S1_GItract_HiSeq_cami_assembly.bam
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S28_Skin_HiSeq_cami_assembly.bam
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S9_Air_HiSeq_cami_assembly.bam
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S6_Oral_HiSeq_cami_assembly.bam
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S1_GItract_HiSeq_cami_assembly.fasta
[2025-07-28 21:23:10.113 UTC] Output reported: /outputs/asmb_files/S28_Skin_HiSeq_cami_assembly.fasta
[2025-07-28 21:23:10.114 UTC] Output reported: /outputs/asmb_files/S9_Air_HiSeq_cami_assembly.fasta
[2025-07-28 21:23:10.114 UTC] Output reported: /outputs/asmb_files/S6_Oral_HiSeq_cami_assembly.fasta
[2025-07-28 21:23:10.114 UTC] Outputs report generated: /outputs/outputs.json
[2025-07-28 21:23:10.114 UTC] Pipeline completed
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Provided resources: mem_gb=184
Job stats:
job                               count
------------------------------  -------
PWY_collation                         1
PWY_collation_biom                    1
PWY_diversity_plots                   1
TAX_collation                         1
TAX_collation_biom                    1
TAX_diversity_plots                   1
add_de_replication_stats              4
all                                   1
bowtie2_build                         4
bowtie2_run                           4
checkm_coverage                       4
checkm_lineage_wf                     4
checkm_plots                          4
checkm_profile                        4
checkm_qa                             4
compress_kraken2_decontaminate        4
copy_annotation_file                  4
cp_geneTPM_files                      1
create_pathways_report                4
gene_annot_geneTPMs                   4
gene_annot_iTPMs                      4
gene_annot_seqExtract                 4
gene_annotation                       4
gene_annotation_grep                  4
gene_prediction                       4
generate_scafftax                     4
gff_to_gtf                            4
join_profiles_tax                     4
kreport2krona_import_text             1
kreport2krona_per_sample              4
krona_import_text                     1
kt_tax_html                           1
make_biom                             1
metabat2_run                          4
pwy_biom_per_sample                   4
rename_verse_summary                  4
run_amrfinder                         4
run_bbtools_stats                     4
run_fastp                             4
run_genes2krona                       4
run_kraken2_classification            4
run_kraken2_decontaminate             4
run_metaspades                        4
run_min_path                          4
run_verse                             4
samtools_to_bam                       4
scaffold_and_read_counts              4
tax_biom_per_sample                   4
tax_classification_genes              4
tax_classification_scaffolds          4
tax_genes_4krona                      4
tax_genes_ABUNtabtax                  4
taxbin_krona_html                     1
taxbin_krona_txt                      4
tpm_normalization                     4
total                               181


    set +o pipefail
    echo "Dependencies:"
    fastp --version
    metaspades.py --version
    bowtie2 --version | awk '{print "bowtie2 version", $3}' | head -n1
    samtools --version | head -n1
    metabat2 2>&1 >/dev/null | grep version
    prodigal -v 2>&1 >/dev/null | head -n2 | tail -n1
    conda list checkm -n checkm | tail -n1 | awk '{print $1, $2}'
    ktImportText | head -n2 | tail -n1 | sed 's/[^a-zA-Z0-9. ]//g' | sed 's/^ *//g'
    metaprokka --version
    cat /usr/local/src/MinPath/MinPath.py | grep version | head -n1
    verse -v | head -n2 | tail -n1
    kraken2 --version | head -n1
    amrfinder --version | awk '{print "AMRFinder version", $1}'
    emapper.py --version | tail -n1 | awk '{print $1}'
    R --version | head -n1
    snakemake --version | awk '{print "Snakemake version", $1}'
    
fastp 0.24.0
Use of uninitialized value in subroutine entry at /opt/conda/bin/metaprokka line 236.
metaprokka 1.15.0
Select jobs to execute...

[Mon Jul 28 19:56:52 2025]
rule run_fastp:
    input: /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz, /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz
    output: /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S9_Air_HiSeq_cami_fastplog.html, /outputs/TEDreads/S9_Air_HiSeq_cami_fastp.json, /outputs/TEDreads/S9_Air_HiSeq_cami_fastplog.txt
    jobid: 16
    reason: Missing output files: /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

[Mon Jul 28 19:56:52 2025]
rule run_fastp:
    input: /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz, /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz
    output: /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S28_Skin_HiSeq_cami_fastplog.html, /outputs/TEDreads/S28_Skin_HiSeq_cami_fastp.json, /outputs/TEDreads/S28_Skin_HiSeq_cami_fastplog.txt
    jobid: 11
    reason: Missing output files: /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

[Mon Jul 28 19:56:52 2025]
rule run_fastp:
    input: /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz, /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz
    output: /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S6_Oral_HiSeq_cami_fastplog.html, /outputs/TEDreads/S6_Oral_HiSeq_cami_fastp.json, /outputs/TEDreads/S6_Oral_HiSeq_cami_fastplog.txt
    jobid: 21
    reason: Missing output files: /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
fastp -i /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz -I /inputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz -o /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz -O /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz -h /outputs/TEDreads/S6_Oral_HiSeq_cami_fastplog.html -j /outputs/TEDreads/S6_Oral_HiSeq_cami_fastp.json --trim_poly_x --cut_window_size 4 --thread 16 --low_complexity_filter --correction --average_qual 10 --length_required 60 --cut_front --cut_front_mean_quality 20 --cut_tail  --cut_tail_mean_quality 15 2>> /outputs/TEDreads/S6_Oral_HiSeq_cami_fastplog.txt
fastp -i /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz -I /inputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz -o /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz -O /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz -h /outputs/TEDreads/S28_Skin_HiSeq_cami_fastplog.html -j /outputs/TEDreads/S28_Skin_HiSeq_cami_fastp.json --trim_poly_x --cut_window_size 4 --thread 16 --low_complexity_filter --correction --average_qual 10 --length_required 60 --cut_front --cut_front_mean_quality 20 --cut_tail  --cut_tail_mean_quality 15 2>> /outputs/TEDreads/S28_Skin_HiSeq_cami_fastplog.txt
fastp -i /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz -I /inputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz -o /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz -O /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz -h /outputs/TEDreads/S9_Air_HiSeq_cami_fastplog.html -j /outputs/TEDreads/S9_Air_HiSeq_cami_fastp.json --trim_poly_x --cut_window_size 4 --thread 16 --low_complexity_filter --correction --average_qual 10 --length_required 60 --cut_front --cut_front_mean_quality 20 --cut_tail  --cut_tail_mean_quality 15 2>> /outputs/TEDreads/S9_Air_HiSeq_cami_fastplog.txt
[Mon Jul 28 19:56:56 2025]
Finished job 16.
1 of 181 steps (1%) done
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_fastp.json.
Select jobs to execute...

[Mon Jul 28 19:56:56 2025]
rule run_kraken2_decontaminate:
    input: /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz
    output: /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S9_Air_HiSeq_cami_kr2outLOG.txt, /outputs/TEDreads/S9_Air_HiSeq_cami_kr2_decontamREPORT.txt, /outputs/TEDreads/S9_Air_HiSeq_cami_kr2_decontamLOG.txt
    jobid: 15
    reason: Missing output files: /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq; Input files updated by another job: /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/decontam_db/decontam_human+mouse_db --paired /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz --unclassified-out /outputs/TEDreads/S9_Air_HiSeq_cami_R#_ted.fastq --output /outputs/TEDreads/S9_Air_HiSeq_cami_kr2outLOG.txt --report /outputs/TEDreads/S9_Air_HiSeq_cami_kr2_decontamREPORT.txt 2>> /outputs/TEDreads/S9_Air_HiSeq_cami_kr2_decontamLOG.txt
[Mon Jul 28 19:56:56 2025]
Finished job 21.
2 of 181 steps (1%) done
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_fastp.json.
[Mon Jul 28 19:56:56 2025]
Finished job 11.
3 of 181 steps (2%) done
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_fastp.json.
Select jobs to execute...

[Mon Jul 28 19:56:56 2025]
rule run_fastp:
    input: /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz, /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz
    output: /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S1_GItract_HiSeq_cami_fastplog.html, /outputs/TEDreads/S1_GItract_HiSeq_cami_fastp.json, /outputs/TEDreads/S1_GItract_HiSeq_cami_fastplog.txt
    jobid: 6
    reason: Missing output files: /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

Select jobs to execute...
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
fastp -i /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz -I /inputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz -o /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz -O /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz -h /outputs/TEDreads/S1_GItract_HiSeq_cami_fastplog.html -j /outputs/TEDreads/S1_GItract_HiSeq_cami_fastp.json --trim_poly_x --cut_window_size 4 --thread 16 --low_complexity_filter --correction --average_qual 10 --length_required 60 --cut_front --cut_front_mean_quality 20 --cut_tail  --cut_tail_mean_quality 15 2>> /outputs/TEDreads/S1_GItract_HiSeq_cami_fastplog.txt
[Mon Jul 28 19:56:59 2025]
Finished job 6.
4 of 181 steps (2%) done
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_fastp.json.
[Mon Jul 28 19:57:01 2025]
Finished job 15.
5 of 181 steps (3%) done
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_R2_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_R1_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_kr2outLOG.txt.

[Mon Jul 28 19:57:01 2025]
rule run_kraken2_decontaminate:
    input: /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz
    output: /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2outLOG.txt, /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2_decontamREPORT.txt, /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2_decontamLOG.txt
    jobid: 20
    reason: Missing output files: /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq; Input files updated by another job: /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz, /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/decontam_db/decontam_human+mouse_db --paired /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz --unclassified-out /outputs/TEDreads/S6_Oral_HiSeq_cami_R#_ted.fastq --output /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2outLOG.txt --report /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2_decontamREPORT.txt 2>> /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2_decontamLOG.txt

[Mon Jul 28 19:57:01 2025]
rule compress_kraken2_decontaminate:
    input: /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq
    output: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz
    jobid: 14
    reason: Missing output files: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz; Input files updated by another job: /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

pigz -c /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq > /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz &&pigz -c /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq > /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz
[Mon Jul 28 19:57:01 2025]
Finished job 14.
6 of 181 steps (3%) done
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_R_1_ted.fastq.
Removing temporary output /outputs/TEDreads/S9_Air_HiSeq_cami_R_2_ted.fastq.
Select jobs to execute...

[Mon Jul 28 19:57:01 2025]
rule run_metaspades:
    input: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta
    jobid: 36
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta; Input files updated by another job: /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metaspades.py -1 /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz --memory 184 --tmp-dir /outputs/tmp -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/ -t 16 --only-assembler
[Mon Jul 28 19:57:06 2025]
Finished job 20.
7 of 181 steps (4%) done
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_R2_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_R1_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_kr2outLOG.txt.
Select jobs to execute...

[Mon Jul 28 19:57:06 2025]
rule run_kraken2_decontaminate:
    input: /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz
    output: /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2outLOG.txt, /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2_decontamREPORT.txt, /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2_decontamLOG.txt
    jobid: 10
    reason: Missing output files: /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq; Input files updated by another job: /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/decontam_db/decontam_human+mouse_db --paired /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz --unclassified-out /outputs/TEDreads/S28_Skin_HiSeq_cami_R#_ted.fastq --output /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2outLOG.txt --report /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2_decontamREPORT.txt 2>> /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2_decontamLOG.txt

[Mon Jul 28 19:57:06 2025]
rule compress_kraken2_decontaminate:
    input: /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq
    output: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    jobid: 19
    reason: Missing output files: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz; Input files updated by another job: /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

pigz -c /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq > /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz &&pigz -c /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq > /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
[Mon Jul 28 19:57:06 2025]
Finished job 19.
8 of 181 steps (4%) done
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_R_1_ted.fastq.
Removing temporary output /outputs/TEDreads/S6_Oral_HiSeq_cami_R_2_ted.fastq.
Select jobs to execute...

[Mon Jul 28 19:57:06 2025]
rule run_metaspades:
    input: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta
    jobid: 42
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta; Input files updated by another job: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metaspades.py -1 /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz --memory 184 --tmp-dir /outputs/tmp -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/ -t 16 --only-assembler
[Mon Jul 28 19:57:11 2025]
Finished job 36.
9 of 181 steps (5%) done
Select jobs to execute...

[Mon Jul 28 19:57:11 2025]
rule run_bbtools_stats:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt
    jobid: 35
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed $'s/_cov_/ cov_/g' /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta && stats.sh in=/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta out=/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt && printf "\nTEDreads mapping stats:\n"  >> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt && rm -rf /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K21 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K33/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/K55 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/pipeline_state /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/misc /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/dataset.info /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*params* /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*.gfa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/run_spades.sh /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*.yaml /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*.paths /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/assembly_graph.fastg
[Mon Jul 28 19:57:11 2025]
Finished job 35.
10 of 181 steps (6%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffolds.fasta.
Select jobs to execute...

[Mon Jul 28 19:57:11 2025]
rule gene_prediction:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna
    jobid: 61
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

prodigal -p meta -i /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta -f gff -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff -a /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa -d /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna -q
[Mon Jul 28 19:57:11 2025]
Finished job 10.
11 of 181 steps (6%) done
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_R1_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_R2_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_kr2outLOG.txt.
Select jobs to execute...

[Mon Jul 28 19:57:11 2025]
rule run_kraken2_decontaminate:
    input: /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz
    output: /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2outLOG.txt, /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2_decontamREPORT.txt, /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2_decontamLOG.txt
    jobid: 5
    reason: Missing output files: /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq; Input files updated by another job: /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz, /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/decontam_db/decontam_human+mouse_db --paired /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz --unclassified-out /outputs/TEDreads/S1_GItract_HiSeq_cami_R#_ted.fastq --output /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2outLOG.txt --report /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2_decontamREPORT.txt 2>> /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2_decontamLOG.txt
[Mon Jul 28 19:57:16 2025]
Finished job 42.
12 of 181 steps (7%) done
Select jobs to execute...

[Mon Jul 28 19:57:16 2025]
rule bowtie2_build:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done
    jobid: 39
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2-build --quiet --threads 16 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.db && touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done
[Mon Jul 28 19:57:16 2025]
Finished job 61.
13 of 181 steps (7%) done
Select jobs to execute...

[Mon Jul 28 19:57:16 2025]
rule run_amrfinder:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
    jobid: 117
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

[Mon Jul 28 19:57:16 2025]
Finished job 5.
14 of 181 steps (8%) done
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_R1_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_R2_te.fastq.gz.
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_kr2outLOG.txt.
Select jobs to execute...
Config file /pipeline/config.yaml is extended by additional config specified via the command line.

[Mon Jul 28 19:57:16 2025]
rule run_kraken2_classification:
    input: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S9_Air_HiSeq_cami_klog.txt, /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt, /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S9_Air_HiSeq_cami_classLOG.txt
    jobid: 13
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt; Input files updated by another job: /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --memory-mapping --paired /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz --output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S9_Air_HiSeq_cami_klog.txt --report /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt 2>> /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S9_Air_HiSeq_cami_classLOG.txt
[Mon Jul 28 19:57:17 2025]
Finished job 39.
15 of 181 steps (8%) done
Select jobs to execute...

[Mon Jul 28 19:57:17 2025]
rule bowtie2_run:
    input: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam
    jobid: 38
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam; Input files updated by another job: /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done, /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2 --phred33 --sensitive-local --no-unal --seed 4 -1 /outputs/TED_out/S9_Air_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S9_Air_HiSeq_cami_R2_ted.fastq.gz -x /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.db -S /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam -p 16 2>> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Running: amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Software directory: '/opt/conda/bin/'
Software version: 3.12.8
WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found
Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1707154055287/_build_env/share/amrfinderplus/data/latest
Database directory: '/opt/conda/share/amrfinderplus/data/2024-07-22.1'
Database version: 2024-07-22.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running blastp
[Mon Jul 28 19:57:18 2025]
Finished job 38.
16 of 181 steps (9%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/bowtie2_build.done.
Select jobs to execute...

[Mon Jul 28 19:57:18 2025]
rule samtools_to_bam:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_colated.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate_sorted.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    jobid: 37
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

samtools sort /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.bam -@ 16 -T /outputs/tmpS9_Air_HiSeq_cami_sort && samtools collate /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.bam -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_colated.bam -@ 16 /outputs/tmpS9_Air_HiSeq_cami_collate && samtools fixmate -m /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_colated.bam /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate.bam -@ 16 && samtools sort /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate.bam -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate_sorted.bam -@ 16 -T /outputs/tmpS9_Air_HiSeq_cami_sort && samtools markdup -r -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate_sorted.bam -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam -@ 16 -T /outputs/tmpS9_Air_HiSeq_cami_markdup && samtools index -b /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam -@ 16
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
Running hmmsearch
[Mon Jul 28 19:57:19 2025]
Finished job 13.
17 of 181 steps (9%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S9_Air_HiSeq_cami_klog.txt.
Select jobs to execute...

[Mon Jul 28 19:57:19 2025]
rule gene_annotation:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    jobid: 84
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

emapper.py -i /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp  --scratch_dir /outputs/tmp --dbmem
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
samtools markdup: warning, unable to calculate estimated library size. Read pairs 9472 should be greater than duplicate pairs 0, which should both be non zero.

