[2022-04-08 20:09:35,030] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-08 20:09:35,030] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-08 20:09:35,030] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-08 20:09:35,031] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-08 20:09:35,031] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-08 20:09:35,031] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLCMBGXL/merged [2022-04-08 20:09:35,508] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-08 20:09:35,508] multiqc [INFO ] This is MultiQC v1.9 [2022-04-08 20:09:35,508] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJLCMBGXL/merged [2022-04-08 20:09:35,508] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJLCMBGXL/merged [2022-04-08 20:09:35,508] multiqc [INFO ] Template : default [2022-04-08 20:09:35,508] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-08 20:09:35,508] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJLCMBGXL/merged [2022-04-08 20:09:35,509] 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 [2022-04-08 20:09:35,509] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17504679/tmppucpiswr [2022-04-08 20:09:35,611] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 20:09:35,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-04-08 20:09:35,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM332_fastqc.html [2022-04-08 20:09:35,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM332_fastqc.html [2022-04-08 20:09:35,786] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM348_fastqc.html [2022-04-08 20:09:35,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM348_fastqc.html [2022-04-08 20:09:35,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM346_fastqc.html [2022-04-08 20:09:35,828] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM346_fastqc.html [2022-04-08 20:09:35,867] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM337_fastqc.html [2022-04-08 20:09:35,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM337_fastqc.html [2022-04-08 20:09:35,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM334_fastqc.html [2022-04-08 20:09:35,912] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM334_fastqc.html [2022-04-08 20:09:35,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM352_fastqc.html [2022-04-08 20:09:35,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM352_fastqc.html [2022-04-08 20:09:35,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM339_fastqc.html [2022-04-08 20:09:35,995] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM339_fastqc.html [2022-04-08 20:09:36,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM354_fastqc.html [2022-04-08 20:09:36,036] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM354_fastqc.html [2022-04-08 20:09:36,076] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM353_fastqc.html [2022-04-08 20:09:36,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM353_fastqc.html [2022-04-08 20:09:36,116] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM335_fastqc.html [2022-04-08 20:09:36,118] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM335_fastqc.html [2022-04-08 20:09:36,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM343_fastqc.html [2022-04-08 20:09:36,159] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM343_fastqc.html [2022-04-08 20:09:36,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_undetermined_fastqc.html [2022-04-08 20:09:36,199] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_undetermined_fastqc.html [2022-04-08 20:09:36,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM351_fastqc.html [2022-04-08 20:09:36,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM351_fastqc.html [2022-04-08 20:09:36,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM341_fastqc.html [2022-04-08 20:09:36,280] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM341_fastqc.html [2022-04-08 20:09:36,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM355_fastqc.html [2022-04-08 20:09:36,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM355_fastqc.html [2022-04-08 20:09:36,361] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM342_fastqc.html [2022-04-08 20:09:36,363] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM342_fastqc.html [2022-04-08 20:09:36,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM345_fastqc.html [2022-04-08 20:09:36,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM345_fastqc.html [2022-04-08 20:09:36,443] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM333_fastqc.html [2022-04-08 20:09:36,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM333_fastqc.html [2022-04-08 20:09:36,486] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM340_fastqc.html [2022-04-08 20:09:36,488] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM340_fastqc.html [2022-04-08 20:09:36,527] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM344_fastqc.html [2022-04-08 20:09:36,529] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM344_fastqc.html [2022-04-08 20:09:36,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM350_fastqc.html [2022-04-08 20:09:36,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM350_fastqc.html [2022-04-08 20:09:36,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM349_fastqc.html [2022-04-08 20:09:36,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM349_fastqc.html [2022-04-08 20:09:36,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM336_fastqc.html [2022-04-08 20:09:36,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM336_fastqc.html [2022-04-08 20:09:36,690] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM347_fastqc.html [2022-04-08 20:09:36,692] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM347_fastqc.html [2022-04-08 20:09:36,730] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM338_fastqc.html [2022-04-08 20:09:36,732] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJLCMBGXL_n01_AKM338_fastqc.html [2022-04-08 20:09:37,069] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 20:09:37,071] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 20:09:37,078] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-08 20:09:37,091] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2022-04-08 20:09:37,100] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-08 20:09:37,105] multiqc [DEBUG ] No samples found: conpair [2022-04-08 20:09:37,110] multiqc [DEBUG ] No samples found: peddy [2022-04-08 20:09:37,114] multiqc [DEBUG ] No samples found: somalier [2022-04-08 20:09:37,119] multiqc [DEBUG ] No samples found: methylQA [2022-04-08 20:09:37,126] multiqc [DEBUG ] No samples found: mosdepth [2022-04-08 20:09:37,130] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-08 20:09:37,133] multiqc [DEBUG ] No samples found: qualimap [2022-04-08 20:09:37,138] multiqc [DEBUG ] No samples found: preseq [2022-04-08 20:09:37,142] multiqc [DEBUG ] No samples found: quast [2022-04-08 20:09:37,146] multiqc [DEBUG ] No samples found: qorts [2022-04-08 20:09:37,151] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-08 20:09:37,155] multiqc [DEBUG ] No samples found: rockhopper [2022-04-08 20:09:37,159] multiqc [DEBUG ] No samples found: rsem [2022-04-08 20:09:37,169] multiqc [DEBUG ] No samples found: rseqc [2022-04-08 20:09:37,173] multiqc [DEBUG ] No samples found: busco [2022-04-08 20:09:37,178] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-08 20:09:37,182] multiqc [DEBUG ] No samples found: disambiguate [2022-04-08 20:09:37,186] multiqc [DEBUG ] No samples found: supernova [2022-04-08 20:09:37,197] multiqc [DEBUG ] No samples found: deeptools [2022-04-08 20:09:37,202] multiqc [DEBUG ] No samples found: sargasso [2022-04-08 20:09:37,206] multiqc [DEBUG ] No samples found: verifybamid [2022-04-08 20:09:37,210] multiqc [DEBUG ] No samples found: mirtrace [2022-04-08 20:09:37,214] multiqc [DEBUG ] No samples found: happy [2022-04-08 20:09:37,219] multiqc [DEBUG ] No samples found: mirtop [2022-04-08 20:09:37,225] multiqc [DEBUG ] No samples found: homer [2022-04-08 20:09:37,229] multiqc [DEBUG ] No samples found: macs2 [2022-04-08 20:09:37,233] multiqc [DEBUG ] No samples found: theta2 [2022-04-08 20:09:37,237] multiqc [DEBUG ] No samples found: snpeff [2022-04-08 20:09:37,243] multiqc [DEBUG ] No samples found: gatk [2022-04-08 20:09:37,247] multiqc [DEBUG ] No samples found: htseq [2022-04-08 20:09:37,252] multiqc [DEBUG ] No samples found: bcftools [2022-04-08 20:09:37,257] multiqc [DEBUG ] No samples found: featureCounts [2022-04-08 20:09:37,262] multiqc [DEBUG ] No samples found: fgbio [2022-04-08 20:09:37,273] multiqc [DEBUG ] No samples found: dragen [2022-04-08 20:09:37,278] multiqc [DEBUG ] No samples found: dedup [2022-04-08 20:09:37,282] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-08 20:09:37,301] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-08 