[2022-03-23 06:31:22,091] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-23 06:31:22,091] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-23 06:31:22,091] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-23 06:31:22,092] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-23 06:31:22,092] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-23 06:31:22,092] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMYYNDRXY/2 [2022-03-23 06:31:22,490] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-23 06:31:22,490] multiqc [INFO ] This is MultiQC v1.9 [2022-03-23 06:31:22,490] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMYYNDRXY/2 [2022-03-23 06:31:22,490] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMYYNDRXY/2 [2022-03-23 06:31:22,490] multiqc [INFO ] Template : default [2022-03-23 06:31:22,491] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-23 06:31:22,491] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMYYNDRXY/2 [2022-03-23 06:31:22,491] 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 [2022-03-23 06:31:22,491] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16535732/tmpug728wyg [2022-03-23 06:31:22,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS189_fastqc.html [2022-03-23 06:31:22,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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HMYYNDRXY_l02_n01_RS164_fastqc.html [2022-03-23 06:31:25,733] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS196_fastqc.html [2022-03-23 06:31:25,735] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS196_fastqc.html [2022-03-23 06:31:25,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW14_fastqc.html [2022-03-23 06:31:25,783] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW14_fastqc.html [2022-03-23 06:31:25,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW15_fastqc.html [2022-03-23 06:31:25,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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HMYYNDRXY_l02_n01_WW8_fastqc.html [2022-03-23 06:31:26,325] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS178_fastqc.html [2022-03-23 06:31:26,327] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS178_fastqc.html [2022-03-23 06:31:26,372] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW31_fastqc.html [2022-03-23 06:31:26,374] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW31_fastqc.html [2022-03-23 06:31:26,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW42_fastqc.html [2022-03-23 06:31:26,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW42_fastqc.html [2022-03-23 06:31:26,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW7_fastqc.html [2022-03-23 06:31:26,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW7_fastqc.html [2022-03-23 06:31:26,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS162_fastqc.html [2022-03-23 06:31:26,516] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS162_fastqc.html [2022-03-23 06:31:26,561] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS174_fastqc.html [2022-03-23 06:31:26,563] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS174_fastqc.html [2022-03-23 06:31:26,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS198_fastqc.html [2022-03-23 06:31:26,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS198_fastqc.html [2022-03-23 06:31:26,655] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS188_fastqc.html [2022-03-23 06:31:26,657] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS188_fastqc.html [2022-03-23 06:31:26,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW35_fastqc.html [2022-03-23 06:31:26,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW35_fastqc.html [2022-03-23 06:31:26,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS205_fastqc.html [2022-03-23 06:31:26,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS205_fastqc.html [2022-03-23 06:31:26,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS153_fastqc.html [2022-03-23 06:31:26,798] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS153_fastqc.html [2022-03-23 06:31:26,843] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS176_fastqc.html [2022-03-23 06:31:26,845] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS176_fastqc.html [2022-03-23 06:31:26,890] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS187_fastqc.html [2022-03-23 06:31:26,892] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS187_fastqc.html [2022-03-23 06:31:26,938] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS203_fastqc.html [2022-03-23 06:31:26,940] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS203_fastqc.html [2022-03-23 06:31:26,985] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS154_fastqc.html [2022-03-23 06:31:26,986] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS154_fastqc.html [2022-03-23 06:31:27,032] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS155_fastqc.html [2022-03-23 06:31:27,034] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS155_fastqc.html [2022-03-23 06:31:27,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS177_fastqc.html [2022-03-23 06:31:27,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS177_fastqc.html [2022-03-23 06:31:27,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW27_fastqc.html [2022-03-23 06:31:27,147] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW27_fastqc.html [2022-03-23 06:31:27,192] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW24_fastqc.html [2022-03-23 06:31:27,194] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW24_fastqc.html [2022-03-23 06:31:27,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW2_fastqc.html [2022-03-23 06:31:27,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_WW2_fastqc.html [2022-03-23 06:31:27,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS179_fastqc.html [2022-03-23 06:31:27,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS179_fastqc.html [2022-03-23 06:31:27,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS202_fastqc.html [2022-03-23 06:31:27,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l02_n01_RS202_fastqc.html [2022-03-23 06:31:27,632] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-23 06:31:27,633] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-23 06:31:27,640] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-23 06:31:27,684] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 97 samples (table) [2022-03-23 06:31:27,694] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-23 06:31:27,697] multiqc [DEBUG ] No samples found: conpair [2022-03-23 06:31:27,700] multiqc [DEBUG ] No samples found: peddy [2022-03-23 06:31:27,703] multiqc [DEBUG ] No samples found: somalier [2022-03-23 06:31:27,706] multiqc [DEBUG ] No samples found: methylQA [2022-03-23 06:31:27,710] multiqc [DEBUG ] No samples found: mosdepth [2022-03-23 06:31:27,713] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-23 06:31:27,716] multiqc [DEBUG ] No samples found: qualimap [2022-03-23 06:31:27,719] multiqc [DEBUG ] No samples found: preseq [2022-03-23 06:31:27,722] multiqc [DEBUG ] No samples found: quast [2022-03-23 06:31:27,724] multiqc [DEBUG ] No samples found: qorts [2022-03-23 06:31:27,728] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-23 06:31:27,731] multiqc [DEBUG ] No samples found: rockhopper [2022-03-23 06:31:27,734] multiqc [DEBUG ] No samples found: rsem [2022-03-23 06:31:27,739] multiqc [DEBUG ] No samples found: rseqc [2022-03-23 06:31:27,742] multiqc [DEBUG ] No samples found: busco [2022-03-23 06:31:27,745] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-23 06:31:27,748] multiqc [DEBUG ] No samples found: disambiguate [2022-03-23 06:31:27,751] multiqc [DEBUG ] No samples found: supernova [2022-03-23 06:31:27,757] multiqc [DEBUG ] No samples found: deeptools [2022-03-23 06:31:27,759] multiqc [DEBUG ] No samples found: sargasso [2022-03-23 06:31:27,763] multiqc [DEBUG ] No samples found: verifybamid [2022-03-23 06:31:27,766] multiqc [DEBUG ] No samples found: mirtrace [2022-03-23 06:31:27,769] multiqc [DEBUG ] No samples found: happy [2022-03-23 06:31:27,772] multiqc [DEBUG ] No samples found: mirtop [2022-03-23 06:31:27,775] multiqc [DEBUG ] No samples found: homer [2022-03-23 06:31:27,778] multiqc [DEBUG ] No samples found: macs2 [2022-03-23 06:31:27,781] multiqc [DEBUG ] No samples found: theta2 [2022-03-23 06:31:27,784] multiqc [DEBUG ] No samples found: snpeff [2022-03-23 06:31:27,788] multiqc [DEBUG ] No samples found: gatk [2022-03-23 06:31:27,791] multiqc [DEBUG ] No samples found: htseq [2022-03-23 06:31:27,794] multiqc [DEBUG ] No samples found: bcftools [2022-03-23 06:31:27,797] multiqc [DEBUG ] No samples found: featureCounts [2022-03-23 06:31:27,801] multiqc [DEBUG ] No samples found: fgbio [2022-03-23 06:31:27,807] multiqc [DEBUG ] No samples found: dragen [2022-03-23 06:31:27,809] multiqc [DEBUG ] No samples found: dedup [2022-03-23 06:31:27,812] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-23 06:31:27,822] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-23 