[2022-04-26 23:17:58,687] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-26 23:17:58,687] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-26 23:17:58,687] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-26 23:17:58,688] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-26 23:17:58,688] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-26 23:17:58,689] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKKG2BGXL/merged [2022-04-26 23:17:59,537] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-26 23:17:59,537] multiqc [INFO ] This is MultiQC v1.9 [2022-04-26 23:17:59,537] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKKG2BGXL/merged [2022-04-26 23:17:59,537] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKKG2BGXL/merged [2022-04-26 23:17:59,537] multiqc [INFO ] Template : default [2022-04-26 23:17:59,537] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-26 23:17:59,538] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKKG2BGXL/merged [2022-04-26 23:17:59,538] 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 [2022-04-26 23:17:59,538] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18666161/tmpg564zucg [2022-04-26 23:17:59,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO17_2_fastqc.html [2022-04-26 23:17:59,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-04-26 23:18:00,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO16_2_fastqc.html [2022-04-26 23:18:00,083] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO16_2_fastqc.html [2022-04-26 23:18:00,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO19_2_fastqc.html [2022-04-26 23:18:00,155] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO19_2_fastqc.html [2022-04-26 23:18:00,194] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK97_fastqc.html [2022-04-26 23:18:00,196] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK97_fastqc.html [2022-04-26 23:18:00,236] multiqc [DEBUG ] 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search pattern filesize limit: HKKG2BGXL_n01_JK101_fastqc.html [2022-04-26 23:18:00,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK101_fastqc.html [2022-04-26 23:18:00,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK98_fastqc.html [2022-04-26 23:18:00,407] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK98_fastqc.html [2022-04-26 23:18:00,446] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_YZ02_fastqc.html [2022-04-26 23:18:00,448] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_YZ02_fastqc.html [2022-04-26 23:18:00,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK94_fastqc.html [2022-04-26 23:18:00,490] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK94_fastqc.html [2022-04-26 23:18:00,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK100_fastqc.html [2022-04-26 23:18:00,533] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK100_fastqc.html [2022-04-26 23:18:00,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO27_fastqc.html [2022-04-26 23:18:00,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO27_fastqc.html [2022-04-26 23:18:00,615] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK99_fastqc.html [2022-04-26 23:18:00,617] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK99_fastqc.html [2022-04-26 23:18:00,656] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_YZ03_fastqc.html [2022-04-26 23:18:00,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_YZ03_fastqc.html [2022-04-26 23:18:00,698] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO25_fastqc.html [2022-04-26 23:18:00,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO25_fastqc.html [2022-04-26 23:18:00,739] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO22_fastqc.html [2022-04-26 23:18:00,741] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO22_fastqc.html [2022-04-26 23:18:00,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO20_2_fastqc.html [2022-04-26 23:18:00,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_DO20_2_fastqc.html [2022-04-26 23:18:00,821] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK95_fastqc.html [2022-04-26 23:18:00,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKG2BGXL_n01_JK95_fastqc.html [2022-04-26 23:18:01,280] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-26 23:18:01,281] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-26 23:18:01,300] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2022-04-26 23:18:01,311] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-26 23:18:01,312] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-26 23:18:01,318] multiqc [DEBUG ] No samples found: conpair [2022-04-26 23:18:01,324] multiqc [DEBUG ] No samples found: peddy [2022-04-26 23:18:01,328] multiqc [DEBUG ] No samples found: somalier [2022-04-26 23:18:01,333] multiqc [DEBUG ] No samples found: methylQA [2022-04-26 23:18:01,341] multiqc [DEBUG ] No samples found: mosdepth [2022-04-26 23:18:01,346] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-26 23:18:01,349] multiqc [DEBUG ] No samples found: qualimap [2022-04-26 23:18:01,354] multiqc [DEBUG ] No samples found: preseq [2022-04-26 23:18:01,359] multiqc [DEBUG ] No samples found: quast [2022-04-26 23:18:01,364] multiqc [DEBUG ] No samples found: qorts [2022-04-26 23:18:01,368] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-26 23:18:01,373] multiqc [DEBUG ] No samples found: rockhopper [2022-04-26 23:18:01,379] multiqc [DEBUG ] No samples found: rsem [2022-04-26 23:18:01,392] multiqc [DEBUG ] No samples found: rseqc [2022-04-26 23:18:01,396] multiqc [DEBUG ] No samples found: busco [2022-04-26 23:18:01,401] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-26 23:18:01,406] multiqc [DEBUG ] No samples found: disambiguate [2022-04-26 23:18:01,412] multiqc [DEBUG ] No