[2024-12-23 03:39:34,236] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-12-23 03:39:34,236] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-12-23 03:39:34,236] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-12-23 03:39:34,239] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-12-23 03:39:34,239] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2024-12-23 03:39:34,239] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-23 03:39:34,271] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-12-23 03:39:34,272] multiqc [INFO ] This is MultiQC v1.9 [2024-12-23 03:39:34,272] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-12-23 03:39:34,272] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/37/e7ca02d7982af22fc837168111caa9/merged [2024-12-23 03:39:34,272] multiqc [INFO ] Template : default [2024-12-23 03:39:34,272] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-12-23 03:39:34,272] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/37/e7ca02d7982af22fc837168111caa9/merged [2024-12-23 03:39:34,272] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2024-12-23 03:39:34,272] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-55304810/tmpb_96t3n6 [2024-12-23 03:39:34,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_8-dam126_GR-bZIP1-2_fastqc.html [2024-12-23 03:39:34,388] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n01_8-dam126_GR-bZIP1-2_fastqc.html [2024-12-23 03:39:34,462] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search 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[2024-12-23 03:39:35,529] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_7-dam126_GR-EV-2_fastqc.html [2024-12-23 03:39:35,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n01_7-dam126_GR-EV-2_fastqc.html [2024-12-23 03:39:35,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_17-2x_dam126-GR-bZIP1_y_bZIP11-2_fastqc.html [2024-12-23 03:39:35,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n01_17-2x_dam126-GR-bZIP1_y_bZIP11-2_fastqc.html [2024-12-23 03:39:35,676] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_1-DAM-GR-EV-1_fastqc.html [2024-12-23 03:39:35,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize 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HLM3CAFX7_n02_7-dam126_GR-EV-2_fastqc.html [2024-12-23 03:39:36,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n02_7-dam126_GR-EV-2_fastqc.html [2024-12-23 03:39:36,593] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_14-GR-bZIP1-2_fastqc.html [2024-12-23 03:39:36,595] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n01_14-GR-bZIP1-2_fastqc.html [2024-12-23 03:39:36,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n02_16-2x_dam126-GR-bZIP1_y_bZIP11-1_fastqc.html [2024-12-23 03:39:36,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n02_16-2x_dam126-GR-bZIP1_y_bZIP11-1_fastqc.html [2024-12-23 03:39:36,730] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n02_3-dam126_GR-EV-1_fastqc.html [2024-12-23 03:39:36,732] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n02_3-dam126_GR-EV-1_fastqc.html [2024-12-23 03:39:36,797] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n01_6-DAM-GR-bZIP1-2_fastqc.html [2024-12-23 03:39:36,799] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n01_6-DAM-GR-bZIP1-2_fastqc.html [2024-12-23 03:39:36,870] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3CAFX7_n02_4-dam126_GR-bZIP1-1_fastqc.html [2024-12-23 03:39:36,872] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3CAFX7_n02_4-dam126_GR-bZIP1-1_fastqc.html [2024-12-23 03:39:37,398] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-23 