Making report
[Mon Jul 28 19:57:20 2025]
Finished job 37.
18 of 181 steps (10%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.sam.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami.bam.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_colated.bam.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate.bam.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_fixmate_sorted.bam.
Select jobs to execute...
AMRFinder took 3 seconds to complete

[Mon Jul 28 19:57:20 2025]
rule compress_kraken2_decontaminate:
    input: /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq
    output: /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz
    jobid: 9
    reason: Missing output files: /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz; Input files updated by another job: /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

pigz -c /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq > /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz &&pigz -c /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq > /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz

[Mon Jul 28 19:57:20 2025]
rule run_bbtools_stats:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt
    jobid: 41
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed $'s/_cov_/ cov_/g' /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta && stats.sh in=/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta out=/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt && printf "\nTEDreads mapping stats:\n"  >> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt && rm -rf /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K21 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K33/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/K55 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/pipeline_state /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/misc /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/dataset.info /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*params* /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*.gfa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/run_spades.sh /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*.yaml /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*.paths /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/assembly_graph.fastg

[Mon Jul 28 19:57:20 2025]
rule scaffold_and_read_counts:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_basecov.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_idx.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_readcount.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov1.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt
    jobid: 48
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

pileup.sh /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true && sort -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt && jgi_summarize_bam_contig_depths /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam --outputDepth /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt && sort /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt | sed '1 s/^/#/' | cut -f 1-3 > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_basecov.txt && samtools idxstats /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_idx.txt && cut -f 1-3 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_idx.txt | sed -e '1s/^/#contigName\tLength\tReadsCount\n/' | sort | grep -v "*" > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_readcount.txt && paste /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_readcount.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_basecov.txt | cut -f 1,2,3,8-14,17 -d $'\t' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov1.txt && awk 'BEGIN{FS=OFS="\t"} NR>1 {if ($2>0 && $3>0) $12=sprintf("%0.2f", $3*1e3/$2); else $12=0; print}'  /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov1.txt | sed -e '1s/^/#NODE\tlen\tReads\t\%ScaffCovered\t\%bpCovered\tplusReads\tminusReads\t\%GC\tMedFold\tstDev\tAveDepth\tRPK\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt

[Mon Jul 28 19:57:20 2025]
rule add_de_replication_stats:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/add_de_replication_stats.done
    jobid: 34
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/add_de_replication_stats.done; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cat /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt <(printf "\nRead alignment de-replication stats:\n") /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_file.txt && mv /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_file.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_stats.txt && touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/add_de_replication_stats.done

[Mon Jul 28 19:57:20 2025]
rule compress_kraken2_decontaminate:
    input: /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq, /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq
    output: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz
    jobid: 4
    reason: Missing output files: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz; Input files updated by another job: /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq, /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

pigz -c /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq > /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz &&pigz -c /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq > /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz

[Mon Jul 28 19:57:20 2025]
rule kreport2krona_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt
    jobid: 12
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

python3 /pipeline/utils/report2krona_wTAXid_last.py --report-file /outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt --no-tax-prefixes -o /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt &&sed -i 's/\tUnclassified\t\t\t\t\t\t\t0/\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\t0/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt

[Mon Jul 28 19:57:20 2025]
rule gff_to_gtf:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf
    jobid: 60
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

/pipeline/utils/gff2gtf.sh /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gff > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf
[Mon Jul 28 19:57:20 2025]
Finished job 34.
19 of 181 steps (10%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_tmp_markdup.txt.
Select jobs to execute...
java -ea -Xmx65096m -cp /opt/conda/opt/bbmap-39.15-0/current/ jgi.CoveragePileup /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true
Namespace(r_file='/outputs/TAXprofiles/readsTAX_plusPFV/reports/S9_Air_HiSeq_cami_taxREPORT.txt', r_dir=None, o_file='/outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt', x_include=False, tax_exclude=True, m_file=None)
[Mon Jul 28 19:57:20 2025]
Finished job 60.
20 of 181 steps (11%) done
[Mon Jul 28 19:57:20 2025]
Finished job 12.
21 of 181 steps (12%) done

[Mon Jul 28 19:57:20 2025]
rule tax_biom_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_4biom.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_json.biom
    jobid: 101
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_json.biom; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed 's/\t/;/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_4biom.txt && biom convert -i /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_4biom.txt -o /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_json.biom --to-json --table-type='OTU table' --process-obs-metadata taxonomy
[Mon Jul 28 19:57:20 2025]
Finished job 9.
22 of 181 steps (12%) done
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_R_1_ted.fastq.
Removing temporary output /outputs/TEDreads/S28_Skin_HiSeq_cami_R_2_ted.fastq.
Select jobs to execute...
[Mon Jul 28 19:57:20 2025]
Finished job 4.
23 of 181 steps (13%) done
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_R_2_ted.fastq.
Removing temporary output /outputs/TEDreads/S1_GItract_HiSeq_cami_R_1_ted.fastq.
Executing jgi.CoveragePileup [/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam, out=/outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt, overwrite=true]

Found samtools 1.21
[Mon Jul 28 19:57:20 2025]
Finished job 117.
24 of 181 steps (13%) done
Could not find sambamba.

[Mon Jul 28 19:57:20 2025]
rule run_verse:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt
    jobid: 59
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.summary.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

verse -a /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf -t 'CDS' -g gene_id -z 0 -s 0 -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam -T 4
[Mon Jul 28 19:57:20 2025]
Finished job 41.
25 of 181 steps (14%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffolds.fasta.
Select jobs to execute...
[Mon Jul 28 19:57:20 2025]
Finished job 59.
26 of 181 steps (14%) done

[Mon Jul 28 19:57:20 2025]
rule tpm_normalization:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_lengths.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_counts.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_coverage.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_RPK.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    jobid: 85
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f4,5,9 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.gtf | sed 's/gene_id //g' | gawk '{print $3,$2-$1+1}' | tr ' ' '\t' | sed '1s/^/gene\tlength\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_lengths.txt && join /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_lengths.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt -t $'\t' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_counts.txt && grep "_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_counts.txt   | awk -v OFS="\t" '{$4 = sprintf("%0.0f", $3*150/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_coverage.txt && grep "_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_coverage.txt | awk -v OFS="\t" '{$5 = sprintf("%0.0f", $3*1e3/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\tRPK\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_RPK.txt && awk -v OFS="\t" 'NR==FNR{sum+= $5; next} FNR==1{print $0,"iTPM"; next} {printf("%s %0.0f\n", $0,$5*1e6/sum)}'  /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_RPK.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_RPK.txt |sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt  

[Mon Jul 28 19:57:20 2025]
rule gene_prediction:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna
    jobid: 65
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

prodigal -p meta -i /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta -f gff -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff -a /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa -d /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna -q

[Mon Jul 28 19:57:20 2025]
rule rename_verse_summary:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
    jobid: 58
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

mv /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.summary.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
[Mon Jul 28 19:57:20 2025]
Finished job 58.
27 of 181 steps (15%) done
Select jobs to execute...
[Mon Jul 28 19:57:20 2025]
Finished job 85.
28 of 181 steps (15%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/verse.CDS.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_lengths.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_counts.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_coverage.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/tmp_RPK.txt.
Reads:                               	21410
Mapped reads:                        	21410
Mapped bases:                        	2937900
Ref scaffolds:                       	6796
Ref bases:                           	1855648

Percent mapped:                      	100.000
Percent proper pairs:                	84.334
Average coverage:                    	1.583
Average coverage with deletions:     	1.583
Standard deviation:                    	0.992
Percent scaffolds with any coverage: 	99.75
Percent of reference bases covered:  	98.22

Time: 	0.573 seconds.
Output depth matrix to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-06-20T09:50:37
Running with 1 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
Thread 0 opened the file: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
Thread 0 processing bam 0: S9_Air_HiSeq_cami_assembly.bam
Thread 0 finished reading bam 0: S9_Air_HiSeq_cami_assembly.bam
Thread 0 finished: S9_Air_HiSeq_cami_assembly.bam with 21410 reads and 16178 readsWellMapped (75.5628%)
Creating depth matrix file: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt
Closing last bam file
Finished
[Mon Jul 28 19:57:21 2025]
Finished job 48.
29 of 181 steps (16%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_basecov.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_idx.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_readcount.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/tmp_scaffcov1.txt.
[Mon Jul 28 19:57:21 2025]
Finished job 101.
30 of 181 steps (17%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_4biom.txt.

[Mon Jul 28 19:57:21 2025]
rule metabat2_run:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done
    jobid: 155
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metabat2 -i /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/mag -m 1500 --maxEdges 250 --unbinned  -t 16 -a /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt && touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done
[Warning!] Negative coverage depth is not allowed for the contig NODE_1_length_1016, column 1: -1.34163e+09
[Mon Jul 28 19:57:21 2025]
Finished job 155.
31 of 181 steps (17%) done
Select jobs to execute...

[Mon Jul 28 19:57:21 2025]
rule run_metaspades:
    input: /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta
    jobid: 30
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta; Input files updated by another job: /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metaspades.py -1 /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz --memory 184 --tmp-dir /outputs/tmp -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/ -t 16 --only-assembler
[Mon Jul 28 19:57:28 2025]
Finished job 65.
32 of 181 steps (18%) done
Select jobs to execute...

[Mon Jul 28 19:57:28 2025]
rule run_amrfinder:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
    jobid: 118
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Running: amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Software directory: '/opt/conda/bin/'
Software version: 3.12.8
WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found
Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1707154055287/_build_env/share/amrfinderplus/data/latest
Database directory: '/opt/conda/share/amrfinderplus/data/2024-07-22.1'
Database version: 2024-07-22.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running blastp
[Mon Jul 28 19:57:30 2025]
Finished job 30.
33 of 181 steps (18%) done
Select jobs to execute...

[Mon Jul 28 19:57:30 2025]
rule bowtie2_build:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done
    jobid: 45
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2-build --quiet --threads 16 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.db && touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done
Running hmmsearch
[Mon Jul 28 19:57:31 2025]
Finished job 45.
34 of 181 steps (19%) done
Select jobs to execute...

[Mon Jul 28 19:57:31 2025]
rule run_metaspades:
    input: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta
    jobid: 24
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta; Input files updated by another job: /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metaspades.py -1 /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz --memory 184 --tmp-dir /outputs/tmp -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/ -t 16 --only-assembler
Making report
AMRFinder took 3 seconds to complete
[Mon Jul 28 19:57:32 2025]
Finished job 118.
35 of 181 steps (19%) done
Select jobs to execute...

[Mon Jul 28 19:57:32 2025]
rule bowtie2_run:
    input: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam
    jobid: 44
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done, /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2 --phred33 --sensitive-local --no-unal --seed 4 -1 /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz -x /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.db -S /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam -p 16 2>> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt
[Mon Jul 28 19:57:33 2025]
Finished job 44.
36 of 181 steps (20%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/bowtie2_build.done.
Select jobs to execute...

[Mon Jul 28 19:57:33 2025]
rule samtools_to_bam:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_colated.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate_sorted.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    jobid: 43
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

samtools sort /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.bam -@ 16 -T /outputs/tmpS6_Oral_HiSeq_cami_sort && samtools collate /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.bam -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_colated.bam -@ 16 /outputs/tmpS6_Oral_HiSeq_cami_collate && samtools fixmate -m /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_colated.bam /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate.bam -@ 16 && samtools sort /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate.bam -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate_sorted.bam -@ 16 -T /outputs/tmpS6_Oral_HiSeq_cami_sort && samtools markdup -r -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate_sorted.bam -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam -@ 16 -T /outputs/tmpS6_Oral_HiSeq_cami_markdup && samtools index -b /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam -@ 16
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
samtools markdup: warning, unable to calculate estimated library size. Read pairs 9960 should be greater than duplicate pairs 0, which should both be non zero.

[Mon Jul 28 19:57:35 2025]
Finished job 43.
37 of 181 steps (20%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.sam.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami.bam.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_colated.bam.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate.bam.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_fixmate_sorted.bam.
Select jobs to execute...

[Mon Jul 28 19:57:35 2025]
rule add_de_replication_stats:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/add_de_replication_stats.done
    jobid: 40
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/add_de_replication_stats.done; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cat /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt <(printf "\nRead alignment de-replication stats:\n") /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_file.txt && mv /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_file.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_stats.txt && touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/add_de_replication_stats.done

[Mon Jul 28 19:57:35 2025]
rule gff_to_gtf:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf
    jobid: 64
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

/pipeline/utils/gff2gtf.sh /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gff > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf

[Mon Jul 28 19:57:35 2025]
rule scaffold_and_read_counts:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_basecov.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_idx.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_readcount.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov1.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt
    jobid: 49
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

pileup.sh /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true && sort -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt && jgi_summarize_bam_contig_depths /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam --outputDepth /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt && sort /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt | sed '1 s/^/#/' | cut -f 1-3 > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_basecov.txt && samtools idxstats /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_idx.txt && cut -f 1-3 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_idx.txt | sed -e '1s/^/#contigName\tLength\tReadsCount\n/' | sort | grep -v "*" > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_readcount.txt && paste /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_readcount.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_basecov.txt | cut -f 1,2,3,8-14,17 -d $'\t' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov1.txt && awk 'BEGIN{FS=OFS="\t"} NR>1 {if ($2>0 && $3>0) $12=sprintf("%0.2f", $3*1e3/$2); else $12=0; print}'  /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov1.txt | sed -e '1s/^/#NODE\tlen\tReads\t\%ScaffCovered\t\%bpCovered\tplusReads\tminusReads\t\%GC\tMedFold\tstDev\tAveDepth\tRPK\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt

[Mon Jul 28 19:57:35 2025]
rule run_bbtools_stats:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt
    jobid: 29
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed $'s/_cov_/ cov_/g' /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta && stats.sh in=/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta out=/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt && printf "\nTEDreads mapping stats:\n"  >> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt && rm -rf /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K21 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K33/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/K55 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/pipeline_state /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/misc /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/dataset.info /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*params* /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*.gfa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/run_spades.sh /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*.yaml /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*.paths /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/assembly_graph.fastg
[Mon Jul 28 19:57:35 2025]
Finished job 40.
38 of 181 steps (21%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_tmp_markdup.txt.
Select jobs to execute...
java -ea -Xmx63560m -cp /opt/conda/opt/bbmap-39.15-0/current/ jgi.CoveragePileup /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true
[Mon Jul 28 19:57:35 2025]
Finished job 64.
39 of 181 steps (22%) done
Executing jgi.CoveragePileup [/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam, out=/outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt, overwrite=true]

Found samtools 1.21
Could not find sambamba.
[Mon Jul 28 19:57:36 2025]
Finished job 29.
40 of 181 steps (22%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffolds.fasta.
Reads:                               	22552
Mapped reads:                        	22552
Mapped bases:                        	3098230
Ref scaffolds:                       	7010
Ref bases:                           	1929842

Percent mapped:                      	100.000
Percent proper pairs:                	83.904
Average coverage:                    	1.605
Average coverage with deletions:     	1.605
Standard deviation:                    	0.935
Percent scaffolds with any coverage: 	99.59
Percent of reference bases covered:  	97.88

Time: 	0.675 seconds.
Output depth matrix to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-06-20T09:50:37
Running with 1 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
Thread 0 opened the file: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
Thread 0 processing bam 0: S6_Oral_HiSeq_cami_assembly.bam
Thread 0 finished reading bam 0: S6_Oral_HiSeq_cami_assembly.bam
Thread 0 finished: S6_Oral_HiSeq_cami_assembly.bam with 22552 reads and 16715 readsWellMapped (74.1176%)
Creating depth matrix file: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt
Closing last bam file
Finished
[Mon Jul 28 19:57:36 2025]
Finished job 49.
41 of 181 steps (23%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_basecov.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_idx.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_readcount.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/tmp_scaffcov1.txt.

[Mon Jul 28 19:57:36 2025]
rule metabat2_run:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done
    jobid: 161
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metabat2 -i /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/mag -m 1500 --maxEdges 250 --unbinned  -t 16 -a /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt && touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done
[Mon Jul 28 19:57:36 2025]
Finished job 161.
42 of 181 steps (23%) done
Select jobs to execute...

[Mon Jul 28 19:57:36 2025]
rule bowtie2_build:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done
    jobid: 33
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2-build --quiet --threads 16 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.db && touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done
[Mon Jul 28 19:57:38 2025]
Finished job 33.
43 of 181 steps (24%) done
Select jobs to execute...

[Mon Jul 28 19:57:38 2025]
rule bowtie2_run:
    input: /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam
    jobid: 32
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam; Input files updated by another job: /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done, /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2 --phred33 --sensitive-local --no-unal --seed 4 -1 /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz -x /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.db -S /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam -p 16 2>> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt
[Mon Jul 28 19:57:39 2025]
Finished job 32.
44 of 181 steps (24%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/bowtie2_build.done.
Select jobs to execute...

