[2022-09-16 20:07:24,990] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-16 20:07:24,990] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-16 20:07:24,990] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-16 20:07:24,991] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-16 20:07:24,991] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-16 20:07:24,991] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGG2JDRX2/merged [2022-09-16 20:07:25,386] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-09-16 20:07:25,387] multiqc [INFO ] This is MultiQC v1.9 [2022-09-16 20:07:25,387] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGG2JDRX2/merged [2022-09-16 20:07:25,387] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGG2JDRX2/merged [2022-09-16 20:07:25,387] multiqc [INFO ] Template : default [2022-09-16 20:07:25,387] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-16 20:07:25,387] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGG2JDRX2/merged [2022-09-16 20:07:25,387] 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 [2022-09-16 20:07:25,387] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24996022/tmpc3lo840a [2022-09-16 20:07:25,515] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2920_fastqc.html [2022-09-16 20:07:25,518] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-09-16 20:07:31,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2938_fastqc.html [2022-09-16 20:07:31,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2938_fastqc.html [2022-09-16 20:07:31,906] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2891_fastqc.html [2022-09-16 20:07:31,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2891_fastqc.html [2022-09-16 20:07:31,950] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY1315_fastqc.html [2022-09-16 20:07:31,952] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY1315_fastqc.html [2022-09-16 20:07:31,994] multiqc 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[2022-09-16 20:07:34,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2933_fastqc.html [2022-09-16 20:07:34,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2933_fastqc.html [2022-09-16 20:07:34,097] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2900_fastqc.html [2022-09-16 20:07:34,099] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2900_fastqc.html [2022-09-16 20:07:34,160] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2943_fastqc.html [2022-09-16 20:07:34,162] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2943_fastqc.html [2022-09-16 20:07:34,209] multiqc 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[2022-09-16 20:07:35,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2936_fastqc.html [2022-09-16 20:07:35,045] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2913_fastqc.html [2022-09-16 20:07:35,047] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2913_fastqc.html [2022-09-16 20:07:35,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2843_fastqc.html [2022-09-16 20:07:35,108] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2843_fastqc.html [2022-09-16 20:07:35,161] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2910_fastqc.html [2022-09-16 20:07:35,163] multiqc 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limit: HGG2JDRX2_n01_DGY2913_fastqc.html [2022-09-16 20:07:35,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2855_fastqc.html [2022-09-16 20:07:35,786] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2855_fastqc.html [2022-09-16 20:07:35,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2854_fastqc.html [2022-09-16 20:07:35,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2854_fastqc.html [2022-09-16 20:07:35,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2917_fastqc.html [2022-09-16 20:07:35,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2917_fastqc.html [2022-09-16 20:07:35,967] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2925_fastqc.html [2022-09-16 20:07:35,969] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2925_fastqc.html [2022-09-16 20:07:36,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2836_fastqc.html [2022-09-16 20:07:36,031] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2836_fastqc.html [2022-09-16 20:07:36,092] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2908_fastqc.html [2022-09-16 20:07:36,094] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2908_fastqc.html [2022-09-16 20:07:36,149] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2856_fastqc.html [2022-09-16 20:07:36,151] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2856_fastqc.html [2022-09-16 20:07:36,209] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2886_fastqc.html [2022-09-16 20:07:36,211] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2886_fastqc.html [2022-09-16 20:07:36,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2835_fastqc.html [2022-09-16 20:07:36,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2835_fastqc.html [2022-09-16 20:07:36,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2946_fastqc.html [2022-09-16 20:07:36,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2946_fastqc.html [2022-09-16 20:07:36,384] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2881_fastqc.html [2022-09-16 20:07:36,386] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2881_fastqc.html [2022-09-16 20:07:36,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2920_fastqc.html [2022-09-16 20:07:36,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2920_fastqc.html [2022-09-16 20:07:36,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2838_fastqc.html [2022-09-16 20:07:36,488] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2838_fastqc.html [2022-09-16 20:07:36,544] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2906_fastqc.html [2022-09-16 20:07:36,546] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2906_fastqc.html [2022-09-16 20:07:36,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2900_fastqc.html [2022-09-16 20:07:36,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n02_DGY2900_fastqc.html [2022-09-16 20:07:36,646] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2935_fastqc.html [2022-09-16 20:07:36,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2935_fastqc.html [2022-09-16 20:07:36,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2888_fastqc.html [2022-09-16 20:07:36,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGG2JDRX2_n01_DGY2888_fastqc.html [2022-09-16 20:07:37,366] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-16 20:07:37,367] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-16 20:07:37,375] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-16 20:07:37,385] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-16 20:07:37,429] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 97 samples (table) [2022-09-16 20:07:37,434] multiqc [DEBUG ] No samples found: conpair [2022-09-16 20:07:37,439] multiqc [DEBUG ] No samples found: peddy [2022-09-16 20:07:37,444] multiqc [DEBUG ] No samples found: somalier [2022-09-16 20:07:37,449] multiqc [DEBUG ] No samples found: methylQA [2022-09-16 20:07:37,457] multiqc [DEBUG ] No samples found: mosdepth [2022-09-16 20:07:37,461] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-16 20:07:37,464] multiqc [DEBUG ] No samples found: qualimap [2022-09-16 20:07:37,469] multiqc [DEBUG ] No samples found: preseq [2022-09-16 20:07:37,474] multiqc [DEBUG ] No samples found: quast [2022-09-16 20:07:37,479] multiqc [DEBUG ] No samples found: qorts [2022-09-16 20:07:37,484] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-16 20:07:37,488] multiqc [DEBUG ] No samples found: rockhopper [2022-09-16 20:07:37,493] multiqc [DEBUG ] No samples found: rsem [2022-09-16 20:07:37,504] multiqc [DEBUG ] No samples found: rseqc [2022-09-16 20:07:37,508] multiqc [DEBUG ] No samples found: busco [2022-09-16 20:07:37,512] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-16 20:07:37,517] multiqc [DEBUG ] No samples found: disambiguate [2022-09-16 20:07:37,521] multiqc [DEBUG ] No samples found: supernova [2022-09-16 20:07:37,533] multiqc [DEBUG ] No samples found: deeptools [2022-09-16 20:07:37,538] multiqc [DEBUG ] No samples found: sargasso [2022-09-16 20:07:37,542] multiqc [DEBUG ] No samples found: verifybamid [2022-09-16 20:07:37,547] multiqc [DEBUG ] No samples found: mirtrace [2022-09-16 20:07:37,551] multiqc [DEBUG ] No samples found: happy [2022-09-16 20:07:37,556] multiqc [DEBUG ] No samples found: mirtop [2022-09-16 20:07:37,562] multiqc [DEBUG ] No samples found: homer [2022-09-16 20:07:37,566] multiqc [DEBUG ] No samples found: macs2 [2022-09-16 20:07:37,571] multiqc [DEBUG ] No samples found: theta2 [2022-09-16 20:07:37,576] multiqc [DEBUG ] No samples found: snpeff [2022-09-16 20:07:37,583] multiqc [DEBUG ] No samples found: gatk [2022-09-16 20:07:37,587] multiqc [DEBUG ] No samples found: htseq [2022-09-16 20:07:37,593] multiqc [DEBUG ] No samples found: bcftools [2022-09-16 20:07:37,597] multiqc [DEBUG ] No samples found: featureCounts [2022-09-16 20:07:37,603] multiqc [DEBUG ] No samples found: fgbio [2022-09-16 20:07:37,616] multiqc [DEBUG ] No samples found: dragen [2022-09-16 