[2021-12-15 16:48:43,601] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-15 16:48:43,601] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-15 16:48:43,601] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-15 16:48:43,602] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-15 16:48:43,602] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-15 16:48:43,602] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5MVLDMXY/merged [2021-12-15 16:48:44,963] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-15 16:48:44,963] multiqc [INFO ] This is MultiQC v1.9 [2021-12-15 16:48:44,963] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5MVLDMXY/merged [2021-12-15 16:48:44,963] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5MVLDMXY/merged [2021-12-15 16:48:44,963] multiqc [INFO ] Template : default [2021-12-15 16:48:44,963] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-15 16:48:44,963] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5MVLDMXY/merged [2021-12-15 16:48:44,963] 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 [2021-12-15 16:48:44,963] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13055183/tmp_5r69icw [2021-12-15 16:48:45,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_sidu032_3_fastqc.html [2021-12-15 16:48:45,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H5MVLDMXY_n02_NR0057.1_fastqc.html [2021-12-15 16:48:45,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0067_fastqc.html [2021-12-15 16:48:45,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0067_fastqc.html [2021-12-15 16:48:45,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0069_fastqc.html [2021-12-15 16:48:45,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0069_fastqc.html [2021-12-15 16:48:45,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0154_fastqc.html [2021-12-15 16:48:45,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0154_fastqc.html [2021-12-15 16:48:45,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0057_fastqc.html [2021-12-15 16:48:45,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0057_fastqc.html [2021-12-15 16:48:46,004] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_sidu036_1_fastqc.html [2021-12-15 16:48:46,006] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_sidu036_1_fastqc.html [2021-12-15 16:48:46,066] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_undetermined_fastqc.html [2021-12-15 16:48:46,068] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_undetermined_fastqc.html [2021-12-15 16:48:46,121] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0061_fastqc.html [2021-12-15 16:48:46,122] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0061_fastqc.html [2021-12-15 16:48:46,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0072_fastqc.html [2021-12-15 16:48:46,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0072_fastqc.html [2021-12-15 16:48:46,249] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_undetermined_fastqc.html [2021-12-15 16:48:46,251] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_undetermined_fastqc.html [2021-12-15 16:48:46,312] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0154.1_fastqc.html [2021-12-15 16:48:46,314] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0154.1_fastqc.html [2021-12-15 16:48:46,378] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_sidu001_4_fastqc.html [2021-12-15 16:48:46,380] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_sidu001_4_fastqc.html [2021-12-15 16:48:46,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_BG0067_fastqc.html [2021-12-15 16:48:46,450] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_BG0067_fastqc.html [2021-12-15 16:48:46,507] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0057_fastqc.html [2021-12-15 16:48:46,509] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0057_fastqc.html [2021-12-15 16:48:46,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_RN0069_fastqc.html [2021-12-15 16:48:46,570] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_RN0069_fastqc.html [2021-12-15 16:48:46,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0057.1_fastqc.html [2021-12-15 16:48:46,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0057.1_fastqc.html [2021-12-15 16:48:46,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0063_fastqc.html [2021-12-15 16:48:46,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0063_fastqc.html [2021-12-15 