[2025-07-28 19:33:28.282 UTC] Starting pipeline: QC, Current time: 2025-07-28 19:33
[2025-07-28 19:33:28.282 UTC] Pipeline version: 0.1.5, nephele_pipeline_utils version: 0.1.55
[2025-07-28 19:33:28.288 UTC] Pipeline arguments:
	--data_type PE
 	--run_cutadapt False
 	--error_rate 0.1
 	--indels False
 	--overlap 3
 	--match_read_wildcards False
 	--match_adapter_wildcards False
 	--adapter_f None
 	--adapter_r None
 	--front_f None
 	--front_r None
 	--anywhere_f None
 	--anywhere_r None
 	--run_qual_trimming True
 	--window_size 4
 	--req_qual 12
 	--lead_qual 30
 	--trail_qual 30
 	--minlen 50
 	--avg_qual 20
 	--run_flash2_merge False
 	--f2_min_overlap 10
 	--f2_max_overlap 315
 	--f2_min_overlap_outie 35
 	--f2_max_mismatch_density 0.25
 	--mapping_file_path /inputs/mapping_file.csv
 	--outputs_dir_path /outputs
[2025-07-28 19:33:28.288 UTC] Pipeline initialized with 4 samples
[2025-07-28 19:33:28.289 UTC] Samples ids: S1_GItract_HiSeq_cami, S28_Skin_HiSeq_cami, S9_Air_HiSeq_cami, S6_Oral_HiSeq_cami
[2025-07-28 19:33:28.289 UTC] Samples info:
[2025-07-28 19:33:28.289 UTC] {'#SampleID': 'S1_GItract_HiSeq_cami', 'TreatmentGroup': 'Gitract', 'ForwardFastqFile': '/inputs/S1_GItract_HiSeq_cami_sub25k.R1.fastq.gz', 'ReverseFastqFile': '/inputs/S1_GItract_HiSeq_cami_sub25k.R2.fastq.gz'}
[2025-07-28 19:33:28.289 UTC] {'#SampleID': 'S28_Skin_HiSeq_cami', 'TreatmentGroup': 'Skin', 'ForwardFastqFile': '/inputs/S28_Skin_HiSeq_cami_sub25k.R1.fastq.gz', 'ReverseFastqFile': '/inputs/S28_Skin_HiSeq_cami_sub25k.R2.fastq.gz'}
[2025-07-28 19:33:28.289 UTC] {'#SampleID': 'S9_Air_HiSeq_cami', 'TreatmentGroup': 'Air', 'ForwardFastqFile': '/inputs/S6_Oral_HiSeq_cami_sub25k.R1.fastq.gz', 'ReverseFastqFile': '/inputs/S6_Oral_HiSeq_cami_sub25k.R2.fastq.gz'}
[2025-07-28 19:33:28.289 UTC] {'#SampleID': 'S6_Oral_HiSeq_cami', 'TreatmentGroup': 'Oral', 'ForwardFastqFile': '/inputs/S9_Air_HiSeq_cami_sub25k.R1.fastq.gz', 'ReverseFastqFile': '/inputs/S9_Air_HiSeq_cami_sub25k.R2.fastq.gz'}
[2025-07-28 19:33:28.289 UTC] Starting pipe...
[2025-07-28 19:33:28.295 UTC] Trying to generate samples
[2025-07-28 19:33:28.295 UTC] Starting Fastqc, outputs in /outputs/multiqc_input.
[2025-07-28 19:33:28.295 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S1_GItract_HiSeq_cami_sub25k.R1.fastq.gz
[2025-07-28 19:33:30.470 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S1_GItract_HiSeq_cami_sub25k.R2.fastq.gz
[2025-07-28 19:33:32.642 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S28_Skin_HiSeq_cami_sub25k.R1.fastq.gz
[2025-07-28 19:33:34.810 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S28_Skin_HiSeq_cami_sub25k.R2.fastq.gz
[2025-07-28 19:33:36.997 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S6_Oral_HiSeq_cami_sub25k.R1.fastq.gz
[2025-07-28 19:33:39.181 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S6_Oral_HiSeq_cami_sub25k.R2.fastq.gz
[2025-07-28 19:33:41.365 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S9_Air_HiSeq_cami_sub25k.R1.fastq.gz
[2025-07-28 19:33:43.538 UTC] trying to run: fastqc -o /outputs/multiqc_input /inputs/S9_Air_HiSeq_cami_sub25k.R2.fastq.gz
[2025-07-28 19:33:45.710 UTC] Finished Fastqc, see /outputs/multiqc_input for outputs.
[2025-07-28 19:33:45.710 UTC] Run Trimmomatic quality trimming selected.
[2025-07-28 19:33:45.710 UTC] Trying to create /outputs/qtrimmed_seqs
[2025-07-28 19:33:45.715 UTC] Trying to run: trimmomatic PE -phred33 /inputs/S1_GItract_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S1_GItract_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
[2025-07-28 19:33:47.351 UTC] TrimmomaticPE: Started with arguments:
 -threads 16 -phred33 /inputs/S1_GItract_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S1_GItract_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
Using templated Output files: /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1U.fastq.gz /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2U.fastq.gz
Input Read Pairs: 25000 Both Surviving: 24915 (99.66%) Forward Only Surviving: 84 (0.34%) Reverse Only Surviving: 1 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

