[2021-02-19 03:14:47,508] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-02-19 03:14:47,508] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-02-19 03:14:47,508] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-19 03:14:47,509] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-02-19 03:14:47,509] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-02-19 03:14:47,509] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3MCHDRXY/merged [2021-02-19 03:14:49,060] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-02-19 03:14:49,060] multiqc [INFO ] This is MultiQC v1.9 [2021-02-19 03:14:49,060] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3MCHDRXY/merged [2021-02-19 03:14:49,060] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3MCHDRXY/merged [2021-02-19 03:14:49,060] multiqc [INFO ] Template : default [2021-02-19 03:14:49,060] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-02-19 03:14:49,060] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3MCHDRXY/merged [2021-02-19 03:14:49,060] 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 [2021-02-19 03:14:49,061] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-2956330/tmpn98jmxcj [2021-02-19 03:14:49,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei048_fastqc.html [2021-02-19 03:14:49,187] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei048_fastqc.html [2021-02-19 03:14:49,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_undetermined_fastqc.html [2021-02-19 03:14:49,231] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_undetermined_fastqc.html [2021-02-19 03:14:49,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei039_fastqc.html [2021-02-19 03:14:49,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei039_fastqc.html [2021-02-19 03:14:49,325] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-19 03:14:49,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-02-19 03:14:49,412] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG136_fastqc.html [2021-02-19 03:14:49,414] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG136_fastqc.html [2021-02-19 03:14:49,454] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG144_fastqc.html [2021-02-19 03:14:49,455] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG144_fastqc.html [2021-02-19 03:14:49,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG135_fastqc.html [2021-02-19 03:14:49,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG135_fastqc.html [2021-02-19 03:14:49,536] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG133_fastqc.html [2021-02-19 03:14:49,538] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG133_fastqc.html [2021-02-19 03:14:49,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG148_fastqc.html [2021-02-19 03:14:49,579] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG148_fastqc.html [2021-02-19 03:14:49,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei054_fastqc.html [2021-02-19 03:14:49,630] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei054_fastqc.html [2021-02-19 03:14:49,691] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG142_fastqc.html [2021-02-19 03:14:49,693] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG142_fastqc.html [2021-02-19 03:14:49,733] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG138_fastqc.html [2021-02-19 03:14:49,735] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG138_fastqc.html [2021-02-19 03:14:49,775] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei051_fastqc.html [2021-02-19 03:14:49,777] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei051_fastqc.html [2021-02-19 03:14:49,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG140_fastqc.html [2021-02-19 03:14:49,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG140_fastqc.html [2021-02-19 03:14:49,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG149_fastqc.html [2021-02-19 03:14:49,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG149_fastqc.html [2021-02-19 03:14:49,907] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG147_fastqc.html [2021-02-19 03:14:49,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG147_fastqc.html [2021-02-19 03:14:49,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG152_fastqc.html [2021-02-19 03:14:49,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG152_fastqc.html [2021-02-19 03:14:49,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG141_fastqc.html [2021-02-19 03:14:49,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG141_fastqc.html [2021-02-19 03:14:50,031] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG145_fastqc.html [2021-02-19 03:14:50,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG145_fastqc.html [2021-02-19 03:14:50,072] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG139_fastqc.html [2021-02-19 03:14:50,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG139_fastqc.html [2021-02-19 03:14:50,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG151_fastqc.html [2021-02-19 03:14:50,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG151_fastqc.html [2021-02-19 03:14:50,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG134_fastqc.html [2021-02-19 03:14:50,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG134_fastqc.html [2021-02-19 03:14:50,228] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei042_fastqc.html [2021-02-19 03:14:50,230] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei042_fastqc.html [2021-02-19 03:14:50,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG146_fastqc.html [2021-02-19 03:14:50,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG146_fastqc.html [2021-02-19 03:14:50,319] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG137_fastqc.html [2021-02-19 03:14:50,320] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG137_fastqc.html [2021-02-19 03:14:50,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG150_fastqc.html [2021-02-19 03:14:50,363] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG150_fastqc.html [2021-02-19 03:14:50,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei045_fastqc.html [2021-02-19 03:14:50,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_dei045_fastqc.html [2021-02-19 03:14:50,492] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG143_fastqc.html [2021-02-19 03:14:50,493] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3MCHDRXY_n01_GG143_fastqc.html [2021-02-19 03:14:50,992] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-19 03:14:50,995] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-02-19 03:14:51,015] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 27 samples (table) [2021-02-19 03:14:51,017] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-02-19 03:14:51,026] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-02-19 03:14:51,033] multiqc [DEBUG ] No samples found: conpair [2021-02-19 03:14:51,041] multiqc [DEBUG ] No samples found: peddy [2021-02-19 03:14:51,046] multiqc [DEBUG ] No samples found: somalier [2021-02-19 03:14:51,052] multiqc [DEBUG ] No samples found: methylQA [2021-02-19 03:14:51,065] multiqc [DEBUG ] No samples found: mosdepth [2021-02-19 03:14:51,071] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-19 03:14:51,076] multiqc [DEBUG ] No samples found: qualimap [2021-02-19 03:14:51,083] multiqc [DEBUG ] No samples found: preseq [2021-02-19 03:14:51,089] multiqc [DEBUG ] No samples found: quast [2021-02-19 03:14:51,095] multiqc [DEBUG ] No samples found: qorts [2021-02-19 03:14:51,102] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-19 03:14:51,110] multiqc [DEBUG ] No samples found: rockhopper [2021-02-19 03:14:51,116] multiqc [DEBUG ] No samples found: rsem [2021-02-19 03:14:51,136] multiqc [DEBUG ] No samples found: rseqc [2021-02-19 03:14:51,145] multiqc [DEBUG ] No samples found: busco [2021-02-19 03:14:51,151] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-19 03:14:51,158] multiqc [DEBUG ] No samples found: disambiguate [2021-02-19 03:14:51,168] multiqc [DEBUG ] No samples found: supernova [2021-02-19 03:14:51,192] multiqc [DEBUG ] No samples found: deeptools [2021-02-19 03:14:51,199] multiqc [DEBUG ] No samples found: sargasso [2021-02-19 03:14:51,204] multiqc [DEBUG ] No samples found: verifybamid [2021-02-19 03:14:51,209] multiqc [DEBUG ] No samples found: mirtrace [2021-02-19 03:14:51,223] multiqc [DEBUG ] No samples found: happy [2021-02-19 03:14:51,230] multiqc [DEBUG ] No samples found: mirtop [2021-02-19 03:14:51,240] multiqc [DEBUG ] No samples found: homer [2021-02-19 03:14:51,249] multiqc [DEBUG ] No samples found: macs2 [2021-02-19 03:14:51,254] multiqc [DEBUG ] No samples found: theta2 [2021-02-19 03:14:51,260] multiqc [DEBUG ] No samples found: snpeff [2021-02-19 03:14:51,270] multiqc [DEBUG ] No samples found: gatk [2021-02-19 03:14:51,276] multiqc [DEBUG ] No samples found: htseq [2021-02-19 03:14:51,284] multiqc [DEBUG ] No samples found: bcftools [2021-02-19 03:14:51,291] multiqc [DEBUG ] No samples found: featureCounts [2021-02-19 03:14:51,301] multiqc [DEBUG ] No samples found: fgbio [2021-02-19 03:14:51,324] multiqc [DEBUG ] No samples found: dragen [2021-02-19 03:14:51,328] multiqc [DEBUG ] No samples found: dedup [2021-02-19 03:14:51,334] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-19 03:14:51,384] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-19 03:14:51,391] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-19 03:14:51,394] multiqc [DEBUG ] No samples found: picard [2021-02-19 03:14:51,402] multiqc [DEBUG ] No samples found: prokka [2021-02-19 03:14:51,406] multiqc [DEBUG ] No samples found: samblaster [2021-02-19 03:14:51,420] multiqc [DEBUG ] No samples found: samtools [2021-02-19 03:14:51,430] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-19 03:14:51,437] multiqc [DEBUG ] No samples found: bamtools [2021-02-19 03:14:51,445] multiqc [DEBUG ] No samples found: jellyfish [2021-02-19 03:14:51,461] multiqc [DEBUG ] No samples found: vcftools [2021-02-19 03:14:51,465] multiqc [DEBUG ] No samples found: longranger [2021-02-19 03:14:51,476] multiqc [DEBUG ] No samples found: stacks [2021-02-19 03:14:51,484] multiqc [DEBUG ] No samples found: varscan2 [2021-02-19 03:14:51,518] multiqc [DEBUG ] No samples found: bbmap [2021-02-19 03:14:51,527] multiqc [DEBUG ] No samples found: bismark [2021-02-19 03:14:51,536] multiqc [DEBUG ] No samples found: biscuit [2021-02-19 03:14:51,542] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-19 03:14:51,549] multiqc [DEBUG ] No samples found: hicup [2021-02-19 03:14:51,558] multiqc [DEBUG ] No samples found: hicpro [2021-02-19 03:14:51,562] multiqc [DEBUG ] No samples found: salmon [2021-02-19 03:14:51,570] multiqc [DEBUG ] No samples found: kallisto [2021-02-19 03:14:51,574] multiqc [DEBUG ] No samples found: slamdunk [2021-02-19 03:14:51,582] multiqc [DEBUG ] No samples found: star [2021-02-19 03:14:51,589] multiqc [DEBUG ] No samples found: hisat2 [2021-02-19 03:14:51,596] multiqc [DEBUG ] No samples found: tophat [2021-02-19 03:14:51,602] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-19 03:14:51,607] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-19 03:14:51,615] multiqc [DEBUG ] No samples found: snpsplit [2021-02-19 03:14:51,622] multiqc [DEBUG ] No samples found: kat [2021-02-19 03:14:51,628] multiqc [DEBUG ] No samples found: leehom [2021-02-19 03:14:51,633] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-19 03:14:51,639] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-19 03:14:51,647] multiqc [DEBUG ] No samples found: cutadapt [2021-02-19 03:14:51,651] multiqc [DEBUG ] No samples found: flexbar [2021-02-19 03:14:51,657] multiqc [DEBUG ] No samples found: kaiju [2021-02-19 03:14:51,663] multiqc [DEBUG ] No samples found: kraken [2021-02-19 03:14:51,670] multiqc [DEBUG ] No samples found: malt [2021-02-19 03:14:51,675] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-19 03:14:51,681] multiqc [DEBUG ] No samples found: sickle [2021-02-19 03:14:51,689] multiqc [DEBUG ] No samples found: skewer [2021-02-19 03:14:51,693] multiqc [DEBUG ] No samples found: sortmerna [2021-02-19 03:14:51,698] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-19 03:14:51,706] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-19 03:14:51,713] multiqc [DEBUG ] No samples found: afterqc [2021-02-19 03:14:51,720] multiqc [DEBUG ] No samples found: fastp [2021-02-19 03:14:52,777] multiqc.modules.fastqc.fastqc [INFO ] Found 27 reports [2021-02-19 03:14:53,156] multiqc [DEBUG ] No samples found: pycoqc [2021-02-19 03:14:53,163] multiqc [DEBUG ] No samples found: minionqc [2021-02-19 03:14:53,171] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-02-19 03:14:53,178] multiqc [DEBUG ] No samples found: clusterflow [2021-02-19 03:14:53,186] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-19 03:14:53,193] multiqc [DEBUG ] No samples found: interop [2021-02-19 03:14:53,201] multiqc [DEBUG ] No samples found: ivar [2021-02-19 03:14:53,208] multiqc [DEBUG ] No samples found: flash [2021-02-19 03:14:53,214] multiqc [DEBUG ] No samples found: seqyclean [2021-02-19 03:14:53,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-02-19 03:14:53,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-02-19 03:14:53,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-02-19 03:14:53,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-02-19 03:14:53,245] multiqc [INFO ] Compressing plot data [2021-02-19 03:14:53,752] multiqc [INFO ] Report : multiqc_report.html [2021-02-19 03:14:53,752] multiqc [INFO ] Data : multiqc_data [2021-02-19 03:14:53,752] multiqc [DEBUG ] Moving data file from '/state/partition1/job-2956330/tmpn98jmxcj/multiqc_data' to '/scratch/gencore/logs/html/H3MCHDRXY/merged/multiqc_data' [2021-02-19 03:14:53,875] multiqc [INFO ] MultiQC complete