[2021-12-23 05:34:32,404] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-23 05:34:32,404] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-23 05:34:32,404] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-23 05:34:32,405] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-23 05:34:32,405] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-23 05:34:32,405] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMKGBGXK/merged [2021-12-23 05:34:33,688] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-23 05:34:33,688] multiqc [INFO ] This is MultiQC v1.9 [2021-12-23 05:34:33,689] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWMKGBGXK/merged [2021-12-23 05:34:33,689] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWMKGBGXK/merged [2021-12-23 05:34:33,689] multiqc [INFO ] Template : default [2021-12-23 05:34:33,689] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-23 05:34:33,689] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWMKGBGXK/merged [2021-12-23 05:34:33,689] 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 [2021-12-23 05:34:33,689] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13270699/tmphh5ewnib [2021-12-23 05:34:33,797] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA23___fastqc.html [2021-12-23 05:34:33,800] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-12-23 05:34:34,945] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA31___fastqc.html [2021-12-23 05:34:34,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA33___fastqc.html [2021-12-23 05:34:34,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA33___fastqc.html [2021-12-23 05:34:35,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA20___fastqc.html [2021-12-23 05:34:35,036] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA20___fastqc.html [2021-12-23 05:34:35,076] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA36___fastqc.html [2021-12-23 05:34:35,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA36___fastqc.html [2021-12-23 05:34:35,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA20___fastqc.html [2021-12-23 05:34:35,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA20___fastqc.html [2021-12-23 05:34:35,164] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA31___fastqc.html [2021-12-23 05:34:35,166] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA31___fastqc.html [2021-12-23 05:34:35,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA30___fastqc.html [2021-12-23 05:34:35,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA30___fastqc.html [2021-12-23 05:34:35,256] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA26___fastqc.html [2021-12-23 05:34:35,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA26___fastqc.html [2021-12-23 05:34:35,301] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA30___fastqc.html [2021-12-23 05:34:35,303] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA30___fastqc.html [2021-12-23 05:34:35,347] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA34___fastqc.html [2021-12-23 05:34:35,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA34___fastqc.html [2021-12-23 05:34:35,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA37___fastqc.html [2021-12-23 05:34:35,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA37___fastqc.html [2021-12-23 05:34:35,440] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA21___fastqc.html [2021-12-23 05:34:35,442] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n02_AA21___fastqc.html [2021-12-23 05:34:35,483] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA36___fastqc.html [2021-12-23 05:34:35,484] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA36___fastqc.html [2021-12-23 05:34:35,528] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_DJ88___fastqc.html [2021-12-23 05:34:35,530] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_DJ88___fastqc.html [2021-12-23 05:34:35,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA40___fastqc.html [2021-12-23 05:34:35,572] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWMKGBGXK_n01_AA40___fastqc.html [2021-12-23 05:34:36,032] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-23 05:34:36,034] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-23 05:34:36,048] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 18 samples (table) [2021-12-23 05:34:36,050] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-23 05:34:36,059] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-23 05:34:36,064] multiqc [DEBUG ] No samples found: conpair [2021-12-23 05:34:36,068] multiqc [DEBUG ] No samples found: peddy [2021-12-23 05:34:36,075] multiqc [DEBUG ] No samples found: somalier [2021-12-23 05:34:36,079] multiqc [DEBUG ] No samples found: methylQA [2021-12-23 05:34:36,085] multiqc [DEBUG ] No samples found: mosdepth [2021-12-23 05:34:36,089] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-23 05:34:36,092] multiqc [DEBUG ] No samples found: qualimap [2021-12-23 05:34:36,097] multiqc [DEBUG ] No samples found: preseq [2021-12-23 05:34:36,101] multiqc [DEBUG ] No samples found: quast [2021-12-23 05:34:36,105] multiqc [DEBUG ] No samples found: qorts [2021-12-23 05:34:36,109] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-23 05:34:36,113] multiqc [DEBUG ] No samples found: rockhopper [2021-12-23 05:34:36,118] multiqc [DEBUG ] No samples found: rsem [2021-12-23 05:34:36,128] multiqc [DEBUG ] No samples found: rseqc [2021-12-23 05:34:36,132] multiqc [DEBUG ] No samples found: busco [2021-12-23 05:34:36,136] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-23 05:34:36,140] multiqc [DEBUG ] No samples found: disambiguate [2021-12-23 05:34:36,144] multiqc [DEBUG ] No samples found: supernova [2021-12-23 