03:39:37,400] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-12-23 03:39:37,408] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-12-23 03:39:37,418] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-12-23 03:39:37,427] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 18 samples (table) [2024-12-23 03:39:37,433] multiqc [DEBUG ] No samples found: conpair [2024-12-23 03:39:37,438] multiqc [DEBUG ] No samples found: peddy [2024-12-23 03:39:37,444] multiqc [DEBUG ] No samples found: somalier [2024-12-23 03:39:37,449] multiqc [DEBUG ] No samples found: methylQA [2024-12-23 03:39:37,459] multiqc [DEBUG ] No samples found: mosdepth [2024-12-23 03:39:37,464] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-12-23 03:39:37,468] multiqc [DEBUG ] No samples found: qualimap [2024-12-23 03:39:37,473] multiqc [DEBUG ] No samples found: preseq [2024-12-23 03:39:37,479] multiqc [DEBUG ] No samples found: quast [2024-12-23 03:39:37,484] multiqc [DEBUG ] No samples found: qorts [2024-12-23 03:39:37,489] multiqc [DEBUG ] No samples found: rna_seqc [2024-12-23 03:39:37,495] multiqc [DEBUG ] No samples found: rockhopper [2024-12-23 03:39:37,500] multiqc [DEBUG ] No samples found: rsem [2024-12-23 03:39:37,513] multiqc [DEBUG ] No samples found: rseqc [2024-12-23 03:39:37,518] multiqc [DEBUG ] No samples found: busco [2024-12-23 03:39:37,524] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-12-23 03:39:37,529] multiqc [DEBUG ] No samples found: disambiguate [2024-12-23 03:39:37,534] multiqc [DEBUG ] No samples found: supernova [2024-12-23 03:39:37,550] multiqc [DEBUG ] No samples found: deeptools [2024-12-23 03:39:37,555] multiqc [DEBUG ] No samples found: sargasso [2024-12-23 03:39:37,560] multiqc [DEBUG ] No samples found: verifybamid [2024-12-23 03:39:37,566] multiqc [DEBUG ] No samples found: mirtrace [2024-12-23 03:39:37,571] multiqc [DEBUG ] No samples found: happy [2024-12-23 03:39:37,576] multiqc [DEBUG ] No samples found: mirtop [2024-12-23 03:39:37,584] multiqc [DEBUG ] No samples found: homer [2024-12-23 03:39:37,589] multiqc [DEBUG ] No samples found: macs2 [2024-12-23 03:39:37,594] multiqc [DEBUG ] No samples found: theta2 [2024-12-23 03:39:37,600] multiqc [DEBUG ] No samples found: snpeff [2024-12-23 03:39:37,608] multiqc [DEBUG ] No samples found: gatk [2024-12-23 03:39:37,613] multiqc [DEBUG ] No samples found: htseq [2024-12-23 03:39:37,619] multiqc [DEBUG ] No samples found: bcftools [2024-12-23 03:39:37,625] multiqc [DEBUG ] No samples found: featureCounts [2024-12-23 03:39:37,632] multiqc [DEBUG ] No samples found: fgbio [2024-12-23 03:39:37,647] multiqc [DEBUG ] No samples found: dragen [2024-12-23 03:39:37,652] multiqc [DEBUG ] No samples found: dedup [2024-12-23 03:39:37,658] multiqc [DEBUG ] No samples found: damageprofiler [2024-12-23 03:39:37,684] multiqc [DEBUG ] No samples found: biobambam2 [2024-12-23 03:39:37,689] multiqc [DEBUG ] No samples found: mtnucratio [2024-12-23 03:39:37,692] multiqc [DEBUG ] No samples found: picard [2024-12-23 03:39:37,697] multiqc [DEBUG ] No samples found: prokka [2024-12-23 03:39:37,702] multiqc [DEBUG ] No samples found: samblaster [2024-12-23 03:39:37,712] multiqc [DEBUG ] No samples found: samtools [2024-12-23 03:39:37,717] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-12-23 03:39:37,723] multiqc [DEBUG ] No samples found: bamtools [2024-12-23 03:39:37,728] multiqc [DEBUG ] No samples found: jellyfish [2024-12-23 03:39:37,737] multiqc [DEBUG ] No samples found: vcftools [2024-12-23 03:39:37,743] multiqc [DEBUG ] No samples found: longranger [2024-12-23 03:39:37,749] multiqc [DEBUG ] No samples found: stacks [2024-12-23 