[Mon Jul 28 19:57:39 2025]
rule samtools_to_bam:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_colated.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate_sorted.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
    jobid: 31
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

samtools sort /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.bam -@ 16 -T /outputs/tmpS28_Skin_HiSeq_cami_sort && samtools collate /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.bam -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_colated.bam -@ 16 /outputs/tmpS28_Skin_HiSeq_cami_collate && samtools fixmate -m /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_colated.bam /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate.bam -@ 16 && samtools sort /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate.bam -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate_sorted.bam -@ 16 -T /outputs/tmpS28_Skin_HiSeq_cami_sort && samtools markdup -r -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate_sorted.bam -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam -@ 16 -T /outputs/tmpS28_Skin_HiSeq_cami_markdup && samtools index -b /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam -@ 16
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[Mon Jul 28 19:57:41 2025]
Finished job 24.
45 of 181 steps (25%) done
Select jobs to execute...

[Mon Jul 28 19:57:41 2025]
rule run_verse:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt
    jobid: 63
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

verse -a /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf -t 'CDS' -g gene_id -z 0 -s 0 -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam -T 4
[Mon Jul 28 19:57:41 2025]
Finished job 63.
46 of 181 steps (25%) done
Select jobs to execute...

[Mon Jul 28 19:57:41 2025]
rule gene_prediction:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna
    jobid: 57
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

prodigal -p meta -i /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta -f gff -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff -a /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa -d /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna -q
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
samtools markdup: warning, unable to calculate estimated library size. Read pairs 10161 should be greater than duplicate pairs 0, which should both be non zero.

[Mon Jul 28 19:57:41 2025]
Finished job 31.
47 of 181 steps (26%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.sam.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami.bam.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_colated.bam.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate.bam.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_fixmate_sorted.bam.
Select jobs to execute...

[Mon Jul 28 19:57:41 2025]
rule add_de_replication_stats:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/add_de_replication_stats.done
    jobid: 28
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/add_de_replication_stats.done; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cat /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt <(printf "\nRead alignment de-replication stats:\n") /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_file.txt && mv /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_file.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_stats.txt && touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/add_de_replication_stats.done

[Mon Jul 28 19:57:41 2025]
rule run_bbtools_stats:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt
    jobid: 23
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed $'s/_cov_/ cov_/g' /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta && stats.sh in=/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta out=/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt && printf "\nTEDreads mapping stats:\n"  >> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt && rm -rf /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K21 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K33/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/K55 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/pipeline_state /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/misc /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/before_rr.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/dataset.info /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*params* /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*.gfa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/first_pe_contigs.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/run_spades.sh /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*.yaml /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*.paths /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/assembly_graph.fastg

[Mon Jul 28 19:57:41 2025]
rule scaffold_and_read_counts:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_basecov.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_idx.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_readcount.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov1.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt
    jobid: 47
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

pileup.sh /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true && sort -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt && jgi_summarize_bam_contig_depths /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam --outputDepth /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt && sort /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt | sed '1 s/^/#/' | cut -f 1-3 > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_basecov.txt && samtools idxstats /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_idx.txt && cut -f 1-3 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_idx.txt | sed -e '1s/^/#contigName\tLength\tReadsCount\n/' | sort | grep -v "*" > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_readcount.txt && paste /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_readcount.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_basecov.txt | cut -f 1,2,3,8-14,17 -d $'\t' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov1.txt && awk 'BEGIN{FS=OFS="\t"} NR>1 {if ($2>0 && $3>0) $12=sprintf("%0.2f", $3*1e3/$2); else $12=0; print}'  /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov1.txt | sed -e '1s/^/#NODE\tlen\tReads\t\%ScaffCovered\t\%bpCovered\tplusReads\tminusReads\t\%GC\tMedFold\tstDev\tAveDepth\tRPK\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt

[Mon Jul 28 19:57:41 2025]
rule tpm_normalization:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_lengths.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_counts.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_coverage.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_RPK.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    jobid: 92
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f4,5,9 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.gtf | sed 's/gene_id //g' | gawk '{print $3,$2-$1+1}' | tr ' ' '\t' | sed '1s/^/gene\tlength\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_lengths.txt && join /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_lengths.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt -t $'\t' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_counts.txt && grep "_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_counts.txt   | awk -v OFS="\t" '{$4 = sprintf("%0.0f", $3*150/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_coverage.txt && grep "_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_coverage.txt | awk -v OFS="\t" '{$5 = sprintf("%0.0f", $3*1e3/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\tRPK\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_RPK.txt && awk -v OFS="\t" 'NR==FNR{sum+= $5; next} FNR==1{print $0,"iTPM"; next} {printf("%s %0.0f\n", $0,$5*1e6/sum)}'  /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_RPK.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_RPK.txt |sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt  

[Mon Jul 28 19:57:41 2025]
rule rename_verse_summary:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
    jobid: 62
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

mv /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.summary.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
[Mon Jul 28 19:57:41 2025]
Finished job 28.
48 of 181 steps (27%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_tmp_markdup.txt.
Select jobs to execute...
java -ea -Xmx67353m -cp /opt/conda/opt/bbmap-39.15-0/current/ jgi.CoveragePileup /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true
[Mon Jul 28 19:57:41 2025]
Finished job 62.
49 of 181 steps (27%) done
[Mon Jul 28 19:57:41 2025]
Finished job 92.
50 of 181 steps (28%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/verse.CDS.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_lengths.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_counts.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_coverage.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/tmp_RPK.txt.
Executing jgi.CoveragePileup [/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam, out=/outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt, overwrite=true]

Found samtools 1.21
Could not find sambamba.
[Mon Jul 28 19:57:41 2025]
Finished job 23.
51 of 181 steps (28%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffolds.fasta.
Reads:                               	22599
Mapped reads:                        	22599
Mapped bases:                        	3097380
Ref scaffolds:                       	6820
Ref bases:                           	1889724

Percent mapped:                      	100.000
Percent proper pairs:                	84.499
Average coverage:                    	1.639
Average coverage with deletions:     	1.639
Standard deviation:                    	1.018
Percent scaffolds with any coverage: 	99.65
Percent of reference bases covered:  	98.08

Time: 	0.638 seconds.
Output depth matrix to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-06-20T09:50:37
Running with 1 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
Thread 0 opened the file: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
Thread 0 processing bam 0: S28_Skin_HiSeq_cami_assembly.bam
Thread 0 finished reading bam 0: S28_Skin_HiSeq_cami_assembly.bam
Thread 0 finished: S28_Skin_HiSeq_cami_assembly.bam with 22599 reads and 16436 readsWellMapped (72.7289%)
Creating depth matrix file: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt
Closing last bam file
Finished
[Mon Jul 28 19:57:42 2025]
Finished job 47.
52 of 181 steps (29%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_basecov.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_idx.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_readcount.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/tmp_scaffcov1.txt.

[Mon Jul 28 19:57:42 2025]
rule bowtie2_build:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done
    jobid: 27
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2-build --quiet --threads 16 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.db && touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done
[Mon Jul 28 19:57:44 2025]
Finished job 27.
53 of 181 steps (29%) done
Select jobs to execute...

[Mon Jul 28 19:57:44 2025]
rule bowtie2_run:
    input: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam
    jobid: 26
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam; Input files updated by another job: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

bowtie2 --phred33 --sensitive-local --no-unal --seed 4 -1 /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz -2 /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz -x /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.db -S /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam -p 16 2>> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt
[Mon Jul 28 19:57:45 2025]
Finished job 26.
54 of 181 steps (30%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/bowtie2_build.done.
Select jobs to execute...

[Mon Jul 28 19:57:45 2025]
rule samtools_to_bam:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.bam, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_colated.bam, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate.bam, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate_sorted.bam, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    jobid: 25
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

samtools sort /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.bam -@ 16 -T /outputs/tmpS1_GItract_HiSeq_cami_sort && samtools collate /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.bam -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_colated.bam -@ 16 /outputs/tmpS1_GItract_HiSeq_cami_collate && samtools fixmate -m /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_colated.bam /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate.bam -@ 16 && samtools sort /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate.bam -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate_sorted.bam -@ 16 -T /outputs/tmpS1_GItract_HiSeq_cami_sort && samtools markdup -r -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate_sorted.bam -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam -@ 16 -T /outputs/tmpS1_GItract_HiSeq_cami_markdup && samtools index -b /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam -@ 16
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[Mon Jul 28 19:57:45 2025]
Finished job 57.
55 of 181 steps (30%) done
Select jobs to execute...

[Mon Jul 28 19:57:45 2025]
rule metabat2_run:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
    jobid: 149
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metabat2 -i /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/mag -m 1500 --maxEdges 250 --unbinned  -t 16 -a /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt && touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
[Mon Jul 28 19:57:45 2025]
Finished job 149.
56 of 181 steps (31%) done
Select jobs to execute...

[Mon Jul 28 19:57:45 2025]
rule gene_prediction:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna
    jobid: 53
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

prodigal -p meta -i /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta -f gff -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff -a /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa -d /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna -q
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
samtools markdup: warning, unable to calculate estimated library size. Read pairs 7304 should be greater than duplicate pairs 0, which should both be non zero.

[Mon Jul 28 19:57:47 2025]
Finished job 25.
57 of 181 steps (31%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.sam.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami.bam.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_colated.bam.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate.bam.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_fixmate_sorted.bam.
Select jobs to execute...

[Mon Jul 28 19:57:47 2025]
rule run_amrfinder:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
    jobid: 116
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Running: amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Software directory: '/opt/conda/bin/'
Software version: 3.12.8
WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found
Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1707154055287/_build_env/share/amrfinderplus/data/latest
Database directory: '/opt/conda/share/amrfinderplus/data/2024-07-22.1'
Database version: 2024-07-22.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Running blastp
Running hmmsearch
[Mon Jul 28 19:57:50 2025]
Finished job 53.
58 of 181 steps (32%) done
Select jobs to execute...

[Mon Jul 28 19:57:50 2025]
rule run_amrfinder:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
    jobid: 115
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Making report
AMRFinder took 3 seconds to complete
[Mon Jul 28 19:57:52 2025]
Finished job 116.
59 of 181 steps (33%) done
Select jobs to execute...

[Mon Jul 28 19:57:52 2025]
rule gff_to_gtf:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf
    jobid: 52
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

/pipeline/utils/gff2gtf.sh /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gff > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf

[Mon Jul 28 19:57:52 2025]
rule scaffold_and_read_counts:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_basecov.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_idx.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_readcount.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov1.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt
    jobid: 46
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

pileup.sh /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true && sort -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt && jgi_summarize_bam_contig_depths /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam --outputDepth /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt && sort /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt | sed '1 s/^/#/' | cut -f 1-3 > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_basecov.txt && samtools idxstats /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_idx.txt && cut -f 1-3 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_idx.txt | sed -e '1s/^/#contigName\tLength\tReadsCount\n/' | sort | grep -v "*" > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_readcount.txt && paste /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_readcount.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_basecov.txt | cut -f 1,2,3,8-14,17 -d $'\t' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov1.txt && awk 'BEGIN{FS=OFS="\t"} NR>1 {if ($2>0 && $3>0) $12=sprintf("%0.2f", $3*1e3/$2); else $12=0; print}'  /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov1.txt | sed -e '1s/^/#NODE\tlen\tReads\t\%ScaffCovered\t\%bpCovered\tplusReads\tminusReads\t\%GC\tMedFold\tstDev\tAveDepth\tRPK\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt

[Mon Jul 28 19:57:52 2025]
rule add_de_replication_stats:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/add_de_replication_stats.done
    jobid: 22
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/add_de_replication_stats.done; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cat /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt <(printf "\nRead alignment de-replication stats:\n") /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_file.txt && mv /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_file.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_stats.txt && touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/add_de_replication_stats.done

[Mon Jul 28 19:57:52 2025]
rule gff_to_gtf:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf
    jobid: 56
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

/pipeline/utils/gff2gtf.sh /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gff > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf
[Mon Jul 28 19:57:52 2025]
Finished job 22.
60 of 181 steps (33%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_tmp_markdup.txt.
Select jobs to execute...
java -ea -Xmx61870m -cp /opt/conda/opt/bbmap-39.15-0/current/ jgi.CoveragePileup /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam out=/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt overwrite=true
[Mon Jul 28 19:57:52 2025]
Finished job 52.
61 of 181 steps (34%) done
[Mon Jul 28 19:57:52 2025]
Finished job 56.
62 of 181 steps (34%) done
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
Executing jgi.CoveragePileup [/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam, out=/outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt, overwrite=true]

amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Running: amrfinder -d /opt/conda/share/amrfinderplus/data/latest --plus --protein /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa --threads 16 --protein_output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt
Software directory: '/opt/conda/bin/'
Software version: 3.12.8
WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found
Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1707154055287/_build_env/share/amrfinderplus/data/latest
Database directory: '/opt/conda/share/amrfinderplus/data/2024-07-22.1'
Database version: 2024-07-22.1
AMRFinder protein-only search
  - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
  - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins
Found samtools 1.21
Running blastp
Could not find sambamba.
Reads:                               	16091
Mapped reads:                        	16091
Mapped bases:                        	2269219
Ref scaffolds:                       	6170
Ref bases:                           	1595786

Percent mapped:                      	100.000
Percent proper pairs:                	88.857
Average coverage:                    	1.422
Average coverage with deletions:     	1.422
Standard deviation:                    	2.259
Percent scaffolds with any coverage: 	99.81
Percent of reference bases covered:  	98.78

Time: 	0.706 seconds.
Output depth matrix to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt
jgi_summarize_bam_contig_depths 2.17 (Bioconda) 2024-06-20T09:50:37
Running with 1 threads to save memory you can reduce the number of threads with the OMP_NUM_THREADS variable
Output matrix to /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt
Opening all bam files and validating headers
Processing bam files with largest_contig=0
Thread 0 opening and reading the header for file: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
Thread 0 opened the file: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
Thread 0 processing bam 0: S1_GItract_HiSeq_cami_assembly.bam
Thread 0 finished reading bam 0: S1_GItract_HiSeq_cami_assembly.bam
Thread 0 finished: S1_GItract_HiSeq_cami_assembly.bam with 16091 reads and 13620 readsWellMapped (84.6436%)
Creating depth matrix file: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt
Closing last bam file
Finished
[Mon Jul 28 19:57:53 2025]
Finished job 46.
63 of 181 steps (35%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_basecov.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_idx.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_readcount.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/tmp_scaffcov1.txt.

[Mon Jul 28 19:57:53 2025]
rule metabat2_run:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done
    jobid: 143
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

metabat2 -i /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/mag -m 1500 --maxEdges 250 --unbinned  -t 16 -a /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt && touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done
[Warning!] Negative coverage depth is not allowed for the contig NODE_1_length_1104, column 1: -1.30668e+09
[Mon Jul 28 19:57:53 2025]
Finished job 143.
64 of 181 steps (35%) done
Select jobs to execute...

[Mon Jul 28 19:57:53 2025]
rule run_verse:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt
    jobid: 55
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

verse -a /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf -t 'CDS' -g gene_id -z 0 -s 0 -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam -T 4
[Mon Jul 28 19:57:53 2025]
Finished job 55.
65 of 181 steps (36%) done
Select jobs to execute...

[Mon Jul 28 19:57:53 2025]
rule run_verse:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt
    jobid: 51
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.summary.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp

verse -a /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf -t 'CDS' -g gene_id -z 0 -s 0 -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam -T 4
[Mon Jul 28 19:57:54 2025]
Finished job 51.
66 of 181 steps (36%) done
Select jobs to execute...

