[2022-07-14 03:51:24,751] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-14 03:51:24,752] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-14 03:51:24,752] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-14 03:51:24,753] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-14 03:51:24,753] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-14 03:51:24,753] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTC5HAFX3/merged [2022-07-14 03:51:25,343] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-14 03:51:25,343] multiqc [INFO ] This is MultiQC v1.9 [2022-07-14 03:51:25,343] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTC5HAFX3/merged [2022-07-14 03:51:25,343] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTC5HAFX3/merged [2022-07-14 03:51:25,343] multiqc [INFO ] Template : default [2022-07-14 03:51:25,343] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-14 03:51:25,344] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTC5HAFX3/merged [2022-07-14 03:51:25,344] 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 [2022-07-14 03:51:25,344] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22170348/tmpgoua89j4 [2022-07-14 03:51:25,456] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-4_fastqc.html [2022-07-14 03:51:25,459] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-4_fastqc.html [2022-07-14 03:51:25,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-5_fastqc.html [2022-07-14 03:51:25,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-5_fastqc.html [2022-07-14 03:51:25,553] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-2_fastqc.html [2022-07-14 03:51:25,555] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-2_fastqc.html [2022-07-14 03:51:25,596] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-14 03:51:25,597] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-14 03:51:25,897] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-6_fastqc.html [2022-07-14 03:51:25,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-6_fastqc.html [2022-07-14 03:51:25,940] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-10_fastqc.html [2022-07-14 03:51:25,941] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-10_fastqc.html [2022-07-14 03:51:25,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-10_fastqc.html [2022-07-14 03:51:25,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-10_fastqc.html [2022-07-14 03:51:26,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-9_fastqc.html [2022-07-14 03:51:26,029] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-9_fastqc.html [2022-07-14 03:51:26,071] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-7_fastqc.html [2022-07-14 03:51:26,073] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-7_fastqc.html [2022-07-14 03:51:26,119] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-8_fastqc.html [2022-07-14 03:51:26,121] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-8_fastqc.html [2022-07-14 03:51:26,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-1_fastqc.html [2022-07-14 03:51:26,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-1_fastqc.html [2022-07-14 03:51:26,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-7_fastqc.html [2022-07-14 03:51:26,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-7_fastqc.html [2022-07-14 03:51:26,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-6_fastqc.html [2022-07-14 03:51:26,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-6_fastqc.html [2022-07-14 03:51:26,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-3_fastqc.html [2022-07-14 03:51:26,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-3_fastqc.html [2022-07-14 03:51:26,354] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-1_fastqc.html [2022-07-14 03:51:26,356] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-1_fastqc.html [2022-07-14 03:51:26,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-9_fastqc.html [2022-07-14 03:51:26,403] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-9_fastqc.html [2022-07-14 03:51:26,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-3_fastqc.html [2022-07-14 03:51:26,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-3_fastqc.html [2022-07-14 03:51:26,497] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_undetermined_fastqc.html [2022-07-14 