[2021-12-15 23:26:11,120] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-15 23:26:11,121] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-15 23:26:11,121] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-15 23:26:11,121] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-15 23:26:11,122] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-15 23:26:11,122] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTWTHBGXK/merged [2021-12-15 23:26:12,562] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-15 23:26:12,562] multiqc [INFO ] This is MultiQC v1.9 [2021-12-15 23:26:12,562] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTWTHBGXK/merged [2021-12-15 23:26:12,562] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTWTHBGXK/merged [2021-12-15 23:26:12,562] multiqc [INFO ] Template : default [2021-12-15 23:26:12,562] 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 23:26:12,562] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTWTHBGXK/merged [2021-12-15 23:26:12,563] 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 23:26:12,563] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13088479/tmpk02lo94m [2021-12-15 23:26:12,664] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK56_fastqc.html [2021-12-15 23:26:12,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK56_fastqc.html [2021-12-15 23:26:12,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK69_fastqc.html [2021-12-15 23:26:12,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK69_fastqc.html [2021-12-15 23:26:12,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK63_fastqc.html [2021-12-15 23:26:12,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK63_fastqc.html [2021-12-15 23:26:12,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK70_fastqc.html [2021-12-15 23:26:12,798] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK70_fastqc.html [2021-12-15 23:26:12,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-15 23:26:12,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-15 23:26:12,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK73_fastqc.html [2021-12-15 23:26:12,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK73_fastqc.html [2021-12-15 23:26:12,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK59_fastqc.html [2021-12-15 23:26:12,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK59_fastqc.html [2021-12-15 23:26:13,038] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK61_fastqc.html [2021-12-15 23:26:13,040] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK61_fastqc.html [2021-12-15 23:26:13,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK71_fastqc.html [2021-12-15 23:26:13,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK71_fastqc.html [2021-12-15 23:26:13,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK72_fastqc.html [2021-12-15 23:26:13,125] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK72_fastqc.html [2021-12-15 23:26:13,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK55_fastqc.html [2021-12-15 23:26:13,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK55_fastqc.html [2021-12-15 23:26:13,209] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK57_fastqc.html [2021-12-15 23:26:13,211] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK57_fastqc.html [2021-12-15 23:26:13,267] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK54_fastqc.html [2021-12-15 23:26:13,269] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK54_fastqc.html [2021-12-15 23:26:13,309] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK65_fastqc.html [2021-12-15 23:26:13,311] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK65_fastqc.html [2021-12-15 23:26:13,353] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK62_fastqc.html [2021-12-15 23:26:13,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK62_fastqc.html [2021-12-15 23:26:13,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK67_fastqc.html [2021-12-15 23:26:13,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK67_fastqc.html [2021-12-15 23:26:13,439] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK58_fastqc.html [2021-12-15 23:26:13,441] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK58_fastqc.html [2021-12-15 23:26:13,482] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK60_fastqc.html [2021-12-15 23:26:13,484] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK60_fastqc.html [2021-12-15 23:26:13,526] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK66_fastqc.html [2021-12-15 23:26:13,528] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK66_fastqc.html [2021-12-15 23:26:13,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_undetermined_fastqc.html [2021-12-15 23:26:13,571] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_undetermined_fastqc.html [2021-12-15 23:26:13,613] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK64_fastqc.html [2021-12-15 23:26:13,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK64_fastqc.html [2021-12-15 23:26:13,658] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK68_fastqc.html [2021-12-15 23:26:13,660] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTWTHBGXK_n01_JK68_fastqc.html [2021-12-15 23:26:14,027] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-15 23:26:14,028] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-15 23:26:14,046] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2021-12-15 23:26:14,047] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-15 23:26:14,058] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-15 23:26:14,062] multiqc [DEBUG ] No samples found: conpair [2021-12-15 23:26:14,071] multiqc [DEBUG ] No samples found: peddy [2021-12-15 23:26:14,079] multiqc [DEBUG ] No samples found: somalier [2021-12-15 23:26:14,082] multiqc [DEBUG ] No samples found: methylQA [2021-12-15 23:26:14,090] multiqc [DEBUG ] No samples found: mosdepth [2021-12-15 23:26:14,095] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-15 23:26:14,098] multiqc [DEBUG ] No samples found: qualimap [2021-12-15 23:26:14,105] multiqc [DEBUG ] No samples found: preseq [2021-12-15 23:26:14,112] multiqc [DEBUG ] No samples found: quast [2021-12-15 23:26:14,120] multiqc [DEBUG ] No samples found: qorts [2021-12-15 23:26:14,124] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-15 23:26:14,132] multiqc [DEBUG ] No samples found: rockhopper [2021-12-15 23:26:14,141] multiqc [DEBUG ] No samples found: rsem [2021-12-15 23:26:14,157] multiqc [DEBUG ] No samples found: rseqc [2021-12-15 23:26:14,161] multiqc [DEBUG ] No samples found: busco [2021-12-15 23:26:14,165] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-15 23:26:14,172] multiqc [DEBUG ] No samples found: disambiguate [2021-12-15 23:26:14,176] multiqc [DEBUG ] No samples found: supernova [2021-12-15 23:26:14,196] multiqc [DEBUG ] No samples found: deeptools [2021-12-15 23:26:14,199] multiqc [DEBUG ] No samples found: sargasso [2021-12-15 23:26:14,203] multiqc [DEBUG ] No samples found: verifybamid [2021-12-15 23:26:14,209] multiqc [DEBUG ] No samples found: mirtrace [2021-12-15 23:26:14,216] multiqc [DEBUG ] No samples found: happy [2021-12-15 23:26:14,221] multiqc [DEBUG ] No samples found: mirtop [2021-12-15 23:26:14,232] multiqc [DEBUG ] No samples found: homer [2021-12-15 23:26:14,237] multiqc [DEBUG ] No samples found: macs2 [2021-12-15 23:26:14,243] multiqc [DEBUG ] No samples found: theta2 [2021-12-15 23:26:14,250] multiqc [DEBUG ] No samples found: snpeff [2021-12-15 23:26:14,254] multiqc [DEBUG ] No samples found: gatk [2021-12-15 23:26:14,261] multiqc [DEBUG ] No samples found: htseq [2021-12-15 23:26:14,265] multiqc [DEBUG ] No samples found: bcftools [2021-12-15 23:26:14,269] multiqc [DEBUG ] No samples found: featureCounts [2021-12-15 23:26:14,276] multiqc [DEBUG ] No samples found: fgbio [2021-12-15 23:26:14,297] multiqc [DEBUG ] No samples found: dragen [2021-12-15 23:26:14,306] multiqc [DEBUG ] No samples found: dedup [2021-12-15 23:26:14,310] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-15 23:26:14,329] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-15 23:26:14,334] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-15 23:26:14,336] multiqc [DEBUG ] No samples found: picard [2021-12-15 23:26:14,343] multiqc [DEBUG ] No samples found: prokka [2021-12-15 23:26:14,348] multiqc [DEBUG ] No samples found: samblaster [2021-12-15 23:26:14,357] multiqc [DEBUG ] No samples found: samtools [2021-12-15 23:26:14,361] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-15 23:26:14,370] multiqc [DEBUG ] No samples found: bamtools [2021-12-15 23:26:14,374] multiqc [DEBUG ] No samples found: jellyfish [2021-12-15 23:26:14,387] multiqc [DEBUG ] No samples found: vcftools [2021-12-15 23:26:14,396] multiqc [DEBUG ] No samples found: longranger [2021-12-15 23:26:14,401] multiqc [DEBUG ] No samples found: stacks [2021-12-15 23:26:14,408] multiqc [DEBUG ] No samples found: varscan2 [2021-12-15 23:26:14,422] multiqc [DEBUG ] No samples found: bbmap [2021-12-15 23:26:14,427] multiqc [DEBUG ] No samples found: bismark [2021-12-15 23:26:14,432] multiqc [DEBUG ] No samples found: biscuit [2021-12-15 23:26:14,439] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-15 23:26:14,444] multiqc [DEBUG ] No samples found: hicup [2021-12-15 23:26:14,449] multiqc [DEBUG ] No samples found: hicpro [2021-12-15 23:26:14,452] multiqc [DEBUG ] No samples found: salmon [2021-12-15 23:26:14,456] multiqc [DEBUG ] No samples found: kallisto [2021-12-15 23:26:14,462] multiqc [DEBUG ] No samples found: slamdunk [2021-12-15 23:26:14,466] multiqc [DEBUG ] No samples found: star [2021-12-15 23:26:14,473] multiqc [DEBUG ] No samples found: hisat2 [2021-12-15 23:26:14,480] multiqc [DEBUG ] No samples found: tophat [2021-12-15 23:26:14,484] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-15 23:26:14,490] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-15 23:26:14,494] multiqc [DEBUG ] No samples found: snpsplit [2021-12-15 23:26:14,497] multiqc [DEBUG ] No samples found: kat [2021-12-15 23:26:14,505] multiqc [DEBUG ] No samples found: leehom [2021-12-15 23:26:14,511] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-15 23:26:14,516] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-15 23:26:14,522] multiqc [DEBUG ] No samples found: cutadapt [2021-12-15 23:26:14,527] multiqc [DEBUG ] No samples found: flexbar [2021-12-15 23:26:14,532] multiqc [DEBUG ] No samples found: kaiju [2021-12-15 23:26:14,538] multiqc [DEBUG ] No samples found: kraken [2021-12-15 23:26:14,544] multiqc [DEBUG ] No samples found: malt [2021-12-15 23:26:14,552] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-15 23:26:14,559] multiqc [DEBUG ] No samples found: sickle [2021-12-15 23:26:14,566] multiqc [DEBUG ] No samples found: skewer [2021-12-15 23:26:14,573] multiqc [DEBUG ] No samples found: sortmerna [2021-12-15 23:26:14,580] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-15 23:26:14,585] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-15 23:26:14,592] multiqc [DEBUG ] No samples found: afterqc [2021-12-15 23:26:14,595] multiqc [DEBUG ] No samples found: fastp [2021-12-15 23:26:16,068] multiqc.modules.fastqc.fastqc [INFO ] Found 21 reports [2021-12-15 23:26:16,523] multiqc [DEBUG ] No samples found: pycoqc [2021-12-15 23:26:16,528] multiqc [DEBUG ] No samples found: minionqc [2021-12-15 23:26:16,534] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-15 23:26:16,539] multiqc [DEBUG ] No samples found: clusterflow [2021-12-15 23:26:16,546] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-15 23:26:16,550] multiqc [DEBUG ] No samples found: interop [2021-12-15 23:26:16,555] multiqc [DEBUG ] No samples found: ivar [2021-12-15 23:26:16,560] multiqc [DEBUG ] No samples found: flash [2021-12-15 23:26:16,565] multiqc [DEBUG ] No samples found: seqyclean [2021-12-15 23:26:16,565] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-15 23:26:16,565] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-15 23:26:16,565] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-15 23:26:16,566] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-15 23:26:16,590] multiqc [INFO ] Compressing plot data [2021-12-15 23:26:16,974] multiqc [INFO ] Report : multiqc_report.html [2021-12-15 23:26:16,974] multiqc [INFO ] Data : multiqc_data [2021-12-15 23:26:16,974] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13088479/tmpk02lo94m/multiqc_data' to '/scratch/gencore/logs/html/HTWTHBGXK/merged/multiqc_data' [2021-12-15 23:26:17,084] multiqc [INFO ] MultiQC complete