[2022-05-06 22:02:57,012] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-06 22:02:57,013] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-06 22:02:57,013] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-06 22:02:57,014] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-06 22:02:57,014] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-06 22:02:57,014] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3N72DRX2/merged [2022-05-06 22:02:57,455] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-06 22:02:57,455] multiqc [INFO ] This is MultiQC v1.9 [2022-05-06 22:02:57,455] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3N72DRX2/merged [2022-05-06 22:02:57,455] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3N72DRX2/merged [2022-05-06 22:02:57,455] multiqc [INFO ] Template : default [2022-05-06 22:02:57,455] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-06 22:02:57,455] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3N72DRX2/merged [2022-05-06 22:02:57,456] 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 [2022-05-06 22:02:57,456] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19169843/tmp2xm_6hve [2022-05-06 22:02:57,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_Tri025a_KD_fastqc.html [2022-05-06 22:02:57,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H3N72DRX2_n01_Hexa002a_KD_fastqc.html [2022-05-06 22:07:31,316] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n01_Hexa002a_KD_fastqc.html [2022-05-06 22:07:31,373] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n01_Tri046a_KD_fastqc.html [2022-05-06 22:07:31,375] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n01_Tri046a_KD_fastqc.html [2022-05-06 22:07:31,424] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_053c_KD_fastqc.html [2022-05-06 22:07:31,426] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n02_053c_KD_fastqc.html [2022-05-06 22:07:31,481] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H3N72DRX2_n01_Tr2_C11I1a_KD_fastqc.html [2022-05-06 22:07:31,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n01_Tr2_C11I1a_KD_fastqc.html [2022-05-06 22:07:31,721] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_124a_KD_fastqc.html [2022-05-06 22:07:31,723] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n02_124a_KD_fastqc.html [2022-05-06 22:07:31,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_Bi070c_KD_fastqc.html [2022-05-06 22:07:31,812] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n02_Bi070c_KD_fastqc.html [2022-05-06 22:07:31,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_Tr4_C6I2b_KD_fastqc.html [2022-05-06 22:07:31,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n02_Tr4_C6I2b_KD_fastqc.html [2022-05-06 22:07:31,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3N72DRX2_n02_Bi043c_KD_fastqc.html [2022-05-06 22:07:31,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3N72DRX2_n02_Bi043c_KD_fastqc.html [2022-05-06 22:07:32,533] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-06 22:07:32,535] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-06 22:07:32,621] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 2344 samples [2022-05-06 22:07:32,630] multiqc.modules.custom_content.custom_content [INFO ] demux_report_L2: Found 2344 samples (table) [2022-05-06 22:07:32,642] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 2344 samples [2022-05-06 22:07:32,651] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2344 samples (table) [2022-05-06 22:07:32,657] multiqc [DEBUG ] No samples found: conpair [2022-05-06 22:07:32,663] multiqc [DEBUG ] No samples found: peddy [2022-05-06 22:07:32,668] multiqc [DEBUG ] No samples found: somalier [2022-05-06 22:07:32,674] multiqc [DEBUG ] No samples found: methylQA [2022-05-06 22:07:32,682] multiqc [DEBUG ] No samples found: mosdepth [2022-05-06 22:07:32,687] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-06 22:07:32,691] multiqc [DEBUG ] No samples found: qualimap [2022-05-06 22:07:32,696] multiqc [DEBUG ] No samples found: preseq [2022-05-06 22:07:32,701] multiqc [DEBUG ] No samples found: quast [2022-05-06 22:07:32,706] multiqc [DEBUG ] No samples found: qorts [2022-05-06 22:07:32,711] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-06 22:07:32,715] multiqc [DEBUG ] No samples found: rockhopper [2022-05-06 22:07:32,720] multiqc [DEBUG ] No samples found: rsem [2022-05-06 22:07:32,733] multiqc [DEBUG ] No samples found: rseqc [2022-05-06 22:07:32,737] multiqc [DEBUG ] No samples found: busco [2022-05-06 22:07:32,742] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-06 22:07:32,747] multiqc [DEBUG ] No samples found: disambiguate [2022-05-06 22:07:32,752] multiqc [DEBUG ] No samples found: supernova [2022-05-06 22:07:32,766] multiqc [DEBUG ] No samples found: deeptools [2022-05-06 22:07:32,771] multiqc [DEBUG ] No samples found: sargasso [2022-05-06 22:07:32,776] multiqc [DEBUG ] No samples found: verifybamid [2022-05-06 22:07:32,781] multiqc [DEBUG ] No samples found: mirtrace [2022-05-06 22:07:32,786] multiqc [DEBUG ] No samples found: happy [2022-05-06 22:07:32,791] multiqc [DEBUG ] No samples found: mirtop [2022-05-06 22:07:32,798] multiqc [DEBUG ] No samples found: homer [2022-05-06 22:07:32,803] multiqc [DEBUG ] No