[2025-01-28 15:56:30,703] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2025-01-28 15:56:30,703] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2025-01-28 15:56:30,704] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2025-01-28 15:56:30,706] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2025-01-28 15:56:30,706] 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}} [2025-01-28 15:56:30,706] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 15:56:30,728] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2025-01-28 15:56:30,728] multiqc [INFO ] This is MultiQC v1.9 [2025-01-28 15:56:30,728] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2025-01-28 15:56:30,728] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/37/61ea828163d9c1c53a9fa51e14f879/merged [2025-01-28 15:56:30,728] multiqc [INFO ] Template : default [2025-01-28 15:56:30,728] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2025-01-28 15:56:30,728] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/37/61ea828163d9c1c53a9fa51e14f879/merged [2025-01-28 15:56:30,729] 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 [2025-01-28 15:56:30,729] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-56556181/tmptwu_sh46 [2025-01-28 15:56:30,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA100_fastqc.html [2025-01-28 15:56:30,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA100_fastqc.html [2025-01-28 15:56:30,881] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-28 15:56:30,882] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2025-01-28 15:56:30,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ81_fastqc.html [2025-01-28 15:56:30,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ81_fastqc.html [2025-01-28 15:56:31,036] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA99_fastqc.html [2025-01-28 15:56:31,038] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA99_fastqc.html [2025-01-28 15:56:31,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_undetermined_fastqc.html [2025-01-28 15:56:31,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_undetermined_fastqc.html [2025-01-28 15:56:31,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA98_fastqc.html [2025-01-28 15:56:31,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA98_fastqc.html [2025-01-28 15:56:31,180] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ76_fastqc.html [2025-01-28 15:56:31,182] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ76_fastqc.html [2025-01-28 15:56:31,226] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA104_fastqc.html [2025-01-28 15:56:31,228] multiqc [DEBUG ] File ignored 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pattern filesize limit: HKL2MBGYW_n01_YZ78_fastqc.html [2025-01-28 15:56:31,416] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA102_fastqc.html [2025-01-28 15:56:31,417] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA102_fastqc.html [2025-01-28 15:56:31,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA97_fastqc.html [2025-01-28 15:56:31,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA97_fastqc.html [2025-01-28 15:56:31,513] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ79_fastqc.html [2025-01-28 15:56:31,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ79_fastqc.html [2025-01-28 15:56:31,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ80_fastqc.html [2025-01-28 15:56:31,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ80_fastqc.html [2025-01-28 15:56:31,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA103_fastqc.html [2025-01-28 15:56:31,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA103_fastqc.html [2025-01-28 15:56:31,654] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ77_fastqc.html [2025-01-28 15:56:31,656] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ77_fastqc.html [2025-01-28 15:56:31,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA101_fastqc.html [2025-01-28 15:56:31,703] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_AA101_fastqc.html [2025-01-28 15:56:31,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ84_fastqc.html [2025-01-28 15:56:31,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ84_fastqc.html [2025-01-28 15:56:31,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ82_fastqc.html [2025-01-28 15:56:31,797] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKL2MBGYW_n01_YZ82_fastqc.html [2025-01-28 15:56:32,251] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 15:56:32,252] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2025-01-28 15:56:32,260] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2025-01-28 15:56:32,270] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2025-01-28 15:56:32,279] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2025-01-28 15:56:32,283] multiqc [DEBUG ] No samples found: conpair [2025-01-28 15:56:32,287] multiqc [DEBUG ] No samples found: peddy [2025-01-28 15:56:32,292] multiqc [DEBUG ] No samples found: somalier [2025-01-28 15:56:32,296] multiqc [DEBUG ] No samples found: methylQA [2025-01-28 15:56:32,303] multiqc [DEBUG ] No samples found: mosdepth [2025-01-28 15:56:32,307] multiqc [DEBUG ] No samples found: phantompeakqualtools [2025-01-28 15:56:32,310] multiqc [DEBUG ] No samples found: qualimap [2025-01-28 15:56:32,314] multiqc [DEBUG ] No samples found: preseq [2025-01-28 15:56:32,319] multiqc [DEBUG ] No samples found: quast [2025-01-28 15:56:32,323] multiqc [DEBUG ] No samples found: qorts [2025-01-28 15:56:32,327] multiqc [DEBUG ] No samples found: rna_seqc [2025-01-28 15:56:32,332] multiqc [DEBUG ] No samples found: rockhopper [2025-01-28 15:56:32,336] multiqc [DEBUG ] No samples found: rsem [2025-01-28 15:56:32,346] multiqc [DEBUG ] No samples found: rseqc [2025-01-28 15:56:32,350] multiqc [DEBUG ] No samples found: busco [2025-01-28 15:56:32,354] multiqc [DEBUG ] No samples found: goleft_indexcov [2025-01-28 15:56:32,358] multiqc [DEBUG ] No samples found: disambiguate [2025-01-28 15:56:32,362] multiqc [DEBUG ] No samples found: supernova [2025-01-28 15:56:32,374] multiqc [DEBUG ] No samples found: deeptools [2025-01-28 15:56:32,378] multiqc [DEBUG ] No samples found: sargasso [2025-01-28 15:56:32,383] multiqc [DEBUG ] No samples found: verifybamid [2025-01-28 15:56:32,387] multiqc [DEBUG ] No samples found: mirtrace [2025-01-28 15:56:32,394] multiqc [DEBUG ] No samples found: happy [2025-01-28 15:56:32,398] multiqc [DEBUG ] No samples found: mirtop [2025-01-28 15:56:32,406] multiqc [DEBUG ] No samples found: homer [2025-01-28 15:56:32,410] multiqc [DEBUG ] No samples found: macs2 [2025-01-28 15:56:32,414] multiqc [DEBUG ] No samples found: theta2 [2025-01-28 15:56:32,419] multiqc [DEBUG ] No samples found: snpeff [2025-01-28 15:56:32,425] multiqc [DEBUG ] No samples found: gatk [2025-01-28 15:56:32,429] multiqc [DEBUG ] No samples found: htseq [2025-01-28 15:56:32,434] multiqc [DEBUG ] No samples found: bcftools [2025-01-28 15:56:32,438] multiqc [DEBUG ] No samples found: featureCounts [2025-01-28 15:56:32,444] multiqc [DEBUG ] No samples found: fgbio [2025-01-28 15:56:32,456] multiqc [DEBUG ] No samples found: dragen [2025-01-28 15:56:32,460] multiqc [DEBUG ] No samples found: dedup [2025-01-28 15:56:32,465] multiqc [DEBUG ] No samples found: damageprofiler [2025-01-28 15:56:32,485] multiqc [DEBUG ] No samples found: biobambam2 [2025-01-28 15:56:32,488] multiqc [DEBUG ] No samples found: mtnucratio [2025-01-28 15:56:32,490] multiqc [DEBUG ] No samples found: picard [2025-01-28 15:56:32,495] multiqc [DEBUG ] No samples found: prokka [2025-01-28 15:56:32,499] multiqc [DEBUG ] No samples found: samblaster [2025-01-28 15:56:32,507] multiqc [DEBUG ] No samples found: samtools [2025-01-28 15:56:32,511] multiqc [DEBUG ] No samples found: sexdeterrmine [2025-01-28 15:56:32,516] multiqc [DEBUG ] No samples found: bamtools [2025-01-28 