[2021-12-12 00:36:59,930] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-12 00:36:59,931] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-12 00:36:59,931] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-12 00:36:59,932] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-12 00:36:59,932] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-12 00:36:59,932] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMN33BGXK/merged [2021-12-12 00:37:01,378] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-12 00:37:01,378] multiqc [INFO ] This is MultiQC v1.9 [2021-12-12 00:37:01,378] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMN33BGXK/merged [2021-12-12 00:37:01,378] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMN33BGXK/merged [2021-12-12 00:37:01,378] multiqc [INFO ] Template : default [2021-12-12 00:37:01,378] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-12 00:37:01,379] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMN33BGXK/merged [2021-12-12 00:37:01,379] 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 [2021-12-12 00:37:01,379] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12989567/tmpx96wj613 [2021-12-12 00:37:01,511] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2769_fastqc.html [2021-12-12 00:37:01,514] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HMN33BGXK_n01_DGY2737_fastqc.html [2021-12-12 00:37:12,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2771_fastqc.html [2021-12-12 00:37:12,790] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2771_fastqc.html [2021-12-12 00:37:12,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2754_fastqc.html [2021-12-12 00:37:12,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2754_fastqc.html [2021-12-12 00:37:12,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2734_fastqc.html [2021-12-12 00:37:12,881] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2734_fastqc.html [2021-12-12 00:37:12,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1734-3_fastqc.html [2021-12-12 00:37:12,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1734-3_fastqc.html [2021-12-12 00:37:12,985] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_undetermined_fastqc.html [2021-12-12 00:37:12,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_undetermined_fastqc.html [2021-12-12 00:37:13,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2767_fastqc.html [2021-12-12 00:37:13,029] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2767_fastqc.html [2021-12-12 00:37:13,072] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2756_fastqc.html [2021-12-12 00:37:13,074] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2756_fastqc.html [2021-12-12 00:37:13,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1736-1_fastqc.html [2021-12-12 00:37:13,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1736-1_fastqc.html [2021-12-12 00:37:13,187] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2781_fastqc.html [2021-12-12 00:37:13,189] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2781_fastqc.html [2021-12-12 00:37:13,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2758_fastqc.html [2021-12-12 00:37:13,234] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2758_fastqc.html [2021-12-12 00:37:13,290] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2691_fastqc.html [2021-12-12 00:37:13,292] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2691_fastqc.html [2021-12-12 00:37:13,350] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1734-1_fastqc.html [2021-12-12 00:37:13,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1734-1_fastqc.html [2021-12-12 00:37:13,407] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2668_fastqc.html [2021-12-12 00:37:13,409] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2668_fastqc.html [2021-12-12 00:37:13,452] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY1734-3_fastqc.html [2021-12-12 00:37:13,454] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY1734-3_fastqc.html [2021-12-12 00:37:13,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2786_fastqc.html [2021-12-12 00:37:13,495] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2786_fastqc.html [2021-12-12 00:37:13,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1657-1_fastqc.html [2021-12-12 00:37:13,561] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY1657-1_fastqc.html [2021-12-12 00:37:13,612] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2687_fastqc.html [2021-12-12 00:37:13,614] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2687_fastqc.html [2021-12-12 00:37:13,669] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2755_fastqc.html [2021-12-12 00:37:13,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2755_fastqc.html [2021-12-12 00:37:13,751] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2779_fastqc.html [2021-12-12 00:37:13,752] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2779_fastqc.html [2021-12-12 00:37:13,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2732_fastqc.html [2021-12-12 00:37:13,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2732_fastqc.html [2021-12-12 00:37:13,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2731_fastqc.html [2021-12-12 00:37:13,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n02_DGY2731_fastqc.html [2021-12-12 00:37:13,932] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2680_fastqc.html [2021-12-12 00:37:13,934] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2680_fastqc.html [2021-12-12 00:37:14,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2744_fastqc.html [2021-12-12 00:37:14,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMN33BGXK_n01_DGY2744_fastqc.html [2021-12-12 00:37:14,547] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-12 00:37:14,548] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-12 00:37:14,557] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-12 00:37:14,607] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 107 samples (table) [2021-12-12 00:37:14,618] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-12 00:37:14,623] multiqc [DEBUG ] No samples found: conpair [2021-12-12 00:37:14,629] multiqc [DEBUG ] No samples found: peddy [2021-12-12 00:37:14,634] multiqc [DEBUG ] No samples found: somalier [2021-12-12 00:37:14,638] multiqc [DEBUG ] No samples found: methylQA [2021-12-12 00:37:14,647] multiqc [DEBUG ] No samples found: mosdepth [2021-12-12 00:37:14,651] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-12 00:37:14,655] multiqc [DEBUG ] No samples found: qualimap [2021-12-12 00:37:14,660] multiqc [DEBUG ] No samples found: preseq [2021-12-12 00:37:14,665] multiqc [DEBUG ] No samples found: quast [2021-12-12 00:37:14,670] multiqc [DEBUG ] No samples found: qorts [2021-12-12 00:37:14,676] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-12 00:37:14,680] multiqc [DEBUG ] No samples found: rockhopper [2021-12-12 00:37:14,685] multiqc [DEBUG ] No samples found: rsem [2021-12-12 00:37:14,701] multiqc [DEBUG ] No samples found: rseqc [2021-12-12 00:37:14,706] multiqc [DEBUG ] No samples found: busco [2021-12-12 00:37:14,713] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-12 00:37:14,717] multiqc [DEBUG ] No samples found: disambiguate [2021-12-12 00:37:14,723] multiqc [DEBUG ] No samples found: supernova [2021-12-12 00:37:14,736] multiqc [DEBUG ] No samples found: deeptools [2021-12-12 00:37:14,741] multiqc [DEBUG ] No samples found: sargasso [2021-12-12 00:37:14,747] multiqc [DEBUG ] No samples found: verifybamid [2021-12-12 00:37:14,752] multiqc [DEBUG ] No samples found: mirtrace [2021-12-12 00:37:14,757] multiqc [DEBUG ] No samples found: happy [2021-12-12 00:37:14,761] multiqc [DEBUG ] No samples found: mirtop [2021-12-12 00:37:14,768] multiqc [DEBUG ] No samples found: homer [2021-12-12 00:37:14,773] multiqc [DEBUG ] No samples found: macs2 [2021-12-12 00:37:14,779] multiqc [DEBUG ] No samples found: theta2 [2021-12-12 00:37:14,784] multiqc [DEBUG ] No samples found: snpeff [2021-12-12 00:37:14,790] multiqc [DEBUG ] No samples found: gatk [2021-12-12 00:37:14,795] multiqc [DEBUG ] No samples found: htseq [2021-12-12 00:37:14,801] multiqc [DEBUG ] No samples found: bcftools [2021-12-12 00:37:14,806] multiqc [DEBUG ] No samples found: featureCounts [2021-12-12 00:37:14,813] multiqc [DEBUG ] No samples found: fgbio [2021-12-12 00:37:14,826] multiqc [DEBUG ] No samples found: dragen [2021-12-12 00:37:14,835] multiqc [DEBUG ] No samples found: dedup [2021-12-12 00:37:14,841] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-12 00:37:14,863] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-12 00:37:14,868] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-12 