[2022-02-05 12:33:46,406] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-05 12:33:46,406] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-05 12:33:46,406] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-05 12:33:46,407] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-05 12:33:46,407] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-05 12:33:46,407] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H72Y2DMXY/merged [2022-02-05 12:33:47,866] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-02-05 12:33:47,866] multiqc [INFO ] This is MultiQC v1.9 [2022-02-05 12:33:47,866] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H72Y2DMXY/merged [2022-02-05 12:33:47,866] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H72Y2DMXY/merged [2022-02-05 12:33:47,866] multiqc [INFO ] Template : default [2022-02-05 12:33:47,866] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-05 12:33:47,866] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H72Y2DMXY/merged [2022-02-05 12:33:47,866] 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 [2022-02-05 12:33:47,867] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-14657191/tmpo5xc2l8j [2022-02-05 12:33:47,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_K562_2_fastqc.html [2022-02-05 12:33:47,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-02-05 12:33:48,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_MDA_1_fastqc.html [2022-02-05 12:33:48,753] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_MDA_1_fastqc.html [2022-02-05 12:33:48,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_K562_1_fastqc.html [2022-02-05 12:33:48,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_K562_1_fastqc.html [2022-02-05 12:33:48,832] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HT29_1_fastqc.html [2022-02-05 12:33:48,834] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HT29_1_fastqc.html [2022-02-05 12:33:48,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_A549_1_fastqc.html [2022-02-05 12:33:48,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_A549_1_fastqc.html [2022-02-05 12:33:48,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HCT116_2_fastqc.html [2022-02-05 12:33:48,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HCT116_2_fastqc.html [2022-02-05 12:33:48,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_undetermined_fastqc.html [2022-02-05 12:33:48,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_undetermined_fastqc.html [2022-02-05 12:33:48,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_K562_2_fastqc.html [2022-02-05 12:33:48,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_K562_2_fastqc.html [2022-02-05 12:33:49,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_undetermined_fastqc.html [2022-02-05 12:33:49,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_undetermined_fastqc.html [2022-02-05 12:33:49,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_PC9_1_fastqc.html [2022-02-05 12:33:49,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_PC9_1_fastqc.html [2022-02-05 12:33:49,118] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_HT29_2_fastqc.html [2022-02-05 12:33:49,119] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_HT29_2_fastqc.html [2022-02-05 12:33:49,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_HCT116_2_fastqc.html [2022-02-05 12:33:49,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_HCT116_2_fastqc.html [2022-02-05 12:33:49,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_MDA_1_fastqc.html [2022-02-05 12:33:49,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_MDA_1_fastqc.html [2022-02-05 12:33:49,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_A549_2_fastqc.html [2022-02-05 12:33:49,241] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_A549_2_fastqc.html [2022-02-05 12:33:49,281] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HT29_2_fastqc.html [2022-02-05 12:33:49,283] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HT29_2_fastqc.html [2022-02-05 