[2021-03-31 20:48:27,304] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-31 20:48:27,304] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-31 20:48:27,304] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-31 20:48:27,305] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-31 20:48:27,305] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-31 20:48:27,305] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HY7FHBGXG/merged [2021-03-31 20:48:28,751] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-03-31 20:48:28,751] multiqc [INFO ] This is MultiQC v1.9 [2021-03-31 20:48:28,751] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HY7FHBGXG/merged [2021-03-31 20:48:28,751] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HY7FHBGXG/merged [2021-03-31 20:48:28,751] multiqc [INFO ] Template : default [2021-03-31 20:48:28,751] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-31 20:48:28,751] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HY7FHBGXG/merged [2021-03-31 20:48:28,751] 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 [2021-03-31 20:48:28,752] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-4477114/tmpbwhgimwn [2021-03-31 20:48:28,859] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS60mR2-noN_fastqc.html [2021-03-31 20:48:28,862] multiqc [DEBUG ] File ignored by longranger/invocation because it 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pattern filesize limit: HY7FHBGXG_n01_2021.MTS10mR2-N_fastqc.html [2021-03-31 20:48:31,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS15mR3-N_fastqc.html [2021-03-31 20:48:31,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS15mR3-N_fastqc.html [2021-03-31 20:48:31,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR3-N_fastqc.html [2021-03-31 20:48:31,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR3-N_fastqc.html [2021-03-31 20:48:31,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-shoot.plusN-45min.rep1_fastqc.html [2021-03-31 20:48:31,966] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-shoot.plusN-45min.rep1_fastqc.html [2021-03-31 20:48:32,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR2-N_fastqc.html [2021-03-31 20:48:32,032] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR2-N_fastqc.html [2021-03-31 20:48:32,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS10mR3-noN_fastqc.html [2021-03-31 20:48:32,095] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS10mR3-noN_fastqc.html [2021-03-31 20:48:32,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR1-noN_fastqc.html [2021-03-31 20:48:32,141] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR1-noN_fastqc.html [2021-03-31 20:48:32,201] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR3-N_fastqc.html [2021-03-31 20:48:32,203] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR3-N_fastqc.html [2021-03-31 20:48:32,269] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS60mR3-N_fastqc.html [2021-03-31 20:48:32,271] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS60mR3-N_fastqc.html [2021-03-31 20:48:32,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR1-N_fastqc.html [2021-03-31 20:48:32,317] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR1-N_fastqc.html [2021-03-31 20:48:32,376] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_bbr01166-root.minusN-45min.rep1_fastqc.html [2021-03-31 20:48:32,377] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_bbr01166-root.minusN-45min.rep1_fastqc.html [2021-03-31 20:48:32,422] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR3-noN_fastqc.html [2021-03-31 20:48:32,424] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS30mR3-noN_fastqc.html [2021-03-31 20:48:32,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS120mR3-noN_fastqc.html [2021-03-31 20:48:32,470] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS120mR3-noN_fastqc.html [2021-03-31 20:48:32,514] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS60mR1-N_fastqc.html [2021-03-31 20:48:32,516] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS60mR1-N_fastqc.html [2021-03-31 20:48:32,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-root.plusN-45min.rep0_fastqc.html [2021-03-31 