[2022-01-28 14:03:01,846] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-28 14:03:01,846] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-28 14:03:01,846] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-28 14:03:01,847] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-28 14:03:01,847] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-28 14:03:01,848] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHHNCAFX3/merged [2022-01-28 14:03:03,556] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-28 14:03:03,556] multiqc [INFO ] This is MultiQC v1.9 [2022-01-28 14:03:03,556] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHHNCAFX3/merged [2022-01-28 14:03:03,556] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHHNCAFX3/merged [2022-01-28 14:03:03,556] multiqc [INFO ] Template : default [2022-01-28 14:03:03,556] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-28 14:03:03,556] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHHNCAFX3/merged [2022-01-28 14:03:03,557] 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 [2022-01-28 14:03:03,557] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14430926/tmpm6bsgpp1 [2022-01-28 14:03:03,663] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11838-ChIP_fastqc.html [2022-01-28 14:03:03,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HHHNCAFX3_n02_2861-log-Input_fastqc.html [2022-01-28 14:03:03,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t0-Input_fastqc.html [2022-01-28 14:03:03,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t0-Input_fastqc.html [2022-01-28 14:03:03,923] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_2861-log-ChIP_fastqc.html [2022-01-28 14:03:03,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_2861-log-ChIP_fastqc.html [2022-01-28 14:03:03,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-log-Input_fastqc.html [2022-01-28 14:03:03,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize 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HHHNCAFX3_n02_11837-Input_fastqc.html [2022-01-28 14:03:04,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_2861-log-ChIP_fastqc.html [2022-01-28 14:03:04,246] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_2861-log-ChIP_fastqc.html [2022-01-28 14:03:04,284] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_undetermined_fastqc.html [2022-01-28 14:03:04,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_undetermined_fastqc.html [2022-01-28 14:03:04,325] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11835-Input_fastqc.html [2022-01-28 14:03:04,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11835-Input_fastqc.html [2022-01-28 14:03:04,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11836-Input_fastqc.html [2022-01-28 14:03:04,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11836-Input_fastqc.html [2022-01-28 14:03:04,404] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11838-Input_fastqc.html [2022-01-28 14:03:04,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11838-Input_fastqc.html [2022-01-28 14:03:04,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t3-Input_fastqc.html [2022-01-28 14:03:04,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t3-Input_fastqc.html [2022-01-28 14:03:04,484] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-log-ChIP_fastqc.html [2022-01-28 14:03:04,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-log-ChIP_fastqc.html [2022-01-28 14:03:04,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11836-ChIP_fastqc.html [2022-01-28 14:03:04,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11836-ChIP_fastqc.html [2022-01-28 14:03:04,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-log-Input_fastqc.html [2022-01-28 14:03:04,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-log-Input_fastqc.html [2022-01-28 14:03:04,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11836-Input_fastqc.html [2022-01-28 14:03:04,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11836-Input_fastqc.html [2022-01-28 14:03:04,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t3-ChIP_fastqc.html [2022-01-28 14:03:04,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_7797-t3-ChIP_fastqc.html [2022-01-28 14:03:04,686] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11836-ChIP_fastqc.html [2022-01-28 14:03:04,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11836-ChIP_fastqc.html [2022-01-28 14:03:04,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t0-ChIP_fastqc.html [2022-01-28 14:03:04,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t0-ChIP_fastqc.html [2022-01-28 14:03:04,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_2861-log-Input_fastqc.html [2022-01-28 14:03:04,767] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_2861-log-Input_fastqc.html [2022-01-28 14:03:04,805] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11838-Input_fastqc.html [2022-01-28 14:03:04,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11838-Input_fastqc.html [2022-01-28 14:03:04,847] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11837-Input_fastqc.html [2022-01-28 14:03:04,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11837-Input_fastqc.html [2022-01-28 14:03:04,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11835-ChIP_fastqc.html [2022-01-28 14:03:04,890] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11835-ChIP_fastqc.html [2022-01-28 14:03:04,927] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11838-ChIP_fastqc.html [2022-01-28 14:03:04,929] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_11838-ChIP_fastqc.html [2022-01-28 14:03:04,967] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t3-Input_fastqc.html [2022-01-28 14:03:04,969] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t3-Input_fastqc.html [2022-01-28 14:03:05,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t0-Input_fastqc.html [2022-01-28 14:03:05,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_7797-t0-Input_fastqc.html [2022-01-28 14:03:05,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11835-Input_fastqc.html [2022-01-28 14:03:05,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n01_11835-Input_fastqc.html [2022-01-28 14:03:05,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHHNCAFX3_n02_undetermined_fastqc.html [2022-01-28 14:03:05,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHHNCAFX3_n02_undetermined_fastqc.html [2022-01-28 14:03:05,547] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-28 14:03:05,549] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-28 14:03:05,563] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2022-01-28 14:03:05,565] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-28 14:03:05,574] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-28 14:03:05,580] multiqc [DEBUG ] No samples found: conpair [2022-01-28 14:03:05,585] multiqc [DEBUG ] No samples found: peddy [2022-01-28 14:03:05,591] multiqc [DEBUG ] No samples found: somalier [2022-01-28 14:03:05,596] multiqc [DEBUG ] No samples found: methylQA [2022-01-28 14:03:05,606] multiqc [DEBUG ] No samples found: mosdepth [2022-01-28 14:03:05,611] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-28 14:03:05,615] multiqc [DEBUG ] No samples found: qualimap [2022-01-28 14:03:05,620] multiqc [DEBUG ] No samples found: preseq [2022-01-28 14:03:05,626] multiqc [DEBUG ] No samples found: quast [2022-01-28 14:03:05,631] multiqc [DEBUG ] No samples found: qorts [2022-01-28 14:03:05,637] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-28 14:03:05,642] multiqc [DEBUG ] No samples found: rockhopper [2022-01-28 14:03:05,648] multiqc [DEBUG ] No samples found: rsem [2022-01-28 14:03:05,659] multiqc [DEBUG ] No samples found: rseqc [2022-01-28 14:03:05,663] multiqc [DEBUG ] No samples found: busco [2022-01-28 14:03:05,668] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-28 14:03:05,674] multiqc [DEBUG ] No samples found: disambiguate [2022-01-28 14:03:05,679] multiqc [DEBUG ] No samples found: supernova [2022-01-28 14:03:05,693] multiqc [DEBUG ] No samples found: deeptools [2022-01-28 14:03:05,698] multiqc [DEBUG ] No samples found: sargasso [2022-01-28 14:03:05,704] multiqc [DEBUG ] No samples found: verifybamid [2022-01-28 14:03:05,710] multiqc [DEBUG ] No samples found: mirtrace [2022-01-28 14:03:05,715] multiqc [DEBUG ] No samples found: happy [2022-01-28 14:03:05,720] multiqc [DEBUG ] No samples found: mirtop [2022-01-28 14:03:05,728] multiqc [DEBUG ] No samples found: homer [2022-01-28 14:03:05,733] multiqc [DEBUG ] No samples found: macs2 [2022-01-28 14:03:05,738] multiqc [DEBUG ] No samples found: theta2 [2022-01-28 14:03:05,744] multiqc [DEBUG ] No samples found: snpeff [2022-01-28 14:03:05,751] multiqc [DEBUG ] No samples found: gatk [2022-01-28 14:03:05,757] multiqc [DEBUG ] No samples found: htseq [2022-01-28 14:03:05,762] multiqc [DEBUG ] No samples found: bcftools [2022-01-28 14:03:05,768] multiqc [DEBUG ] No samples found: featureCounts [2022-01-28 14:03:05,775] multiqc [DEBUG ] No samples found: fgbio [2022-01-28 14:03:05,789] multiqc [DEBUG ] No samples found: dragen [2022-01-28 14:03:05,795] multiqc [DEBUG ] No samples