[2021-12-21 03:39:58,149] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-21 03:39:58,149] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-21 03:39:58,149] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-21 03:39:58,150] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-21 03:39:58,150] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-21 03:39:58,150] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGL5JAFX3/merged [2021-12-21 03:39:58,549] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-21 03:39:58,549] multiqc [INFO ] This is MultiQC v1.9 [2021-12-21 03:39:58,549] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGL5JAFX3/merged [2021-12-21 03:39:58,549] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGL5JAFX3/merged [2021-12-21 03:39:58,549] multiqc [INFO ] Template : default [2021-12-21 03:39:58,549] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-21 03:39:58,549] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGL5JAFX3/merged [2021-12-21 03:39:58,550] 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 [2021-12-21 03:39:58,550] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13227763/tmpcxa5ou4y [2021-12-21 03:39:58,649] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-4_fastqc.html [2021-12-21 03:39:58,652] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-12-21 03:39:59,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-13_fastqc.html [2021-12-21 03:39:59,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-13_fastqc.html [2021-12-21 03:39:59,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-10_fastqc.html [2021-12-21 03:39:59,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-10_fastqc.html [2021-12-21 03:39:59,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-11_fastqc.html [2021-12-21 03:39:59,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-11_fastqc.html [2021-12-21 03:39:59,410] multiqc [DEBUG 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HGL5JAFX3_n02_as1-6_fastqc.html [2021-12-21 03:39:59,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-6_fastqc.html [2021-12-21 03:39:59,734] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-15_fastqc.html [2021-12-21 03:39:59,736] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-15_fastqc.html [2021-12-21 03:39:59,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-18_fastqc.html [2021-12-21 03:39:59,783] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-18_fastqc.html [2021-12-21 03:39:59,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_undetermined_fastqc.html [2021-12-21 03:39:59,828] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_undetermined_fastqc.html [2021-12-21 03:39:59,870] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-13_fastqc.html [2021-12-21 03:39:59,872] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-13_fastqc.html [2021-12-21 03:39:59,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-2_fastqc.html [2021-12-21 03:39:59,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-2_fastqc.html [2021-12-21 03:39:59,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-8_fastqc.html [2021-12-21 03:39:59,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-8_fastqc.html [2021-12-21 03:40:00,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-16_fastqc.html [2021-12-21 03:40:00,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-16_fastqc.html [2021-12-21 03:40:00,055] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-11_fastqc.html [2021-12-21 03:40:00,057] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-11_fastqc.html [2021-12-21 03:40:00,101] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-14_fastqc.html [2021-12-21 03:40:00,103] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-14_fastqc.html [2021-12-21 03:40:00,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-5_fastqc.html [2021-12-21 03:40:00,147] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-5_fastqc.html [2021-12-21 03:40:00,191] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-3_fastqc.html [2021-12-21 03:40:00,193] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-3_fastqc.html [2021-12-21 03:40:00,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-15_fastqc.html [2021-12-21 03:40:00,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-15_fastqc.html [2021-12-21 03:40:00,283] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-5_fastqc.html [2021-12-21 03:40:00,285] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-5_fastqc.html [2021-12-21 03:40:00,329] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-17_fastqc.html [2021-12-21 03:40:00,331] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-17_fastqc.html [2021-12-21 03:40:00,375] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-2_fastqc.html [2021-12-21 03:40:00,377] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-2_fastqc.html [2021-12-21 03:40:00,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_undetermined_fastqc.html [2021-12-21 03:40:00,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_undetermined_fastqc.html [2021-12-21 03:40:00,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-3_fastqc.html [2021-12-21 03:40:00,464] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-3_fastqc.html [2021-12-21 03:40:00,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-10_fastqc.html [2021-12-21 03:40:00,511] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-10_fastqc.html [2021-12-21 03:40:00,554] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-9_fastqc.html [2021-12-21 03:40:00,556] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-9_fastqc.html [2021-12-21 03:40:00,602] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-6_fastqc.html [2021-12-21 03:40:00,604] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n01_as1-6_fastqc.html [2021-12-21 03:40:00,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-7_fastqc.html [2021-12-21 03:40:00,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-7_fastqc.html [2021-12-21 