12:33:49,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_PC9_2_fastqc.html [2022-02-05 12:33:49,324] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_PC9_2_fastqc.html [2022-02-05 12:33:49,363] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_A549_1_fastqc.html [2022-02-05 12:33:49,364] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_A549_1_fastqc.html [2022-02-05 12:33:49,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HCT116_1_fastqc.html [2022-02-05 12:33:49,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n01_HCT116_1_fastqc.html [2022-02-05 12:33:49,446] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H72Y2DMXY_n02_K562_1_fastqc.html [2022-02-05 12:33:49,448] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H72Y2DMXY_n02_K562_1_fastqc.html [2022-02-05 12:33:49,784] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-05 12:33:49,786] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-05 12:33:49,793] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-05 12:33:49,799] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 12 samples (table) [2022-02-05 12:33:49,809] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-05 12:33:49,814] multiqc [DEBUG ] No samples found: conpair [2022-02-05 12:33:49,819] multiqc [DEBUG ] No samples found: peddy [2022-02-05 12:33:49,824] multiqc [DEBUG ] No samples found: somalier [2022-02-05 12:33:49,829] multiqc [DEBUG ] No samples found: methylQA [2022-02-05 12:33:49,838] multiqc [DEBUG ] No samples found: mosdepth [2022-02-05 12:33:49,843] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-05 12:33:49,846] multiqc [DEBUG ] No samples found: qualimap [2022-02-05 12:33:49,852] multiqc [DEBUG ] No samples found: preseq [2022-02-05 12:33:49,857] multiqc [DEBUG ] No samples found: quast [2022-02-05 12:33:49,862] multiqc [DEBUG ] No samples found: qorts [2022-02-05 12:33:49,867] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-05 12:33:49,872] multiqc [DEBUG ] No samples found: rockhopper [2022-02-05 12:33:49,877] multiqc [DEBUG ] No samples found: rsem [2022-02-05 12:33:49,888] multiqc [DEBUG ] No samples found: rseqc [2022-02-05 12:33:49,892] multiqc [DEBUG ] No samples found: busco [2022-02-05 12:33:49,897] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-05 12:33:49,902] multiqc [DEBUG ] No samples found: disambiguate [2022-02-05 12:33:49,907] multiqc [DEBUG ] No samples found: supernova [2022-02-05 12:33:49,921] multiqc [DEBUG ] No samples found: deeptools [2022-02-05 12:33:49,926] multiqc [DEBUG ] No samples found: sargasso [2022-02-05 12:33:49,930] multiqc [DEBUG ] No samples found: verifybamid [2022-02-05 12:33:49,936] multiqc [DEBUG ] No samples found: mirtrace [2022-02-05 12:33:49,941] multiqc [DEBUG ] No samples found: happy [2022-02-05 12:33:49,946] multiqc [DEBUG ] No samples found: mirtop [2022-02-05 12:33:49,952] multiqc [DEBUG ] No samples found: homer [2022-02-05 12:33:49,957] multiqc [DEBUG ] No samples found: macs2 [2022-02-05 12:33:49,962] multiqc [DEBUG ] No samples found: theta2 [2022-02-05 12:33:49,967] multiqc [DEBUG ] No samples found: snpeff [2022-02-05 12:33:49,974] multiqc [DEBUG ] No samples found: gatk [2022-02-05 12:33:49,979] multiqc [DEBUG ] No samples found: htseq [2022-02-05 12:33:49,984] multiqc [DEBUG ] No samples found: bcftools [2022-02-05 12:33:49,989] multiqc [DEBUG ] No samples found: featureCounts [2022-02-05 12:33:49,996] multiqc [DEBUG ] No samples found: fgbio [2022-02-05 12:33:50,008] multiqc [DEBUG ] No samples found: dragen [2022-02-05 12:33:50,013] multiqc [DEBUG ] No samples found: dedup [2022-02-05 12:33:50,018] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-05 12:33:50,042] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-05 12:33:50,047] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-05 12:33:50,049] multiqc [DEBUG ] No samples found: picard [2022-02-05 12:33:50,055] multiqc [DEBUG ] No samples found: prokka [2022-02-05 12:33:50,059] multiqc [DEBUG ] No samples found: samblaster [2022-02-05 12:33:50,068] multiqc [DEBUG ] No samples found: samtools [2022-02-05 