03:39:37,754] multiqc [DEBUG ] No samples found: varscan2 [2024-12-23 03:39:37,772] multiqc [DEBUG ] No samples found: bbmap [2024-12-23 03:39:37,778] multiqc [DEBUG ] No samples found: bismark [2024-12-23 03:39:37,784] multiqc [DEBUG ] No samples found: biscuit [2024-12-23 03:39:37,790] multiqc [DEBUG ] No samples found: hicexplorer [2024-12-23 03:39:37,796] multiqc [DEBUG ] No samples found: hicup [2024-12-23 03:39:37,801] multiqc [DEBUG ] No samples found: hicpro [2024-12-23 03:39:37,807] multiqc [DEBUG ] No samples found: salmon [2024-12-23 03:39:37,812] multiqc [DEBUG ] No samples found: kallisto [2024-12-23 03:39:37,818] multiqc [DEBUG ] No samples found: slamdunk [2024-12-23 03:39:37,824] multiqc [DEBUG ] No samples found: star [2024-12-23 03:39:37,829] multiqc [DEBUG ] No samples found: hisat2 [2024-12-23 03:39:37,834] multiqc [DEBUG ] No samples found: tophat [2024-12-23 03:39:37,839] multiqc [DEBUG ] No samples found: bowtie2 [2024-12-23 03:39:37,845] multiqc [DEBUG ] No samples found: bowtie1 [2024-12-23 03:39:37,850] multiqc [DEBUG ] No samples found: snpsplit [2024-12-23 03:39:37,855] multiqc [DEBUG ] No samples found: kat [2024-12-23 03:39:37,860] multiqc [DEBUG ] No samples found: leehom [2024-12-23 03:39:37,865] multiqc [DEBUG ] No samples found: adapterRemoval [2024-12-23 03:39:37,870] multiqc [DEBUG ] No samples found: clipandmerge [2024-12-23 03:39:37,875] multiqc [DEBUG ] No samples found: cutadapt [2024-12-23 03:39:37,880] multiqc [DEBUG ] No samples found: flexbar [2024-12-23 03:39:37,885] multiqc [DEBUG ] No samples found: kaiju [2024-12-23 03:39:37,891] multiqc [DEBUG ] No samples found: kraken [2024-12-23 03:39:37,896] multiqc [DEBUG ] No samples found: malt [2024-12-23 03:39:37,901] multiqc [DEBUG ] No samples found: trimmomatic [2024-12-23 03:39:37,906] multiqc [DEBUG ] No samples found: sickle [2024-12-23 03:39:37,912] multiqc [DEBUG ] No samples found: skewer [2024-12-23 03:39:37,917] multiqc [DEBUG ] No samples found: sortmerna [2024-12-23 03:39:37,922] multiqc [DEBUG ] No samples found: biobloomtools [2024-12-23 03:39:37,927] multiqc [DEBUG ] No samples found: fastq_screen [2024-12-23 03:39:37,932] multiqc [DEBUG ] No samples found: afterqc [2024-12-23 03:39:37,937] multiqc [DEBUG ] No samples found: fastp [2024-12-23 03:39:39,199] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2024-12-23 03:39:39,860] multiqc [DEBUG ] No samples found: pycoqc [2024-12-23 03:39:39,865] multiqc [DEBUG ] No samples found: minionqc [2024-12-23 03:39:39,871] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-12-23 03:39:39,877] multiqc [DEBUG ] No samples found: clusterflow [2024-12-23 03:39:39,882] multiqc [DEBUG ] No samples found: bcl2fastq [2024-12-23 03:39:39,888] multiqc [DEBUG ] No samples found: interop [2024-12-23 03:39:39,893] multiqc [DEBUG ] No samples found: ivar [2024-12-23 03:39:39,899] multiqc [DEBUG ] No samples found: flash [2024-12-23 03:39:39,904] multiqc [DEBUG ] No samples found: seqyclean [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-12-23 03:39:39,904] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-12-23 03:39:39,905] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-12-23 03:39:39,951] multiqc [INFO ] Compressing plot data [2024-12-23 03:39:40,731] multiqc [INFO ] Report : multiqc_report.html [2024-12-23 03:39:40,731] multiqc [INFO ] Data : multiqc_data [2024-12-23 03:39:40,731] multiqc [DEBUG ] Moving data file from '/state/partition1/job-55304810/tmpb_96t3n6/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/37/e7ca02d7982af22fc837168111caa9/merged/multiqc_data' [2024-12-23 03:39:40,860] multiqc [INFO ] MultiQC complete