03:51:26,499] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_undetermined_fastqc.html [2022-07-14 03:51:26,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-5_fastqc.html [2022-07-14 03:51:26,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-5_fastqc.html [2022-07-14 03:51:26,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-11_fastqc.html [2022-07-14 03:51:26,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-11_fastqc.html [2022-07-14 03:51:26,626] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-8_fastqc.html [2022-07-14 03:51:26,628] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-8_fastqc.html [2022-07-14 03:51:26,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-4_fastqc.html [2022-07-14 03:51:26,676] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-4_fastqc.html [2022-07-14 03:51:26,723] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_undetermined_fastqc.html [2022-07-14 03:51:26,725] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_undetermined_fastqc.html [2022-07-14 03:51:26,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-2_fastqc.html [2022-07-14 03:51:26,766] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n02_as5-2_fastqc.html [2022-07-14 03:51:26,811] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-11_fastqc.html [2022-07-14 03:51:26,813] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTC5HAFX3_n01_as5-11_fastqc.html [2022-07-14 03:51:27,173] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-14 03:51:27,175] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-14 03:51:27,191] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-14 03:51:27,197] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 12 samples (table) [2022-07-14 03:51:27,198] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-14 03:51:27,203] multiqc [DEBUG ] No samples found: conpair [2022-07-14 03:51:27,208] multiqc [DEBUG ] No samples found: peddy [2022-07-14 03:51:27,214] multiqc [DEBUG ] No samples found: somalier [2022-07-14 03:51:27,219] multiqc [DEBUG ] No samples found: methylQA [2022-07-14 03:51:27,227] multiqc [DEBUG ] No samples found: mosdepth [2022-07-14 03:51:27,232] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-14 03:51:27,235] multiqc [DEBUG ] No samples found: qualimap [2022-07-14 03:51:27,240] multiqc [DEBUG ] No samples found: preseq [2022-07-14 03:51:27,245] multiqc [DEBUG ] No samples found: quast [2022-07-14 03:51:27,250] multiqc [DEBUG ] No samples found: qorts [2022-07-14 03:51:27,255] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-14 03:51:27,260] multiqc [DEBUG ] No samples found: rockhopper [2022-07-14 03:51:27,265] multiqc [DEBUG ] No samples found: rsem [2022-07-14 03:51:27,275] multiqc [DEBUG ] No samples found: rseqc [2022-07-14 03:51:27,280] multiqc [DEBUG ] No samples found: busco [2022-07-14 03:51:27,284] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-14 03:51:27,289] multiqc [DEBUG ] No samples found: disambiguate [2022-07-14 03:51:27,294] multiqc [DEBUG ] No samples found: supernova [2022-07-14 03:51:27,309] multiqc [DEBUG ] No samples found: deeptools [2022-07-14 03:51:27,315] multiqc [DEBUG ] No samples found: sargasso [2022-07-14 03:51:27,321] multiqc [DEBUG ] No samples found: verifybamid [2022-07-14 03:51:27,325] multiqc [DEBUG ] No samples found: mirtrace [2022-07-14 03:51:27,331] multiqc [DEBUG ] No samples found: happy [2022-07-14 03:51:27,336] multiqc [DEBUG ] No samples found: mirtop [2022-07-14 03:51:27,345] multiqc [DEBUG ] No samples found: homer [2022-07-14 03:51:27,349] multiqc [DEBUG ] No samples found: macs2 [2022-07-14 03:51:27,354] multiqc [DEBUG ] No samples found: theta2 [2022-07-14 03:51:27,361] multiqc [DEBUG ] No samples found: snpeff [2022-07-14 03:51:27,370] multiqc [DEBUG ] No samples found: gatk [2022-07-14 03:51:27,374] multiqc [DEBUG ] No samples found: htseq [2022-07-14 03:51:27,381] multiqc [DEBUG ] No samples found: bcftools [2022-07-14 03:51:27,387] multiqc [DEBUG ] No samples found: featureCounts [2022-07-14 03:51:27,393] multiqc [DEBUG ] No samples found: fgbio [2022-07-14 03:51:27,408] multiqc [DEBUG ] No samples found: dragen [2022-07-14 03:51:27,412] multiqc [DEBUG ] No samples found: dedup [2022-07-14 03:51:27,417] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-14 03:51:27,441] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-14 03:51:27,446] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-14 