16:48:46,738] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_mook198_2_fastqc.html [2021-12-15 16:48:46,740] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_mook198_2_fastqc.html [2021-12-15 16:48:46,822] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0154_fastqc.html [2021-12-15 16:48:46,824] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_NR0154_fastqc.html [2021-12-15 16:48:46,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_BG0063_fastqc.html [2021-12-15 16:48:46,890] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_BG0063_fastqc.html [2021-12-15 16:48:46,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0062_fastqc.html [2021-12-15 16:48:46,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_BG0062_fastqc.html [2021-12-15 16:48:47,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0068_fastqc.html [2021-12-15 16:48:47,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_RN0068_fastqc.html [2021-12-15 16:48:47,086] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_mook198_2_fastqc.html [2021-12-15 16:48:47,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_mook198_2_fastqc.html [2021-12-15 16:48:47,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n01_Pf3D7_fastqc.html [2021-12-15 16:48:47,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n01_Pf3D7_fastqc.html [2021-12-15 16:48:47,215] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0154.1_fastqc.html [2021-12-15 16:48:47,217] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5MVLDMXY_n02_NR0154.1_fastqc.html [2021-12-15 16:48:47,701] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-15 16:48:47,702] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-15 16:48:47,718] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2021-12-15 16:48:47,727] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-15 16:48:47,729] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-15 16:48:47,734] multiqc [DEBUG ] No samples found: conpair [2021-12-15 16:48:47,739] multiqc [DEBUG ] No samples found: peddy [2021-12-15 16:48:47,744] multiqc [DEBUG ] No samples found: somalier [2021-12-15 16:48:47,748] multiqc [DEBUG ] No samples found: methylQA [2021-12-15 16:48:47,755] multiqc [DEBUG ] No samples found: mosdepth [2021-12-15 16:48:47,758] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-15 16:48:47,762] multiqc [DEBUG ] No samples found: qualimap [2021-12-15 16:48:47,765] multiqc [DEBUG ] No samples found: preseq [2021-12-15 16:48:47,770] multiqc [DEBUG ] No samples found: quast [2021-12-15 16:48:47,775] multiqc [DEBUG ] No samples found: qorts [2021-12-15 16:48:47,780] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-15 16:48:47,784] multiqc [DEBUG ] No samples found: rockhopper [2021-12-15 16:48:47,789] multiqc [DEBUG ] No samples found: rsem [2021-12-15 16:48:47,798] multiqc [DEBUG ] No samples found: rseqc [2021-12-15 16:48:47,802] multiqc [DEBUG ] No samples found: busco [2021-12-15 16:48:47,808] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-15 16:48:47,812] multiqc [DEBUG ] No samples found: disambiguate [2021-12-15 16:48:47,816] multiqc [DEBUG ] No samples found: supernova [2021-12-15 16:48:47,828] multiqc [DEBUG ] No samples found: deeptools [2021-12-15 16:48:47,833] multiqc [DEBUG ] No samples found: sargasso [2021-12-15 16:48:47,837] multiqc [DEBUG ] No samples found: verifybamid [2021-12-15 16:48:47,842] multiqc [DEBUG ] No samples found: mirtrace [2021-12-15 16:48:47,846] multiqc [DEBUG ] No samples found: happy [2021-12-15 16:48:47,851] multiqc [DEBUG ] No samples found: mirtop [2021-12-15 16:48:47,857] multiqc [DEBUG ] No samples found: homer [2021-12-15 16:48:47,862] multiqc [DEBUG ] No samples found: macs2 [2021-12-15 16:48:47,866] multiqc [DEBUG ] No samples found: theta2 [2021-12-15 16:48:47,871] multiqc [DEBUG ] No samples found: snpeff [2021-12-15 16:48:47,877] multiqc [DEBUG ] No samples found: gatk [2021-12-15 16:48:47,881] multiqc [DEBUG ] No samples found: htseq [2021-12-15 16:48:47,886] multiqc [DEBUG ] No samples found: bcftools [2021-12-15 16:48:47,890] multiqc [DEBUG ] No samples found: featureCounts [2021-12-15 16:48:47,895] multiqc [DEBUG ] No samples found: fgbio [2021-12-15 16:48:47,906] multiqc [DEBUG ] No samples found: dragen [2021-12-15 16:48:47,910] multiqc [DEBUG ] No samples found: dedup [2021-12-15 16:48:47,914] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-15 16:48:47,932] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-15 