[2021-06-25 00:12:21,352] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-06-25 00:12:21,352] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-06-25 00:12:21,352] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-06-25 00:12:21,353] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-06-25 00:12:21,353] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-06-25 00:12:21,353] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGMJ7DRXY/merged [2021-06-25 00:12:22,714] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-06-25 00:12:22,714] multiqc [INFO ] This is MultiQC v1.9 [2021-06-25 00:12:22,714] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGMJ7DRXY/merged [2021-06-25 00:12:22,714] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGMJ7DRXY/merged [2021-06-25 00:12:22,714] multiqc [INFO ] Template : default [2021-06-25 00:12:22,714] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-06-25 00:12:22,714] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGMJ7DRXY/merged [2021-06-25 00:12:22,714] 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 [2021-06-25 00:12:22,715] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8036771/tmpgsmg_w62 [2021-06-25 00:12:22,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-p1107NLSmyc-plusN-03_fastqc.html [2021-06-25 00:12:22,840] multiqc [DEBUG ] File ignored by 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[2021-06-25 00:12:26,563] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT6468-minusN-02_fastqc.html [2021-06-25 00:12:26,654] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-root.plusN-1hr.rep4_fastqc.html [2021-06-25 00:12:26,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-root.plusN-1hr.rep4_fastqc.html [2021-06-25 00:12:26,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-p1107NLSmyc-minusN-03_fastqc.html [2021-06-25 00:12:26,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-p1107NLSmyc-minusN-03_fastqc.html [2021-06-25 00:12:26,826] multiqc [DEBUG ] File 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[2021-06-25 00:12:27,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_202105-W22-root.plusN-1hr.rep1_fastqc.html [2021-06-25 00:12:27,197] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_202105-W22-root.minusN-1hr.rep2_fastqc.html [2021-06-25 00:12:27,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_202105-W22-root.minusN-1hr.rep2_fastqc.html [2021-06-25 00:12:27,243] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT4432-plusN-02_fastqc.html [2021-06-25 00:12:27,245] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT4432-plusN-02_fastqc.html [2021-06-25 00:12:27,301] multiqc [DEBUG ] File ignored by 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[2021-06-25 00:12:27,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210503-UT6201-minusN-03_fastqc.html [2021-06-25 00:12:27,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-UT3125-plusN-01_fastqc.html [2021-06-25 00:12:27,975] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-UT3125-plusN-01_fastqc.html [2021-06-25 00:12:28,044] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-shoot.minusN-1hr.rep2_fastqc.html [2021-06-25 00:12:28,045] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-shoot.minusN-1hr.rep2_fastqc.html [2021-06-25 00:12:28,104] multiqc [DEBUG ] File ignored by 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pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-G2plantUT5628-plusN-01_fastqc.html [2021-06-25 00:12:28,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT6468-plusN-01_fastqc.html [2021-06-25 00:12:28,282] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT6468-plusN-01_fastqc.html [2021-06-25 00:12:28,369] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-shoot.plusN-1hr.rep4_fastqc.html [2021-06-25 00:12:28,371] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-shoot.plusN-1hr.rep4_fastqc.html [2021-06-25 00:12:28,417] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-G2plantUT5628-minusN-03_fastqc.html [2021-06-25 00:12:28,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210504-G2plantUT5628-minusN-03_fastqc.html [2021-06-25 00:12:28,464] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT1855-minusN-03_fastqc.html [2021-06-25 