00:37:14,870] multiqc [DEBUG ] No samples found: picard [2021-12-12 00:37:14,875] multiqc [DEBUG ] No samples found: prokka [2021-12-12 00:37:14,880] multiqc [DEBUG ] No samples found: samblaster [2021-12-12 00:37:14,890] multiqc [DEBUG ] No samples found: samtools [2021-12-12 00:37:14,896] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-12 00:37:14,901] multiqc [DEBUG ] No samples found: bamtools [2021-12-12 00:37:14,906] multiqc [DEBUG ] No samples found: jellyfish [2021-12-12 00:37:14,916] multiqc [DEBUG ] No samples found: vcftools [2021-12-12 00:37:14,922] multiqc [DEBUG ] No samples found: longranger [2021-12-12 00:37:14,927] multiqc [DEBUG ] No samples found: stacks [2021-12-12 00:37:14,932] multiqc [DEBUG ] No samples found: varscan2 [2021-12-12 00:37:14,946] multiqc [DEBUG ] No samples found: bbmap [2021-12-12 00:37:14,951] multiqc [DEBUG ] No samples found: bismark [2021-12-12 00:37:14,956] multiqc [DEBUG ] No samples found: biscuit [2021-12-12 00:37:14,961] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-12 00:37:14,966] multiqc [DEBUG ] No samples found: hicup [2021-12-12 00:37:14,971] multiqc [DEBUG ] No samples found: hicpro [2021-12-12 00:37:14,976] multiqc [DEBUG ] No samples found: salmon [2021-12-12 00:37:14,981] multiqc [DEBUG ] No samples found: kallisto [2021-12-12 00:37:14,986] multiqc [DEBUG ] No samples found: slamdunk [2021-12-12 00:37:14,991] multiqc [DEBUG ] No samples found: star [2021-12-12 00:37:14,996] multiqc [DEBUG ] No samples found: hisat2 [2021-12-12 00:37:15,001] multiqc [DEBUG ] No samples found: tophat [2021-12-12 00:37:15,006] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-12 00:37:15,011] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-12 00:37:15,016] multiqc [DEBUG ] No samples found: snpsplit [2021-12-12 00:37:15,021] multiqc [DEBUG ] No samples found: kat [2021-12-12 00:37:15,026] multiqc [DEBUG ] No samples found: leehom [2021-12-12 00:37:15,031] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-12 00:37:15,035] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-12 00:37:15,040] multiqc [DEBUG ] No samples found: cutadapt [2021-12-12 00:37:15,045] multiqc [DEBUG ] No samples found: flexbar [2021-12-12 00:37:15,050] multiqc [DEBUG ] No samples found: kaiju [2021-12-12 00:37:15,055] multiqc [DEBUG ] No samples found: kraken [2021-12-12 00:37:15,060] multiqc [DEBUG ] No samples found: malt [2021-12-12 00:37:15,065] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-12 00:37:15,070] multiqc [DEBUG ] No samples found: sickle [2021-12-12 00:37:15,075] multiqc [DEBUG ] No samples found: skewer [2021-12-12 00:37:15,080] multiqc [DEBUG ] No samples found: sortmerna [2021-12-12 00:37:15,084] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-12 00:37:15,089] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-12 00:37:15,094] multiqc [DEBUG ] No samples found: afterqc [2021-12-12 00:37:15,100] multiqc [DEBUG ] No samples found: fastp [2021-12-12 00:37:34,325] multiqc.modules.fastqc.fastqc [INFO ] Found 214 reports [2021-12-12 00:37:52,819] multiqc [DEBUG ] No samples found: pycoqc [2021-12-12 00:37:52,824] multiqc [DEBUG ] No samples found: minionqc [2021-12-12 00:37:52,829] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-12 00:37:52,834] multiqc [DEBUG ] No samples found: clusterflow [2021-12-12 00:37:52,839] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-12 00:37:52,844] multiqc [DEBUG ] No samples found: interop [2021-12-12 00:37:52,849] multiqc [DEBUG ] No samples found: ivar [2021-12-12 00:37:52,854] multiqc [DEBUG ] No samples found: flash [2021-12-12 00:37:52,859] multiqc [DEBUG ] No samples found: seqyclean [2021-12-12 00:37:52,859] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-12 00:37:52,859] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-12 00:37:52,859] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-12 00:37:52,859] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-12 00:37:53,105] multiqc [INFO ] Compressing plot data [2021-12-12 00:37:53,185] multiqc [INFO ] Report : multiqc_report.html [2021-12-12 00:37:53,185] multiqc [INFO ] Data : multiqc_data [2021-12-12 00:37:53,186] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12989567/tmpx96wj613/multiqc_data' to '/scratch/gencore/logs/html/HMN33BGXK/merged/multiqc_data' [2021-12-12 00:37:53,327] multiqc [INFO ] MultiQC complete