20:09:37,306] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-08 20:09:37,308] multiqc [DEBUG ] No samples found: picard [2022-04-08 20:09:37,312] multiqc [DEBUG ] No samples found: prokka [2022-04-08 20:09:37,316] multiqc [DEBUG ] No samples found: samblaster [2022-04-08 20:09:37,324] multiqc [DEBUG ] No samples found: samtools [2022-04-08 20:09:37,328] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-08 20:09:37,333] multiqc [DEBUG ] No samples found: bamtools [2022-04-08 20:09:37,337] multiqc [DEBUG ] No samples found: jellyfish [2022-04-08 20:09:37,343] multiqc [DEBUG ] No samples found: vcftools [2022-04-08 20:09:37,348] multiqc [DEBUG ] No samples found: longranger [2022-04-08 20:09:37,352] multiqc [DEBUG ] No samples found: stacks [2022-04-08 20:09:37,356] multiqc [DEBUG ] No samples found: varscan2 [2022-04-08 20:09:37,368] multiqc [DEBUG ] No samples found: bbmap [2022-04-08 20:09:37,373] multiqc [DEBUG ] No samples found: bismark [2022-04-08 20:09:37,377] multiqc [DEBUG ] No samples found: biscuit [2022-04-08 20:09:37,381] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-08 20:09:37,386] multiqc [DEBUG ] No samples found: hicup [2022-04-08 20:09:37,390] multiqc [DEBUG ] No samples found: hicpro [2022-04-08 20:09:37,394] multiqc [DEBUG ] No samples found: salmon [2022-04-08 20:09:37,398] multiqc [DEBUG ] No samples found: kallisto [2022-04-08 20:09:37,402] multiqc [DEBUG ] No samples found: slamdunk [2022-04-08 20:09:37,407] multiqc [DEBUG ] No samples found: star [2022-04-08 20:09:37,411] multiqc [DEBUG ] No samples found: hisat2 [2022-04-08 20:09:37,415] multiqc [DEBUG ] No samples found: tophat [2022-04-08 20:09:37,419] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-08 20:09:37,424] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-08 20:09:37,428] multiqc [DEBUG ] No samples found: snpsplit [2022-04-08 20:09:37,432] multiqc [DEBUG ] No samples found: kat [2022-04-08 20:09:37,436] multiqc [DEBUG ] No samples found: leehom [2022-04-08 20:09:37,440] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-08 20:09:37,444] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-08 20:09:37,448] multiqc [DEBUG ] No samples found: cutadapt [2022-04-08 20:09:37,452] multiqc [DEBUG ] No samples found: flexbar [2022-04-08 20:09:37,457] multiqc [DEBUG ] No samples found: kaiju [2022-04-08 20:09:37,461] multiqc [DEBUG ] No samples found: kraken [2022-04-08 20:09:37,465] multiqc [DEBUG ] No samples found: malt [2022-04-08 20:09:37,469] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-08 20:09:37,473] multiqc [DEBUG ] No samples found: sickle [2022-04-08 20:09:37,478] multiqc [DEBUG ] No samples found: skewer [2022-04-08 20:09:37,482] multiqc [DEBUG ] No samples found: sortmerna [2022-04-08 20:09:37,486] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-08 20:09:37,490] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-08 20:09:37,494] multiqc [DEBUG ] No samples found: afterqc [2022-04-08 20:09:37,498] multiqc [DEBUG ] No samples found: fastp [2022-04-08 20:09:39,206] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2022-04-08 20:09:39,741] multiqc [DEBUG ] No samples found: pycoqc [2022-04-08 20:09:39,745] multiqc [DEBUG ] No samples found: minionqc [2022-04-08 20:09:39,750] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-08 20:09:39,754] multiqc [DEBUG ] No samples found: clusterflow [2022-04-08 20:09:39,761] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-08 20:09:39,765] multiqc [DEBUG ] No samples found: interop [2022-04-08 20:09:39,770] multiqc [DEBUG ] No samples found: ivar [2022-04-08 20:09:39,774] multiqc [DEBUG ] No samples found: flash [2022-04-08 20:09:39,778] multiqc [DEBUG ] No samples found: seqyclean [2022-04-08 20:09:39,779] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-08 20:09:39,779] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-08 20:09:39,779] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-08 20:09:39,779] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-08 20:09:39,808] multiqc [INFO ] Compressing plot data [2022-04-08 20:09:40,277] multiqc [INFO ] Report : multiqc_report.html [2022-04-08 20:09:40,277] multiqc [INFO ] Data : multiqc_data [2022-04-08 20:09:40,278] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17504679/tmppucpiswr/multiqc_data' to '/scratch/gencore/logs/html/HJLCMBGXL/merged/multiqc_data' [2022-04-08 20:09:40,397] multiqc [INFO ] MultiQC complete