20:48:32,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-root.plusN-45min.rep0_fastqc.html [2021-03-31 20:48:32,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR2-noN_fastqc.html [2021-03-31 20:48:32,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR2-noN_fastqc.html [2021-03-31 20:48:32,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR1-N_fastqc.html [2021-03-31 20:48:32,714] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS20mR1-N_fastqc.html [2021-03-31 20:48:32,758] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR3-noN_fastqc.html [2021-03-31 20:48:32,760] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS5mR3-noN_fastqc.html [2021-03-31 20:48:32,805] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-root.plusN-45min.rep1_fastqc.html [2021-03-31 20:48:32,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_W22-root.plusN-45min.rep1_fastqc.html [2021-03-31 20:48:32,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS90mR3-N_fastqc.html [2021-03-31 20:48:32,852] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HY7FHBGXG_n01_2021.MTS90mR3-N_fastqc.html [2021-03-31 20:48:33,435] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-31 20:48:33,437] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-31 20:48:33,454] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-31 20:48:33,486] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 71 samples (table) [2021-03-31 20:48:33,488] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-31 20:48:33,494] multiqc [DEBUG ] No samples found: conpair [2021-03-31 20:48:33,499] multiqc [DEBUG ] No samples found: peddy [2021-03-31 20:48:33,504] multiqc [DEBUG ] No samples found: somalier [2021-03-31 20:48:33,509] multiqc [DEBUG ] No samples found: methylQA [2021-03-31 20:48:33,518] multiqc [DEBUG ] No samples found: mosdepth [2021-03-31 20:48:33,523] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-31 20:48:33,526] multiqc [DEBUG ] No samples found: qualimap [2021-03-31 20:48:33,532] multiqc [DEBUG ] No samples found: preseq [2021-03-31 20:48:33,537] multiqc [DEBUG ] No samples found: quast [2021-03-31 20:48:33,542] multiqc [DEBUG ] No samples found: qorts [2021-03-31 20:48:33,548] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-31 20:48:33,553] multiqc [DEBUG ] No samples found: rockhopper [2021-03-31 20:48:33,557] multiqc [DEBUG ] No samples found: rsem [2021-03-31 20:48:33,570] multiqc [DEBUG ] No samples found: rseqc [2021-03-31 20:48:33,574] multiqc [DEBUG ] No samples found: busco [2021-03-31 20:48:33,579] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-31 20:48:33,584] multiqc [DEBUG ] No samples found: disambiguate [2021-03-31 20:48:33,589] multiqc [DEBUG ] No samples found: supernova [2021-03-31 20:48:33,604] multiqc [DEBUG ] No samples found: deeptools [2021-03-31 20:48:33,609] multiqc [DEBUG ] No samples found: sargasso [2021-03-31 20:48:33,614] multiqc [DEBUG ] No samples found: verifybamid [2021-03-31 20:48:33,623] multiqc [DEBUG ] No samples found: mirtrace [2021-03-31 20:48:33,629] multiqc [DEBUG ] No samples found: happy [2021-03-31 20:48:33,634] multiqc [DEBUG ] No samples found: mirtop [2021-03-31 20:48:33,640] multiqc [DEBUG ] No samples found: homer [2021-03-31 20:48:33,646] multiqc [DEBUG ] No samples found: macs2 [2021-03-31 20:48:33,650] multiqc [DEBUG ] No samples found: theta2 [2021-03-31 20:48:33,656] multiqc [DEBUG ] No samples found: snpeff [2021-03-31 20:48:33,664] multiqc [DEBUG ] No samples found: gatk [2021-03-31 20:48:33,669] multiqc [DEBUG ] No samples found: htseq [2021-03-31 20:48:33,675] multiqc [DEBUG ] No samples found: bcftools [2021-03-31 20:48:33,680] multiqc [DEBUG ] No samples found: featureCounts [2021-03-31 20:48:33,687] multiqc [DEBUG ] No samples found: fgbio [2021-03-31 20:48:33,703] multiqc [DEBUG ] No samples found: dragen [2021-03-31 20:48:33,708] multiqc [DEBUG ] No samples found: dedup [2021-03-31 20:48:33,712] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-31 20:48:33,737] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-31 20:48:33,740] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-31 20:48:33,743] multiqc [DEBUG ] No samples found: picard [2021-03-31 20:48:33,747] multiqc [DEBUG ] No samples found: prokka [2021-03-31 