[2021-01-29 19:23:06,495] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-01-29 19:23:06,495] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-01-29 19:23:06,495] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-29 19:23:06,496] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-01-29 19:23:06,496] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-01-29 19:23:06,496] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JHLT4/1 [2021-01-29 19:23:08,002] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-01-29 19:23:08,002] multiqc [INFO ] This is MultiQC v1.9 [2021-01-29 19:23:08,002] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-JHLT4/1 [2021-01-29 19:23:08,002] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-JHLT4/1 [2021-01-29 19:23:08,002] multiqc [INFO ] Template : default [2021-01-29 19:23:08,002] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-01-29 19:23:08,002] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-JHLT4/1 [2021-01-29 19:23:08,003] 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 [2021-01-29 19:23:08,003] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1940964/tmpi9rbcz9s [2021-01-29 19:23:08,111] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1794_d10_redo_fastqc.html [2021-01-29 19:23:08,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1794_d10_redo_fastqc.html [2021-01-29 19:23:08,157] multiqc [DEBUG ] File ignored by 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000000000-JHLT4_l01_n01_1800_d10_redo_fastqc.html [2021-01-29 19:23:18,197] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1803_d06_redo_fastqc.html [2021-01-29 19:23:18,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1803_d06_redo_fastqc.html [2021-01-29 19:23:18,243] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1790_d02_redo_fastqc.html [2021-01-29 19:23:18,245] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1790_d02_redo_fastqc.html [2021-01-29 19:23:18,288] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1794_d02_redo_fastqc.html [2021-01-29 19:23:18,290] multiqc [DEBUG ] File ignored by 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000000000-JHLT4_l01_n02_1801_d08_redo_fastqc.html [2021-01-29 19:23:18,426] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1801_d08_redo_fastqc.html [2021-01-29 19:23:18,470] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1794_d04_redo_fastqc.html [2021-01-29 19:23:18,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1794_d04_redo_fastqc.html [2021-01-29 19:23:18,515] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1795_d02_redo_fastqc.html [2021-01-29 19:23:18,517] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1795_d02_redo_fastqc.html [2021-01-29 19:23:18,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1802_d06_redo_fastqc.html [2021-01-29 19:23:18,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1802_d06_redo_fastqc.html [2021-01-29 19:23:18,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_pDZ_amp_redo_fastqc.html [2021-01-29 19:23:18,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_pDZ_amp_redo_fastqc.html [2021-01-29 19:23:18,655] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1796_d04_redo_fastqc.html [2021-01-29 19:23:18,657] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1796_d04_redo_fastqc.html [2021-01-29 19:23:18,703] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1802_d06_redo_fastqc.html [2021-01-29 19:23:18,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1802_d06_redo_fastqc.html [2021-01-29 19:23:18,748] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1797_d12_redo_fastqc.html [2021-01-29 19:23:18,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1797_d12_redo_fastqc.html [2021-01-29 19:23:18,794] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1788_d12_redo_fastqc.html [2021-01-29 19:23:18,796] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1788_d12_redo_fastqc.html [2021-01-29 19:23:18,839] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1800_d12_redo_fastqc.html [2021-01-29 19:23:18,841] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1800_d12_redo_fastqc.html [2021-01-29 19:23:18,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1793_d10_redo_fastqc.html [2021-01-29 19:23:18,887] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1793_d10_redo_fastqc.html [2021-01-29 19:23:18,930] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1787_d06_redo_fastqc.html [2021-01-29 19:23:18,932] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1787_d06_redo_fastqc.html [2021-01-29 19:23:18,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1795_d12_redo_fastqc.html [2021-01-29 19:23:18,977] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1795_d12_redo_fastqc.html [2021-01-29 19:23:19,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1788_d08_redo_fastqc.html [2021-01-29 19:23:19,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n02_1788_d08_redo_fastqc.html [2021-01-29 19:23:19,065] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1793_d02_redo_fastqc.html [2021-01-29 19:23:19,067] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-JHLT4_l01_n01_1793_d02_redo_fastqc.html [2021-01-29 19:23:19,402] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-29 19:23:19,403] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-29 19:23:19,451] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 90 samples (table) [2021-01-29 19:23:19,452] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-01-29 19:23:19,462] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-01-29 19:23:19,466] multiqc [DEBUG ] No samples found: conpair [2021-01-29 19:23:19,470] multiqc [DEBUG ] No samples found: peddy [2021-01-29 19:23:19,475] multiqc [DEBUG ] No samples found: somalier [2021-01-29 19:23:19,479] multiqc [DEBUG ] No samples found: methylQA [2021-01-29 19:23:19,485] multiqc [DEBUG ] No samples found: mosdepth [2021-01-29 19:23:19,489] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-29 19:23:19,492] multiqc [DEBUG ] No samples found: qualimap [2021-01-29 19:23:19,497] multiqc [DEBUG ] No samples found: preseq [2021-01-29 19:23:19,501] multiqc [DEBUG ] No samples found: quast [2021-01-29 19:23:19,505] multiqc [DEBUG ] No samples found: qorts [2021-01-29 19:23:19,509] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-29 19:23:19,513] multiqc [DEBUG ] No samples found: rockhopper [2021-01-29 19:23:19,517] multiqc [DEBUG ] No samples found: rsem [2021-01-29 19:23:19,526] multiqc [DEBUG ] No samples found: rseqc [2021-01-29 19:23:19,530] multiqc [DEBUG ] No samples found: busco [2021-01-29 19:23:19,534] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-29 19:23:19,538] multiqc [DEBUG ] No samples found: disambiguate [2021-01-29 19:23:19,542] multiqc [DEBUG ] No samples found: supernova [2021-01-29 19:23:19,553] multiqc [DEBUG ] No samples found: deeptools [2021-01-29 19:23:19,557] multiqc [DEBUG ] No samples found: sargasso [2021-01-29 19:23:19,561] multiqc [DEBUG ] No samples found: verifybamid [2021-01-29 19:23:19,565] multiqc [DEBUG ] No samples found: mirtrace [2021-01-29 19:23:19,569] multiqc [DEBUG ] No samples found: happy [2021-01-29 19:23:19,573] multiqc [DEBUG ] No samples found: mirtop [2021-01-29 19:23:19,579] multiqc [DEBUG ] No samples found: homer [2021-01-29 19:23:19,582] multiqc [DEBUG ] No samples found: macs2 [2021-01-29 19:23:19,586] multiqc [DEBUG ] No samples found: theta2 [2021-01-29 19:23:19,590] multiqc [DEBUG ] No samples found: snpeff [2021-01-29 19:23:19,596] multiqc [DEBUG ] No samples found: gatk [2021-01-29 19:23:19,600] multiqc [DEBUG ] No samples found: htseq [2021-01-29 19:23:19,605] multiqc [DEBUG ] No samples found: bcftools [2021-01-29 19:23:19,609] multiqc [DEBUG ] No samples found: featureCounts [2021-01-29 19:23:19,614] multiqc [DEBUG ] No samples found: fgbio [2021-01-29 19:23:19,624] multiqc [DEBUG ] No samples found: dragen [2021-01-29 19:23:19,628] multiqc [DEBUG ] No samples found: dedup [2021-01-29 19:23:19,633] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-29 19:23:19,650] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-29 19:23:19,654] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-29 19:23:19,657] multiqc [DEBUG ] No samples found: picard [2021-01-29 19:23:19,661] multiqc [DEBUG ] No samples found: prokka [2021-01-29 19:23:19,664] multiqc [DEBUG ] No samples found: samblaster [2021-01-29 19:23:19,671] multiqc [DEBUG ] No samples found: samtools [2021-01-29 19:23:19,675] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-29 19:23:19,680] multiqc [DEBUG ] No samples found: bamtools [2021-01-29 19:23:19,683] multiqc [DEBUG ] No samples found: jellyfish [2021-01-29 19:23:19,689] multiqc [DEBUG ] No samples found: vcftools [2021-01-29 19:23:19,694] multiqc [DEBUG ] No samples found: longranger [2021-01-29 19:23:19,698] multiqc [DEBUG ] No samples found: stacks [2021-01-29 19:23:19,702] multiqc [DEBUG ] No samples found: varscan2 [2021-01-29 19:23:19,713] multiqc [DEBUG ] No samples found: bbmap [2021-01-29 19:23:19,717] multiqc [DEBUG ] No samples found: bismark [2021-01-29 19:23:19,722] multiqc [DEBUG ] No samples found: biscuit [2021-01-29 19:23:19,726] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-29 19:23:19,730] multiqc [DEBUG ] No samples found: hicup [2021-01-29 19:23:19,734] multiqc [DEBUG ] No samples found: hicpro [2021-01-29 19:23:19,737] multiqc [DEBUG ] No samples found: salmon [2021-01-29 19:23:19,741] multiqc [DEBUG ] No samples found: kallisto [2021-01-29 19:23:19,745] multiqc [DEBUG ] No samples found: slamdunk [2021-01-29 19:23:19,749] multiqc [DEBUG ] No samples found: star [2021-01-29 19:23:19,753] multiqc [DEBUG ] No samples found: hisat2 [2021-01-29 19:23:19,757] multiqc [DEBUG ] No samples found: tophat [2021-01-29 19:23:19,761] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-29 19:23:19,765] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-29 19:23:19,769] multiqc [DEBUG ] No samples found: snpsplit [2021-01-29 19:23:19,773] multiqc [DEBUG ] No samples found: kat [2021-01-29 19:23:19,777] multiqc [DEBUG ] No samples found: leehom [2021-01-29 19:23:19,781] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-29 19:23:19,785] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-29 19:23:19,789] multiqc [DEBUG ] No samples found: cutadapt [2021-01-29 19:23:19,793] multiqc [DEBUG ] No samples found: flexbar [2021-01-29 19:23:19,797] multiqc [DEBUG ] No samples found: kaiju [2021-01-29 19:23:19,803] multiqc [DEBUG ] No samples found: kraken [2021-01-29 19:23:19,807] multiqc [DEBUG ] No samples found: malt [2021-01-29 19:23:19,811] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-29 19:23:19,815] multiqc [DEBUG ] No samples found: sickle [2021-01-29 19:23:19,819] multiqc [DEBUG ] No samples found: skewer [2021-01-29 19:23:19,822] multiqc [DEBUG ] No samples found: sortmerna [2021-01-29 19:23:19,826] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-29 19:23:19,830] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-29 19:23:19,834] multiqc [DEBUG ] No samples found: afterqc [2021-01-29 19:23:19,838] multiqc [DEBUG ] No samples found: fastp [2021-01-29 19:23:20,853] multiqc.modules.fastqc.fastqc [INFO ] Found 180 reports [2021-01-29 19:23:41,475] multiqc [DEBUG ] No samples found: pycoqc [2021-01-29 19:23:41,480] multiqc [DEBUG ] No samples found: minionqc [2021-01-29 19:23:41,484] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-01-29 19:23:41,488] multiqc [DEBUG ] No samples found: clusterflow [2021-01-29 19:23:41,492] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-29 19:23:41,496] multiqc [DEBUG ] No samples found: interop [2021-01-29 19:23:41,501] multiqc [DEBUG ] No samples found: ivar [2021-01-29 19:23:41,505] multiqc [DEBUG ] No samples found: flash [2021-01-29 19:23:41,509] multiqc [DEBUG ] No samples found: seqyclean [2021-01-29 19:23:41,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-01-29 19:23:41,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-01-29 19:23:41,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-01-29 19:23:41,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-01-29 19:23:41,509] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-01-29 19:23:41,715] multiqc [INFO ] Compressing plot data [2021-01-29 19:23:41,781] multiqc [INFO ] Report : multiqc_report.html [2021-01-29 19:23:41,781] multiqc [INFO ] Data : multiqc_data [2021-01-29 19:23:41,781] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1940964/tmpi9rbcz9s/multiqc_data' to '/scratch/gencore/logs/html/000000000-JHLT4/1/multiqc_data' [2021-01-29 19:23:41,906] multiqc [INFO ] MultiQC complete