[2021-08-10 10:06:47,240] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-10 10:06:47,240] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-10 10:06:47,240] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-10 10:06:47,241] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-10 10:06:47,241] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-10 10:06:47,241] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGG72DRXY/merged [2021-08-10 10:06:48,792] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-10 10:06:48,792] multiqc [INFO ] This is MultiQC v1.9 [2021-08-10 10:06:48,792] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGG72DRXY/merged [2021-08-10 10:06:48,792] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGG72DRXY/merged [2021-08-10 10:06:48,792] multiqc [INFO ] Template : default [2021-08-10 10:06:48,793] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-10 10:06:48,793] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGG72DRXY/merged [2021-08-10 10:06:48,793] 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 [2021-08-10 10:06:48,793] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9289566/tmpq3x63ixk [2021-08-10 10:06:48,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1735-3_fastqc.html [2021-08-10 10:06:48,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-08-10 10:06:52,996] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1733-2_fastqc.html [2021-08-10 10:06:53,044] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1731-1_fastqc.html [2021-08-10 10:06:53,046] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1731-1_fastqc.html [2021-08-10 10:06:53,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1748-1_fastqc.html [2021-08-10 10:06:53,089] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1748-1_fastqc.html [2021-08-10 10:06:53,146] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1743-1_fastqc.html [2021-08-10 10:06:53,148] multiqc [DEBUG 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[2021-08-10 10:06:53,652] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1740-3_fastqc.html [2021-08-10 10:06:53,654] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1740-3_fastqc.html [2021-08-10 10:06:53,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1222-3_fastqc.html [2021-08-10 10:06:53,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1222-3_fastqc.html [2021-08-10 10:06:53,733] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_500-2_fastqc.html [2021-08-10 10:06:53,735] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_500-2_fastqc.html [2021-08-10 10:06:53,777] multiqc [DEBUG ] 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10:06:54,197] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_3-2_fastqc.html [2021-08-10 10:06:54,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1735-1_fastqc.html [2021-08-10 10:06:54,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1735-1_fastqc.html [2021-08-10 10:06:54,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_undetermined_fastqc.html [2021-08-10 10:06:54,280] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_undetermined_fastqc.html [2021-08-10 10:06:54,332] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_3-3_fastqc.html [2021-08-10 10:06:54,334] multiqc [DEBUG ] 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filesize limit: HGG72DRXY_n01_1222-2_fastqc.html [2021-08-10 10:06:54,697] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1222-4_fastqc.html [2021-08-10 10:06:54,699] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1222-4_fastqc.html [2021-08-10 10:06:54,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1733-4_fastqc.html [2021-08-10 10:06:54,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1733-4_fastqc.html [2021-08-10 10:06:54,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1735-2_fastqc.html [2021-08-10 10:06:54,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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[2021-08-10 10:06:55,017] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1657-3_fastqc.html [2021-08-10 10:06:55,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1657-3_fastqc.html [2021-08-10 10:06:55,057] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1741-3_fastqc.html [2021-08-10 10:06:55,059] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1741-3_fastqc.html [2021-08-10 10:06:55,099] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1751-1_fastqc.html [2021-08-10 