12:33:50,073] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-05 12:33:50,079] multiqc [DEBUG ] No samples found: bamtools [2022-02-05 12:33:50,083] multiqc [DEBUG ] No samples found: jellyfish [2022-02-05 12:33:50,092] multiqc [DEBUG ] No samples found: vcftools [2022-02-05 12:33:50,097] multiqc [DEBUG ] No samples found: longranger [2022-02-05 12:33:50,103] multiqc [DEBUG ] No samples found: stacks [2022-02-05 12:33:50,108] multiqc [DEBUG ] No samples found: varscan2 [2022-02-05 12:33:50,122] multiqc [DEBUG ] No samples found: bbmap [2022-02-05 12:33:50,127] multiqc [DEBUG ] No samples found: bismark [2022-02-05 12:33:50,132] multiqc [DEBUG ] No samples found: biscuit [2022-02-05 12:33:50,138] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-05 12:33:50,143] multiqc [DEBUG ] No samples found: hicup [2022-02-05 12:33:50,149] multiqc [DEBUG ] No samples found: hicpro [2022-02-05 12:33:50,153] multiqc [DEBUG ] No samples found: salmon [2022-02-05 12:33:50,158] multiqc [DEBUG ] No samples found: kallisto [2022-02-05 12:33:50,163] multiqc [DEBUG ] No samples found: slamdunk [2022-02-05 12:33:50,169] multiqc [DEBUG ] No samples found: star [2022-02-05 12:33:50,174] multiqc [DEBUG ] No samples found: hisat2 [2022-02-05 12:33:50,179] multiqc [DEBUG ] No samples found: tophat [2022-02-05 12:33:50,184] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-05 12:33:50,189] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-05 12:33:50,194] multiqc [DEBUG ] No samples found: snpsplit [2022-02-05 12:33:50,199] multiqc [DEBUG ] No samples found: kat [2022-02-05 12:33:50,203] multiqc [DEBUG ] No samples found: leehom [2022-02-05 12:33:50,209] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-05 12:33:50,213] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-05 12:33:50,218] multiqc [DEBUG ] No samples found: cutadapt [2022-02-05 12:33:50,223] multiqc [DEBUG ] No samples found: flexbar [2022-02-05 12:33:50,228] multiqc [DEBUG ] No samples found: kaiju [2022-02-05 12:33:50,233] multiqc [DEBUG ] No samples found: kraken [2022-02-05 12:33:50,238] multiqc [DEBUG ] No samples found: malt [2022-02-05 12:33:50,243] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-05 12:33:50,248] multiqc [DEBUG ] No samples found: sickle [2022-02-05 12:33:50,253] multiqc [DEBUG ] No samples found: skewer [2022-02-05 12:33:50,258] multiqc [DEBUG ] No samples found: sortmerna [2022-02-05 12:33:50,262] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-05 12:33:50,267] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-05 12:33:50,272] multiqc [DEBUG ] No samples found: afterqc [2022-02-05 12:33:50,277] multiqc [DEBUG ] No samples found: fastp [2022-02-05 12:33:53,680] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-02-05 12:33:54,040] multiqc [DEBUG ] No samples found: pycoqc [2022-02-05 12:33:54,044] multiqc [DEBUG ] No samples found: minionqc [2022-02-05 12:33:54,049] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-05 12:33:54,054] multiqc [DEBUG ] No samples found: clusterflow [2022-02-05 12:33:54,059] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-05 12:33:54,064] multiqc [DEBUG ] No samples found: interop [2022-02-05 12:33:54,069] multiqc [DEBUG ] No samples found: ivar [2022-02-05 12:33:54,074] multiqc [DEBUG ] No samples found: flash [2022-02-05 12:33:54,079] multiqc [DEBUG ] No samples found: seqyclean [2022-02-05 12:33:54,079] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-05 12:33:54,079] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-05 12:33:54,079] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-05 12:33:54,079] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-05 12:33:54,107] multiqc [INFO ] Compressing plot data [2022-02-05 12:33:54,563] multiqc [INFO ] Report : multiqc_report.html [2022-02-05 12:33:54,563] multiqc [INFO ] Data : multiqc_data [2022-02-05 12:33:54,563] multiqc [DEBUG ] Moving data file from '/state/partition1/job-14657191/tmpo5xc2l8j/multiqc_data' to '/scratch/gencore/logs/html/H72Y2DMXY/merged/multiqc_data' [2022-02-05 12:33:54,687] multiqc [INFO ] MultiQC complete