20:48:33,752] multiqc [DEBUG ] No samples found: samblaster [2021-03-31 20:48:33,763] multiqc [DEBUG ] No samples found: samtools [2021-03-31 20:48:33,769] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-31 20:48:33,776] multiqc [DEBUG ] No samples found: bamtools [2021-03-31 20:48:33,781] multiqc [DEBUG ] No samples found: jellyfish [2021-03-31 20:48:33,791] multiqc [DEBUG ] No samples found: vcftools [2021-03-31 20:48:33,796] multiqc [DEBUG ] No samples found: longranger [2021-03-31 20:48:33,802] multiqc [DEBUG ] No samples found: stacks [2021-03-31 20:48:33,808] multiqc [DEBUG ] No samples found: varscan2 [2021-03-31 20:48:33,827] multiqc [DEBUG ] No samples found: bbmap [2021-03-31 20:48:33,831] multiqc [DEBUG ] No samples found: bismark [2021-03-31 20:48:33,837] multiqc [DEBUG ] No samples found: biscuit [2021-03-31 20:48:33,841] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-31 20:48:33,846] multiqc [DEBUG ] No samples found: hicup [2021-03-31 20:48:33,851] multiqc [DEBUG ] No samples found: hicpro [2021-03-31 20:48:33,855] multiqc [DEBUG ] No samples found: salmon [2021-03-31 20:48:33,861] multiqc [DEBUG ] No samples found: kallisto [2021-03-31 20:48:33,867] multiqc [DEBUG ] No samples found: slamdunk [2021-03-31 20:48:33,871] multiqc [DEBUG ] No samples found: star [2021-03-31 20:48:33,876] multiqc [DEBUG ] No samples found: hisat2 [2021-03-31 20:48:33,881] multiqc [DEBUG ] No samples found: tophat [2021-03-31 20:48:33,886] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-31 20:48:33,890] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-31 20:48:33,895] multiqc [DEBUG ] No samples found: snpsplit [2021-03-31 20:48:33,900] multiqc [DEBUG ] No samples found: kat [2021-03-31 20:48:33,904] multiqc [DEBUG ] No samples found: leehom [2021-03-31 20:48:33,909] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-31 20:48:33,914] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-31 20:48:33,918] multiqc [DEBUG ] No samples found: cutadapt [2021-03-31 20:48:33,923] multiqc [DEBUG ] No samples found: flexbar [2021-03-31 20:48:33,927] multiqc [DEBUG ] No samples found: kaiju [2021-03-31 20:48:33,933] multiqc [DEBUG ] No samples found: kraken [2021-03-31 20:48:33,939] multiqc [DEBUG ] No samples found: malt [2021-03-31 20:48:33,943] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-31 20:48:33,947] multiqc [DEBUG ] No samples found: sickle [2021-03-31 20:48:33,953] multiqc [DEBUG ] No samples found: skewer [2021-03-31 20:48:33,959] multiqc [DEBUG ] No samples found: sortmerna [2021-03-31 20:48:33,963] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-31 20:48:33,974] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-31 20:48:33,979] multiqc [DEBUG ] No samples found: afterqc [2021-03-31 20:48:33,984] multiqc [DEBUG ] No samples found: fastp [2021-03-31 20:48:40,155] multiqc.modules.fastqc.fastqc [INFO ] Found 71 reports [2021-03-31 20:48:41,554] multiqc [DEBUG ] No samples found: pycoqc [2021-03-31 20:48:41,558] multiqc [DEBUG ] No samples found: minionqc [2021-03-31 20:48:41,562] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-31 20:48:41,567] multiqc [DEBUG ] No samples found: clusterflow [2021-03-31 20:48:41,572] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-31 20:48:41,577] multiqc [DEBUG ] No samples found: interop [2021-03-31 20:48:41,582] multiqc [DEBUG ] No samples found: ivar [2021-03-31 20:48:41,587] multiqc [DEBUG ] No samples found: flash [2021-03-31 20:48:41,592] multiqc [DEBUG ] No samples found: seqyclean [2021-03-31 20:48:41,592] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-31 20:48:41,592] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-31 20:48:41,592] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-31 20:48:41,592] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-31 20:48:41,674] multiqc [INFO ] Compressing plot data [2021-03-31 20:48:42,887] multiqc [INFO ] Report : multiqc_report.html [2021-03-31 20:48:42,887] multiqc [INFO ] Data : multiqc_data [2021-03-31 20:48:42,887] multiqc [DEBUG ] Moving data file from '/state/partition1/job-4477114/tmpbwhgimwn/multiqc_data' to '/scratch/gencore/logs/html/HY7FHBGXG/merged/multiqc_data' [2021-03-31 20:48:43,023] multiqc [INFO ] MultiQC complete