00:12:28,466] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210510-UT1855-minusN-03_fastqc.html [2021-06-25 00:12:28,526] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210503-KN1-plusN-02_fastqc.html [2021-06-25 00:12:28,528] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210503-KN1-plusN-02_fastqc.html [2021-06-25 00:12:28,588] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210503-p1107NLSmyc-minusN-01_fastqc.html [2021-06-25 00:12:28,590] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_ZmTARGET.20210503-p1107NLSmyc-minusN-01_fastqc.html [2021-06-25 00:12:28,652] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-root.minusN-1hr.rep1_fastqc.html [2021-06-25 00:12:28,654] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGMJ7DRXY_n01_G2UFMu00214-root.minusN-1hr.rep1_fastqc.html [2021-06-25 00:12:29,082] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-25 00:12:29,086] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-06-25 00:12:29,095] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-06-25 00:12:29,192] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 218 samples (table) [2021-06-25 00:12:29,202] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-06-25 00:12:29,236] multiqc [DEBUG ] No samples found: conpair [2021-06-25 00:12:29,244] multiqc [DEBUG ] No samples found: peddy [2021-06-25 00:12:29,252] multiqc [DEBUG ] No samples found: somalier [2021-06-25 00:12:29,258] multiqc [DEBUG ] No samples found: methylQA [2021-06-25 00:12:29,266] multiqc [DEBUG ] No samples found: mosdepth [2021-06-25 00:12:29,271] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-06-25 00:12:29,274] multiqc [DEBUG ] No samples found: qualimap [2021-06-25 00:12:29,279] multiqc [DEBUG ] No samples found: preseq [2021-06-25 00:12:29,283] multiqc [DEBUG ] No samples found: quast [2021-06-25 00:12:29,288] multiqc [DEBUG ] No samples found: qorts [2021-06-25 00:12:29,293] multiqc [DEBUG ] No samples found: rna_seqc [2021-06-25 00:12:29,298] multiqc [DEBUG ] No samples found: rockhopper [2021-06-25 00:12:29,302] multiqc [DEBUG ] No samples found: rsem [2021-06-25 00:12:29,312] multiqc [DEBUG ] No samples found: rseqc [2021-06-25 00:12:29,317] multiqc [DEBUG ] No samples found: busco [2021-06-25 00:12:29,323] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-06-25 00:12:29,327] multiqc [DEBUG ] No samples found: disambiguate [2021-06-25 00:12:29,332] multiqc [DEBUG ] No samples found: supernova [2021-06-25 00:12:29,343] multiqc [DEBUG ] No samples found: deeptools [2021-06-25 00:12:29,348] multiqc [DEBUG ] No samples found: sargasso [2021-06-25 00:12:29,353] multiqc [DEBUG ] No samples found: verifybamid [2021-06-25 00:12:29,357] multiqc [DEBUG ] No samples found: mirtrace [2021-06-25 00:12:29,363] multiqc [DEBUG ] No samples found: happy [2021-06-25 00:12:29,371] multiqc [DEBUG ] No samples found: mirtop [2021-06-25 00:12:29,381] multiqc [DEBUG ] No samples found: homer [2021-06-25 00:12:29,389] multiqc [DEBUG ] No samples found: macs2 [2021-06-25 00:12:29,398] multiqc [DEBUG ] No samples found: theta2 [2021-06-25 00:12:29,405] multiqc [DEBUG ] No samples found: snpeff [2021-06-25 00:12:29,415] multiqc [DEBUG ] No samples found: gatk [2021-06-25 00:12:29,423] multiqc [DEBUG ] No samples found: htseq [2021-06-25 00:12:29,432] multiqc [DEBUG ] No samples found: bcftools [2021-06-25 00:12:29,440] multiqc [DEBUG ] No samples found: featureCounts [2021-06-25 00:12:29,451] multiqc [DEBUG ] No samples found: fgbio [2021-06-25 00:12:29,469] multiqc [DEBUG ] No samples found: dragen [2021-06-25 00:12:29,474] multiqc [DEBUG ] No samples found: dedup [2021-06-25 00:12:29,479] multiqc [DEBUG ] No samples found: damageprofiler [2021-06-25 00:12:29,499] multiqc [DEBUG ] No samples found: biobambam2 [2021-06-25 00:12:29,503] multiqc [DEBUG ] No samples found: mtnucratio [2021-06-25 00:12:29,506] multiqc [DEBUG ] No samples found: picard [2021-06-25 00:12:29,510] multiqc [DEBUG ] No samples found: prokka [2021-06-25 00:12:29,515] multiqc [DEBUG ] No samples found: samblaster [2021-06-25 00:12:29,523] multiqc [DEBUG ] No samples found: samtools [2021-06-25 00:12:29,528] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-06-25 00:12:29,532] multiqc [DEBUG ] No samples found: bamtools [2021-06-25 00:12:29,537] multiqc [DEBUG ] No samples found: jellyfish [2021-06-25 00:12:29,544] multiqc [DEBUG ] No samples found: vcftools [2021-06-25 00:12:29,549] multiqc [DEBUG ] No samples found: longranger [2021-06-25 00:12:29,554] multiqc [DEBUG ] No samples found: stacks [2021-06-25 00:12:29,559] multiqc [DEBUG ] No samples found: varscan2 [2021-06-25 00:12:29,572] multiqc [DEBUG ] No samples found: bbmap [2021-06-25 00:12:29,577] multiqc [DEBUG ] No samples found: bismark [2021-06-25 00:12:29,582] multiqc [DEBUG ] No samples found: biscuit [2021-06-25 00:12:29,588] multiqc [DEBUG ] No samples found: hicexplorer [2021-06-25 00:12:29,593] multiqc [DEBUG ] No samples found: hicup [2021-06-25 00:12:29,598] multiqc [DEBUG ] No samples found: hicpro [2021-06-25 00:12:29,602] multiqc [DEBUG ] No samples found: salmon [2021-06-25 00:12:29,607] multiqc [DEBUG ] No samples found: kallisto [2021-06-25 00:12:29,616] multiqc [DEBUG ] No samples found: slamdunk [2021-06-25 00:12:29,624] multiqc [DEBUG ] No samples found: star [2021-06-25 00:12:29,633] multiqc [DEBUG ] No samples found: hisat2 [2021-06-25 00:12:29,642] multiqc [DEBUG ] No samples found: tophat [2021-06-25 00:12:29,650] multiqc [DEBUG ] No samples found: bowtie2 [2021-06-25 00:12:29,659] multiqc [DEBUG ] No samples found: bowtie1 [2021-06-25 00:12:29,668] multiqc [DEBUG ] No samples found: snpsplit [2021-06-25 00:12:29,676] multiqc [DEBUG ] No samples found: kat [2021-06-25 00:12:29,684] multiqc [DEBUG ] No samples found: leehom [2021-06-25 00:12:29,691] multiqc [DEBUG ] No samples found: adapterRemoval [2021-06-25 00:12:29,699] multiqc [DEBUG ] No samples found: clipandmerge [2021-06-25 00:12:29,707] multiqc [DEBUG ] No samples found: cutadapt [2021-06-25 00:12:29,716] multiqc [DEBUG ] No samples found: flexbar [2021-06-25 00:12:29,724] multiqc [DEBUG ] No samples found: kaiju [2021-06-25 00:12:29,732] multiqc [DEBUG ] No samples found: kraken [2021-06-25 00:12:29,740] multiqc [DEBUG ] No samples found: malt [2021-06-25 00:12:29,748] multiqc [DEBUG ] No samples found: trimmomatic [2021-06-25 00:12:29,757] multiqc [DEBUG ] No samples found: sickle [2021-06-25 00:12:29,764] multiqc [DEBUG ] No samples found: skewer [2021-06-25 00:12:29,769] multiqc [DEBUG ] No samples found: sortmerna [2021-06-25 00:12:29,777] multiqc [DEBUG ] No samples found: biobloomtools [2021-06-25 00:12:29,785] multiqc [DEBUG ] No samples found: fastq_screen [2021-06-25 00:12:29,795] multiqc [DEBUG ] No samples found: afterqc [2021-06-25 00:12:29,804] multiqc [DEBUG ] No samples found: fastp [2021-06-25 00:12:31,812] multiqc.modules.fastqc.fastqc [WARNING] Couldn't read 'HGMJ7DRXY_n01_ZmTARGET.20210510-UT6468-minusN-01_fastqc.zip' - Bad zip file [2021-06-25 00:12:31,812] multiqc.modules.fastqc.fastqc [DEBUG ] Bad zip file error: File is not a zip file [2021-06-25 00:12:38,539] multiqc.modules.fastqc.fastqc [INFO ] Found 94 reports [2021-06-25 00:12:39,754] multiqc [DEBUG ] No samples found: pycoqc [2021-06-25 00:12:39,763] multiqc [DEBUG ] No samples found: minionqc [2021-06-25 00:12:39,772] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-06-25 00:12:39,781] multiqc [DEBUG ] No samples found: clusterflow [2021-06-25 00:12:39,789] multiqc [DEBUG ] No samples found: bcl2fastq [2021-06-25 00:12:39,801] multiqc [DEBUG ] No samples found: interop [2021-06-25 00:12:39,808] multiqc [DEBUG ] No samples found: ivar [2021-06-25 00:12:39,818] multiqc [DEBUG ] No samples found: flash [2021-06-25 00:12:39,827] multiqc [DEBUG ] No samples found: seqyclean [2021-06-25 00:12:39,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-06-25 00:12:39,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-06-25 00:12:39,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-06-25 00:12:39,828] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-06-25 00:12:39,935] multiqc [INFO ] Compressing plot data [2021-06-25 00:12:41,578] multiqc [INFO ] Report : multiqc_report.html [2021-06-25 00:12:41,578] multiqc [INFO ] Data : multiqc_data [2021-06-25 00:12:41,578] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8036771/tmpgsmg_w62/multiqc_data' to '/scratch/gencore/logs/html/HGMJ7DRXY/merged/multiqc_data' [2021-06-25 00:12:41,705] multiqc [INFO ] MultiQC complete