15:56:32,520] multiqc [DEBUG ] No samples found: jellyfish [2025-01-28 15:56:32,526] multiqc [DEBUG ] No samples found: vcftools [2025-01-28 15:56:32,530] multiqc [DEBUG ] No samples found: longranger [2025-01-28 15:56:32,534] multiqc [DEBUG ] No samples found: stacks [2025-01-28 15:56:32,539] multiqc [DEBUG ] No samples found: varscan2 [2025-01-28 15:56:32,550] multiqc [DEBUG ] No samples found: bbmap [2025-01-28 15:56:32,555] multiqc [DEBUG ] No samples found: bismark [2025-01-28 15:56:32,559] multiqc [DEBUG ] No samples found: biscuit [2025-01-28 15:56:32,563] multiqc [DEBUG ] No samples found: hicexplorer [2025-01-28 15:56:32,567] multiqc [DEBUG ] No samples found: hicup [2025-01-28 15:56:32,572] multiqc [DEBUG ] No samples found: hicpro [2025-01-28 15:56:32,575] multiqc [DEBUG ] No samples found: salmon [2025-01-28 15:56:32,579] multiqc [DEBUG ] No samples found: kallisto [2025-01-28 15:56:32,585] multiqc [DEBUG ] No samples found: slamdunk [2025-01-28 15:56:32,590] multiqc [DEBUG ] No samples found: star [2025-01-28 15:56:32,594] multiqc [DEBUG ] No samples found: hisat2 [2025-01-28 15:56:32,599] multiqc [DEBUG ] No samples found: tophat [2025-01-28 15:56:32,603] multiqc [DEBUG ] No samples found: bowtie2 [2025-01-28 15:56:32,608] multiqc [DEBUG ] No samples found: bowtie1 [2025-01-28 15:56:32,612] multiqc [DEBUG ] No samples found: snpsplit [2025-01-28 15:56:32,615] multiqc [DEBUG ] No samples found: kat [2025-01-28 15:56:32,619] multiqc [DEBUG ] No samples found: leehom [2025-01-28 15:56:32,624] multiqc [DEBUG ] No samples found: adapterRemoval [2025-01-28 15:56:32,628] multiqc [DEBUG ] No samples found: clipandmerge [2025-01-28 15:56:32,632] multiqc [DEBUG ] No samples found: cutadapt [2025-01-28 15:56:32,636] multiqc [DEBUG ] No samples found: flexbar [2025-01-28 15:56:32,640] multiqc [DEBUG ] No samples found: kaiju [2025-01-28 15:56:32,644] multiqc [DEBUG ] No samples found: kraken [2025-01-28 15:56:32,649] multiqc [DEBUG ] No samples found: malt [2025-01-28 15:56:32,653] multiqc [DEBUG ] No samples found: trimmomatic [2025-01-28 15:56:32,656] multiqc [DEBUG ] No samples found: sickle [2025-01-28 15:56:32,660] multiqc [DEBUG ] No samples found: skewer [2025-01-28 15:56:32,664] multiqc [DEBUG ] No samples found: sortmerna [2025-01-28 15:56:32,668] multiqc [DEBUG ] No samples found: biobloomtools [2025-01-28 15:56:32,672] multiqc [DEBUG ] No samples found: fastq_screen [2025-01-28 15:56:32,676] multiqc [DEBUG ] No samples found: afterqc [2025-01-28 15:56:32,681] multiqc [DEBUG ] No samples found: fastp [2025-01-28 15:56:34,088] multiqc.modules.fastqc.fastqc [INFO ] Found 19 reports [2025-01-28 15:56:34,479] multiqc [DEBUG ] No samples found: pycoqc [2025-01-28 15:56:34,484] multiqc [DEBUG ] No samples found: minionqc [2025-01-28 15:56:34,488] multiqc [DEBUG ] No samples found: multivcfanalyzer [2025-01-28 15:56:34,492] multiqc [DEBUG ] No samples found: clusterflow [2025-01-28 15:56:34,497] multiqc [DEBUG ] No samples found: bcl2fastq [2025-01-28 15:56:34,501] multiqc [DEBUG ] No samples found: interop [2025-01-28 15:56:34,505] multiqc [DEBUG ] No samples found: ivar [2025-01-28 15:56:34,509] multiqc [DEBUG ] No samples found: flash [2025-01-28 15:56:34,513] multiqc [DEBUG ] No samples found: seqyclean [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,513] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2025-01-28 15:56:34,514] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2025-01-28 15:56:34,537] multiqc [INFO ] Compressing plot data [2025-01-28 15:56:34,903] multiqc [INFO ] Report : multiqc_report.html [2025-01-28 15:56:34,903] multiqc [INFO ] Data : multiqc_data [2025-01-28 15:56:34,903] multiqc [DEBUG ] Moving data file from '/state/partition1/job-56556181/tmptwu_sh46/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/37/61ea828163d9c1c53a9fa51e14f879/merged/multiqc_data' [2025-01-28 15:56:35,061] multiqc [INFO ] MultiQC complete