[Mon Jul 28 19:57:54 2025]
rule rename_verse_summary:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
    jobid: 50
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

mv /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.summary.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_stats.txt

[Mon Jul 28 19:57:54 2025]
rule tpm_normalization:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_lengths.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_counts.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_coverage.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_RPK.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    jobid: 71
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f4,5,9 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.gtf | sed 's/gene_id //g' | gawk '{print $3,$2-$1+1}' | tr ' ' '\t' | sed '1s/^/gene\tlength\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_lengths.txt && join /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_lengths.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt -t $'\t' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_counts.txt && grep "_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_counts.txt   | awk -v OFS="\t" '{$4 = sprintf("%0.0f", $3*150/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_coverage.txt && grep "_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_coverage.txt | awk -v OFS="\t" '{$5 = sprintf("%0.0f", $3*1e3/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\tRPK\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_RPK.txt && awk -v OFS="\t" 'NR==FNR{sum+= $5; next} FNR==1{print $0,"iTPM"; next} {printf("%s %0.0f\n", $0,$5*1e6/sum)}'  /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_RPK.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_RPK.txt |sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt  

[Mon Jul 28 19:57:54 2025]
rule rename_verse_summary:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_stats.txt
    jobid: 54
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_stats.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.summary.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

mv /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.summary.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_stats.txt

[Mon Jul 28 19:57:54 2025]
rule tpm_normalization:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_lengths.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_counts.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_coverage.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_RPK.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    jobid: 78
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f4,5,9 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.gtf | sed 's/gene_id //g' | gawk '{print $3,$2-$1+1}' | tr ' ' '\t' | sed '1s/^/gene\tlength\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_lengths.txt && join /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_lengths.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt -t $'\t' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_counts.txt && grep "_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_counts.txt   | awk -v OFS="\t" '{$4 = sprintf("%0.0f", $3*150/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_coverage.txt && grep "_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_coverage.txt | awk -v OFS="\t" '{$5 = sprintf("%0.0f", $3*1e3/$2)}1' | sort | sed -e '1s/^/#name\tlen\treads\tcov\tRPK\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_RPK.txt && awk -v OFS="\t" 'NR==FNR{sum+= $5; next} FNR==1{print $0,"iTPM"; next} {printf("%s %0.0f\n", $0,$5*1e6/sum)}'  /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_RPK.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_RPK.txt |sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt  
[Mon Jul 28 19:57:54 2025]
Finished job 50.
67 of 181 steps (37%) done
Select jobs to execute...
Running hmmsearch
[Mon Jul 28 19:57:54 2025]
Finished job 54.
68 of 181 steps (38%) done
[Mon Jul 28 19:57:54 2025]
Finished job 71.
69 of 181 steps (38%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/verse.CDS.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_lengths.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_counts.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_coverage.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/tmp_RPK.txt.
[Mon Jul 28 19:57:54 2025]
Finished job 78.
70 of 181 steps (39%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/verse.CDS.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_lengths.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_counts.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_coverage.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/tmp_RPK.txt.
Making report
AMRFinder took 3 seconds to complete
[Mon Jul 28 19:57:56 2025]
Finished job 115.
71 of 181 steps (39%) done
[1;32mFunctional annotation of hits...[0m
0 1.430511474609375e-06 0.00 q/s (% mem usage: 1.60, % mem avail: 98.35)
[1;34mTime to load the DB into memory: 43.91850423812866[0m
500 46.32048749923706 10.79 q/s (% mem usage: 24.10, % mem avail: 75.92)
1000 48.45026516914368 20.64 q/s (% mem usage: 24.10, % mem avail: 75.92)
1500 50.428914308547974 29.74 q/s (% mem usage: 24.10, % mem avail: 75.92)
2000 52.50036096572876 38.09 q/s (% mem usage: 24.10, % mem avail: 75.92)
2500 54.37030100822449 45.98 q/s (% mem usage: 24.10, % mem avail: 75.92)
3000 56.08794069290161 53.49 q/s (% mem usage: 24.10, % mem avail: 75.92)
3500 57.770729303359985 60.58 q/s (% mem usage: 24.10, % mem avail: 75.92)
4000 59.47996211051941 67.25 q/s (% mem usage: 24.10, % mem avail: 75.92)
4500 61.20136380195618 73.53 q/s (% mem usage: 24.10, % mem avail: 75.92)
5000 62.84288287162781 79.56 q/s (% mem usage: 24.10, % mem avail: 75.92)
5500 64.80037021636963 84.88 q/s (% mem usage: 24.10, % mem avail: 75.92)
6000 66.7541778087616 89.88 q/s (% mem usage: 24.10, % mem avail: 75.92)
6167 70.95333433151245 86.92 q/s (% mem usage: 1.80, % mem avail: 98.19)
[Mon Jul 28 20:16:38 2025]
Finished job 84.
72 of 181 steps (40%) done

[Mon Jul 28 20:16:38 2025]
rule checkm_lineage_wf:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    jobid: 142
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp, mem_gb=184

checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
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    Finished aligning 39 of 43 (90.70%) marker genes.
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    Finished aligning 41 of 43 (95.35%) marker genes.
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    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.

    Finished processing 1 of 2 (50.00%) bins (current: mag.tooShort).
                                                                     
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[Mon Jul 28 20:18:16 2025]
Finished job 142.
73 of 181 steps (40%) done
Select jobs to execute...

[Mon Jul 28 20:18:16 2025]
rule checkm_coverage:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    jobid: 145
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.bam 2>/dev/null
Activating conda environment: checkm
[Mon Jul 28 20:18:18 2025]
Finished job 145.
74 of 181 steps (41%) done
Select jobs to execute...

[Mon Jul 28 20:18:18 2025]
rule checkm_lineage_wf:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    jobid: 154
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp, mem_gb=184

checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished processing 0 of 2 (0.00%) bins.
    Finished processing 1 of 2 (50.00%) bins.
    Finished processing 2 of 2 (100.00%) bins.
    Finished processing 0 of 2 (0.00%) bins.
    Finished processing 1 of 2 (50.00%) bins.
    Finished processing 2 of 2 (100.00%) bins.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
    Finished extracting 0 of 43 (0.00%) HMMs.
    Finished extracting 1 of 43 (2.33%) HMMs.
    Finished extracting 2 of 43 (4.65%) HMMs.
    Finished extracting 3 of 43 (6.98%) HMMs.
    Finished extracting 4 of 43 (9.30%) HMMs.
    Finished extracting 5 of 43 (11.63%) HMMs.
    Finished extracting 6 of 43 (13.95%) HMMs.
    Finished extracting 7 of 43 (16.28%) HMMs.
    Finished extracting 8 of 43 (18.60%) HMMs.
    Finished extracting 9 of 43 (20.93%) HMMs.
    Finished extracting 10 of 43 (23.26%) HMMs.
    Finished extracting 11 of 43 (25.58%) HMMs.
    Finished extracting 12 of 43 (27.91%) HMMs.
    Finished extracting 13 of 43 (30.23%) HMMs.
    Finished extracting 14 of 43 (32.56%) HMMs.
    Finished extracting 15 of 43 (34.88%) HMMs.
    Finished extracting 16 of 43 (37.21%) HMMs.
    Finished extracting 17 of 43 (39.53%) HMMs.
    Finished extracting 18 of 43 (41.86%) HMMs.
    Finished extracting 19 of 43 (44.19%) HMMs.
    Finished extracting 20 of 43 (46.51%) HMMs.
    Finished extracting 21 of 43 (48.84%) HMMs.
    Finished extracting 22 of 43 (51.16%) HMMs.
    Finished extracting 23 of 43 (53.49%) HMMs.
    Finished extracting 24 of 43 (55.81%) HMMs.
    Finished extracting 25 of 43 (58.14%) HMMs.
    Finished extracting 26 of 43 (60.47%) HMMs.
    Finished extracting 27 of 43 (62.79%) HMMs.
    Finished extracting 28 of 43 (65.12%) HMMs.
    Finished extracting 29 of 43 (67.44%) HMMs.
    Finished extracting 30 of 43 (69.77%) HMMs.
    Finished extracting 31 of 43 (72.09%) HMMs.
    Finished extracting 32 of 43 (74.42%) HMMs.
    Finished extracting 33 of 43 (76.74%) HMMs.
    Finished extracting 34 of 43 (79.07%) HMMs.
    Finished extracting 35 of 43 (81.40%) HMMs.
    Finished extracting 36 of 43 (83.72%) HMMs.
    Finished extracting 37 of 43 (86.05%) HMMs.
    Finished extracting 38 of 43 (88.37%) HMMs.
    Finished extracting 39 of 43 (90.70%) HMMs.
    Finished extracting 40 of 43 (93.02%) HMMs.
    Finished extracting 41 of 43 (95.35%) HMMs.
    Finished extracting 42 of 43 (97.67%) HMMs.
    Finished extracting 43 of 43 (100.00%) HMMs.
    Finished aligning 0 of 43 (0.00%) marker genes.
    Finished aligning 1 of 43 (2.33%) marker genes.
    Finished aligning 2 of 43 (4.65%) marker genes.
    Finished aligning 3 of 43 (6.98%) marker genes.
    Finished aligning 4 of 43 (9.30%) marker genes.
    Finished aligning 5 of 43 (11.63%) marker genes.
    Finished aligning 6 of 43 (13.95%) marker genes.
    Finished aligning 7 of 43 (16.28%) marker genes.
    Finished aligning 8 of 43 (18.60%) marker genes.
    Finished aligning 9 of 43 (20.93%) marker genes.
    Finished aligning 10 of 43 (23.26%) marker genes.
    Finished aligning 11 of 43 (25.58%) marker genes.
    Finished aligning 12 of 43 (27.91%) marker genes.
    Finished aligning 13 of 43 (30.23%) marker genes.
    Finished aligning 14 of 43 (32.56%) marker genes.
    Finished aligning 15 of 43 (34.88%) marker genes.
    Finished aligning 16 of 43 (37.21%) marker genes.
    Finished aligning 17 of 43 (39.53%) marker genes.
    Finished aligning 18 of 43 (41.86%) marker genes.
    Finished aligning 19 of 43 (44.19%) marker genes.
    Finished aligning 20 of 43 (46.51%) marker genes.
    Finished aligning 21 of 43 (48.84%) marker genes.
    Finished aligning 22 of 43 (51.16%) marker genes.
    Finished aligning 23 of 43 (53.49%) marker genes.
    Finished aligning 24 of 43 (55.81%) marker genes.
    Finished aligning 25 of 43 (58.14%) marker genes.
    Finished aligning 26 of 43 (60.47%) marker genes.
    Finished aligning 27 of 43 (62.79%) marker genes.
    Finished aligning 28 of 43 (65.12%) marker genes.
    Finished aligning 29 of 43 (67.44%) marker genes.
    Finished aligning 30 of 43 (69.77%) marker genes.
    Finished aligning 31 of 43 (72.09%) marker genes.
    Finished aligning 32 of 43 (74.42%) marker genes.
    Finished aligning 33 of 43 (76.74%) marker genes.
    Finished aligning 34 of 43 (79.07%) marker genes.
    Finished aligning 35 of 43 (81.40%) marker genes.
    Finished aligning 36 of 43 (83.72%) marker genes.
    Finished aligning 37 of 43 (86.05%) marker genes.
    Finished aligning 38 of 43 (88.37%) marker genes.
    Finished aligning 39 of 43 (90.70%) marker genes.
    Finished aligning 40 of 43 (93.02%) marker genes.
    Finished aligning 41 of 43 (95.35%) marker genes.
    Finished aligning 42 of 43 (97.67%) marker genes.
    Finished aligning 43 of 43 (100.00%) marker genes.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.

    Finished processing 1 of 2 (50.00%) bins (current: mag.tooShort).
                                                                     
    Finished processing 2 of 2 (100.00%) bins (current: mag.lowDepth).
    Finished processing 0 of 2 (0.00%) bins.
    Finished processing 1 of 2 (50.00%) bins.
    Finished processing 2 of 2 (100.00%) bins.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
    Finished processing 0 of 2 (0.00%) bins.
    Finished processing 1 of 2 (50.00%) bins.
    Finished processing 2 of 2 (100.00%) bins.
    Finished processing 0 of 2 (0.00%) bins.
    Finished processing 1 of 2 (50.00%) bins.
    Finished processing 2 of 2 (100.00%) bins.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
[Mon Jul 28 20:19:59 2025]
Finished job 154.
75 of 181 steps (41%) done
Select jobs to execute...

[Mon Jul 28 20:19:59 2025]
rule checkm_lineage_wf:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    jobid: 148
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp, mem_gb=184

checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished extracting 0 of 43 (0.00%) HMMs.
    Finished extracting 1 of 43 (2.33%) HMMs.
    Finished extracting 2 of 43 (4.65%) HMMs.
    Finished extracting 3 of 43 (6.98%) HMMs.
    Finished extracting 4 of 43 (9.30%) HMMs.
    Finished extracting 5 of 43 (11.63%) HMMs.
    Finished extracting 6 of 43 (13.95%) HMMs.
    Finished extracting 7 of 43 (16.28%) HMMs.
    Finished extracting 8 of 43 (18.60%) HMMs.
    Finished extracting 9 of 43 (20.93%) HMMs.
    Finished extracting 10 of 43 (23.26%) HMMs.
    Finished extracting 11 of 43 (25.58%) HMMs.
    Finished extracting 12 of 43 (27.91%) HMMs.
    Finished extracting 13 of 43 (30.23%) HMMs.
    Finished extracting 14 of 43 (32.56%) HMMs.
    Finished extracting 15 of 43 (34.88%) HMMs.
    Finished extracting 16 of 43 (37.21%) HMMs.
    Finished extracting 17 of 43 (39.53%) HMMs.
    Finished extracting 18 of 43 (41.86%) HMMs.
    Finished extracting 19 of 43 (44.19%) HMMs.
    Finished extracting 20 of 43 (46.51%) HMMs.
    Finished extracting 21 of 43 (48.84%) HMMs.
    Finished extracting 22 of 43 (51.16%) HMMs.
    Finished extracting 23 of 43 (53.49%) HMMs.
    Finished extracting 24 of 43 (55.81%) HMMs.
    Finished extracting 25 of 43 (58.14%) HMMs.
    Finished extracting 26 of 43 (60.47%) HMMs.
    Finished extracting 27 of 43 (62.79%) HMMs.
    Finished extracting 28 of 43 (65.12%) HMMs.
    Finished extracting 29 of 43 (67.44%) HMMs.
    Finished extracting 30 of 43 (69.77%) HMMs.
    Finished extracting 31 of 43 (72.09%) HMMs.
    Finished extracting 32 of 43 (74.42%) HMMs.
    Finished extracting 33 of 43 (76.74%) HMMs.
    Finished extracting 34 of 43 (79.07%) HMMs.
    Finished extracting 35 of 43 (81.40%) HMMs.
    Finished extracting 36 of 43 (83.72%) HMMs.
    Finished extracting 37 of 43 (86.05%) HMMs.
    Finished extracting 38 of 43 (88.37%) HMMs.
    Finished extracting 39 of 43 (90.70%) HMMs.
    Finished extracting 40 of 43 (93.02%) HMMs.
    Finished extracting 41 of 43 (95.35%) HMMs.
    Finished extracting 42 of 43 (97.67%) HMMs.
    Finished extracting 43 of 43 (100.00%) HMMs.
    Finished aligning 0 of 43 (0.00%) marker genes.
    Finished aligning 1 of 43 (2.33%) marker genes.
    Finished aligning 2 of 43 (4.65%) marker genes.
    Finished aligning 3 of 43 (6.98%) marker genes.
    Finished aligning 4 of 43 (9.30%) marker genes.
    Finished aligning 5 of 43 (11.63%) marker genes.
    Finished aligning 6 of 43 (13.95%) marker genes.
    Finished aligning 7 of 43 (16.28%) marker genes.
    Finished aligning 8 of 43 (18.60%) marker genes.
    Finished aligning 9 of 43 (20.93%) marker genes.
    Finished aligning 10 of 43 (23.26%) marker genes.
    Finished aligning 11 of 43 (25.58%) marker genes.
    Finished aligning 12 of 43 (27.91%) marker genes.
    Finished aligning 13 of 43 (30.23%) marker genes.
    Finished aligning 14 of 43 (32.56%) marker genes.
    Finished aligning 15 of 43 (34.88%) marker genes.
    Finished aligning 16 of 43 (37.21%) marker genes.
    Finished aligning 17 of 43 (39.53%) marker genes.
    Finished aligning 18 of 43 (41.86%) marker genes.
    Finished aligning 19 of 43 (44.19%) marker genes.
    Finished aligning 20 of 43 (46.51%) marker genes.
    Finished aligning 21 of 43 (48.84%) marker genes.
    Finished aligning 22 of 43 (51.16%) marker genes.
    Finished aligning 23 of 43 (53.49%) marker genes.
    Finished aligning 24 of 43 (55.81%) marker genes.
    Finished aligning 25 of 43 (58.14%) marker genes.
    Finished aligning 26 of 43 (60.47%) marker genes.
    Finished aligning 27 of 43 (62.79%) marker genes.
    Finished aligning 28 of 43 (65.12%) marker genes.
    Finished aligning 29 of 43 (67.44%) marker genes.
    Finished aligning 30 of 43 (69.77%) marker genes.
    Finished aligning 31 of 43 (72.09%) marker genes.
    Finished aligning 32 of 43 (74.42%) marker genes.
    Finished aligning 33 of 43 (76.74%) marker genes.
    Finished aligning 34 of 43 (79.07%) marker genes.
    Finished aligning 35 of 43 (81.40%) marker genes.
    Finished aligning 36 of 43 (83.72%) marker genes.
    Finished aligning 37 of 43 (86.05%) marker genes.
    Finished aligning 38 of 43 (88.37%) marker genes.
    Finished aligning 39 of 43 (90.70%) marker genes.
    Finished aligning 40 of 43 (93.02%) marker genes.
    Finished aligning 41 of 43 (95.35%) marker genes.
    Finished aligning 42 of 43 (97.67%) marker genes.
    Finished aligning 43 of 43 (100.00%) marker genes.
    Finished parsing hits for 1 of 1 (100.00%) bins.

    Finished processing 1 of 1 (100.00%) bins (current: mag.tooShort).
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
[Mon Jul 28 20:22:04 2025]
Finished job 148.
76 of 181 steps (42%) done
Select jobs to execute...