[2025-07-28 19:33:47.351 UTC] Trying to run: trimmomatic PE -phred33 /inputs/S28_Skin_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S28_Skin_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
[2025-07-28 19:33:49.024 UTC] TrimmomaticPE: Started with arguments:
 -threads 16 -phred33 /inputs/S28_Skin_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S28_Skin_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
Using templated Output files: /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1U.fastq.gz /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2U.fastq.gz
Input Read Pairs: 25000 Both Surviving: 24915 (99.66%) Forward Only Surviving: 84 (0.34%) Reverse Only Surviving: 1 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

[2025-07-28 19:33:49.025 UTC] Trying to run: trimmomatic PE -phred33 /inputs/S6_Oral_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S6_Oral_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
[2025-07-28 19:33:50.680 UTC] TrimmomaticPE: Started with arguments:
 -threads 16 -phred33 /inputs/S6_Oral_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S6_Oral_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
Using templated Output files: /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1U.fastq.gz /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2U.fastq.gz
Input Read Pairs: 25000 Both Surviving: 24924 (99.70%) Forward Only Surviving: 76 (0.30%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

[2025-07-28 19:33:50.680 UTC] Trying to run: trimmomatic PE -phred33 /inputs/S9_Air_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S9_Air_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
[2025-07-28 19:33:52.366 UTC] TrimmomaticPE: Started with arguments:
 -threads 16 -phred33 /inputs/S9_Air_HiSeq_cami_sub25k.R1.fastq.gz /inputs/S9_Air_HiSeq_cami_sub25k.R2.fastq.gz -baseout /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami.fastq.gz LEADING:30 TRAILING:30 SLIDINGWINDOW:4:12 MINLEN:50 AVGQUAL:20
Using templated Output files: /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1U.fastq.gz /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2U.fastq.gz
Input Read Pairs: 25000 Both Surviving: 24921 (99.68%) Forward Only Surviving: 79 (0.32%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

[2025-07-28 19:33:52.367 UTC] Trying to run multiqc on /outputs/multiqc_input.
[2025-07-28 19:33:54.369 UTC] 
[2025-07-28 19:33:54.369 UTC] Finished multiqc.
[2025-07-28 19:33:54.369 UTC] Generating outputs report: /outputs/outputs.json
[2025-07-28 19:33:54.373 UTC] Output reported: /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_1P.fastq.gz
[2025-07-28 19:33:54.373 UTC] Output reported: /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_1P.fastq.gz
[2025-07-28 19:33:54.373 UTC] Output reported: /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_1P.fastq.gz
[2025-07-28 19:33:54.374 UTC] Output reported: /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_1P.fastq.gz
[2025-07-28 19:33:54.374 UTC] Output reported: /outputs/qtrimmed_seqs/S1_GItract_HiSeq_cami_2P.fastq.gz
[2025-07-28 19:33:54.374 UTC] Output reported: /outputs/qtrimmed_seqs/S28_Skin_HiSeq_cami_2P.fastq.gz
[2025-07-28 19:33:54.374 UTC] Output reported: /outputs/qtrimmed_seqs/S9_Air_HiSeq_cami_2P.fastq.gz
[2025-07-28 19:33:54.374 UTC] Output reported: /outputs/qtrimmed_seqs/S6_Oral_HiSeq_cami_2P.fastq.gz
[2025-07-28 19:33:54.375 UTC] Output reported: /outputs/multiqc_report.html
[2025-07-28 19:33:54.376 UTC] Outputs report generated: /outputs/outputs.json
[2025-07-28 19:33:54.376 UTC] Pipeline completed