samples found: supernova [2022-04-26 23:18:01,427] multiqc [DEBUG ] No samples found: deeptools [2022-04-26 23:18:01,432] multiqc [DEBUG ] No samples found: sargasso [2022-04-26 23:18:01,436] multiqc [DEBUG ] No samples found: verifybamid [2022-04-26 23:18:01,441] multiqc [DEBUG ] No samples found: mirtrace [2022-04-26 23:18:01,447] multiqc [DEBUG ] No samples found: happy [2022-04-26 23:18:01,452] multiqc [DEBUG ] No samples found: mirtop [2022-04-26 23:18:01,459] multiqc [DEBUG ] No samples found: homer [2022-04-26 23:18:01,465] multiqc [DEBUG ] No samples found: macs2 [2022-04-26 23:18:01,470] multiqc [DEBUG ] No samples found: theta2 [2022-04-26 23:18:01,475] multiqc [DEBUG ] No samples found: snpeff [2022-04-26 23:18:01,482] multiqc [DEBUG ] No samples found: gatk [2022-04-26 23:18:01,487] multiqc [DEBUG ] No samples found: htseq [2022-04-26 23:18:01,493] multiqc [DEBUG ] No samples found: bcftools [2022-04-26 23:18:01,497] multiqc [DEBUG ] No samples found: featureCounts [2022-04-26 23:18:01,505] multiqc [DEBUG ] No samples found: fgbio [2022-04-26 23:18:01,520] multiqc [DEBUG ] No samples found: dragen [2022-04-26 23:18:01,525] multiqc [DEBUG ] No samples found: dedup [2022-04-26 23:18:01,529] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-26 23:18:01,555] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-26 23:18:01,560] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-26 23:18:01,562] multiqc [DEBUG ] No samples found: picard [2022-04-26 23:18:01,568] multiqc [DEBUG ] No samples found: prokka [2022-04-26 23:18:01,574] multiqc [DEBUG ] No samples found: samblaster [2022-04-26 23:18:01,584] multiqc [DEBUG ] No samples found: samtools [2022-04-26 23:18:01,589] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-26 23:18:01,596] multiqc [DEBUG ] No samples found: bamtools [2022-04-26 23:18:01,601] multiqc [DEBUG ] No samples found: jellyfish [2022-04-26 23:18:01,611] multiqc [DEBUG ] No samples found: vcftools [2022-04-26 23:18:01,616] multiqc [DEBUG ] No samples found: longranger [2022-04-26 23:18:01,621] multiqc [DEBUG ] No samples found: stacks [2022-04-26 23:18:01,625] multiqc [DEBUG ] No samples found: varscan2 [2022-04-26 23:18:01,642] multiqc [DEBUG ] No samples found: bbmap [2022-04-26 23:18:01,647] multiqc [DEBUG ] No samples found: bismark [2022-04-26 23:18:01,652] multiqc [DEBUG ] No samples found: biscuit [2022-04-26 23:18:01,662] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-26 23:18:01,668] multiqc [DEBUG ] No samples found: hicup [2022-04-26 23:18:01,672] multiqc [DEBUG ] No samples found: hicpro [2022-04-26 23:18:01,677] multiqc [DEBUG ] No samples found: salmon [2022-04-26 23:18:01,682] multiqc [DEBUG ] No samples found: kallisto [2022-04-26 23:18:01,686] multiqc [DEBUG ] No samples found: slamdunk [2022-04-26 23:18:01,691] multiqc [DEBUG ] No samples found: star [2022-04-26 23:18:01,696] multiqc [DEBUG ] No samples found: hisat2 [2022-04-26 23:18:01,701] multiqc [DEBUG ] No samples found: tophat [2022-04-26 23:18:01,706] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-26 23:18:01,711] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-26 23:18:01,717] multiqc [DEBUG ] No samples found: snpsplit [2022-04-26 23:18:01,722] multiqc [DEBUG ] No samples found: kat [2022-04-26 23:18:01,727] multiqc [DEBUG ] No samples found: leehom [2022-04-26 23:18:01,733] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-26 23:18:01,738] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-26 23:18:01,744] multiqc [DEBUG ] No samples found: cutadapt [2022-04-26 23:18:01,749] multiqc [DEBUG ] No samples found: flexbar [2022-04-26 23:18:01,755] multiqc [DEBUG ] No samples found: kaiju [2022-04-26 23:18:01,760] multiqc [DEBUG ] No samples found: kraken [2022-04-26 23:18:01,765] multiqc [DEBUG ] No samples found: malt [2022-04-26 23:18:01,771] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-26 23:18:01,775] multiqc [DEBUG ] No samples found: sickle [2022-04-26 23:18:01,780] multiqc [DEBUG ] No samples found: skewer [2022-04-26 23:18:01,785] multiqc [DEBUG ] No samples found: sortmerna [2022-04-26 23:18:01,789] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-26 23:18:01,794] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-26 23:18:01,799] multiqc [DEBUG ] No samples found: afterqc [2022-04-26 23:18:01,804] multiqc [DEBUG ] No samples found: fastp [2022-04-26 23:18:03,604] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-04-26 23:18:04,135] multiqc [DEBUG ] No samples found: pycoqc [2022-04-26 23:18:04,140] multiqc [DEBUG ] No samples found: minionqc [2022-04-26 23:18:04,146] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-26 23:18:04,151] multiqc [DEBUG ] No samples found: clusterflow [2022-04-26 23:18:04,156] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-26 23:18:04,162] multiqc [DEBUG ] No samples found: interop [2022-04-26 23:18:04,166] multiqc [DEBUG ] No samples found: ivar [2022-04-26 23:18:04,171] multiqc [DEBUG ] No samples found: flash [2022-04-26 23:18:04,176] multiqc [DEBUG ] No samples found: seqyclean [2022-04-26 23:18:04,177] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-26 23:18:04,177] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-26 23:18:04,177] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-26 23:18:04,177] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-26 23:18:04,205] multiqc [INFO ] Compressing plot data [2022-04-26 23:18:04,651] multiqc [INFO ] Report : multiqc_report.html [2022-04-26 23:18:04,651] multiqc [INFO ] Data : multiqc_data [2022-04-26 23:18:04,651] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18666161/tmpg564zucg/multiqc_data' to '/scratch/gencore/logs/html/HKKG2BGXL/merged/multiqc_data' [2022-04-26 23:18:04,776] multiqc [INFO ] MultiQC complete