[Mon Jul 28 20:22:04 2025]
rule checkm_lineage_wf:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    jobid: 160
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp, mem_gb=184

checkm lineage_wf --tab_table --nt --pplacer_threads 48 -t 48 -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished extracting 0 of 43 (0.00%) HMMs.
    Finished extracting 1 of 43 (2.33%) HMMs.
    Finished extracting 2 of 43 (4.65%) HMMs.
    Finished extracting 3 of 43 (6.98%) HMMs.
    Finished extracting 4 of 43 (9.30%) HMMs.
    Finished extracting 5 of 43 (11.63%) HMMs.
    Finished extracting 6 of 43 (13.95%) HMMs.
    Finished extracting 7 of 43 (16.28%) HMMs.
    Finished extracting 8 of 43 (18.60%) HMMs.
    Finished extracting 9 of 43 (20.93%) HMMs.
    Finished extracting 10 of 43 (23.26%) HMMs.
    Finished extracting 11 of 43 (25.58%) HMMs.
    Finished extracting 12 of 43 (27.91%) HMMs.
    Finished extracting 13 of 43 (30.23%) HMMs.
    Finished extracting 14 of 43 (32.56%) HMMs.
    Finished extracting 15 of 43 (34.88%) HMMs.
    Finished extracting 16 of 43 (37.21%) HMMs.
    Finished extracting 17 of 43 (39.53%) HMMs.
    Finished extracting 18 of 43 (41.86%) HMMs.
    Finished extracting 19 of 43 (44.19%) HMMs.
    Finished extracting 20 of 43 (46.51%) HMMs.
    Finished extracting 21 of 43 (48.84%) HMMs.
    Finished extracting 22 of 43 (51.16%) HMMs.
    Finished extracting 23 of 43 (53.49%) HMMs.
    Finished extracting 24 of 43 (55.81%) HMMs.
    Finished extracting 25 of 43 (58.14%) HMMs.
    Finished extracting 26 of 43 (60.47%) HMMs.
    Finished extracting 27 of 43 (62.79%) HMMs.
    Finished extracting 28 of 43 (65.12%) HMMs.
    Finished extracting 29 of 43 (67.44%) HMMs.
    Finished extracting 30 of 43 (69.77%) HMMs.
    Finished extracting 31 of 43 (72.09%) HMMs.
    Finished extracting 32 of 43 (74.42%) HMMs.
    Finished extracting 33 of 43 (76.74%) HMMs.
    Finished extracting 34 of 43 (79.07%) HMMs.
    Finished extracting 35 of 43 (81.40%) HMMs.
    Finished extracting 36 of 43 (83.72%) HMMs.
    Finished extracting 37 of 43 (86.05%) HMMs.
    Finished extracting 38 of 43 (88.37%) HMMs.
    Finished extracting 39 of 43 (90.70%) HMMs.
    Finished extracting 40 of 43 (93.02%) HMMs.
    Finished extracting 41 of 43 (95.35%) HMMs.
    Finished extracting 42 of 43 (97.67%) HMMs.
    Finished extracting 43 of 43 (100.00%) HMMs.
    Finished aligning 0 of 43 (0.00%) marker genes.
    Finished aligning 1 of 43 (2.33%) marker genes.
    Finished aligning 2 of 43 (4.65%) marker genes.
    Finished aligning 3 of 43 (6.98%) marker genes.
    Finished aligning 4 of 43 (9.30%) marker genes.
    Finished aligning 5 of 43 (11.63%) marker genes.
    Finished aligning 6 of 43 (13.95%) marker genes.
    Finished aligning 7 of 43 (16.28%) marker genes.
    Finished aligning 8 of 43 (18.60%) marker genes.
    Finished aligning 9 of 43 (20.93%) marker genes.
    Finished aligning 10 of 43 (23.26%) marker genes.
    Finished aligning 11 of 43 (25.58%) marker genes.
    Finished aligning 12 of 43 (27.91%) marker genes.
    Finished aligning 13 of 43 (30.23%) marker genes.
    Finished aligning 14 of 43 (32.56%) marker genes.
    Finished aligning 15 of 43 (34.88%) marker genes.
    Finished aligning 16 of 43 (37.21%) marker genes.
    Finished aligning 17 of 43 (39.53%) marker genes.
    Finished aligning 18 of 43 (41.86%) marker genes.
    Finished aligning 19 of 43 (44.19%) marker genes.
    Finished aligning 20 of 43 (46.51%) marker genes.
    Finished aligning 21 of 43 (48.84%) marker genes.
    Finished aligning 22 of 43 (51.16%) marker genes.
    Finished aligning 23 of 43 (53.49%) marker genes.
    Finished aligning 24 of 43 (55.81%) marker genes.
    Finished aligning 25 of 43 (58.14%) marker genes.
    Finished aligning 26 of 43 (60.47%) marker genes.
    Finished aligning 27 of 43 (62.79%) marker genes.
    Finished aligning 28 of 43 (65.12%) marker genes.
    Finished aligning 29 of 43 (67.44%) marker genes.
    Finished aligning 30 of 43 (69.77%) marker genes.
    Finished aligning 31 of 43 (72.09%) marker genes.
    Finished aligning 32 of 43 (74.42%) marker genes.
    Finished aligning 33 of 43 (76.74%) marker genes.
    Finished aligning 34 of 43 (79.07%) marker genes.
    Finished aligning 35 of 43 (81.40%) marker genes.
    Finished aligning 36 of 43 (83.72%) marker genes.
    Finished aligning 37 of 43 (86.05%) marker genes.
    Finished aligning 38 of 43 (88.37%) marker genes.
    Finished aligning 39 of 43 (90.70%) marker genes.
    Finished aligning 40 of 43 (93.02%) marker genes.
    Finished aligning 41 of 43 (95.35%) marker genes.
    Finished aligning 42 of 43 (97.67%) marker genes.
    Finished aligning 43 of 43 (100.00%) marker genes.
    Finished parsing hits for 1 of 1 (100.00%) bins.

    Finished processing 1 of 1 (100.00%) bins (current: mag.tooShort).
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished processing 0 of 1 (0.00%) bins.
    Finished processing 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
[Mon Jul 28 20:24:03 2025]
Finished job 160.
77 of 181 steps (43%) done
Select jobs to execute...

[Mon Jul 28 20:24:03 2025]
rule checkm_coverage:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    jobid: 157
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.bam 2>/dev/null
Activating conda environment: checkm
[Mon Jul 28 20:24:05 2025]
Finished job 157.
78 of 181 steps (43%) done
Select jobs to execute...

[Mon Jul 28 20:24:05 2025]
rule checkm_coverage:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    jobid: 163
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.bam 2>/dev/null
Activating conda environment: checkm
[Mon Jul 28 20:24:07 2025]
Finished job 163.
79 of 181 steps (44%) done
Select jobs to execute...

[Mon Jul 28 20:24:07 2025]
rule checkm_coverage:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    jobid: 151
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm coverage -x fa -t 48 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.bam 2>/dev/null
Activating conda environment: checkm
[Mon Jul 28 20:24:10 2025]
Finished job 151.
80 of 181 steps (44%) done
Select jobs to execute...

[Mon Jul 28 20:24:10 2025]
rule checkm_qa:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    jobid: 153
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/ && checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
[Mon Jul 28 20:24:13 2025]
Finished job 153.
81 of 181 steps (45%) done
Select jobs to execute...

[Mon Jul 28 20:24:13 2025]
rule checkm_qa:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    jobid: 159
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/ && checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
[Mon Jul 28 20:24:17 2025]
Finished job 159.
82 of 181 steps (45%) done
Select jobs to execute...

[Mon Jul 28 20:24:17 2025]
rule checkm_qa:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    jobid: 147
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/ && checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished parsing hits for 1 of 1 (100.00%) bins.
    Finished parsing hits for 1 of 1 (100.00%) bins.
[Mon Jul 28 20:24:20 2025]
Finished job 147.
83 of 181 steps (46%) done
Select jobs to execute...

[Mon Jul 28 20:24:20 2025]
rule checkm_qa:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    jobid: 141
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 48
    resources: tmpdir=/docker_tmp

checkm qa -o 2 --tab_table -t 48 -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/ && checkm tree_qa -o 2 --tab_table -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/
Activating conda environment: checkm
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
    Finished parsing hits for 1 of 2 (50.00%) bins.
    Finished parsing hits for 2 of 2 (100.00%) bins.
[Mon Jul 28 20:24:24 2025]
Finished job 141.
84 of 181 steps (46%) done
Select jobs to execute...

[Mon Jul 28 20:24:24 2025]
rule checkm_profile:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    jobid: 162
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

checkm profile -q /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt --tab_table -f /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_plots:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
    jobid: 164
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


            checkm coding_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95 || true
            checkm marker_plot --image_type pdf  -x fa --dpi 400 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            checkm nx_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
            
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_plots:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
    jobid: 166
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


            checkm coding_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95 || true
            checkm marker_plot --image_type pdf  -x fa --dpi 400 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            checkm nx_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
            
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_profile:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    jobid: 144
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

checkm profile -q /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt --tab_table -f /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule tax_classification_scaffolds:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt
    jobid: 133
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 --memory-mapping --threads 16 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly.fasta --output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt --report /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt

[Mon Jul 28 20:24:24 2025]
rule checkm_plots:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
    jobid: 165
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


            checkm coding_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95 || true
            checkm marker_plot --image_type pdf  -x fa --dpi 400 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            checkm nx_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
            
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_profile:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    jobid: 150
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

checkm profile -q /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt --tab_table -f /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_plots:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
    jobid: 167
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/lineage.ms, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


            checkm coding_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ 95 || true
            checkm marker_plot --image_type pdf  -x fa --dpi 400 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            checkm nx_plot --image_type pdf  -x fa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/ /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/ || true
            touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done
            
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule checkm_profile:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    jobid: 156
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

checkm profile -q /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_coverage.txt --tab_table -f /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
Activating conda environment: checkm

[Mon Jul 28 20:24:24 2025]
rule gene_annotation_grep:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.COG.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt
    jobid: 83
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        grep "NODE_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,11 | sed -e 's/\t-//g' | grep -e $'\t' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,5 > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.COG.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,12 | grep "ko:" | sed 's/ko://g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,13 | grep "ko" | sed 's/,map.*//g' | sed 's/ko/map/g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt || true
        
[Mon Jul 28 20:24:24 2025]
Finished job 83.
85 of 181 steps (47%) done
Select jobs to execute...

[Mon Jul 28 20:24:24 2025]
rule gene_annot_iTPMs:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    jobid: 112
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt        
        

[Mon Jul 28 20:24:24 2025]
rule gene_annot_seqExtract:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
    jobid: 105
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.fna; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        seqtk subseq /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.faa
        seqtk subseq /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.fna
        seqtk subseq /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.faa
        seqtk subseq /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
        

[Mon Jul 28 20:24:24 2025]
rule copy_annotation_file:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    jobid: 82
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

[Mon Jul 28 20:24:24 2025]
Finished job 112.
86 of 181 steps (48%) done
Select jobs to execute...

[Mon Jul 28 20:24:24 2025]
rule gene_annot_geneTPMs:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt
    jobid: 111
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        cut -f1,7 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt | sed $'s/#KO.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/KO_list.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt |         sed '1s/^/#KO\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt

        cut -f1,7 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt | sed $'s/#EC.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/EC_list.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt |         sed '1s/^/#EC\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt
        
[Mon Jul 28 20:24:24 2025]
Finished job 105.
87 of 181 steps (48%) done
Select jobs to execute...
[Mon Jul 28 20:24:24 2025]
Finished job 111.
88 of 181 steps (49%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
[Mon Jul 28 20:24:25 2025]
Finished job 162.
89 of 181 steps (49%) done

[Mon Jul 28 20:24:25 2025]
rule taxbin_krona_txt:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    output: /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt
    jobid: 172
    reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

join /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -t $'\t' | cut -f6,10,11 | sed -e 's/..__/\t/g' | sed -e 's/\tunresolved//g' | sed -e '1 s/^/#/' > /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt

[Mon Jul 28 20:24:25 2025]
rule join_profiles_tax:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt
    jobid: 158
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -f1,5 > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt && cut /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt -f1,6-11,13,15,17,19,23 > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt && paste /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt && join /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt -t $'\t' | cut -f 1,3,4,6,7-19 | sed 's/[^\t]*_assembly: //g' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt
[Mon Jul 28 20:24:25 2025]
Finished job 144.
90 of 181 steps (50%) done
[Mon Jul 28 20:24:25 2025]
Finished job 150.
91 of 181 steps (50%) done
[Mon Jul 28 20:24:25 2025]
Finished job 156.
92 of 181 steps (51%) done
Select jobs to execute...

[Mon Jul 28 20:24:25 2025]
rule taxbin_krona_txt:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    output: /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt
    jobid: 170
    reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

join /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -t $'\t' | cut -f6,10,11 | sed -e 's/..__/\t/g' | sed -e 's/\tunresolved//g' | sed -e '1 s/^/#/' > /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt

[Mon Jul 28 20:24:25 2025]
rule join_profiles_tax:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt
    jobid: 140
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -f1,5 > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt && cut /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt -f1,6-11,13,15,17,19,23 > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt && paste /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt && join /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt -t $'\t' | cut -f 1,3,4,6,7-19 | sed 's/[^\t]*_assembly: //g' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt

[Mon Jul 28 20:24:25 2025]
rule join_profiles_tax:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt
    jobid: 146
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -f1,5 > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt && cut /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt -f1,6-11,13,15,17,19,23 > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt && paste /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt && join /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt -t $'\t' | cut -f 1,3,4,6,7-19 | sed 's/[^\t]*_assembly: //g' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt

[Mon Jul 28 20:24:25 2025]
rule join_profiles_tax:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt
    jobid: 152
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -f1,5 > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt && cut /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_qa.txt -f1,6-11,13,15,17,19,23 > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt && paste /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt && join /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt -t $'\t' | cut -f 1,3,4,6,7-19 | sed 's/[^\t]*_assembly: //g' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt

[Mon Jul 28 20:24:25 2025]
rule taxbin_krona_txt:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    output: /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt
    jobid: 169
    reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

join /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -t $'\t' | cut -f6,10,11 | sed -e 's/..__/\t/g' | sed -e 's/\tunresolved//g' | sed -e '1 s/^/#/' > /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt

[Mon Jul 28 20:24:25 2025]
rule taxbin_krona_txt:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    output: /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt
    jobid: 171
    reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

join /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt -t $'\t' | cut -f6,10,11 | sed -e 's/..__/\t/g' | sed -e 's/\tunresolved//g' | sed -e '1 s/^/#/' > /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt

[Mon Jul 28 20:24:25 2025]
Job 173: rule make_biom
        Making biom file from 'Taxonomy (contained)' column in output of checkm tree_qa,
        '{sample}_assembly: mapped reads' column in checkm profiles, and metadata.
        metadata: /inputs/mapping_file.csv
        input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt
        output: /outputs/TAXprofiles/MAGs_TAX/MAG-based_Counts+TAX.biom
        jobid: 173
Reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/MAG-based_Counts+TAX.biom; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_profiles.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tax.txt

[Mon Jul 28 20:24:25 2025]
Finished job 172.
93 of 181 steps (51%) done
[Mon Jul 28 20:24:25 2025]
Finished job 158.
94 of 181 steps (52%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt.
[Mon Jul 28 20:24:25 2025]
Finished job 170.
95 of 181 steps (52%) done
[Mon Jul 28 20:24:25 2025]
Finished job 140.
96 of 181 steps (53%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt.
[Mon Jul 28 20:24:25 2025]
Finished job 146.
97 of 181 steps (54%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt.
Select jobs to execute...
[Mon Jul 28 20:24:25 2025]
Finished job 169.
98 of 181 steps (54%) done
[Mon Jul 28 20:24:25 2025]
Finished job 152.
99 of 181 steps (55%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp1.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/tmp2.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_tmpsum.txt.
[Mon Jul 28 20:24:25 2025]
Finished job 171.
100 of 181 steps (55%) done

[Mon Jul 28 20:24:25 2025]
rule taxbin_krona_html:
    input: /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt
    output: /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html
    jobid: 168
    reason: Missing output files: /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html; Input files updated by another job: /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt
    resources: tmpdir=/docker_tmp

ktImportText /outputs/TAXprofiles/MAGs_TAX/bin/S1_GItract_HiSeq_cami_4krona.txt /outputs/TAXprofiles/MAGs_TAX/bin/S28_Skin_HiSeq_cami_4krona.txt /outputs/TAXprofiles/MAGs_TAX/bin/S9_Air_HiSeq_cami_4krona.txt /outputs/TAXprofiles/MAGs_TAX/bin/S6_Oral_HiSeq_cami_4krona.txt -o /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html
Select jobs to execute...
[Mon Jul 28 20:24:25 2025]
Finished job 168.
101 of 181 steps (56%) done
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
cp /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt && cut -f 1,5 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
[Mon Jul 28 20:24:26 2025]
Finished job 82.
102 of 181 steps (56%) done

[Mon Jul 28 20:24:26 2025]
rule run_min_path:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt
    jobid: 87
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt ]; then
            python3 /usr/local/src/MinPath/MinPath.py -any /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -map /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -mps /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.mps                 -report /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt -details /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt >> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt is empty, so run_min_path will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        fi
        
[Mon Jul 28 20:24:26 2025]
Finished job 133.
103 of 181 steps (57%) done
Select jobs to execute...