16:48:47,937] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-15 16:48:47,939] multiqc [DEBUG ] No samples found: picard [2021-12-15 16:48:47,944] multiqc [DEBUG ] No samples found: prokka [2021-12-15 16:48:47,948] multiqc [DEBUG ] No samples found: samblaster [2021-12-15 16:48:47,955] multiqc [DEBUG ] No samples found: samtools [2021-12-15 16:48:47,959] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-15 16:48:47,965] multiqc [DEBUG ] No samples found: bamtools [2021-12-15 16:48:47,969] multiqc [DEBUG ] No samples found: jellyfish [2021-12-15 16:48:47,980] multiqc [DEBUG ] No samples found: vcftools [2021-12-15 16:48:47,984] multiqc [DEBUG ] No samples found: longranger [2021-12-15 16:48:47,988] multiqc [DEBUG ] No samples found: stacks [2021-12-15 16:48:47,991] multiqc [DEBUG ] No samples found: varscan2 [2021-12-15 16:48:48,009] multiqc [DEBUG ] No samples found: bbmap [2021-12-15 16:48:48,013] multiqc [DEBUG ] No samples found: bismark [2021-12-15 16:48:48,018] multiqc [DEBUG ] No samples found: biscuit [2021-12-15 16:48:48,022] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-15 16:48:48,027] multiqc [DEBUG ] No samples found: hicup [2021-12-15 16:48:48,033] multiqc [DEBUG ] No samples found: hicpro [2021-12-15 16:48:48,038] multiqc [DEBUG ] No samples found: salmon [2021-12-15 16:48:48,042] multiqc [DEBUG ] No samples found: kallisto [2021-12-15 16:48:48,046] multiqc [DEBUG ] No samples found: slamdunk [2021-12-15 16:48:48,050] multiqc [DEBUG ] No samples found: star [2021-12-15 16:48:48,054] multiqc [DEBUG ] No samples found: hisat2 [2021-12-15 16:48:48,058] multiqc [DEBUG ] No samples found: tophat [2021-12-15 16:48:48,064] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-15 16:48:48,068] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-15 16:48:48,073] multiqc [DEBUG ] No samples found: snpsplit [2021-12-15 16:48:48,077] multiqc [DEBUG ] No samples found: kat [2021-12-15 16:48:48,081] multiqc [DEBUG ] No samples found: leehom [2021-12-15 16:48:48,085] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-15 16:48:48,089] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-15 16:48:48,093] multiqc [DEBUG ] No samples found: cutadapt [2021-12-15 16:48:48,098] multiqc [DEBUG ] No samples found: flexbar [2021-12-15 16:48:48,102] multiqc [DEBUG ] No samples found: kaiju [2021-12-15 16:48:48,106] multiqc [DEBUG ] No samples found: kraken [2021-12-15 16:48:48,111] multiqc [DEBUG ] No samples found: malt [2021-12-15 16:48:48,115] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-15 16:48:48,120] multiqc [DEBUG ] No samples found: sickle [2021-12-15 16:48:48,124] multiqc [DEBUG ] No samples found: skewer [2021-12-15 16:48:48,128] multiqc [DEBUG ] No samples found: sortmerna [2021-12-15 16:48:48,132] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-15 16:48:48,136] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-15 16:48:48,140] multiqc [DEBUG ] No samples found: afterqc [2021-12-15 16:48:48,144] multiqc [DEBUG ] No samples found: fastp [2021-12-15 16:48:54,220] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2021-12-15 16:48:54,705] multiqc [DEBUG ] No samples found: pycoqc [2021-12-15 16:48:54,710] multiqc [DEBUG ] No samples found: minionqc [2021-12-15 16:48:54,716] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-15 16:48:54,721] multiqc [DEBUG ] No samples found: clusterflow [2021-12-15 16:48:54,727] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-15 16:48:54,732] multiqc [DEBUG ] No samples found: interop [2021-12-15 16:48:54,736] multiqc [DEBUG ] No samples found: ivar [2021-12-15 16:48:54,741] multiqc [DEBUG ] No samples found: flash [2021-12-15 16:48:54,745] multiqc [DEBUG ] No samples found: seqyclean [2021-12-15 16:48:54,745] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-15 16:48:54,745] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-15 16:48:54,745] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-15 16:48:54,745] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-15 16:48:54,785] multiqc [INFO ] Compressing plot data [2021-12-15 16:48:55,442] multiqc [INFO ] Report : multiqc_report.html [2021-12-15 16:48:55,442] multiqc [INFO ] Data : multiqc_data [2021-12-15 16:48:55,442] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13055183/tmp_5r69icw/multiqc_data' to '/scratch/gencore/logs/html/H5MVLDMXY/merged/multiqc_data' [2021-12-15 16:48:55,553] multiqc [INFO ] MultiQC complete