2026-07-21 17:34:43 - Preparing your machine to run the pipeline for job 3c0967ef0743
2026-07-21 17:36:47 - Pre-processing completed
[2026-07-21 17:36:51.628 UTC] Starting pipeline: QC, Current time: 2026-07-21 17:36
[2026-07-21 17:36:51.629 UTC] Pipeline version: 0.2.2, nephele_pipeline_utils version: 0.1.61
[2026-07-21 17:36:51.633 UTC] Pipeline arguments:
	--data_type PE
 	--run_cutadapt False
 	--error_rate 0.1
 	--indels True
 	--overlap 3
 	--match_read_wildcards False
 	--match_adapter_wildcards True
 	--adapter_f None
 	--adapter_r None
 	--front_f None
 	--front_r None
 	--anywhere_f None
 	--anywhere_r None
 	--run_qual_trimming False
 	--trim None
 	--truncation None
 	--window_size 4
 	--req_qual 12
 	--lead_qual 3
 	--trail_qual 3
 	--minlen 30
 	--avg_qual 0
 	--run_pair_reads False
 	--run_bbmerge False
 	--strictness default
 	--output_dag True
 	--mapping_file_path /inputs/mapping_file.csv
 	--inputs_dir_path /inputs
 	--outputs_dir_path /outputs
[2026-07-21 17:36:51.633 UTC] Pipeline initialized with 3 samples
[2026-07-21 17:36:51.633 UTC] Samples ids: SRR12904817, SRR12904818, SRR12904821
[2026-07-21 17:36:51.633 UTC] Samples info:
[2026-07-21 17:36:51.633 UTC] {'#SampleID': 'SRR12904817', 'Description': 'SRR12904817', 'TreatmentGroup': '12 month', 'ForwardFastqFile': 'SRR12904817_1_2Msub.fastq.gz', 'ReverseFastqFile': 'SRR12904817_2_2Msub.fastq.gz'}
[2026-07-21 17:36:51.633 UTC] {'#SampleID': 'SRR12904818', 'Description': 'SRR12904818', 'TreatmentGroup': '12 month', 'ForwardFastqFile': 'SRR12904818_1_2Msub.fastq.gz', 'ReverseFastqFile': 'SRR12904818_2_2Msub.fastq.gz'}
[2026-07-21 17:36:51.633 UTC] {'#SampleID': 'SRR12904821', 'Description': 'SRR12904821', 'TreatmentGroup': '1 month', 'ForwardFastqFile': 'SRR12904821_1_2Msub.fastq.gz', 'ReverseFastqFile': 'SRR12904821_2_2Msub.fastq.gz'}
[2026-07-21 17:36:51.639 UTC] Running command: bash -c snakemake --dag -f -s /pipeline/Snakefile -p --cores all --keep-going --keep-incomplete --config num_threads=16 outputs_dir_path=/outputs logs_dir_path=/outputs/logs multiqc_in_dir=multiqc_input limits_file=limits.txt multiqc_config_file=multiqc_config.yaml data_type=PE run_cutadapt=False cutadapt_args='--cores 16 --overlap 3 --error-rate 0.1' cutadapt_out_dir_name=adapter_trimmed run_qual_trimming=False trimo_args='MINLEN:30 SLIDINGWINDOW:4:12 LEADING:3 AVGQUAL:0 TRAILING:3' trim_out_dir_name=quality_trimmed run_pair_reads=False pair_reads_dir_name=pairing run_bbmerge=False bbmerge_dir_name=merging strictness=default samples='{"SRR12904817": {"fwd_fastq": "/inputs/SRR12904817_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904817_R2.fastq.gz"}, "SRR12904818": {"fwd_fastq": "/inputs/SRR12904818_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904818_R2.fastq.gz"}, "SRR12904821": {"fwd_fastq": "/inputs/SRR12904821_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904821_R2.fastq.gz"}}' | dot -Tpdf > /outputs/logs/dag.pdf
Building DAG of jobs...
[2026-07-21 17:36:52.269 UTC] Running command: bash -c snakemake -s /pipeline/Snakefile -p --cores all --keep-going --keep-incomplete --config num_threads=16 outputs_dir_path=/outputs logs_dir_path=/outputs/logs multiqc_in_dir=multiqc_input limits_file=limits.txt multiqc_config_file=multiqc_config.yaml data_type=PE run_cutadapt=False cutadapt_args='--cores 16 --overlap 3 --error-rate 0.1' cutadapt_out_dir_name=adapter_trimmed run_qual_trimming=False trimo_args='MINLEN:30 SLIDINGWINDOW:4:12 LEADING:3 AVGQUAL:0 TRAILING:3' trim_out_dir_name=quality_trimmed run_pair_reads=False pair_reads_dir_name=pairing run_bbmerge=False bbmerge_dir_name=merging strictness=default samples='{"SRR12904817": {"fwd_fastq": "/inputs/SRR12904817_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904817_R2.fastq.gz"}, "SRR12904818": {"fwd_fastq": "/inputs/SRR12904818_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904818_R2.fastq.gz"}, "SRR12904821": {"fwd_fastq": "/inputs/SRR12904821_R1.fastq.gz", "rev_fastq": "/inputs/SRR12904821_R2.fastq.gz"}}'
Assuming unrestricted shared filesystem usage.
host: 20ed1ad10daf
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job stats:
job        count
-------  -------
all            1
fastqc         3
multiqc        1
total          5