03:51:27,448] multiqc [DEBUG ] No samples found: picard [2022-07-14 03:51:27,454] multiqc [DEBUG ] No samples found: prokka [2022-07-14 03:51:27,458] multiqc [DEBUG ] No samples found: samblaster [2022-07-14 03:51:27,466] multiqc [DEBUG ] No samples found: samtools [2022-07-14 03:51:27,472] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-14 03:51:27,476] multiqc [DEBUG ] No samples found: bamtools [2022-07-14 03:51:27,481] multiqc [DEBUG ] No samples found: jellyfish [2022-07-14 03:51:27,490] multiqc [DEBUG ] No samples found: vcftools [2022-07-14 03:51:27,496] multiqc [DEBUG ] No samples found: longranger [2022-07-14 03:51:27,500] multiqc [DEBUG ] No samples found: stacks [2022-07-14 03:51:27,505] multiqc [DEBUG ] No samples found: varscan2 [2022-07-14 03:51:27,527] multiqc [DEBUG ] No samples found: bbmap [2022-07-14 03:51:27,534] multiqc [DEBUG ] No samples found: bismark [2022-07-14 03:51:27,540] multiqc [DEBUG ] No samples found: biscuit [2022-07-14 03:51:27,544] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-14 03:51:27,549] multiqc [DEBUG ] No samples found: hicup [2022-07-14 03:51:27,554] multiqc [DEBUG ] No samples found: hicpro [2022-07-14 03:51:27,559] multiqc [DEBUG ] No samples found: salmon [2022-07-14 03:51:27,564] multiqc [DEBUG ] No samples found: kallisto [2022-07-14 03:51:27,570] multiqc [DEBUG ] No samples found: slamdunk [2022-07-14 03:51:27,574] multiqc [DEBUG ] No samples found: star [2022-07-14 03:51:27,580] multiqc [DEBUG ] No samples found: hisat2 [2022-07-14 03:51:27,585] multiqc [DEBUG ] No samples found: tophat [2022-07-14 03:51:27,589] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-14 03:51:27,595] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-14 03:51:27,601] multiqc [DEBUG ] No samples found: snpsplit [2022-07-14 03:51:27,605] multiqc [DEBUG ] No samples found: kat [2022-07-14 03:51:27,610] multiqc [DEBUG ] No samples found: leehom [2022-07-14 03:51:27,615] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-14 03:51:27,619] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-14 03:51:27,624] multiqc [DEBUG ] No samples found: cutadapt [2022-07-14 03:51:27,628] multiqc [DEBUG ] No samples found: flexbar [2022-07-14 03:51:27,633] multiqc [DEBUG ] No samples found: kaiju [2022-07-14 03:51:27,637] multiqc [DEBUG ] No samples found: kraken [2022-07-14 03:51:27,644] multiqc [DEBUG ] No samples found: malt [2022-07-14 03:51:27,648] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-14 03:51:27,653] multiqc [DEBUG ] No samples found: sickle [2022-07-14 03:51:27,659] multiqc [DEBUG ] No samples found: skewer [2022-07-14 03:51:27,663] multiqc [DEBUG ] No samples found: sortmerna [2022-07-14 03:51:27,668] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-14 03:51:27,675] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-14 03:51:27,680] multiqc [DEBUG ] No samples found: afterqc [2022-07-14 03:51:27,686] multiqc [DEBUG ] No samples found: fastp [2022-07-14 03:51:28,286] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-07-14 03:51:28,802] multiqc [DEBUG ] No samples found: pycoqc [2022-07-14 03:51:28,807] multiqc [DEBUG ] No samples found: minionqc [2022-07-14 03:51:28,812] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-14 03:51:28,818] multiqc [DEBUG ] No samples found: clusterflow [2022-07-14 03:51:28,824] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-14 03:51:28,830] multiqc [DEBUG ] No samples found: interop [2022-07-14 03:51:28,835] multiqc [DEBUG ] No samples found: ivar [2022-07-14 03:51:28,841] multiqc [DEBUG ] No samples found: flash [2022-07-14 03:51:28,846] multiqc [DEBUG ] No samples found: seqyclean [2022-07-14 03:51:28,847] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-14 03:51:28,847] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-14 03:51:28,847] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-14 03:51:28,847] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-14 03:51:28,875] multiqc [INFO ] Compressing plot data [2022-07-14 03:51:29,318] multiqc [INFO ] Report : multiqc_report.html [2022-07-14 03:51:29,318] multiqc [INFO ] Data : multiqc_data [2022-07-14 03:51:29,318] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22170348/tmpgoua89j4/multiqc_data' to '/scratch/gencore/logs/html/HTC5HAFX3/merged/multiqc_data' [2022-07-14 03:51:29,442] multiqc [INFO ] MultiQC complete