20:07:37,620] multiqc [DEBUG ] No samples found: dedup [2022-09-16 20:07:37,625] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-16 20:07:37,647] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-16 20:07:37,652] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-16 20:07:37,655] multiqc [DEBUG ] No samples found: picard [2022-09-16 20:07:37,659] multiqc [DEBUG ] No samples found: prokka [2022-09-16 20:07:37,663] multiqc [DEBUG ] No samples found: samblaster [2022-09-16 20:07:37,671] multiqc [DEBUG ] No samples found: samtools [2022-09-16 20:07:37,676] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-16 20:07:37,680] multiqc [DEBUG ] No samples found: bamtools [2022-09-16 20:07:37,684] multiqc [DEBUG ] No samples found: jellyfish [2022-09-16 20:07:37,691] multiqc [DEBUG ] No samples found: vcftools [2022-09-16 20:07:37,696] multiqc [DEBUG ] No samples found: longranger [2022-09-16 20:07:37,701] multiqc [DEBUG ] No samples found: stacks [2022-09-16 20:07:37,706] multiqc [DEBUG ] No samples found: varscan2 [2022-09-16 20:07:37,719] multiqc [DEBUG ] No samples found: bbmap [2022-09-16 20:07:37,724] multiqc [DEBUG ] No samples found: bismark [2022-09-16 20:07:37,729] multiqc [DEBUG ] No samples found: biscuit [2022-09-16 20:07:37,733] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-16 20:07:37,738] multiqc [DEBUG ] No samples found: hicup [2022-09-16 20:07:37,743] multiqc [DEBUG ] No samples found: hicpro [2022-09-16 20:07:37,747] multiqc [DEBUG ] No samples found: salmon [2022-09-16 20:07:37,751] multiqc [DEBUG ] No samples found: kallisto [2022-09-16 20:07:37,756] multiqc [DEBUG ] No samples found: slamdunk [2022-09-16 20:07:37,760] multiqc [DEBUG ] No samples found: star [2022-09-16 20:07:37,765] multiqc [DEBUG ] No samples found: hisat2 [2022-09-16 20:07:37,770] multiqc [DEBUG ] No samples found: tophat [2022-09-16 20:07:37,774] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-16 20:07:37,779] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-16 20:07:37,783] multiqc [DEBUG ] No samples found: snpsplit [2022-09-16 20:07:37,787] multiqc [DEBUG ] No samples found: kat [2022-09-16 20:07:37,792] multiqc [DEBUG ] No samples found: leehom [2022-09-16 20:07:37,796] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-16 20:07:37,800] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-16 20:07:37,805] multiqc [DEBUG ] No samples found: cutadapt [2022-09-16 20:07:37,809] multiqc [DEBUG ] No samples found: flexbar [2022-09-16 20:07:37,813] multiqc [DEBUG ] No samples found: kaiju [2022-09-16 20:07:37,818] multiqc [DEBUG ] No samples found: kraken [2022-09-16 20:07:37,822] multiqc [DEBUG ] No samples found: malt [2022-09-16 20:07:37,826] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-16 20:07:37,831] multiqc [DEBUG ] No samples found: sickle [2022-09-16 20:07:37,835] multiqc [DEBUG ] No samples found: skewer [2022-09-16 20:07:37,839] multiqc [DEBUG ] No samples found: sortmerna [2022-09-16 20:07:37,843] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-16 20:07:37,849] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-16 20:07:37,853] multiqc [DEBUG ] No samples found: afterqc [2022-09-16 20:07:37,857] multiqc [DEBUG ] No samples found: fastp [2022-09-16 20:07:47,561] multiqc.modules.fastqc.fastqc [INFO ] Found 194 reports [2022-09-16 20:08:08,442] multiqc [DEBUG ] No samples found: pycoqc [2022-09-16 20:08:08,446] multiqc [DEBUG ] No samples found: minionqc [2022-09-16 20:08:08,452] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-16 20:08:08,456] multiqc [DEBUG ] No samples found: clusterflow [2022-09-16 20:08:08,461] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-16 20:08:08,466] multiqc [DEBUG ] No samples found: interop [2022-09-16 20:08:08,471] multiqc [DEBUG ] No samples found: ivar [2022-09-16 20:08:08,476] multiqc [DEBUG ] No samples found: flash [2022-09-16 20:08:08,480] multiqc [DEBUG ] No samples found: seqyclean [2022-09-16 20:08:08,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-16 20:08:08,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-16 20:08:08,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-16 20:08:08,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-16 20:08:08,708] multiqc [INFO ] Compressing plot data [2022-09-16 20:08:08,773] multiqc [INFO ] Report : multiqc_report.html [2022-09-16 20:08:08,773] multiqc [INFO ] Data : multiqc_data [2022-09-16 20:08:08,773] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24996022/tmpc3lo840a/multiqc_data' to '/scratch/gencore/logs/html/HGG2JDRX2/merged/multiqc_data' [2022-09-16 20:08:08,904] multiqc [INFO ] MultiQC complete