[2022-03-19 12:45:53,562] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-19 12:45:53,562] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-19 12:45:53,562] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-19 12:45:53,563] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-19 12:45:53,563] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-19 12:45:53,563] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKKFHAFX3/merged [2022-03-19 12:45:54,038] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-19 12:45:54,038] multiqc [INFO ] This is MultiQC v1.9 [2022-03-19 12:45:54,039] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKKFHAFX3/merged [2022-03-19 12:45:54,039] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKKFHAFX3/merged [2022-03-19 12:45:54,039] multiqc [INFO ] Template : default [2022-03-19 12:45:54,039] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-19 12:45:54,039] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKKFHAFX3/merged [2022-03-19 12:45:54,039] 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 [2022-03-19 12:45:54,039] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16292014/tmp6ba_5yvz [2022-03-19 12:45:54,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_B5_fastqc.html [2022-03-19 12:45:54,154] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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[2022-03-19 12:45:54,846] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_DNA_11539_fastqc.html [2022-03-19 12:45:54,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_undetermined_fastqc.html [2022-03-19 12:45:54,887] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_undetermined_fastqc.html [2022-03-19 12:45:54,925] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_DNA_11536_fastqc.html [2022-03-19 12:45:54,927] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_DNA_11536_fastqc.html [2022-03-19 12:45:54,966] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_B6_fastqc.html [2022-03-19 12:45:54,968] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_B6_fastqc.html [2022-03-19 12:45:55,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_B3_fastqc.html [2022-03-19 12:45:55,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_B3_fastqc.html [2022-03-19 12:45:55,049] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V4_fastqc.html [2022-03-19 12:45:55,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V4_fastqc.html [2022-03-19 12:45:55,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11537_fastqc.html [2022-03-19 12:45:55,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11537_fastqc.html [2022-03-19 12:45:55,131] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_B6_fastqc.html [2022-03-19 12:45:55,133] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_B6_fastqc.html [2022-03-19 12:45:55,172] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_B3_fastqc.html [2022-03-19 12:45:55,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_B3_fastqc.html [2022-03-19 12:45:55,214] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11539_fastqc.html [2022-03-19 12:45:55,216] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11539_fastqc.html [2022-03-19 12:45:55,254] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V3_fastqc.html [2022-03-19 12:45:55,256] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V3_fastqc.html [2022-03-19 12:45:55,296] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V5_fastqc.html [2022-03-19 12:45:55,298] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V5_fastqc.html [2022-03-19 12:45:55,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V1_fastqc.html [2022-03-19 12:45:55,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V1_fastqc.html [2022-03-19 12:45:55,377] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11224_fastqc.html [2022-03-19 12:45:55,379] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_DNA_11224_fastqc.html [2022-03-19 12:45:55,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V2_fastqc.html [2022-03-19 12:45:55,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_V2_fastqc.html [2022-03-19 12:45:55,457] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V2_fastqc.html [2022-03-19 12:45:55,459] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V2_fastqc.html [2022-03-19 12:45:55,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n02_DNA_11224_fastqc.html [2022-03-19 12:45:55,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n02_DNA_11224_fastqc.html [2022-03-19 12:45:55,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V3_fastqc.html [2022-03-19 12:45:55,540] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_V3_fastqc.html [2022-03-19 12:45:55,579] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKKFHAFX3_n01_undetermined_fastqc.html [2022-03-19 12:45:55,581] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKKFHAFX3_n01_undetermined_fastqc.html [2022-03-19 12:45:56,135] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-19 12:45:56,137] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-19 12:45:56,151] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2022-03-19 12:45:56,153] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-19 12:45:56,163] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-19 12:45:56,168] multiqc [DEBUG ] No samples found: conpair [2022-03-19 12:45:56,173] multiqc [DEBUG ] No samples found: peddy [2022-03-19 12:45:56,178] multiqc [DEBUG ] No samples found: somalier [2022-03-19 12:45:56,182] multiqc [DEBUG ] No samples found: methylQA [2022-03-19 12:45:56,191] multiqc [DEBUG ] No samples found: mosdepth [2022-03-19 12:45:56,195] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-19 12:45:56,199] multiqc [DEBUG ] No samples found: qualimap [2022-03-19 12:45:56,204] multiqc [DEBUG ] No samples found: preseq [2022-03-19 12:45:56,209] multiqc [DEBUG ] No samples found: quast [2022-03-19 12:45:56,213] multiqc [DEBUG ] No samples found: qorts [2022-03-19 12:45:56,218] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-19 12:45:56,223] multiqc [DEBUG ] No samples found: rockhopper [2022-03-19 12:45:56,228] multiqc [DEBUG ] No samples found: rsem [2022-03-19 12:45:56,239] multiqc [DEBUG ] No samples found: rseqc [2022-03-19 12:45:56,243] multiqc [DEBUG ] No samples found: busco [2022-03-19 12:45:56,248] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-19 12:45:56,253] multiqc [DEBUG ] No samples found: disambiguate [2022-03-19 12:45:56,257] multiqc [DEBUG ] No samples found: supernova [2022-03-19 12:45:56,271] multiqc [DEBUG ] No samples found: deeptools [2022-03-19 12:45:56,276] multiqc [DEBUG ] No samples found: sargasso [2022-03-19 12:45:56,280] multiqc [DEBUG ] No samples found: verifybamid [2022-03-19 12:45:56,285] multiqc [DEBUG ] No samples found: mirtrace [2022-03-19 12:45:56,290] multiqc [DEBUG ] No samples found: happy [2022-03-19 12:45:56,295] multiqc [DEBUG ] No samples found: mirtop [2022-03-19 12:45:56,301] multiqc [DEBUG ] No samples found: homer [2022-03-19 12:45:56,306] multiqc [DEBUG ] No samples found: macs2 [2022-03-19 12:45:56,310] multiqc [DEBUG ] No samples found: theta2 [2022-03-19 12:45:56,315] multiqc [DEBUG ] No samples found: snpeff [2022-03-19 12:45:56,322] multiqc [DEBUG ] No samples found: gatk [2022-03-19 12:45:56,327] multiqc [DEBUG ] No samples found: htseq [2022-03-19 12:45:56,332] multiqc [DEBUG ] No samples found: bcftools [2022-03-19 12:45:56,337] multiqc [DEBUG ] No samples found: featureCounts [2022-03-19 12:45:56,343] multiqc [DEBUG ] No samples found: fgbio [2022-03-19 12:45:56,357] multiqc [DEBUG ] No samples found: dragen [2022-03-19 12:45:56,362] multiqc [DEBUG ] No samples found: dedup [2022-03-19 12:45:56,367] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-19 12:45:56,392] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-19 12:45:56,397] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-19 12:45:56,400] multiqc [DEBUG ] No samples found: picard [2022-03-19 12:45:56,405] multiqc [DEBUG ] No samples found: prokka [2022-03-19 12:45:56,409] multiqc [DEBUG ] No samples found: samblaster [2022-03-19 12:45:56,418] multiqc [DEBUG ] No samples found: samtools [2022-03-19 12:45:56,422] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-19 12:45:56,428] multiqc [DEBUG ] No samples found: bamtools [2022-03-19 12:45:56,432] multiqc [DEBUG ] No samples found: jellyfish [2022-03-19 12:45:56,439] multiqc [DEBUG ] No samples found: vcftools [2022-03-19 12:45:56,444] multiqc [DEBUG ] No samples found: longranger [2022-03-19 12:45:56,449] multiqc [DEBUG ] No samples found: stacks [2022-03-19 12:45:56,454] multiqc [DEBUG ] No samples found: varscan2 [2022-03-19 12:45:56,469] multiqc [DEBUG ] No samples found: bbmap [2022-03-19 12:45:56,474] multiqc [DEBUG ] No samples found: bismark [2022-03-19 12:45:56,479] multiqc [DEBUG ] No samples found: biscuit [2022-03-19 12:45:56,484] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-19 12:45:56,489] multiqc [DEBUG ] No samples found: hicup [2022-03-19 12:45:56,494] multiqc [DEBUG ] No samples found: hicpro [2022-03-19 12:45:56,498] multiqc [DEBUG ] No samples found: salmon [2022-03-19 12:45:56,503] multiqc [DEBUG ] No samples found: kallisto [2022-03-19 12:45:56,507] multiqc [DEBUG ] No samples found: slamdunk [2022-03-19 12:45:56,512] multiqc [DEBUG ] No samples found: star [2022-03-19 12:45:56,517] multiqc [DEBUG ] No samples found: hisat2 [2022-03-19 12:45:56,522] multiqc [DEBUG ] No samples found: tophat [2022-03-19 12:45:56,526] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-19 12:45:56,531] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-19 12:45:56,536] multiqc [DEBUG ] No samples found: snpsplit [2022-03-19 12:45:56,540] multiqc [DEBUG ] No samples found: kat [2022-03-19 12:45:56,544] multiqc [DEBUG ] No samples found: leehom [2022-03-19 12:45:56,549] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-19 12:45:56,554] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-19 12:45:56,558] multiqc [DEBUG ] No samples found: cutadapt [2022-03-19 12:45:56,563] multiqc [DEBUG ] No samples found: flexbar [2022-03-19 12:45:56,567] multiqc [DEBUG ] No samples found: kaiju [2022-03-19 12:45:56,572] multiqc [DEBUG ] No samples found: kraken [2022-03-19 12:45:56,577] multiqc [DEBUG ] No samples found: malt [2022-03-19 12:45:56,582] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-19 12:45:56,586] multiqc [DEBUG ] No samples found: sickle [2022-03-19 12:45:56,591] multiqc [DEBUG ] No samples found: skewer [2022-03-19 12:45:56,595] multiqc [DEBUG ] No samples found: sortmerna [2022-03-19 12:45:56,599] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-19 12:45:56,604] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-19 12:45:56,609] multiqc [DEBUG ] No samples found: afterqc [2022-03-19 12:45:56,614] multiqc [DEBUG ] No samples found: fastp [2022-03-19 12:45:57,339] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2022-03-19 12:45:57,631] multiqc [DEBUG ] No samples found: pycoqc [2022-03-19 12:45:57,636] multiqc [DEBUG ] No samples found: minionqc [2022-03-19 12:45:57,641] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-19 12:45:57,646] multiqc [DEBUG ] No samples found: clusterflow [2022-03-19 12:45:57,651] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-19 12:45:57,656] multiqc [DEBUG ] No samples found: interop [2022-03-19 12:45:57,660] multiqc [DEBUG ] No samples found: ivar [2022-03-19 12:45:57,666] multiqc [DEBUG ] No samples found: flash [2022-03-19 12:45:57,671] multiqc [DEBUG ] No samples found: seqyclean [2022-03-19 12:45:57,671] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-19 12:45:57,671] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-19 12:45:57,671] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-19 12:45:57,671] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-19 12:45:57,711] multiqc [INFO ] Compressing plot data [2022-03-19 12:45:58,262] multiqc [INFO ] Report : multiqc_report.html [2022-03-19 12:45:58,262] multiqc [INFO ] Data : multiqc_data [2022-03-19 12:45:58,262] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16292014/tmp6ba_5yvz/multiqc_data' to '/scratch/gencore/logs/html/HKKFHAFX3/merged/multiqc_data' [2022-03-19 12:45:58,393] multiqc [INFO ] MultiQC complete