10:06:55,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1751-1_fastqc.html [2021-08-10 10:06:55,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1740-1_fastqc.html [2021-08-10 10:06:55,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1740-1_fastqc.html [2021-08-10 10:06:55,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1743-2_fastqc.html [2021-08-10 10:06:55,206] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1743-2_fastqc.html [2021-08-10 10:06:55,245] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1728-1_fastqc.html [2021-08-10 10:06:55,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1728-1_fastqc.html [2021-08-10 10:06:55,304] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1747-1_fastqc.html [2021-08-10 10:06:55,306] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1747-1_fastqc.html [2021-08-10 10:06:55,360] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1-2_fastqc.html [2021-08-10 10:06:55,361] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1-2_fastqc.html [2021-08-10 10:06:55,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n02_1-1_fastqc.html [2021-08-10 10:06:55,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n02_1-1_fastqc.html [2021-08-10 10:06:55,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_1726-1_fastqc.html [2021-08-10 10:06:55,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_1726-1_fastqc.html [2021-08-10 10:06:55,535] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG72DRXY_n01_3-1_fastqc.html [2021-08-10 10:06:55,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG72DRXY_n01_3-1_fastqc.html [2021-08-10 10:06:56,065] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-10 10:06:56,067] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-10 10:06:56,075] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-10 10:06:56,104] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 63 samples (table) [2021-08-10 10:06:56,114] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-10 10:06:56,118] multiqc [DEBUG ] No samples found: conpair [2021-08-10 10:06:56,123] multiqc [DEBUG ] No samples found: peddy [2021-08-10 10:06:56,128] multiqc [DEBUG ] No samples found: somalier [2021-08-10 10:06:56,133] multiqc [DEBUG ] No samples found: methylQA [2021-08-10 10:06:56,142] multiqc [DEBUG ] No samples found: mosdepth [2021-08-10 10:06:56,146] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-10 10:06:56,149] multiqc [DEBUG ] No samples found: qualimap [2021-08-10 10:06:56,154] multiqc [DEBUG ] No samples found: preseq [2021-08-10 10:06:56,159] multiqc [DEBUG ] No samples found: quast [2021-08-10 10:06:56,163] multiqc [DEBUG ] No samples found: qorts [2021-08-10 10:06:56,168] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-10 10:06:56,173] multiqc [DEBUG ] No samples found: rockhopper [2021-08-10 10:06:56,179] multiqc [DEBUG ] No samples found: rsem [2021-08-10 10:06:56,189] multiqc [DEBUG ] No samples found: rseqc [2021-08-10 10:06:56,193] multiqc [DEBUG ] No samples found: busco [2021-08-10 10:06:56,198] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-10 10:06:56,203] multiqc [DEBUG ] No samples found: disambiguate [2021-08-10 10:06:56,207] multiqc [DEBUG ] No samples found: supernova [2021-08-10 10:06:56,219] multiqc [DEBUG ] No samples found: deeptools [2021-08-10 10:06:56,224] multiqc [DEBUG ] No samples found: sargasso [2021-08-10 10:06:56,228] multiqc [DEBUG ] No samples found: verifybamid [2021-08-10 10:06:56,233] multiqc [DEBUG ] No samples found: mirtrace [2021-08-10 10:06:56,244] multiqc [DEBUG ] No samples found: happy [2021-08-10 10:06:56,248] multiqc [DEBUG ] No samples found: mirtop [2021-08-10 10:06:56,254] multiqc [DEBUG ] No samples found: homer [2021-08-10 10:06:56,259] multiqc [DEBUG ] No samples found: macs2 [2021-08-10 10:06:56,263] multiqc [DEBUG ] No samples found: theta2 [2021-08-10 10:06:56,268] multiqc [DEBUG ] No samples found: snpeff [2021-08-10 10:06:56,274] multiqc [DEBUG ] No samples found: gatk [2021-08-10 10:06:56,278] multiqc [DEBUG ] No samples found: htseq [2021-08-10 10:06:56,284] multiqc [DEBUG ] No samples found: bcftools [2021-08-10 10:06:56,288] multiqc [DEBUG ] No samples found: featureCounts [2021-08-10 10:06:56,295] multiqc [DEBUG ] No samples found: fgbio [2021-08-10 10:06:56,307] multiqc [DEBUG ] No samples found: dragen [2021-08-10 10:06:56,311] multiqc [DEBUG ] No samples found: dedup [2021-08-10 10:06:56,316] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-10 