found: dedup [2022-01-28 14:03:05,800] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-28 14:03:05,824] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-28 14:03:05,830] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-28 14:03:05,832] multiqc [DEBUG ] No samples found: picard [2022-01-28 14:03:05,837] multiqc [DEBUG ] No samples found: prokka [2022-01-28 14:03:05,842] multiqc [DEBUG ] No samples found: samblaster [2022-01-28 14:03:05,851] multiqc [DEBUG ] No samples found: samtools [2022-01-28 14:03:05,856] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-28 14:03:05,862] multiqc [DEBUG ] No samples found: bamtools [2022-01-28 14:03:05,866] multiqc [DEBUG ] No samples found: jellyfish [2022-01-28 14:03:05,874] multiqc [DEBUG ] No samples found: vcftools [2022-01-28 14:03:05,879] multiqc [DEBUG ] No samples found: longranger [2022-01-28 14:03:05,884] multiqc [DEBUG ] No samples found: stacks [2022-01-28 14:03:05,889] multiqc [DEBUG ] No samples found: varscan2 [2022-01-28 14:03:05,903] multiqc [DEBUG ] No samples found: bbmap [2022-01-28 14:03:05,908] multiqc [DEBUG ] No samples found: bismark [2022-01-28 14:03:05,914] multiqc [DEBUG ] No samples found: biscuit [2022-01-28 14:03:05,919] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-28 14:03:05,925] multiqc [DEBUG ] No samples found: hicup [2022-01-28 14:03:05,931] multiqc [DEBUG ] No samples found: hicpro [2022-01-28 14:03:05,936] multiqc [DEBUG ] No samples found: salmon [2022-01-28 14:03:05,941] multiqc [DEBUG ] No samples found: kallisto [2022-01-28 14:03:05,947] multiqc [DEBUG ] No samples found: slamdunk [2022-01-28 14:03:05,952] multiqc [DEBUG ] No samples found: star [2022-01-28 14:03:05,957] multiqc [DEBUG ] No samples found: hisat2 [2022-01-28 14:03:05,962] multiqc [DEBUG ] No samples found: tophat [2022-01-28 14:03:05,967] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-28 14:03:05,972] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-28 14:03:05,977] multiqc [DEBUG ] No samples found: snpsplit [2022-01-28 14:03:05,987] multiqc [DEBUG ] No samples found: kat [2022-01-28 14:03:05,991] multiqc [DEBUG ] No samples found: leehom [2022-01-28 14:03:05,997] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-28 14:03:06,001] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-28 14:03:06,006] multiqc [DEBUG ] No samples found: cutadapt [2022-01-28 14:03:06,011] multiqc [DEBUG ] No samples found: flexbar [2022-01-28 14:03:06,016] multiqc [DEBUG ] No samples found: kaiju [2022-01-28 14:03:06,021] multiqc [DEBUG ] No samples found: kraken [2022-01-28 14:03:06,027] multiqc [DEBUG ] No samples found: malt [2022-01-28 14:03:06,031] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-28 14:03:06,036] multiqc [DEBUG ] No samples found: sickle [2022-01-28 14:03:06,041] multiqc [DEBUG ] No samples found: skewer [2022-01-28 14:03:06,046] multiqc [DEBUG ] No samples found: sortmerna [2022-01-28 14:03:06,051] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-28 14:03:06,056] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-28 14:03:06,061] multiqc [DEBUG ] No samples found: afterqc [2022-01-28 14:03:06,066] multiqc [DEBUG ] No samples found: fastp [2022-01-28 14:03:06,805] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2022-01-28 14:03:07,094] multiqc [DEBUG ] No samples found: pycoqc [2022-01-28 14:03:07,099] multiqc [DEBUG ] No samples found: minionqc [2022-01-28 14:03:07,104] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-28 14:03:07,114] multiqc [DEBUG ] No samples found: clusterflow [2022-01-28 14:03:07,118] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-28 14:03:07,124] multiqc [DEBUG ] No samples found: interop [2022-01-28 14:03:07,129] multiqc [DEBUG ] No samples found: ivar [2022-01-28 14:03:07,135] multiqc [DEBUG ] No samples found: flash [2022-01-28 14:03:07,140] multiqc [DEBUG ] No samples found: seqyclean [2022-01-28 14:03:07,140] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-28 14:03:07,140] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-28 14:03:07,140] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-28 14:03:07,140] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-28 14:03:07,181] multiqc [INFO ] Compressing plot data [2022-01-28 14:03:07,744] multiqc [INFO ] Report : multiqc_report.html [2022-01-28 14:03:07,744] multiqc [INFO ] Data : multiqc_data [2022-01-28 14:03:07,744] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14430926/tmpm6bsgpp1/multiqc_data' to '/scratch/gencore/logs/html/HHHNCAFX3/merged/multiqc_data' [2022-01-28 14:03:07,870] multiqc [INFO ] MultiQC complete