[Mon Jul 28 20:24:26 2025]
rule tax_classification_scaffolds:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt
    jobid: 137
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 --memory-mapping --threads 16 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly.fasta --output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt --report /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt

[Mon Jul 28 20:24:26 2025]
rule generate_scafftax:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt
    jobid: 132
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt && paste /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt <(cut -f2-3 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt) > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt
[Mon Jul 28 20:24:26 2025]
Finished job 132.
104 of 181 steps (57%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt.
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Mon Jul 28 20:24:27 2025]
Finished job 173.
105 of 181 steps (58%) done
[Mon Jul 28 20:24:29 2025]
Finished job 137.
106 of 181 steps (59%) done

[Mon Jul 28 20:24:29 2025]
rule tax_classification_genes:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
    jobid: 122
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --threads 16  --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna --memory-mapping --output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt --report /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt

[Mon Jul 28 20:24:29 2025]
rule generate_scafftax:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt
    jobid: 136
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt && paste /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt <(cut -f2-3 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt) > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt
[Mon Jul 28 20:24:29 2025]
Finished job 136.
107 of 181 steps (59%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt.
Select jobs to execute...
[Mon Jul 28 20:24:31 2025]
Finished job 122.
108 of 181 steps (60%) done

[Mon Jul 28 20:24:31 2025]
rule tax_genes_ABUNtabtax:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    jobid: 121
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt &&paste /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt <(cut -f2-3 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt) > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt 

[Mon Jul 28 20:24:31 2025]
rule run_kraken2_classification:
    input: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S6_Oral_HiSeq_cami_klog.txt, /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt, /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S6_Oral_HiSeq_cami_classLOG.txt
    jobid: 18
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt; Input files updated by another job: /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --memory-mapping --paired /outputs/TED_out/S6_Oral_HiSeq_cami_R1_ted.fastq.gz /outputs/TED_out/S6_Oral_HiSeq_cami_R2_ted.fastq.gz --output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S6_Oral_HiSeq_cami_klog.txt --report /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt 2>> /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S6_Oral_HiSeq_cami_classLOG.txt
[Mon Jul 28 20:24:31 2025]
Finished job 121.
109 of 181 steps (60%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt.
Select jobs to execute...

[Mon Jul 28 20:24:31 2025]
rule tax_genes_4krona:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    output: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt
    jobid: 129
    reason: Missing output files: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f6-8 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt | awk -F'\t' 'NR>1{k = $3; sum[k]+= $1; name[k]=$2} END { print; for (k in sum) print sum[k], name[k], k}' OFS="	" |sed -e '1 s/^/#iTPM\tTAXname\tTAXid\n/' > /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt
[Mon Jul 28 20:24:31 2025]
Finished job 129.
110 of 181 steps (61%) done
Select jobs to execute...
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
[Mon Jul 28 20:24:32 2025]
Finished job 167.
111 of 181 steps (61%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/metabat2_run.done.
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
[Mon Jul 28 20:24:33 2025]
Finished job 164.
112 of 181 steps (62%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/metabat2_run.done.
[Mon Jul 28 20:24:34 2025]
Finished job 18.
113 of 181 steps (62%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S6_Oral_HiSeq_cami_klog.txt.

[Mon Jul 28 20:24:34 2025]
rule kreport2krona_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    jobid: 17
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

python3 /pipeline/utils/report2krona_wTAXid_last.py --report-file /outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt --no-tax-prefixes -o /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt &&sed -i 's/\tUnclassified\t\t\t\t\t\t\t0/\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\t0/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt

[Mon Jul 28 20:24:34 2025]
rule tax_classification_genes:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
    jobid: 124
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna
    wildcards: sample=S9_Air_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --threads 16  --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes.fna --memory-mapping --output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt --report /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
Namespace(r_file='/outputs/TAXprofiles/readsTAX_plusPFV/reports/S6_Oral_HiSeq_cami_taxREPORT.txt', r_dir=None, o_file='/outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt', x_include=False, tax_exclude=True, m_file=None)
[Mon Jul 28 20:24:34 2025]
Finished job 17.
114 of 181 steps (63%) done
Select jobs to execute...

[Mon Jul 28 20:24:34 2025]
rule tax_biom_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_4biom.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_json.biom
    jobid: 102
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_json.biom; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed 's/\t/;/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_4biom.txt && biom convert -i /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_4biom.txt -o /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_json.biom --to-json --table-type='OTU table' --process-obs-metadata taxonomy
[Mon Jul 28 20:24:35 2025]
Finished job 87.
115 of 181 steps (64%) done
Select jobs to execute...

[Mon Jul 28 20:24:35 2025]
rule create_pathways_report:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    jobid: 86
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt ]; then
            grep 'minpath\ 1' /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt is empty, so create_pathways_report will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        fi
        
[Mon Jul 28 20:24:35 2025]
Finished job 86.
116 of 181 steps (64%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_report.txt.
Select jobs to execute...

[Mon Jul 28 20:24:35 2025]
rule run_genes2krona:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt
    jobid: 81
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -a -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt -a -s /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt ]; then
            python3 /pipeline/utils/genes2KronaTable.py -i /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt            -m /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -H /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt -n S9_Air_HiSeq_cami -c /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt            -l /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt -o /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt &&            sed '1s/^/#/' /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt &&            cp /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt
        else
            echo "One of the input file is empty, so run_genes2krona will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt
        fi
        
[Mon Jul 28 20:24:35 2025]
Finished job 102.
117 of 181 steps (65%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_4biom.txt.
Select jobs to execute...
[Mon Jul 28 20:24:35 2025]
Finished job 81.
118 of 181 steps (65%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt.

[Mon Jul 28 20:24:35 2025]
rule pwy_biom_per_sample:
    input: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_4biom.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom
    jobid: 97
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt ]; then
            sed 's/\t/;/g' /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_4biom.txt
            biom convert -i /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_4biom.txt -o /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom --to-json --table-type='Pathway table' --process-obs-metadata taxonomy || touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom
        else
            echo "The input file /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt is empty, so pwy_biom_per_sample will not run. All output file(s) from this step are empty."
            touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_4biom.txt /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom
        fi
        
[Mon Jul 28 20:24:36 2025]
Finished job 124.
119 of 181 steps (66%) done
Select jobs to execute...

[Mon Jul 28 20:24:36 2025]
rule tax_genes_ABUNtabtax:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    jobid: 123
    reason: Missing output files: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt &&paste /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt <(cut -f2-3 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt) > /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt 

[Mon Jul 28 20:24:36 2025]
rule tax_classification_genes:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
    jobid: 126
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --threads 16  --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna --memory-mapping --output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt --report /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
[Mon Jul 28 20:24:36 2025]
Finished job 123.
120 of 181 steps (66%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt.
Select jobs to execute...

[Mon Jul 28 20:24:36 2025]
rule tax_genes_4krona:
    input: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    output: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt
    jobid: 130
    reason: Missing output files: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    wildcards: sample=S9_Air_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f6-8 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt | awk -F'\t' 'NR>1{k = $3; sum[k]+= $1; name[k]=$2} END { print; for (k in sum) print sum[k], name[k], k}' OFS="	" |sed -e '1 s/^/#iTPM\tTAXname\tTAXid\n/' > /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt
[Mon Jul 28 20:24:36 2025]
Finished job 130.
121 of 181 steps (67%) done
Select jobs to execute...
[Mon Jul 28 20:24:36 2025]
Finished job 97.
122 of 181 steps (67%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_4biom.txt.
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
[Mon Jul 28 20:24:36 2025]
Finished job 166.
123 of 181 steps (68%) done
Removing temporary output /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/metabat2_run.done.
[Mon Jul 28 20:24:38 2025]
Finished job 126.
124 of 181 steps (69%) done

[Mon Jul 28 20:24:38 2025]
rule run_kraken2_classification:
    input: /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S1_GItract_HiSeq_cami_klog.txt, /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt, /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S1_GItract_HiSeq_cami_classLOG.txt
    jobid: 3
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt; Input files updated by another job: /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --memory-mapping --paired /outputs/TED_out/S1_GItract_HiSeq_cami_R1_ted.fastq.gz /outputs/TED_out/S1_GItract_HiSeq_cami_R2_ted.fastq.gz --output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S1_GItract_HiSeq_cami_klog.txt --report /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt 2>> /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S1_GItract_HiSeq_cami_classLOG.txt

[Mon Jul 28 20:24:38 2025]
rule tax_genes_ABUNtabtax:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    jobid: 125
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt &&paste /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt <(cut -f2-3 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt) > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt 
[Mon Jul 28 20:24:38 2025]
Finished job 125.
125 of 181 steps (69%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt.
Select jobs to execute...

[Mon Jul 28 20:24:38 2025]
rule tax_genes_4krona:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    output: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt
    jobid: 131
    reason: Missing output files: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f6-8 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt | awk -F'\t' 'NR>1{k = $3; sum[k]+= $1; name[k]=$2} END { print; for (k in sum) print sum[k], name[k], k}' OFS="	" |sed -e '1 s/^/#iTPM\tTAXname\tTAXid\n/' > /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt
[Mon Jul 28 20:24:38 2025]
Finished job 131.
126 of 181 steps (70%) done
Select jobs to execute...
/opt/conda/envs/checkm/lib/python3.8/site-packages/checkm/plot/nxPlot.py:83: UserWarning: FixedFormatter should only be used together with FixedLocator
  axes.set_yticklabels(kbpLabels)
[Mon Jul 28 20:24:39 2025]
Finished job 165.
127 of 181 steps (70%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/metabat2_run.done.
[Mon Jul 28 20:24:40 2025]
Finished job 3.
128 of 181 steps (71%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S1_GItract_HiSeq_cami_klog.txt.

[Mon Jul 28 20:24:41 2025]
rule kreport2krona_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt
    jobid: 2
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

python3 /pipeline/utils/report2krona_wTAXid_last.py --report-file /outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt --no-tax-prefixes -o /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt &&sed -i 's/\tUnclassified\t\t\t\t\t\t\t0/\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\t0/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt

[Mon Jul 28 20:24:41 2025]
rule tax_classification_scaffolds:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt
    jobid: 139
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 --memory-mapping --threads 16 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly.fasta --output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt --report /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt
Namespace(r_file='/outputs/TAXprofiles/readsTAX_plusPFV/reports/S1_GItract_HiSeq_cami_taxREPORT.txt', r_dir=None, o_file='/outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt', x_include=False, tax_exclude=True, m_file=None)
[Mon Jul 28 20:24:41 2025]
Finished job 2.
129 of 181 steps (71%) done
Select jobs to execute...

[Mon Jul 28 20:24:41 2025]
rule tax_biom_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_4biom.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_json.biom
    jobid: 99
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_json.biom; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed 's/\t/;/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_4biom.txt && biom convert -i /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_4biom.txt -o /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_json.biom --to-json --table-type='OTU table' --process-obs-metadata taxonomy
[Mon Jul 28 20:24:42 2025]
Finished job 99.
130 of 181 steps (72%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_4biom.txt.
Select jobs to execute...
[Mon Jul 28 20:24:43 2025]
Finished job 139.
131 of 181 steps (72%) done

[Mon Jul 28 20:24:43 2025]
rule gene_annotation:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    jobid: 77
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

emapper.py -i /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp  --scratch_dir /outputs/tmp --dbmem

[Mon Jul 28 20:24:43 2025]
rule generate_scafftax:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt
    jobid: 138
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt && paste /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt <(cut -f2-3 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt) > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt
[Mon Jul 28 20:24:43 2025]
Finished job 138.
132 of 181 steps (73%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt.
Select jobs to execute...
[1;32mFunctional annotation of hits...[0m
0 9.5367431640625e-07 0.00 q/s (% mem usage: 1.70, % mem avail: 98.34)
[1;34mTime to load the DB into memory: 43.6709463596344[0m
500 45.88734197616577 10.90 q/s (% mem usage: 24.00, % mem avail: 75.99)
1000 48.1089072227478 20.79 q/s (% mem usage: 24.00, % mem avail: 75.99)
1500 50.35313606262207 29.79 q/s (% mem usage: 24.00, % mem avail: 75.99)
2000 52.69320201873779 37.96 q/s (% mem usage: 24.00, % mem avail: 75.99)
2500 55.01206398010254 45.44 q/s (% mem usage: 24.00, % mem avail: 75.99)
3000 57.24099040031433 52.41 q/s (% mem usage: 24.00, % mem avail: 75.99)
3500 59.47359824180603 58.85 q/s (% mem usage: 24.00, % mem avail: 75.99)
4000 61.663384437561035 64.87 q/s (% mem usage: 24.00, % mem avail: 75.99)
4500 64.1161539554596 70.19 q/s (% mem usage: 24.00, % mem avail: 75.99)
5000 66.49703431129456 75.19 q/s (% mem usage: 24.00, % mem avail: 75.99)
5500 68.78789114952087 79.96 q/s (% mem usage: 24.00, % mem avail: 75.99)
6000 71.08689570426941 84.40 q/s (% mem usage: 24.00, % mem avail: 75.99)
6295 74.20494174957275 84.83 q/s (% mem usage: 23.90, % mem avail: 76.05)
[Mon Jul 28 20:43:51 2025]
Finished job 77.
133 of 181 steps (73%) done

[Mon Jul 28 20:43:51 2025]
rule tax_classification_genes:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt
    jobid: 120
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --threads 16  --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna --memory-mapping --output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt --report /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_classLOG.txt

[Mon Jul 28 20:43:51 2025]
rule gene_annotation_grep:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.COG.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt
    jobid: 76
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        grep "NODE_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,11 | sed -e 's/\t-//g' | grep -e $'\t' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,5 > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.COG.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,12 | grep "ko:" | sed 's/ko://g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,13 | grep "ko" | sed 's/,map.*//g' | sed 's/ko/map/g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt || true
        
[Mon Jul 28 20:43:51 2025]
Finished job 76.
134 of 181 steps (74%) done
Select jobs to execute...

[Mon Jul 28 20:43:51 2025]
rule gene_annot_iTPMs:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    jobid: 110
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt        
        

[Mon Jul 28 20:43:51 2025]
rule gene_annot_seqExtract:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
    jobid: 104
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.fna; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        seqtk subseq /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.faa
        seqtk subseq /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.fna
        seqtk subseq /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.faa
        seqtk subseq /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
        

[Mon Jul 28 20:43:51 2025]
rule copy_annotation_file:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    jobid: 75
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

[Mon Jul 28 20:43:51 2025]
Finished job 110.
135 of 181 steps (75%) done
Select jobs to execute...

[Mon Jul 28 20:43:51 2025]
rule gene_annot_geneTPMs:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt
    jobid: 109
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        cut -f1,7 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt | sed $'s/#KO.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/KO_list.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt |         sed '1s/^/#KO\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt

        cut -f1,7 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt | sed $'s/#EC.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/EC_list.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt |         sed '1s/^/#EC\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt
        
[Mon Jul 28 20:43:52 2025]
Finished job 104.
136 of 181 steps (75%) done
Select jobs to execute...
[Mon Jul 28 20:43:52 2025]
Finished job 109.
137 of 181 steps (76%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
cp /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt && cut -f 1,5 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
[Mon Jul 28 20:43:53 2025]
Finished job 75.
138 of 181 steps (76%) done

[Mon Jul 28 20:43:53 2025]
rule run_min_path:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt
    jobid: 80
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt ]; then
            python3 /usr/local/src/MinPath/MinPath.py -any /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -map /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -mps /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.mps                 -report /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt -details /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt >> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt is empty, so run_min_path will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        fi
        
[Mon Jul 28 20:43:53 2025]
Finished job 120.
139 of 181 steps (77%) done
Select jobs to execute...

[Mon Jul 28 20:43:53 2025]
rule tax_classification_scaffolds:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt
    jobid: 135
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --confidence 0.05 --memory-mapping --threads 16 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly.fasta --output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt --report /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_taxREPORT.txt 2>> /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXclassLOG.txt

[Mon Jul 28 20:43:53 2025]
rule tax_genes_ABUNtabtax:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    jobid: 119
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt &&paste /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt <(cut -f2-3 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt) > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt 
[Mon Jul 28 20:43:53 2025]
Finished job 119.
140 of 181 steps (77%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_tmptax.txt.
Select jobs to execute...

[Mon Jul 28 20:43:53 2025]
rule tax_genes_4krona:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    output: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt
    jobid: 128
    reason: Missing output files: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f6-8 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt | awk -F'\t' 'NR>1{k = $3; sum[k]+= $1; name[k]=$2} END { print; for (k in sum) print sum[k], name[k], k}' OFS="	" |sed -e '1 s/^/#iTPM\tTAXname\tTAXid\n/' > /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt
[Mon Jul 28 20:43:53 2025]
Finished job 128.
141 of 181 steps (78%) done
Select jobs to execute...

