[2022-08-25 04:57:50,229] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-08-25 04:57:50,229] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-08-25 04:57:50,229] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-08-25 04:57:50,230] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-08-25 04:57:50,230] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-08-25 04:57:50,230] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVVYVAFX3/merged [2022-08-25 04:57:50,839] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-08-25 04:57:50,839] multiqc [INFO ] This is MultiQC v1.9 [2022-08-25 04:57:50,839] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVVYVAFX3/merged [2022-08-25 04:57:50,839] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVVYVAFX3/merged [2022-08-25 04:57:50,839] multiqc [INFO ] Template : default [2022-08-25 04:57:50,839] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-08-25 04:57:50,839] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVVYVAFX3/merged [2022-08-25 04:57:50,840] 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 [2022-08-25 04:57:50,840] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24098992/tmpzwlbe2zg [2022-08-25 04:57:50,948] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-08-25 04:57:50,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-08-25 04:57:51,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_7_fastqc.html [2022-08-25 04:57:51,316] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_7_fastqc.html [2022-08-25 04:57:51,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_9_fastqc.html [2022-08-25 04:57:51,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_9_fastqc.html [2022-08-25 04:57:51,398] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_12_fastqc.html [2022-08-25 04:57:51,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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HVVYVAFX3_n02_dad4_13_fastqc.html [2022-08-25 04:57:51,582] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_undetermined_fastqc.html [2022-08-25 04:57:51,583] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_undetermined_fastqc.html [2022-08-25 04:57:51,623] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_10_fastqc.html [2022-08-25 04:57:51,625] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_10_fastqc.html [2022-08-25 04:57:51,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_5_fastqc.html [2022-08-25 04:57:51,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_5_fastqc.html [2022-08-25 04:57:51,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_9_fastqc.html [2022-08-25 04:57:51,709] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_9_fastqc.html [2022-08-25 04:57:51,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_1_fastqc.html [2022-08-25 04:57:51,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_1_fastqc.html [2022-08-25 04:57:51,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_4_fastqc.html [2022-08-25 04:57:51,791] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_4_fastqc.html [2022-08-25 04:57:51,832] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_8_fastqc.html [2022-08-25 04:57:51,834] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_8_fastqc.html [2022-08-25 04:57:51,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_2_fastqc.html [2022-08-25 04:57:51,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_2_fastqc.html [2022-08-25 04:57:51,916] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_5_fastqc.html [2022-08-25 04:57:51,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_5_fastqc.html [2022-08-25 04:57:51,957] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_3_fastqc.html [2022-08-25 04:57:51,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_3_fastqc.html [2022-08-25 04:57:51,999] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_13_fastqc.html [2022-08-25 04:57:52,001] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_13_fastqc.html [2022-08-25 04:57:52,044] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_11_fastqc.html [2022-08-25 04:57:52,046] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_11_fastqc.html [2022-08-25 04:57:52,084] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_12_fastqc.html [2022-08-25 04:57:52,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_12_fastqc.html [2022-08-25 04:57:52,134] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_11_fastqc.html [2022-08-25 04:57:52,136] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_11_fastqc.html [2022-08-25 04:57:52,176] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_4_fastqc.html [2022-08-25 04:57:52,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_4_fastqc.html [2022-08-25 04:57:52,218] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_7_fastqc.html [2022-08-25 04:57:52,220] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_7_fastqc.html [2022-08-25 04:57:52,259] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_6_fastqc.html [2022-08-25 04:57:52,261] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_6_fastqc.html [2022-08-25 04:57:52,300] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_1_fastqc.html [2022-08-25 04:57:52,302] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_1_fastqc.html [2022-08-25 04:57:52,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_3_fastqc.html [2022-08-25 04:57:52,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_3_fastqc.html [2022-08-25 04:57:52,383] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_8_fastqc.html [2022-08-25 04:57:52,385] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_8_fastqc.html [2022-08-25 04:57:52,425] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_2_fastqc.html [2022-08-25 04:57:52,427] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_2_fastqc.html [2022-08-25 04:57:52,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_6_fastqc.html [2022-08-25 04:57:52,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_6_fastqc.html [2022-08-25 04:57:52,511] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_14_fastqc.html [2022-08-25 04:57:52,513] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n02_dad4_14_fastqc.html [2022-08-25 04:57:52,557] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_10_fastqc.html [2022-08-25 04:57:52,559] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVVYVAFX3_n01_dad4_10_fastqc.html [2022-08-25 04:57:53,074] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-25 04:57:53,076] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-25 04:57:53,090] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 15 samples (table) [2022-08-25 04:57:53,100] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-08-25 04:57:53,102] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-08-25 04:57:53,107] multiqc [DEBUG ] No samples found: conpair [2022-08-25 04:57:53,112] multiqc [DEBUG ] No samples found: peddy [2022-08-25 04:57:53,118] multiqc [DEBUG ] No samples found: somalier [2022-08-25 04:57:53,124] multiqc [DEBUG ] No samples found: methylQA [2022-08-25 04:57:53,137] multiqc [DEBUG ] No samples found: mosdepth [2022-08-25 04:57:53,144] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-08-25 04:57:53,148] multiqc [DEBUG ] No samples found: qualimap [2022-08-25 04:57:53,153] multiqc [DEBUG ] No samples found: preseq [2022-08-25 04:57:53,157] multiqc [DEBUG ] No samples found: quast [2022-08-25 04:57:53,164] multiqc [DEBUG ] No samples found: qorts [2022-08-25 04:57:53,170] multiqc [DEBUG ] No samples found: rna_seqc [2022-08-25 04:57:53,175] multiqc [DEBUG ] No samples found: rockhopper [2022-08-25 04:57:53,180] multiqc [DEBUG ] No samples found: rsem [2022-08-25 04:57:53,192] multiqc [DEBUG ] No samples found: rseqc [2022-08-25 04:57:53,198] multiqc [DEBUG ] No samples found: busco [2022-08-25 04:57:53,204] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-08-25 04:57:53,210] multiqc [DEBUG ] No samples found: disambiguate [2022-08-25 04:57:53,216] multiqc [DEBUG ] No samples found: supernova [2022-08-25 04:57:53,233] multiqc [DEBUG ] No samples found: deeptools [2022-08-25 04:57:53,238] multiqc [DEBUG ] No samples found: sargasso [2022-08-25 04:57:53,243] multiqc [DEBUG ] No samples found: verifybamid [2022-08-25 04:57:53,249] multiqc [DEBUG ] No samples found: mirtrace [2022-08-25 04:57:53,256] multiqc [DEBUG ] No samples found: happy [2022-08-25 04:57:53,263] multiqc [DEBUG ] No samples found: mirtop [2022-08-25 04:57:53,272] multiqc [DEBUG ] No samples found: homer [2022-08-25 04:57:53,279] multiqc [DEBUG ] No samples found: macs2 [2022-08-25 04:57:53,284] multiqc [DEBUG ] No samples found: theta2 [2022-08-25 04:57:53,289] multiqc [DEBUG ] No samples found: snpeff [2022-08-25 04:57:53,297] multiqc [DEBUG ] No samples found: gatk [2022-08-25 04:57:53,301] multiqc [DEBUG ] No samples found: htseq [2022-08-25 04:57:53,307] multiqc [DEBUG ] No samples found: bcftools [2022-08-25 04:57:53,312] multiqc [DEBUG ] No samples found: featureCounts [2022-08-25 04:57:53,322] multiqc [DEBUG ] No samples found: fgbio [2022-08-25 04:57:53,338] multiqc [DEBUG ] No samples found: dragen [2022-08-25 04:57:53,343] multiqc [DEBUG ] No samples found: dedup [2022-08-25 04:57:53,349] multiqc [DEBUG ] No samples found: damageprofiler [2022-08-25 04:57:53,373] multiqc [DEBUG ] No samples found: biobambam2 [2022-08-25 04:57:53,381] multiqc [DEBUG ] No samples found: mtnucratio [2022-08-25 04:57:53,383] multiqc [DEBUG ] No samples found: picard [2022-08-25 04:57:53,388] multiqc [DEBUG ] No samples found: prokka [2022-08-25 04:57:53,393] multiqc [DEBUG ] No samples found: samblaster [2022-08-25 04:57:53,402] multiqc [DEBUG ] No samples found: samtools [2022-08-25 04:57:53,407] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-08-25 04:57:53,412] multiqc [DEBUG ] No samples found: bamtools [2022-08-25 04:57:53,417] multiqc [DEBUG ] No samples found: jellyfish [2022-08-25 04:57:53,424] multiqc [DEBUG ] No samples found: vcftools [2022-08-25 04:57:53,430] multiqc [DEBUG ] No samples found: longranger [2022-08-25 04:57:53,434] multiqc [DEBUG ] No samples found: stacks [2022-08-25 04:57:53,439] multiqc [DEBUG ] No samples found: varscan2 [2022-08-25 04:57:53,452] multiqc [DEBUG ] No samples found: bbmap [2022-08-25 04:57:53,457] multiqc [DEBUG ] No samples found: bismark [2022-08-25 04:57:53,464] multiqc [DEBUG ] No samples found: biscuit [2022-08-25 04:57:53,471] multiqc [DEBUG ] No samples found: hicexplorer [2022-08-25 04:57:53,477] multiqc [DEBUG ] No samples found: hicup [2022-08-25 04:57:53,484] multiqc [DEBUG ] No samples found: hicpro [2022-08-25 04:57:53,488] multiqc [DEBUG ] No samples found: salmon [2022-08-25 04:57:53,495] multiqc [DEBUG ] No samples found: kallisto [2022-08-25 04:57:53,500] multiqc [DEBUG ] No samples found: slamdunk [2022-08-25 04:57:53,505] multiqc [DEBUG ] No samples found: star [2022-08-25 04:57:53,510] multiqc [DEBUG ] No samples found: hisat2 [2022-08-25 04:57:53,518] multiqc [DEBUG ] No samples found: tophat [2022-08-25 04:57:53,525] multiqc [DEBUG ] No samples found: bowtie2 [2022-08-25 04:57:53,530] multiqc [DEBUG ] No samples found: bowtie1 [2022-08-25 04:57:53,535] multiqc [DEBUG ] No samples found: snpsplit [2022-08-25 04:57:53,541] multiqc [DEBUG ] No samples found: kat [2022-08-25 04:57:53,545] multiqc [DEBUG ] No samples found: leehom [2022-08-25 04:57:53,550] multiqc [DEBUG ] No samples found: adapterRemoval [2022-08-25 04:57:53,554] multiqc [DEBUG ] No samples found: clipandmerge [2022-08-25 04:57:53,559] multiqc [DEBUG ] No samples found: cutadapt [2022-08-25 04:57:53,563] multiqc [DEBUG ] No samples found: flexbar [2022-08-25 04:57:53,568] multiqc [DEBUG ] No samples found: kaiju [2022-08-25 04:57:53,573] multiqc [DEBUG ] No samples found: kraken [2022-08-25 04:57:53,578] multiqc [DEBUG ] No samples found: malt [2022-08-25 04:57:53,584] multiqc [DEBUG ] No samples found: trimmomatic [2022-08-25 04:57:53,588] multiqc [DEBUG ] No samples found: sickle [2022-08-25 04:57:53,593] multiqc [DEBUG ] No samples found: skewer [2022-08-25 04:57:53,598] multiqc [DEBUG ] No samples found: sortmerna [2022-08-25 04:57:53,603] multiqc [DEBUG ] No samples found: biobloomtools [2022-08-25 04:57:53,608] multiqc [DEBUG ] No samples found: fastq_screen [2022-08-25 04:57:53,612] multiqc [DEBUG ] No samples found: afterqc [2022-08-25 04:57:53,618] multiqc [DEBUG ] No samples found: fastp [2022-08-25 04:57:54,346] multiqc.modules.fastqc.fastqc [INFO ] Found 30 reports [2022-08-25 04:57:54,964] multiqc [DEBUG ] No samples found: pycoqc [2022-08-25 04:57:54,969] multiqc [DEBUG ] No samples found: minionqc [2022-08-25 04:57:54,974] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-08-25 04:57:54,979] multiqc [DEBUG ] No samples found: clusterflow [2022-08-25 04:57:54,984] multiqc [DEBUG ] No samples found: bcl2fastq [2022-08-25 04:57:54,989] multiqc [DEBUG ] No samples found: interop [2022-08-25 04:57:54,994] multiqc [DEBUG ] No samples found: ivar [2022-08-25 04:57:54,999] multiqc [DEBUG ] No samples found: flash [2022-08-25 04:57:55,005] multiqc [DEBUG ] No samples found: seqyclean [2022-08-25 04:57:55,005] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-08-25 04:57:55,005] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-08-25 04:57:55,005] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-08-25 04:57:55,005] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-08-25 04:57:55,042] multiqc [INFO ] Compressing plot data [2022-08-25 04:57:55,580] multiqc [INFO ] Report : multiqc_report.html [2022-08-25 04:57:55,580] multiqc [INFO ] Data : multiqc_data [2022-08-25 04:57:55,580] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24098992/tmpzwlbe2zg/multiqc_data' to '/scratch/gencore/logs/html/HVVYVAFX3/merged/multiqc_data' [2022-08-25 04:57:55,719] multiqc [INFO ] MultiQC complete