 * cutadapt: 4.9
 * trimmomatic: 0.39
 * bbtools: java -ea -Xmx22402m -Xms22402m -cp /usr/local/src/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 --version
BBTools version 39.38
For help, please run the shellscript with no parameters, or look in /docs/.
 * fastqc: FastQC v0.12.1
 * multiqc: multiqc, version 1.33
Select jobs to execute...
Execute 3 jobs...

[Tue Jul 21 17:36:54 2026]
localrule fastqc:
    input: /inputs/SRR12904821_R1.fastq.gz, /inputs/SRR12904821_R2.fastq.gz
    output: /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.html
    jobid: 3
    reason: Missing output files: /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.html
    wildcards: sample=SRR12904821
    resources: tmpdir=/docker_tmp
Shell command: None

[Tue Jul 21 17:36:54 2026]
localrule fastqc:
    input: /inputs/SRR12904817_R1.fastq.gz, /inputs/SRR12904817_R2.fastq.gz
    output: /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.html
    jobid: 1
    reason: Missing output files: /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip
    wildcards: sample=SRR12904817
    resources: tmpdir=/docker_tmp
Shell command: None

[Tue Jul 21 17:36:54 2026]
localrule fastqc:
    input: /inputs/SRR12904818_R1.fastq.gz, /inputs/SRR12904818_R2.fastq.gz
    output: /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.html
    jobid: 2
    reason: Missing output files: /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip
    wildcards: sample=SRR12904818
    resources: tmpdir=/docker_tmp
Shell command: None
application/gzip
application/gzip
application/gzip
application/gzip
application/gzip
application/gzip
[Tue Jul 21 17:37:29 2026]
Finished jobid: 3 (Rule: fastqc)
1 of 5 steps (20%) done
[Tue Jul 21 17:37:29 2026]
Finished jobid: 2 (Rule: fastqc)
2 of 5 steps (40%) done
[Tue Jul 21 17:37:29 2026]
Finished jobid: 1 (Rule: fastqc)
3 of 5 steps (60%) done
Select jobs to execute...
Execute 1 jobs...

[Tue Jul 21 17:37:29 2026]
localrule multiqc:
    input: /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip
    output: /outputs/multiqc_report.html
    jobid: 4
    reason: Missing output files: /outputs/multiqc_report.html; Input files updated by another job: /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip
    resources: tmpdir=/docker_tmp
Shell command: None

/// MultiQC 🔍 v1.33

            config | Loading config settings from: multiqc_config.yaml
     version_check | MultiQC Version v1.35 now available!
       file_search | Search path: /outputs/multiqc_input

            fastqc | Found 6 reports

     write_results | Data        : /outputs/multiqc_report_data
     write_results | Report      : /outputs/multiqc_report.html
           multiqc | MultiQC complete
[Tue Jul 21 17:37:32 2026]
Finished jobid: 4 (Rule: multiqc)
4 of 5 steps (80%) done
Select jobs to execute...
Execute 1 jobs...

[Tue Jul 21 17:37:32 2026]
localrule all:
    input: /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.html, /outputs/multiqc_report.html
    jobid: 0
    reason: Input files updated by another job: /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904818_R1_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904818_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904817_R2_fastqc.zip, /outputs/multiqc_input/initial_qc/SRR12904821_R2_fastqc.zip, /outputs/multiqc_report.html, /outputs/multiqc_input/initial_qc/SRR12904817_R1_fastqc.html, /outputs/multiqc_input/initial_qc/SRR12904821_R1_fastqc.html
    resources: tmpdir=/docker_tmp
Shell command: None
[Tue Jul 21 17:37:32 2026]
Finished jobid: 0 (Rule: all)
5 of 5 steps (100%) done
Complete log(s): /pipeline/.snakemake/log/2026-07-21T173652.698758.snakemake.log
[2026-07-21 17:37:34.051 UTC] Generating outputs report: /outputs/outputs.json
[2026-07-21 17:37:34.054 UTC] Output reported: /outputs/multiqc_report.html
[2026-07-21 17:37:34.055 UTC] Outputs report generated: /outputs/outputs.json
[2026-07-21 17:37:34.056 UTC] Pipeline completed