10:06:56,339] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-10 10:06:56,343] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-10 10:06:56,345] multiqc [DEBUG ] No samples found: picard [2021-08-10 10:06:56,355] multiqc [DEBUG ] No samples found: prokka [2021-08-10 10:06:56,360] multiqc [DEBUG ] No samples found: samblaster [2021-08-10 10:06:56,370] multiqc [DEBUG ] No samples found: samtools [2021-08-10 10:06:56,375] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-10 10:06:56,380] multiqc [DEBUG ] No samples found: bamtools [2021-08-10 10:06:56,384] multiqc [DEBUG ] No samples found: jellyfish [2021-08-10 10:06:56,390] multiqc [DEBUG ] No samples found: vcftools [2021-08-10 10:06:56,395] multiqc [DEBUG ] No samples found: longranger [2021-08-10 10:06:56,399] multiqc [DEBUG ] No samples found: stacks [2021-08-10 10:06:56,404] multiqc [DEBUG ] No samples found: varscan2 [2021-08-10 10:06:56,416] multiqc [DEBUG ] No samples found: bbmap [2021-08-10 10:06:56,421] multiqc [DEBUG ] No samples found: bismark [2021-08-10 10:06:56,426] multiqc [DEBUG ] No samples found: biscuit [2021-08-10 10:06:56,430] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-10 10:06:56,435] multiqc [DEBUG ] No samples found: hicup [2021-08-10 10:06:56,439] multiqc [DEBUG ] No samples found: hicpro [2021-08-10 10:06:56,443] multiqc [DEBUG ] No samples found: salmon [2021-08-10 10:06:56,449] multiqc [DEBUG ] No samples found: kallisto [2021-08-10 10:06:56,454] multiqc [DEBUG ] No samples found: slamdunk [2021-08-10 10:06:56,459] multiqc [DEBUG ] No samples found: star [2021-08-10 10:06:56,463] multiqc [DEBUG ] No samples found: hisat2 [2021-08-10 10:06:56,467] multiqc [DEBUG ] No samples found: tophat [2021-08-10 10:06:56,472] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-10 10:06:56,476] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-10 10:06:56,481] multiqc [DEBUG ] No samples found: snpsplit [2021-08-10 10:06:56,485] multiqc [DEBUG ] No samples found: kat [2021-08-10 10:06:56,489] multiqc [DEBUG ] No samples found: leehom [2021-08-10 10:06:56,493] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-10 10:06:56,497] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-10 10:06:56,501] multiqc [DEBUG ] No samples found: cutadapt [2021-08-10 10:06:56,505] multiqc [DEBUG ] No samples found: flexbar [2021-08-10 10:06:56,510] multiqc [DEBUG ] No samples found: kaiju [2021-08-10 10:06:56,515] multiqc [DEBUG ] No samples found: kraken [2021-08-10 10:06:56,519] multiqc [DEBUG ] No samples found: malt [2021-08-10 10:06:56,523] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-10 10:06:56,528] multiqc [DEBUG ] No samples found: sickle [2021-08-10 10:06:56,532] multiqc [DEBUG ] No samples found: skewer [2021-08-10 10:06:56,536] multiqc [DEBUG ] No samples found: sortmerna [2021-08-10 10:06:56,540] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-10 10:06:56,545] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-10 10:06:56,549] multiqc [DEBUG ] No samples found: afterqc [2021-08-10 10:06:56,554] multiqc [DEBUG ] No samples found: fastp [2021-08-10 10:07:02,138] multiqc.modules.fastqc.fastqc [INFO ] Found 126 reports [2021-08-10 10:07:22,065] multiqc [DEBUG ] No samples found: pycoqc [2021-08-10 10:07:22,070] multiqc [DEBUG ] No samples found: minionqc [2021-08-10 10:07:22,074] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-10 10:07:22,079] multiqc [DEBUG ] No samples found: clusterflow [2021-08-10 10:07:22,083] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-10 10:07:22,088] multiqc [DEBUG ] No samples found: interop [2021-08-10 10:07:22,093] multiqc [DEBUG ] No samples found: ivar [2021-08-10 10:07:22,097] multiqc [DEBUG ] No samples found: flash [2021-08-10 10:07:22,102] multiqc [DEBUG ] No samples found: seqyclean [2021-08-10 10:07:22,102] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-10 10:07:22,102] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-10 10:07:22,102] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-10 10:07:22,102] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-10 10:07:22,246] multiqc [INFO ] Compressing plot data [2021-08-10 10:07:22,291] multiqc [INFO ] Report : multiqc_report.html [2021-08-10 10:07:22,291] multiqc [INFO ] Data : multiqc_data [2021-08-10 10:07:22,291] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9289566/tmpq3x63ixk/multiqc_data' to '/scratch/gencore/logs/html/HGG72DRXY/merged/multiqc_data' [2021-08-10 10:07:22,429] multiqc [INFO ] MultiQC complete