samples found: macs2 [2022-05-06 22:07:32,807] multiqc [DEBUG ] No samples found: theta2 [2022-05-06 22:07:32,812] multiqc [DEBUG ] No samples found: snpeff [2022-05-06 22:07:32,820] multiqc [DEBUG ] No samples found: gatk [2022-05-06 22:07:32,825] multiqc [DEBUG ] No samples found: htseq [2022-05-06 22:07:32,830] multiqc [DEBUG ] No samples found: bcftools [2022-05-06 22:07:32,835] multiqc [DEBUG ] No samples found: featureCounts [2022-05-06 22:07:32,842] multiqc [DEBUG ] No samples found: fgbio [2022-05-06 22:07:32,856] multiqc [DEBUG ] No samples found: dragen [2022-05-06 22:07:32,861] multiqc [DEBUG ] No samples found: dedup [2022-05-06 22:07:32,866] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-06 22:07:32,890] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-06 22:07:32,895] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-06 22:07:32,898] multiqc [DEBUG ] No samples found: picard [2022-05-06 22:07:32,903] multiqc [DEBUG ] No samples found: prokka [2022-05-06 22:07:32,908] multiqc [DEBUG ] No samples found: samblaster [2022-05-06 22:07:32,917] multiqc [DEBUG ] No samples found: samtools [2022-05-06 22:07:32,922] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-06 22:07:32,927] multiqc [DEBUG ] No samples found: bamtools [2022-05-06 22:07:32,932] multiqc [DEBUG ] No samples found: jellyfish [2022-05-06 22:07:32,941] multiqc [DEBUG ] No samples found: vcftools [2022-05-06 22:07:32,946] multiqc [DEBUG ] No samples found: longranger [2022-05-06 22:07:32,951] multiqc [DEBUG ] No samples found: stacks [2022-05-06 22:07:32,956] multiqc [DEBUG ] No samples found: varscan2 [2022-05-06 22:07:32,970] multiqc [DEBUG ] No samples found: bbmap [2022-05-06 22:07:32,975] multiqc [DEBUG ] No samples found: bismark [2022-05-06 22:07:32,980] multiqc [DEBUG ] No samples found: biscuit [2022-05-06 22:07:32,985] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-06 22:07:32,990] multiqc [DEBUG ] No samples found: hicup [2022-05-06 22:07:32,995] multiqc [DEBUG ] No samples found: hicpro [2022-05-06 22:07:33,000] multiqc [DEBUG ] No samples found: salmon [2022-05-06 22:07:33,004] multiqc [DEBUG ] No samples found: kallisto [2022-05-06 22:07:33,009] multiqc [DEBUG ] No samples found: slamdunk [2022-05-06 22:07:33,014] multiqc [DEBUG ] No samples found: star [2022-05-06 22:07:33,019] multiqc [DEBUG ] No samples found: hisat2 [2022-05-06 22:07:33,024] multiqc [DEBUG ] No samples found: tophat [2022-05-06 22:07:33,029] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-06 22:07:33,034] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-06 22:07:33,039] multiqc [DEBUG ] No samples found: snpsplit [2022-05-06 22:07:33,043] multiqc [DEBUG ] No samples found: kat [2022-05-06 22:07:33,048] multiqc [DEBUG ] No samples found: leehom [2022-05-06 22:07:33,053] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-06 22:07:33,057] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-06 22:07:33,062] multiqc [DEBUG ] No samples found: cutadapt [2022-05-06 22:07:33,067] multiqc [DEBUG ] No samples found: flexbar [2022-05-06 22:07:33,072] multiqc [DEBUG ] No samples found: kaiju [2022-05-06 22:07:33,077] multiqc [DEBUG ] No samples found: kraken [2022-05-06 22:07:33,082] multiqc [DEBUG ] No samples found: malt [2022-05-06 22:07:33,087] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-06 22:07:33,092] multiqc [DEBUG ] No samples found: sickle [2022-05-06 22:07:33,096] multiqc [DEBUG ] No samples found: skewer [2022-05-06 22:07:33,101] multiqc [DEBUG ] No samples found: sortmerna [2022-05-06 22:07:33,106] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-06 22:07:33,111] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-06 22:07:33,115] multiqc [DEBUG ] No samples found: afterqc [2022-05-06 22:07:33,120] multiqc [DEBUG ] No samples found: fastp [2022-05-06 22:12:30,866] multiqc.modules.fastqc.fastqc [INFO ] Found 4688 reports [2022-05-06 22:18:09,404] multiqc [DEBUG ] No samples found: pycoqc [2022-05-06 22:18:09,409] multiqc [DEBUG ] No samples found: minionqc [2022-05-06 22:18:09,415] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-06 22:18:09,420] multiqc [DEBUG ] No samples found: clusterflow [2022-05-06 22:18:09,425] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-06 22:18:09,430] multiqc [DEBUG ] No samples found: interop [2022-05-06 22:18:09,436] multiqc [DEBUG ] No samples found: ivar [2022-05-06 22:18:09,441] multiqc [DEBUG ] No samples found: flash [2022-05-06 22:18:09,446] multiqc [DEBUG ] No samples found: seqyclean [2022-05-06 22:18:09,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report Lane 2'. [2022-05-06 22:18:09,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-06 22:18:09,446] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-06 22:18:09,480] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 4688 samples [2022-05-06 22:18:09,500] multiqc [INFO ] Compressing plot data [2022-05-06 22:18:12,226] multiqc [INFO ] Report : multiqc_report.html [2022-05-06 22:18:12,227] multiqc [INFO ] Data : multiqc_data [2022-05-06 22:18:12,227] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19169843/tmp2xm_6hve/multiqc_data' to '/scratch/gencore/logs/html/H3N72DRX2/merged/multiqc_data' [2022-05-06 22:18:12,664] multiqc [INFO ] MultiQC complete