[2022-09-15 12:20:44,415] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-15 12:20:44,415] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-15 12:20:44,415] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-15 12:20:44,416] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-15 12:20:44,416] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-15 12:20:44,416] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNCMMDSX3/merged [2022-09-15 12:20:44,815] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-15 12:20:44,815] multiqc [INFO ] This is MultiQC v1.9 [2022-09-15 12:20:44,815] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNCMMDSX3/merged [2022-09-15 12:20:44,815] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNCMMDSX3/merged [2022-09-15 12:20:44,815] multiqc [INFO ] Template : default [2022-09-15 12:20:44,815] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-15 12:20:44,815] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNCMMDSX3/merged [2022-09-15 12:20:44,815] 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 [2022-09-15 12:20:44,816] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24849014/tmplmmtyl1k [2022-09-15 12:20:44,961] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bchi_096_fastqc.html [2022-09-15 12:20:44,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HNCMMDSX3_n02_Bath_077_fastqc.html [2022-09-15 12:21:10,182] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_060_fastqc.html [2022-09-15 12:21:10,184] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_060_fastqc.html [2022-09-15 12:21:10,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_095_fastqc.html [2022-09-15 12:21:10,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_095_fastqc.html [2022-09-15 12:21:10,299] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bchi_067_fastqc.html [2022-09-15 12:21:10,301] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bchi_067_fastqc.html [2022-09-15 12:21:10,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_006_fastqc.html [2022-09-15 12:21:10,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_006_fastqc.html [2022-09-15 12:21:10,415] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_007_fastqc.html [2022-09-15 12:21:10,417] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_007_fastqc.html [2022-09-15 12:21:10,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_026_fastqc.html [2022-09-15 12:21:10,481] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bath_026_fastqc.html [2022-09-15 12:21:10,542] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bchi_003_fastqc.html [2022-09-15 12:21:10,544] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bchi_003_fastqc.html [2022-09-15 12:21:10,604] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_014_fastqc.html [2022-09-15 12:21:10,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_014_fastqc.html [2022-09-15 12:21:10,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_052_fastqc.html [2022-09-15 12:21:10,665] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n01_Bath_052_fastqc.html [2022-09-15 12:21:10,724] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bchi_049_fastqc.html [2022-09-15 12:21:10,726] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMMDSX3_n02_Bchi_049_fastqc.html [2022-09-15 12:21:11,336] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-15 12:21:11,338] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-15 12:21:11,433] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 193 samples (table) [2022-09-15 12:21:11,442] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-15 12:21:11,444] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-15 12:21:11,449] multiqc [DEBUG ] No samples found: conpair [2022-09-15 12:21:11,454] multiqc [DEBUG ] No samples found: peddy [2022-09-15 12:21:11,459] multiqc [DEBUG ] No samples found: somalier [2022-09-15 12:21:11,464] multiqc [DEBUG ] No samples found: methylQA [2022-09-15 12:21:11,472] multiqc [DEBUG ] No samples found: mosdepth [2022-09-15 12:21:11,476] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-15 12:21:11,480] multiqc [DEBUG ] No samples found: qualimap [2022-09-15 12:21:11,484] multiqc [DEBUG ] No samples found: preseq [2022-09-15 12:21:11,489] multiqc [DEBUG ] No samples found: quast [2022-09-15 12:21:11,494] multiqc [DEBUG ] No samples found: qorts [2022-09-15 12:21:11,498] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-15 12:21:11,503] multiqc [DEBUG ] No samples found: rockhopper [2022-09-15 12:21:11,507] multiqc [DEBUG ] No samples found: rsem [2022-09-15 12:21:11,519] multiqc [DEBUG ] No samples found: rseqc [2022-09-15 12:21:11,523] multiqc [DEBUG ] No samples found: busco [2022-09-15 12:21:11,528] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-15 12:21:11,532] multiqc [DEBUG ] No samples found: disambiguate [2022-09-15 12:21:11,537] multiqc [DEBUG ] No samples found: supernova [2022-09-15 12:21:11,549] multiqc [DEBUG ] No samples found: deeptools [2022-09-15 12:21:11,553] multiqc [DEBUG ] No samples found: sargasso [2022-09-15 12:21:11,558] multiqc [DEBUG ] No samples found: verifybamid [2022-09-15 12:21:11,563] multiqc [DEBUG ] No samples found: mirtrace [2022-09-15 12:21:11,568] multiqc [DEBUG ] No samples found: happy [2022-09-15 12:21:11,572] multiqc [DEBUG ] No samples found: mirtop [2022-09-15 12:21:11,579] multiqc [DEBUG ] No samples found: homer [2022-09-15 12:21:11,583] multiqc [DEBUG ] No samples found: macs2 [2022-09-15 12:21:11,588] multiqc [DEBUG ] No samples found: theta2 [2022-09-15 12:21:11,592] multiqc [DEBUG ] No samples found: snpeff [2022-09-15 12:21:11,599] multiqc [DEBUG ] No samples found: gatk [2022-09-15 12:21:11,608] multiqc [DEBUG ] No samples found: htseq [2022-09-15 12:21:11,620] multiqc [DEBUG ] No samples found: bcftools [2022-09-15 12:21:11,632] multiqc [DEBUG ] No samples found: featureCounts [2022-09-15 12:21:11,643] multiqc [DEBUG ] No samples found: fgbio [2022-09-15 12:21:11,669] multiqc [DEBUG ] No samples found: dragen [2022-09-15 12:21:11,680] multiqc [DEBUG ] No samples found: dedup [2022-09-15 12:21:11,684] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-15 12:21:11,738] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-15 12:21:11,743] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-15 12:21:11,745] multiqc [DEBUG ] No samples found: picard [2022-09-15 12:21:11,763] multiqc [DEBUG ] No samples found: prokka [2022-09-15 12:21:11,782] multiqc [DEBUG ] No samples found: samblaster [2022-09-15 12:21:11,812] multiqc [DEBUG ] No samples found: samtools [2022-09-15 12:21:11,817] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-15 12:21:11,829] multiqc [DEBUG ] No samples found: bamtools [2022-09-15 12:21:11,840] multiqc [DEBUG ] No samples found: jellyfish [2022-09-15 12:21:11,861] multiqc [DEBUG ] No samples found: vcftools [2022-09-15 12:21:11,872] multiqc [DEBUG ] No samples found: longranger [2022-09-15 12:21:11,883] multiqc [DEBUG ] No samples found: stacks [2022-09-15 12:21:11,896] multiqc [DEBUG ] No samples found: varscan2 [2022-09-15 12:21:11,944] multiqc [DEBUG ] No samples found: bbmap [2022-09-15 12:21:11,949] multiqc [DEBUG ] No samples found: bismark [2022-09-15 12:21:11,954] multiqc [DEBUG ] No samples found: biscuit [2022-09-15 12:21:11,965] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-15 12:21:11,970] multiqc [DEBUG ] No samples found: hicup [2022-09-15 12:21:11,975] multiqc [DEBUG ] No samples found: hicpro [2022-09-15 12:21:11,984] multiqc [DEBUG ] No samples found: salmon [2022-09-15 12:21:11,995] multiqc [DEBUG ] No samples found: kallisto [2022-09-15 12:21:12,006] multiqc [DEBUG ] No samples found: slamdunk [2022-09-15 12:21:12,025] multiqc [DEBUG ] No samples found: star [2022-09-15 12:21:12,036] multiqc [DEBUG ] No samples found: hisat2 [2022-09-15 12:21:12,041] multiqc [DEBUG ] No samples found: tophat [2022-09-15 12:21:12,052] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-15 12:21:12,057] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-15 12:21:12,069] multiqc [DEBUG ] No samples found: snpsplit [2022-09-15 12:21:12,074] multiqc [DEBUG ] No samples found: kat [2022-09-15 12:21:12,085] multiqc [DEBUG ] No samples found: leehom [2022-09-15 12:21:12,096] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-15 12:21:12,100] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-15 12:21:12,112] multiqc [DEBUG ] No samples found: cutadapt [2022-09-15 12:21:12,123] multiqc [DEBUG ] No samples found: flexbar [2022-09-15 12:21:12,139] multiqc [DEBUG ] No samples found: kaiju [2022-09-15 12:21:12,151] multiqc [DEBUG ] No samples found: kraken [2022-09-15 12:21:12,163] multiqc [DEBUG ] No samples found: malt [2022-09-15 12:21:12,181] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-15 12:21:12,193] multiqc [DEBUG ] No samples found: sickle [2022-09-15 12:21:12,211] multiqc [DEBUG ] No samples found: skewer [2022-09-15 12:21:12,223] multiqc [DEBUG ] No samples found: sortmerna [2022-09-15 12:21:12,242] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-15 12:21:12,263] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-15 12:21:12,276] multiqc [DEBUG ] No samples found: afterqc [2022-09-15 12:21:12,288] multiqc [DEBUG ] No samples found: fastp [2022-09-15 12:22:19,367] multiqc.modules.fastqc.fastqc [INFO ] Found 386 reports [2022-09-15 12:22:54,315] multiqc [DEBUG ] No samples found: pycoqc [2022-09-15 12:22:54,334] multiqc [DEBUG ] No samples found: minionqc [2022-09-15 12:22:54,346] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-15 12:22:54,365] multiqc [DEBUG ] No samples found: clusterflow [2022-09-15 12:22:54,384] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-15 12:22:54,397] multiqc [DEBUG ] No samples found: interop [2022-09-15 12:22:54,410] multiqc [DEBUG ] No samples found: ivar [2022-09-15 12:22:54,422] multiqc [DEBUG ] No samples found: flash [2022-09-15 12:22:54,434] multiqc [DEBUG ] No samples found: seqyclean [2022-09-15 12:22:54,434] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-15 12:22:54,434] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-15 12:22:54,434] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-15 12:22:54,434] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-15 12:22:54,874] multiqc [INFO ] Compressing plot data [2022-09-15 12:22:55,005] multiqc [INFO ] Report : multiqc_report.html [2022-09-15 12:22:55,006] multiqc [INFO ] Data : multiqc_data [2022-09-15 12:22:55,006] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24849014/tmplmmtyl1k/multiqc_data' to '/scratch/gencore/logs/html/HNCMMDSX3/merged/multiqc_data' [2022-09-15 12:22:55,395] multiqc [INFO ] MultiQC complete