[Mon Jul 28 20:43:53 2025]
rule kt_tax_html:
    input: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt
    output: /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html
    jobid: 127
    reason: Missing output files: /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html; Input files updated by another job: /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt
    resources: tmpdir=/docker_tmp

ktImportTaxonomy /outputs/TAXprofiles/geneTAX_plusPFV/bin/S1_GItract_HiSeq_cami_4krona.txt /outputs/TAXprofiles/geneTAX_plusPFV/bin/S28_Skin_HiSeq_cami_4krona.txt /outputs/TAXprofiles/geneTAX_plusPFV/bin/S9_Air_HiSeq_cami_4krona.txt /outputs/TAXprofiles/geneTAX_plusPFV/bin/S6_Oral_HiSeq_cami_4krona.txt -m 1 -q 2 -t 3 -d 10 -tax /dbs/wgsa2/KronaTools_taxonomy -o /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html
   [ WARNING ]  Score column already in use; not reading scores.
[Mon Jul 28 20:43:56 2025]
Finished job 135.
142 of 181 steps (78%) done
Select jobs to execute...

[Mon Jul 28 20:43:56 2025]
rule generate_scafftax:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt
    jobid: 134
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

cut -f2-3 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt | sed -e 's/ (taxid /\t/g' | sed -e 's/)$//g' | sort | sed '1s/^/#contigName\tTAXname\tTAXid\n/' > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt && paste /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt <(cut -f2-3 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt) > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt

[Mon Jul 28 20:43:56 2025]
rule gene_annotation:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    jobid: 91
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S6_Oral_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

emapper.py -i /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp  --scratch_dir /outputs/tmp --dbmem
[Mon Jul 28 20:43:56 2025]
Finished job 134.
143 of 181 steps (79%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_klog.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAXtmp_tax.txt.
Select jobs to execute...
   [ WARNING ]  The following taxonomy IDs were not found in the local
                database and were set to root (if they were recently added to
                NCBI, use updateTaxonomy.sh to update the local database):
                2829812 2932268 2892440 3020908 3020829
[Mon Jul 28 20:43:57 2025]
Finished job 127.
144 of 181 steps (80%) done
[Mon Jul 28 20:44:02 2025]
Finished job 80.
145 of 181 steps (80%) done

[Mon Jul 28 20:44:02 2025]
rule create_pathways_report:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    jobid: 79
    reason: Missing output files: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt ]; then
            grep 'minpath\ 1' /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt is empty, so create_pathways_report will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        fi
        
[Mon Jul 28 20:44:02 2025]
Finished job 79.
146 of 181 steps (81%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_report.txt.
Select jobs to execute...

[Mon Jul 28 20:44:02 2025]
rule run_genes2krona:
    input: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    output: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt
    jobid: 74
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -a -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt -a -s /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt ]; then
            python3 /pipeline/utils/genes2KronaTable.py -i /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt            -m /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -H /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt -n S28_Skin_HiSeq_cami -c /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt            -l /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt -o /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt &&            sed '1s/^/#/' /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt > /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt &&            cp /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt
        else
            echo "One of the input file is empty, so run_genes2krona will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt
        fi
        
[Mon Jul 28 20:44:02 2025]
Finished job 74.
147 of 181 steps (81%) done
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt.
Removing temporary output /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt.
Select jobs to execute...

[Mon Jul 28 20:44:02 2025]
rule pwy_biom_per_sample:
    input: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_4biom.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom
    jobid: 96
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt ]; then
            sed 's/\t/;/g' /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_4biom.txt
            biom convert -i /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_4biom.txt -o /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom --to-json --table-type='Pathway table' --process-obs-metadata taxonomy || touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom
        else
            echo "The input file /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt is empty, so pwy_biom_per_sample will not run. All output file(s) from this step are empty."
            touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_4biom.txt /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom
        fi
        
[Mon Jul 28 20:44:03 2025]
Finished job 96.
148 of 181 steps (82%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_4biom.txt.
Select jobs to execute...
[1;32mFunctional annotation of hits...[0m
0 1.1920928955078125e-06 0.00 q/s (% mem usage: 1.70, % mem avail: 98.33)
[1;34mTime to load the DB into memory: 44.192787170410156[0m
500 46.8285813331604 10.68 q/s (% mem usage: 24.00, % mem avail: 75.99)
1000 49.31543684005737 20.28 q/s (% mem usage: 24.00, % mem avail: 75.99)
1500 51.747321128845215 28.99 q/s (% mem usage: 24.00, % mem avail: 75.99)
2000 54.35421705245972 36.80 q/s (% mem usage: 24.00, % mem avail: 75.99)
2500 56.94709396362305 43.90 q/s (% mem usage: 24.00, % mem avail: 75.99)
3000 59.429240465164185 50.48 q/s (% mem usage: 24.00, % mem avail: 75.99)
3500 61.9109308719635 56.53 q/s (% mem usage: 24.00, % mem avail: 75.99)
4000 64.3509213924408 62.16 q/s (% mem usage: 24.00, % mem avail: 75.99)
4500 66.99748420715332 67.17 q/s (% mem usage: 24.00, % mem avail: 75.99)
5000 69.29953956604004 72.15 q/s (% mem usage: 24.00, % mem avail: 75.99)
5500 71.87106823921204 76.53 q/s (% mem usage: 24.00, % mem avail: 75.99)
6000 74.62084221839905 80.41 q/s (% mem usage: 24.00, % mem avail: 75.99)
6308 79.84468746185303 79.00 q/s (% mem usage: 1.60, % mem avail: 98.39)
[Mon Jul 28 21:03:28 2025]
Finished job 91.
149 of 181 steps (82%) done

[Mon Jul 28 21:03:29 2025]
rule run_kraken2_classification:
    input: /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz
    output: /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S28_Skin_HiSeq_cami_klog.txt, /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt, /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S28_Skin_HiSeq_cami_classLOG.txt
    jobid: 8
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt; Input files updated by another job: /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz, /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz
    wildcards: sample=S28_Skin_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

kraken2 --use-names --gzip-compressed --threads 16 --confidence 0.05 --db /dbs/wgsa2/classification_db/plusPFV_Mar2023 --memory-mapping --paired /outputs/TED_out/S28_Skin_HiSeq_cami_R1_ted.fastq.gz /outputs/TED_out/S28_Skin_HiSeq_cami_R2_ted.fastq.gz --output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S28_Skin_HiSeq_cami_klog.txt --report /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt 2>> /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S28_Skin_HiSeq_cami_classLOG.txt

[Mon Jul 28 21:03:29 2025]
rule gene_annotation_grep:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.COG.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt
    jobid: 90
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        grep "NODE_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,11 | sed -e 's/\t-//g' | grep -e $'\t' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,5 > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.COG.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,12 | grep "ko:" | sed 's/ko://g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,13 | grep "ko" | sed 's/,map.*//g' | sed 's/ko/map/g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt || true
        
[Mon Jul 28 21:03:29 2025]
Finished job 90.
150 of 181 steps (83%) done
Select jobs to execute...

[Mon Jul 28 21:03:29 2025]
rule copy_annotation_file:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    jobid: 89
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp

[Mon Jul 28 21:03:29 2025]
rule gene_annot_iTPMs:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    jobid: 114
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt        
        

[Mon Jul 28 21:03:29 2025]
rule gene_annot_seqExtract:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
    jobid: 106
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.faa; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        seqtk subseq /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.faa
        seqtk subseq /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.fna
        seqtk subseq /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.faa
        seqtk subseq /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
        
[Mon Jul 28 21:03:29 2025]
Finished job 114.
151 of 181 steps (83%) done
Select jobs to execute...

[Mon Jul 28 21:03:29 2025]
rule gene_annot_geneTPMs:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt
    jobid: 113
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        cut -f1,7 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt | sed $'s/#KO.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/KO_list.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt |         sed '1s/^/#KO\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt

        cut -f1,7 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt | sed $'s/#EC.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/EC_list.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt |         sed '1s/^/#EC\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt
        
[Mon Jul 28 21:03:29 2025]
Finished job 106.
152 of 181 steps (84%) done
Select jobs to execute...
[Mon Jul 28 21:03:29 2025]
Finished job 113.
153 of 181 steps (85%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
cp /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt && cut -f 1,5 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
[Mon Jul 28 21:03:30 2025]
Finished job 89.
154 of 181 steps (85%) done

[Mon Jul 28 21:03:30 2025]
rule run_min_path:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt
    jobid: 94
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt ]; then
            python3 /usr/local/src/MinPath/MinPath.py -any /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -map /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -mps /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.mps                 -report /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt -details /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt >> /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt is empty, so run_min_path will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        fi
        
[Mon Jul 28 21:03:31 2025]
Finished job 8.
155 of 181 steps (86%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/klogs/S28_Skin_HiSeq_cami_klog.txt.
Select jobs to execute...

[Mon Jul 28 21:03:31 2025]
rule gene_annotation:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.hits, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.seed_orthologs, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    jobid: 70
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa
    wildcards: sample=S1_GItract_HiSeq_cami
    threads: 16
    resources: tmpdir=/docker_tmp, mem_gb=184

emapper.py -i /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa -o annots --output_dir /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ --cpu 16 --itype proteins --block_size 4 --index_chunks 2 --data_dir /dbs/wgsa2/eggnog_data --override --temp_dir /outputs/tmp  --scratch_dir /outputs/tmp --dbmem

[Mon Jul 28 21:03:31 2025]
rule kreport2krona_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt
    jobid: 7
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

python3 /pipeline/utils/report2krona_wTAXid_last.py --report-file /outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt --no-tax-prefixes -o /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt &&sed -i 's/\tUnclassified\t\t\t\t\t\t\t0/\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\tUnclassified\t0/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt
Namespace(r_file='/outputs/TAXprofiles/readsTAX_plusPFV/reports/S28_Skin_HiSeq_cami_taxREPORT.txt', r_dir=None, o_file='/outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt', x_include=False, tax_exclude=True, m_file=None)
[Mon Jul 28 21:03:31 2025]
Finished job 7.
156 of 181 steps (86%) done
Select jobs to execute...

[Mon Jul 28 21:03:31 2025]
rule kreport2krona_import_text:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html
    jobid: 1
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    resources: tmpdir=/docker_tmp

ktImportText /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt -o /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html

[Mon Jul 28 21:03:31 2025]
rule TAX_collation:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX+Lineage.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Lineage.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/TAX_collationR.log
    jobid: 178
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts.txt; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S9_Air_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S1_GItract_HiSeq_cami_wTAXid_4krona.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bin/S6_Oral_HiSeq_cami_wTAXid_4krona.txt
    resources: tmpdir=/docker_tmp

find /outputs/TAXprofiles/readsTAX_plusPFV/bin//*_4krona.txt -type f -empty -delete && ls -1 /outputs/TAXprofiles/readsTAX_plusPFV/bin/ | xargs basename -a -s _wTAXid_4krona.txt > /outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt && Rscript /pipeline/utils/TableMerging_TAX_v4.R --binDIR /outputs/TAXprofiles/readsTAX_plusPFV/bin/ --sccList /outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt --outdir /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/ --genesDIR NA 2>&1 >/outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/TAX_collationR.log

[Mon Jul 28 21:03:31 2025]
rule tax_biom_per_sample:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt
    output: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_4biom.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_json.biom
    jobid: 100
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_json.biom; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt
    wildcards: sample=S28_Skin_HiSeq_cami
    resources: tmpdir=/docker_tmp

sed 's/\t/;/g' /outputs/TAXprofiles/readsTAX_plusPFV/bin/S28_Skin_HiSeq_cami_wTAXid_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_4biom.txt && biom convert -i /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_4biom.txt -o /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_json.biom --to-json --table-type='OTU table' --process-obs-metadata taxonomy
[Mon Jul 28 21:03:31 2025]
Finished job 1.
157 of 181 steps (87%) done
[Mon Jul 28 21:03:32 2025]
Finished job 100.
158 of 181 steps (87%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_4biom.txt.
[Mon Jul 28 21:03:34 2025]
Finished job 178.
159 of 181 steps (88%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/SccList.txt.
Select jobs to execute...

[Mon Jul 28 21:03:34 2025]
rule TAX_collation_biom:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage.txt, /inputs/mapping_file.csv
    output: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/tmp_.txt
    jobid: 177
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage.txt
    resources: tmpdir=/docker_tmp

sed '1s/Lineage/taxonomy/' /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage.txt > /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/tmp_.txt && biom convert -i /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/tmp_.txt -m <(sed '1s/^/#/' /inputs/mapping_file.csv) -o /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom --to-json --table-type='OTU table' --process-obs-metadata taxonomy

[Mon Jul 28 21:03:34 2025]
rule TAX_diversity_plots:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_TAX.txt, /inputs/mapping_file.csv
    output: /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt, /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_diversity_plots.done
    jobid: 180
    reason: Missing output files: /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_diversity_plots.done; Input files updated by another job: /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_TAX.txt, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts.txt
    resources: tmpdir=/docker_tmp


            sed 's/^#//g' /inputs/mapping_file.csv > /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt
            Rscript /pipeline/utils/DiversityPlots_TAX_v3.R --wdir /outputs/tmp --indir /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/ --mfile /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt --outdir /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/ || echo "ERROR: Failed to generate TAX_diversity_plots"
            touch /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_diversity_plots.done
            
Loading required package: data.table
Loading required package: fossil
Loading required package: sp
[Mon Jul 28 21:03:35 2025]
Finished job 177.
160 of 181 steps (88%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/tmp_.txt.
Loading required package: maps
Loading required package: shapefiles
Loading required package: foreign

Attaching package: ‘shapefiles’

The following objects are masked from ‘package:foreign’:

    read.dbf, write.dbf

Loading required package: ggplot2
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
Loading required package: ampvis2
All packages loaded successfully
Warning message:
In dir.create(path$outdir) :
  '/outputs/TAXprofiles/readsTAX_plusPFV/DivPlots' already exists
Warning message:
In tables$meta <- read.table(paste0(args$mfile), header = T, sep = "\t",  :
  Coercing LHS to a list
Warning message:
In alpha1$reads = colSums(tables$counts) : Coercing LHS to a list
Warning message:
In sst$meta = tables$meta : Coercing LHS to a list
Warning message:
Could not find a column named one of "OTU, ASV, #OTU ID" in otutable. Using row names as OTU ID's. 
107 OTUs not present in more than 0.01% relative abundance in any sample have been filtered 
Before: 353 OTUs
After: 246 OTUs
107 OTUs not present in more than 0.01% relative abundance in any sample have been filtered 
Before: 353 OTUs
After: 246 OTUs
Warning messages:
1: In vegan::metaMDS(data$abund, distance = distmeasure, trace = FALSE,  :
  stress is (nearly) zero: you may have insufficient data
2: In postMDS(out$points, dis, plot = max(0, plot - 1), ...) :
  skipping half-change scaling: too few points below threshold
Warning message:
In scale_fill_gradientn(colours = color.pal, trans = plot_colorscale,  :
  log-10 transformation introduced infinite values.
The following sample(s) have not been rarefied (less than 24795.25 reads):
S28_Skin_HiSeq_cami, S6_Oral_HiSeq_cami, S9_Air_HiSeq_cami
0 samples have been filtered.
[Mon Jul 28 21:03:39 2025]
Finished job 94.
161 of 181 steps (89%) done
Select jobs to execute...

[Mon Jul 28 21:03:39 2025]
rule create_pathways_report:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    jobid: 93
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt ]; then
            grep 'minpath\ 1' /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt is empty, so create_pathways_report will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        fi
        
[Mon Jul 28 21:03:39 2025]
Finished job 93.
162 of 181 steps (90%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_report.txt.
Select jobs to execute...

[Mon Jul 28 21:03:39 2025]
rule run_genes2krona:
    input: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    output: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt
    jobid: 88
    reason: Missing output files: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -a -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt -a -s /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt ]; then
            python3 /pipeline/utils/genes2KronaTable.py -i /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt            -m /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -H /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt -n S6_Oral_HiSeq_cami -c /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt            -l /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt -o /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt &&            sed '1s/^/#/' /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt > /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt &&            cp /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt
        else
            echo "One of the input file is empty, so run_genes2krona will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt
        fi
        
Warning messages:
1: In max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
3: In max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
4: In max(ids, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
[Mon Jul 28 21:03:39 2025]
Finished job 180.
163 of 181 steps (90%) done
Removing temporary output /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/tmp_mapping_file.txt.
[Mon Jul 28 21:03:39 2025]
Finished job 88.
164 of 181 steps (91%) done
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt.
Removing temporary output /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt.
Select jobs to execute...