05:34:36,156] multiqc [DEBUG ] No samples found: deeptools [2021-12-23 05:34:36,160] multiqc [DEBUG ] No samples found: sargasso [2021-12-23 05:34:36,164] multiqc [DEBUG ] No samples found: verifybamid [2021-12-23 05:34:36,168] multiqc [DEBUG ] No samples found: mirtrace [2021-12-23 05:34:36,172] multiqc [DEBUG ] No samples found: happy [2021-12-23 05:34:36,177] multiqc [DEBUG ] No samples found: mirtop [2021-12-23 05:34:36,182] multiqc [DEBUG ] No samples found: homer [2021-12-23 05:34:36,186] multiqc [DEBUG ] No samples found: macs2 [2021-12-23 05:34:36,189] multiqc [DEBUG ] No samples found: theta2 [2021-12-23 05:34:36,194] multiqc [DEBUG ] No samples found: snpeff [2021-12-23 05:34:36,199] multiqc [DEBUG ] No samples found: gatk [2021-12-23 05:34:36,203] multiqc [DEBUG ] No samples found: htseq [2021-12-23 05:34:36,208] multiqc [DEBUG ] No samples found: bcftools [2021-12-23 05:34:36,212] multiqc [DEBUG ] No samples found: featureCounts [2021-12-23 05:34:36,217] multiqc [DEBUG ] No samples found: fgbio [2021-12-23 05:34:36,230] multiqc [DEBUG ] No samples found: dragen [2021-12-23 05:34:36,234] multiqc [DEBUG ] No samples found: dedup [2021-12-23 05:34:36,238] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-23 05:34:36,259] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-23 05:34:36,262] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-23 05:34:36,265] multiqc [DEBUG ] No samples found: picard [2021-12-23 05:34:36,269] multiqc [DEBUG ] No samples found: prokka [2021-12-23 05:34:36,272] multiqc [DEBUG ] No samples found: samblaster [2021-12-23 05:34:36,281] multiqc [DEBUG ] No samples found: samtools [2021-12-23 05:34:36,285] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-23 05:34:36,289] multiqc [DEBUG ] No samples found: bamtools [2021-12-23 05:34:36,293] multiqc [DEBUG ] No samples found: jellyfish [2021-12-23 05:34:36,301] multiqc [DEBUG ] No samples found: vcftools [2021-12-23 05:34:36,305] multiqc [DEBUG ] No samples found: longranger [2021-12-23 05:34:36,309] multiqc [DEBUG ] No samples found: stacks [2021-12-23 05:34:36,313] multiqc [DEBUG ] No samples found: varscan2 [2021-12-23 05:34:36,334] multiqc [DEBUG ] No samples found: bbmap [2021-12-23 05:34:36,338] multiqc [DEBUG ] No samples found: bismark [2021-12-23 05:34:36,343] multiqc [DEBUG ] No samples found: biscuit [2021-12-23 05:34:36,347] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-23 05:34:36,351] multiqc [DEBUG ] No samples found: hicup [2021-12-23 05:34:36,355] multiqc [DEBUG ] No samples found: hicpro [2021-12-23 05:34:36,359] multiqc [DEBUG ] No samples found: salmon [2021-12-23 05:34:36,363] multiqc [DEBUG ] No samples found: kallisto [2021-12-23 05:34:36,367] multiqc [DEBUG ] No samples found: slamdunk [2021-12-23 05:34:36,371] multiqc [DEBUG ] No samples found: star [2021-12-23 05:34:36,375] multiqc [DEBUG ] No samples found: hisat2 [2021-12-23 05:34:36,379] multiqc [DEBUG ] No samples found: tophat [2021-12-23 05:34:36,383] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-23 05:34:36,387] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-23 05:34:36,391] multiqc [DEBUG ] No samples found: snpsplit [2021-12-23 05:34:36,394] multiqc [DEBUG ] No samples found: kat [2021-12-23 05:34:36,398] multiqc [DEBUG ] No samples found: leehom [2021-12-23 05:34:36,402] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-23 05:34:36,405] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-23 05:34:36,409] multiqc [DEBUG ] No samples found: cutadapt [2021-12-23 05:34:36,413] multiqc [DEBUG ] No samples found: flexbar [2021-12-23 05:34:36,417] multiqc [DEBUG ] No samples found: kaiju [2021-12-23 05:34:36,421] multiqc [DEBUG ] No samples found: kraken [2021-12-23 05:34:36,425] multiqc [DEBUG ] No samples found: malt [2021-12-23 05:34:36,428] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-23 05:34:36,432] multiqc [DEBUG ] No samples found: sickle [2021-12-23 05:34:36,436] multiqc [DEBUG ] No samples found: skewer [2021-12-23 05:34:36,440] multiqc [DEBUG ] No samples found: sortmerna [2021-12-23 05:34:36,443] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-23 05:34:36,447] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-23 05:34:36,451] multiqc [DEBUG ] No samples found: afterqc [2021-12-23 05:34:36,455] multiqc [DEBUG ] No samples found: fastp [2021-12-23 05:34:38,914] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2021-12-23 05:34:39,661] multiqc [DEBUG ] No samples found: pycoqc [2021-12-23 05:34:39,665] multiqc [DEBUG ] No samples found: minionqc [2021-12-23 05:34:39,669] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-23 05:34:39,673] multiqc [DEBUG ] No samples found: clusterflow [2021-12-23 05:34:39,678] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-23 05:34:39,682] multiqc [DEBUG ] No samples found: interop [2021-12-23 05:34:39,686] multiqc [DEBUG ] No samples found: ivar [2021-12-23 05:34:39,690] multiqc [DEBUG ] No samples found: flash [2021-12-23 05:34:39,694] multiqc [DEBUG ] No samples found: seqyclean [2021-12-23 05:34:39,694] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-23 05:34:39,694] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-23 05:34:39,694] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-23 05:34:39,694] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-23 05:34:39,736] multiqc [INFO ] Compressing plot data [2021-12-23 05:34:40,388] multiqc [INFO ] Report : multiqc_report.html [2021-12-23 05:34:40,388] multiqc [INFO ] Data : multiqc_data [2021-12-23 05:34:40,388] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13270699/tmphh5ewnib/multiqc_data' to '/scratch/gencore/logs/html/HWMKGBGXK/merged/multiqc_data' [2021-12-23 05:34:40,514] multiqc [INFO ] MultiQC complete