06:31:27,825] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-23 06:31:27,827] multiqc [DEBUG ] No samples found: picard [2022-03-23 06:31:27,830] multiqc [DEBUG ] No samples found: prokka [2022-03-23 06:31:27,833] multiqc [DEBUG ] No samples found: samblaster [2022-03-23 06:31:27,837] multiqc [DEBUG ] No samples found: samtools [2022-03-23 06:31:27,840] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-23 06:31:27,843] multiqc [DEBUG ] No samples found: bamtools [2022-03-23 06:31:27,846] multiqc [DEBUG ] No samples found: jellyfish [2022-03-23 06:31:27,851] multiqc [DEBUG ] No samples found: vcftools [2022-03-23 06:31:27,854] multiqc [DEBUG ] No samples found: longranger [2022-03-23 06:31:27,857] multiqc [DEBUG ] No samples found: stacks [2022-03-23 06:31:27,860] multiqc [DEBUG ] No samples found: varscan2 [2022-03-23 06:31:27,866] multiqc [DEBUG ] No samples found: bbmap [2022-03-23 06:31:27,869] multiqc [DEBUG ] No samples found: bismark [2022-03-23 06:31:27,872] multiqc [DEBUG ] No samples found: biscuit [2022-03-23 06:31:27,875] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-23 06:31:27,878] multiqc [DEBUG ] No samples found: hicup [2022-03-23 06:31:27,881] multiqc [DEBUG ] No samples found: hicpro [2022-03-23 06:31:27,884] multiqc [DEBUG ] No samples found: salmon [2022-03-23 06:31:27,887] multiqc [DEBUG ] No samples found: kallisto [2022-03-23 06:31:27,890] multiqc [DEBUG ] No samples found: slamdunk [2022-03-23 06:31:27,893] multiqc [DEBUG ] No samples found: star [2022-03-23 06:31:27,896] multiqc [DEBUG ] No samples found: hisat2 [2022-03-23 06:31:27,899] multiqc [DEBUG ] No samples found: tophat [2022-03-23 06:31:27,902] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-23 06:31:27,905] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-23 06:31:27,908] multiqc [DEBUG ] No samples found: snpsplit [2022-03-23 06:31:27,911] multiqc [DEBUG ] No samples found: kat [2022-03-23 06:31:27,914] multiqc [DEBUG ] No samples found: leehom [2022-03-23 06:31:27,917] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-23 06:31:27,920] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-23 06:31:27,923] multiqc [DEBUG ] No samples found: cutadapt [2022-03-23 06:31:27,926] multiqc [DEBUG ] No samples found: flexbar [2022-03-23 06:31:27,929] multiqc [DEBUG ] No samples found: kaiju [2022-03-23 06:31:27,931] multiqc [DEBUG ] No samples found: kraken [2022-03-23 06:31:27,934] multiqc [DEBUG ] No samples found: malt [2022-03-23 06:31:27,937] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-23 06:31:27,940] multiqc [DEBUG ] No samples found: sickle [2022-03-23 06:31:27,943] multiqc [DEBUG ] No samples found: skewer [2022-03-23 06:31:27,946] multiqc [DEBUG ] No samples found: sortmerna [2022-03-23 06:31:27,949] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-23 06:31:27,952] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-23 06:31:27,955] multiqc [DEBUG ] No samples found: afterqc [2022-03-23 06:31:27,958] multiqc [DEBUG ] No samples found: fastp [2022-03-23 06:31:34,221] multiqc.modules.fastqc.fastqc [INFO ] Found 97 reports [2022-03-23 06:31:35,485] multiqc [DEBUG ] No samples found: pycoqc [2022-03-23 06:31:35,488] multiqc [DEBUG ] No samples found: minionqc [2022-03-23 06:31:35,491] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-23 06:31:35,494] multiqc [DEBUG ] No samples found: clusterflow [2022-03-23 06:31:35,497] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-23 06:31:35,500] multiqc [DEBUG ] No samples found: interop [2022-03-23 06:31:35,503] multiqc [DEBUG ] No samples found: ivar [2022-03-23 06:31:35,506] multiqc [DEBUG ] No samples found: flash [2022-03-23 06:31:35,509] multiqc [DEBUG ] No samples found: seqyclean [2022-03-23 06:31:35,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-03-23 06:31:35,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-03-23 06:31:35,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-03-23 06:31:35,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-23 06:31:35,510] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-23 06:31:35,621] multiqc [INFO ] Compressing plot data [2022-03-23 06:31:37,338] multiqc [INFO ] Report : multiqc_report.html [2022-03-23 06:31:37,338] multiqc [INFO ] Data : multiqc_data [2022-03-23 06:31:37,338] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16535732/tmpug728wyg/multiqc_data' to '/scratch/gencore/logs/html/HMYYNDRXY/2/multiqc_data' [2022-03-23 06:31:37,442] multiqc [INFO ] MultiQC complete