[Mon Jul 28 21:03:39 2025]
rule pwy_biom_per_sample:
    input: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_4biom.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom
    jobid: 98
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt
    wildcards: sample=S6_Oral_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt ]; then
            sed 's/\t/;/g' /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_4biom.txt
            biom convert -i /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_4biom.txt -o /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom --to-json --table-type='Pathway table' --process-obs-metadata taxonomy || touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom
        else
            echo "The input file /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt is empty, so pwy_biom_per_sample will not run. All output file(s) from this step are empty."
            touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_4biom.txt /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom
        fi
        
[Mon Jul 28 21:03:40 2025]
Finished job 98.
165 of 181 steps (91%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_4biom.txt.
[1;32mFunctional annotation of hits...[0m
0 9.5367431640625e-07 0.00 q/s (% mem usage: 1.70, % mem avail: 98.34)
[1;34mTime to load the DB into memory: 43.430256366729736[0m
500 44.49396634101868 11.24 q/s (% mem usage: 24.00, % mem avail: 76.00)
1000 45.54652118682861 21.96 q/s (% mem usage: 24.00, % mem avail: 76.00)
1500 46.70880174636841 32.11 q/s (% mem usage: 24.00, % mem avail: 76.00)
2000 47.92656636238098 41.73 q/s (% mem usage: 24.00, % mem avail: 76.00)
2500 49.00889301300049 51.01 q/s (% mem usage: 24.00, % mem avail: 76.00)
3000 50.091384172439575 59.89 q/s (% mem usage: 24.00, % mem avail: 76.00)
3500 51.22920370101929 68.32 q/s (% mem usage: 24.00, % mem avail: 76.00)
4000 52.2130401134491 76.61 q/s (% mem usage: 24.00, % mem avail: 76.00)
4500 53.26687049865723 84.48 q/s (% mem usage: 24.00, % mem avail: 76.00)
5000 54.38299536705017 91.94 q/s (% mem usage: 24.00, % mem avail: 76.00)
5500 55.4233341217041 99.24 q/s (% mem usage: 24.00, % mem avail: 76.00)
5855 59.75114870071411 97.99 q/s (% mem usage: 1.60, % mem avail: 98.38)
[Mon Jul 28 21:22:52 2025]
Finished job 70.
166 of 181 steps (92%) done
Select jobs to execute...

[Mon Jul 28 21:22:52 2025]
rule gene_annotation_grep:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.COG.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt
    jobid: 69
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        grep "NODE_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,11 | sed -e 's/\t-//g' | grep -e $'\t' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f 1,5 > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.COG.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,12 | grep "ko:" | sed 's/ko://g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt || true
        grep "NODE_" /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.emapper.annotations | cut -f1,13 | grep "ko" | sed 's/,map.*//g' | sed 's/ko/map/g' | awk '{n=split($2,s,",");for (i=1;i<=n;i++) {$2=s[i];print}}' | sed -e 's/\s/\t/g' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.KEGGmap.txt || true
        
[Mon Jul 28 21:22:52 2025]
Finished job 69.
167 of 181 steps (92%) done
Select jobs to execute...

[Mon Jul 28 21:22:52 2025]
rule gene_annot_seqExtract:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
    jobid: 103
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.fna; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        seqtk subseq /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.faa
        seqtk subseq /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.fna
        seqtk subseq /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.faa /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.faa
        seqtk subseq /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes.fna /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
        

[Mon Jul 28 21:22:52 2025]
rule gene_annot_iTPMs:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    jobid: 108
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
        awk -v OFS="\t" 'NR==FNR { id[$1]=$0; next } ($1 in id){ print $2, id[$1]}'  /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt | sed '1s/^/#KO\tnodeID\tlen\treads\tcov\tiRPK\tiTPM\n/' > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt        
        

[Mon Jul 28 21:22:52 2025]
rule copy_annotation_file:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    jobid: 68
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp

[Mon Jul 28 21:22:52 2025]
Finished job 108.
168 of 181 steps (93%) done
Select jobs to execute...

[Mon Jul 28 21:22:52 2025]
rule gene_annot_geneTPMs:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt
    jobid: 107
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        cut -f1,7 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ko.txt | sed $'s/#KO.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/KO_list.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt |         sed '1s/^/#KO\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt

        cut -f1,7 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/ANNOTgenes_ABUNtab.ec.txt | sed $'s/#EC.*//g' | awk -F'\t' -f /pipeline/utils/calc_geneTPM.awk > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt
        awk -F'\t' -f /pipeline/utils/join2files_f2.awk /pipeline/utils/EC_list.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt |         sed '1s/^/#EC\tgeneTPM\tgeneNAME\n/'> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt
        
[Mon Jul 28 21:22:52 2025]
Finished job 103.
169 of 181 steps (93%) done
[Mon Jul 28 21:22:52 2025]
Finished job 107.
170 of 181 steps (94%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ko.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/tmp_geneTPMtab.ec.txt.
Select jobs to execute...

[Mon Jul 28 21:22:52 2025]
rule cp_geneTPM_files:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/genebin/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt
    jobid: 176
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/genebin/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt
    resources: tmpdir=/docker_tmp

Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Config file /pipeline/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
cp /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt && cut -f 1,5 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_ABUNtab.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Select jobs to execute...
cp /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt /outputs/PWYprofiles/keggPWYs.MP/genebin/
[Mon Jul 28 21:22:54 2025]
Finished job 68.
171 of 181 steps (94%) done
Select jobs to execute...

[Mon Jul 28 21:22:54 2025]
rule run_min_path:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt
    jobid: 73
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt ]; then
            python3 /usr/local/src/MinPath/MinPath.py -any /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -map /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -mps /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.mps                 -report /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt -details /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt >> /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt is empty, so run_min_path will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.details.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.minpath.log.txt
        fi
        
[Mon Jul 28 21:22:54 2025]
Finished job 176.
172 of 181 steps (95%) done
[Mon Jul 28 21:23:02 2025]
Finished job 73.
173 of 181 steps (96%) done
Select jobs to execute...

[Mon Jul 28 21:23:02 2025]
rule create_pathways_report:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    jobid: 72
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt ]; then
            grep 'minpath\ 1' /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        else
            echo "The input file /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt is empty, so create_pathways_report will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
        fi
        
[Mon Jul 28 21:23:02 2025]
Finished job 72.
174 of 181 steps (96%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_report.txt.
Select jobs to execute...

[Mon Jul 28 21:23:02 2025]
rule run_genes2krona:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt
    output: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt
    jobid: 67
    reason: Missing output files: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt; Input files updated by another job: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt -a -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt -a -s /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt ]; then
            python3 /pipeline/utils/genes2KronaTable.py -i /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt            -m /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-ko2map-092022.txt -H /dbs/wgsa2/minpath_data/KEGG_myfiles_0922/KEGG-HRCHY-092022.txt -n S1_GItract_HiSeq_cami -c /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt            -l /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/ko2gg.report.txt -o /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt &&            sed '1s/^/#/' /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt > /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt &&            cp /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt
        else
            echo "One of the input file is empty, so run_genes2krona will not run. All output file(s) from this step are empty."
            touch /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt
        fi
        
[Mon Jul 28 21:23:02 2025]
Finished job 67.
175 of 181 steps (97%) done
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_annots.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_TPM.txt.
Removing temporary output /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/tmp_4kr.txt.
Select jobs to execute...

[Mon Jul 28 21:23:02 2025]
rule pwy_biom_per_sample:
    input: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_4biom.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom
    jobid: 95
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt
    wildcards: sample=S1_GItract_HiSeq_cami
    resources: tmpdir=/docker_tmp


        if [ -s /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt ]; then
            sed 's/\t/;/g' /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt | sed 's/;/\t/1' | nl -n ln |sed '1s/^/\t/' | sed '1s/1\s\+\t#/\t/' | sed 's/\s\+\t/\t/g' | sed '1s/LINEAGE/taxonomy/' | sed -e '1s/Level.*/taxonomy/' > /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_4biom.txt
            biom convert -i /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_4biom.txt -o /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom --to-json --table-type='Pathway table' --process-obs-metadata taxonomy || touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom
        else
            echo "The input file /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt is empty, so pwy_biom_per_sample will not run. All output file(s) from this step are empty."
            touch /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_4biom.txt /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom
        fi
        

[Mon Jul 28 21:23:02 2025]
rule krona_import_text:
    input: /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html
    jobid: 66
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html; Input files updated by another job: /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt
    resources: tmpdir=/docker_tmp

ktImportText /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/pathways/S1_GItract_HiSeq_cami_4krona.txt /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/pathways/S28_Skin_HiSeq_cami_4krona.txt /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/pathways/S9_Air_HiSeq_cami_4krona.txt /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/pathways/S6_Oral_HiSeq_cami_4krona.txt -o /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html

[Mon Jul 28 21:23:02 2025]
rule PWY_collation:
    input: /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt
    output: /outputs/PWYprofiles/keggPWYs.MP/SccList.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY+allTiers.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_allTiers.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_PWY.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_geneTPMtable.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/PWY_collation.log
    jobid: 175
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_PWY.txt; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/genebin/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S28_Skin_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S1_GItract_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S9_Air_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/pwybin/S6_Oral_HiSeq_cami_4krona.txt, /outputs/PWYprofiles/keggPWYs.MP/genebin/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt
    resources: tmpdir=/docker_tmp

find /outputs/PWYprofiles/keggPWYs.MP/pwybin//*.txt -type f -empty -delete && find /outputs/PWYprofiles/keggPWYs.MP/genebin//*.txt -type f -empty -delete && ls -1 /outputs/PWYprofiles/keggPWYs.MP/pwybin/ | xargs basename -a -s _4krona.txt > /outputs/PWYprofiles/keggPWYs.MP/SccList.txt && head /outputs/PWYprofiles/keggPWYs.MP/SccList.txt &&Rscript /pipeline/utils/TableMerging_PWY_v4.R --binDIR /outputs/PWYprofiles/keggPWYs.MP/pwybin/ --sccList /outputs/PWYprofiles/keggPWYs.MP/SccList.txt --outdir /outputs/PWYprofiles/keggPWYs.MP/merged_tables/ --genesDIR /outputs/PWYprofiles/keggPWYs.MP/genebin/ 2>&1 >/outputs/PWYprofiles/keggPWYs.MP/merged_tables/PWY_collation.log
[Mon Jul 28 21:23:02 2025]
Finished job 66.
176 of 181 steps (97%) done
[Mon Jul 28 21:23:03 2025]
Finished job 95.
177 of 181 steps (98%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_4biom.txt.
[Mon Jul 28 21:23:04 2025]
Finished job 175.
178 of 181 steps (98%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/SccList.txt.
Select jobs to execute...

[Mon Jul 28 21:23:04 2025]
rule PWY_collation_biom:
    input: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers.txt, /inputs/mapping_file.csv
    output: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers_json.biom, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/tmp_.txt
    jobid: 174
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers_json.biom; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers.txt
    resources: tmpdir=/docker_tmp

sed '1s/allTiers/taxonomy/' /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers.txt > /outputs/PWYprofiles/keggPWYs.MP/merged_tables/tmp_.txt && biom convert -i /outputs/PWYprofiles/keggPWYs.MP/merged_tables/tmp_.txt -m <(sed '1s/^/#/' /inputs/mapping_file.csv) -o /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers_json.biom --to-json --table-type='Pathway table' --process-obs-metadata taxonomy

[Mon Jul 28 21:23:04 2025]
rule PWY_diversity_plots:
    input: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_PWY.txt, /inputs/mapping_file.csv
    output: /outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt, /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_diversity_plots.done
    jobid: 179
    reason: Missing output files: /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_diversity_plots.done; Input files updated by another job: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+PWY.txt, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_PWY.txt
    resources: tmpdir=/docker_tmp


            sed 's/^#//g' /inputs/mapping_file.csv > /outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt
            Rscript /pipeline/utils/DiversityPlots_PWY_v3.R --wdir /outputs/tmp --indir /outputs/PWYprofiles/keggPWYs.MP/merged_tables/ --mfile /outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt --outdir /outputs/PWYprofiles/keggPWYs.MP/DivPlots/ || echo "ERROR: Failed to generate PWY_diversity_plots"
            touch /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_diversity_plots.done
            
Loading required package: data.table
[Mon Jul 28 21:23:05 2025]
Finished job 174.
179 of 181 steps (99%) done
Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/merged_tables/tmp_.txt.
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Attaching package: ‘shapefiles’

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── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ lubridate 1.9.4     ✔ tibble    3.2.1
✔ purrr     1.0.4     ✔ tidyr     1.3.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::between()     masks data.table::between()
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ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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    IQR, mad, sd, var, xtabs

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    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
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All packages loaded successfully
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Failed to locate timezone database 
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In dir.create(path$outdir) :
  '/outputs/PWYprofiles/keggPWYs.MP/DivPlots' already exists
Warning message:
In tables$meta <- read.table(paste0(args$mfile), header = T, sep = "\t",  :
  Coercing LHS to a list
Warning message:
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  skipping half-change scaling: too few points below threshold
Warning messages:
1: The data has already been normalised. Setting normalise = TRUE (the default) will normalise the data again and the relative abundance information about the original data of which the provided data is a subset will be lost. 
2: In scale_fill_gradientn(colours = color.pal, trans = plot_colorscale,  :
  log-10 transformation introduced infinite values.
[Mon Jul 28 21:23:09 2025]
Finished job 179.
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Removing temporary output /outputs/PWYprofiles/keggPWYs.MP/DivPlots/tmp_mapping_file.txt.
Select jobs to execute...

[Mon Jul 28 21:23:09 2025]
localrule all:
    input: /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html, /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom, /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom, /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom, /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_json.biom, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html, /outputs/TAXprofiles/MAGs_TAX/MAG-based_Counts+TAX.biom, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom, /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_diversity_plots.done, /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_diversity_plots.done
    jobid: 0
    reason: Input files updated by another job: /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/PWYprofiles/keggPWYs.MP/DivPlots/PWY_diversity_plots.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/TAXprofiles/MAGs_TAX/TAXplots_MAGx.html, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S9_Air_HiSeq_cami_json.biom, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/PWYprofiles/keggPWYs.MP/merged_tables/merged_Counts+allTiers_json.biom, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/S9_Air_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ec.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S6_Oral_HiSeq_cami_json.biom, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/TAXprofiles/geneTAX_plusPFV/TAXplots_genesTAX_plusPFV.html, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/S28_Skin_HiSeq_cami_assembly_scaffCoverage.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/PWYprofiles/keggPWYs.MP/bioms/S1_GItract_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S28_Skin_HiSeq_cami_json.biom, /outputs/PWYprofiles/keggPWYs.MP/bioms/S9_Air_HiSeq_cami_json.biom, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S1_GItract_HiSeq_cami_json.biom, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/annotations/S1_GItract_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ko.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/S6_Oral_HiSeq_cami_geneTPMtab.ko.txt, /outputs/TAXprofiles/readsTAX_plusPFV/TAXplots_readsTAX_plusPFV.html, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/PREDgenes_stats.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/S6_Oral_HiSeq_cami_assembly_depths.txt, /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/TAX_diversity_plots.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/mag_SUMMARY.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/AMRs/AMRs.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.faa, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/TAXprofiles/readsTAX_plusPFV/bioms/S6_Oral_HiSeq_cami_json.biom, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ec.txt, /outputs/PWYprofiles/keggPWYs.MP/bioms/S28_Skin_HiSeq_cami_json.biom, /outputs/TAXprofiles/MAGs_TAX/MAG-based_Counts+TAX.biom, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/genesTAX_plusPFV/geneTAX_ABUNtab+tax.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/scaffTAX_plusPFV/scaffTAX_scaffCovr+tax.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/checkm_plots.done, /outputs/PWYprofiles/keggPWYs.MP/PWYplots_ko2gg.html, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/add_de_replication_stats.done, /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/genes/annotations/S9_Air_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/genes/AMRs/AMRs_info.txt, /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/S1_GItract_HiSeq_cami_assembly_depths.txt, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/annots.ko.fna, /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/genes/annotations/S28_Skin_HiSeq_cami_geneTPMtab.ko.txt, /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/genes/annotations/annots.ec.fna
    resources: tmpdir=/docker_tmp

[Mon Jul 28 21:23:09 2025]
Finished job 0.
181 of 181 steps (100%) done
Complete log: .snakemake/log/2025-07-28T195649.459768.snakemake.log

    set +o pipefail
    echo "Cleaning output..."
    rm -rf /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*.bt2 /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*.bt2 /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*.bt2 /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*.bt2 /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/*.done /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/*.done /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/*.done /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/*.done /outputs/asmbMetaSpades/S1_GItract_HiSeq_cami_asmb/MAGs/magsQA/QCplots/*.done /outputs/asmbMetaSpades/S28_Skin_HiSeq_cami_asmb/MAGs/magsQA/QCplots/*.done /outputs/asmbMetaSpades/S9_Air_HiSeq_cami_asmb/MAGs/magsQA/QCplots/*.done /outputs/asmbMetaSpades/S6_Oral_HiSeq_cami_asmb/MAGs/magsQA/QCplots/*.done /outputs/PWYprofiles/keggPWYs.MP/DivPlots/*.done /outputs/TAXprofiles/readsTAX_plusPFV/DivPlots/*.done /outputs/TAXprofiles/readsTAX_plusPFV/klogs/
    
        rm -rf /outputs/TED_out/
        cp /outputs/TAXprofiles/readsTAX_plusPFV/merged_tables/merged_Counts+Lineage_json.biom /outputs/for_analyze_with_microbiomedb.biom