03:40:00,693] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-1_fastqc.html [2021-12-21 03:40:00,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGL5JAFX3_n02_as1-1_fastqc.html [2021-12-21 03:40:01,015] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 03:40:01,016] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 03:40:01,023] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-21 03:40:01,033] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2021-12-21 03:40:01,042] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-21 03:40:01,046] multiqc [DEBUG ] No samples found: conpair [2021-12-21 03:40:01,052] multiqc [DEBUG ] No samples found: peddy [2021-12-21 03:40:01,057] multiqc [DEBUG ] No samples found: somalier [2021-12-21 03:40:01,061] multiqc [DEBUG ] No samples found: methylQA [2021-12-21 03:40:01,069] multiqc [DEBUG ] No samples found: mosdepth [2021-12-21 03:40:01,073] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-21 03:40:01,076] multiqc [DEBUG ] No samples found: qualimap [2021-12-21 03:40:01,082] multiqc [DEBUG ] No samples found: preseq [2021-12-21 03:40:01,087] multiqc [DEBUG ] No samples found: quast [2021-12-21 03:40:01,091] multiqc [DEBUG ] No samples found: qorts [2021-12-21 03:40:01,095] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-21 03:40:01,099] multiqc [DEBUG ] No samples found: rockhopper [2021-12-21 03:40:01,103] multiqc [DEBUG ] No samples found: rsem [2021-12-21 03:40:01,117] multiqc [DEBUG ] No samples found: rseqc [2021-12-21 03:40:01,122] multiqc [DEBUG ] No samples found: busco [2021-12-21 03:40:01,126] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-21 03:40:01,130] multiqc [DEBUG ] No samples found: disambiguate [2021-12-21 03:40:01,135] multiqc [DEBUG ] No samples found: supernova [2021-12-21 03:40:01,144] multiqc [DEBUG ] No samples found: deeptools [2021-12-21 03:40:01,148] multiqc [DEBUG ] No samples found: sargasso [2021-12-21 03:40:01,153] multiqc [DEBUG ] No samples found: verifybamid [2021-12-21 03:40:01,157] multiqc [DEBUG ] No samples found: mirtrace [2021-12-21 03:40:01,162] multiqc [DEBUG ] No samples found: happy [2021-12-21 03:40:01,166] multiqc [DEBUG ] No samples found: mirtop [2021-12-21 03:40:01,171] multiqc [DEBUG ] No samples found: homer [2021-12-21 03:40:01,174] multiqc [DEBUG ] No samples found: macs2 [2021-12-21 03:40:01,180] multiqc [DEBUG ] No samples found: theta2 [2021-12-21 03:40:01,184] multiqc [DEBUG ] No samples found: snpeff [2021-12-21 03:40:01,190] multiqc [DEBUG ] No samples found: gatk [2021-12-21 03:40:01,194] multiqc [DEBUG ] No samples found: htseq [2021-12-21 03:40:01,199] multiqc [DEBUG ] No samples found: bcftools [2021-12-21 03:40:01,207] multiqc [DEBUG ] No samples found: featureCounts [2021-12-21 03:40:01,212] multiqc [DEBUG ] No samples found: fgbio [2021-12-21 03:40:01,222] multiqc [DEBUG ] No samples found: dragen [2021-12-21 03:40:01,227] multiqc [DEBUG ] No samples found: dedup [2021-12-21 03:40:01,232] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-21 03:40:01,261] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-21 03:40:01,265] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-21 03:40:01,267] multiqc [DEBUG ] No samples found: picard [2021-12-21 03:40:01,272] multiqc [DEBUG ] No samples found: prokka [2021-12-21 03:40:01,278] multiqc [DEBUG ] No samples found: samblaster [2021-12-21 03:40:01,285] multiqc [DEBUG ] No samples found: samtools [2021-12-21 03:40:01,289] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-21 03:40:01,293] multiqc [DEBUG ] No samples found: bamtools [2021-12-21 03:40:01,297] multiqc [DEBUG ] No samples found: jellyfish [2021-12-21 03:40:01,303] multiqc [DEBUG ] No samples found: vcftools [2021-12-21 03:40:01,307] multiqc [DEBUG ] No samples found: longranger [2021-12-21 03:40:01,312] multiqc [DEBUG ] No samples found: stacks [2021-12-21 03:40:01,316] multiqc [DEBUG ] No samples found: varscan2 [2021-12-21 03:40:01,327] multiqc [DEBUG ] No samples found: bbmap [2021-12-21 03:40:01,331] multiqc [DEBUG ] No samples found: bismark [2021-12-21 03:40:01,335] multiqc [DEBUG ] No samples found: biscuit [2021-12-21 03:40:01,338] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-21 03:40:01,342] multiqc [DEBUG ] No samples found: hicup [2021-12-21 03:40:01,348] multiqc [DEBUG ] No samples found: hicpro [2021-12-21 03:40:01,354] multiqc [DEBUG ] No samples found: salmon [2021-12-21 03:40:01,357] multiqc [DEBUG ] No samples found: kallisto [2021-12-21 03:40:01,361] multiqc [DEBUG ] No samples found: slamdunk [2021-12-21 03:40:01,365] multiqc [DEBUG ] No samples found: star [2021-12-21 03:40:01,369] multiqc [DEBUG ] No samples found: hisat2 [2021-12-21 03:40:01,373] multiqc [DEBUG ] No samples found: tophat [2021-12-21 03:40:01,376] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-21 03:40:01,380] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-21 03:40:01,384] multiqc [DEBUG ] No samples found: snpsplit [2021-12-21 03:40:01,388] multiqc [DEBUG ] No samples found: kat [2021-12-21 03:40:01,391] multiqc [DEBUG ] No samples found: leehom [2021-12-21 03:40:01,396] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-21 03:40:01,400] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-21 03:40:01,403] multiqc [DEBUG ] No samples found: cutadapt [2021-12-21 03:40:01,407] multiqc [DEBUG ] No samples found: flexbar [2021-12-21 03:40:01,411] multiqc [DEBUG ] No samples found: kaiju [2021-12-21 03:40:01,414] multiqc [DEBUG ] No samples found: kraken [2021-12-21 03:40:01,418] multiqc [DEBUG ] No samples found: malt [2021-12-21 03:40:01,424] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-21 03:40:01,428] multiqc [DEBUG ] No samples found: sickle [2021-12-21 03:40:01,431] multiqc [DEBUG ] No samples found: skewer [2021-12-21 03:40:01,435] multiqc [DEBUG ] No samples found: sortmerna [2021-12-21 03:40:01,439] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-21 03:40:01,444] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-21 03:40:01,448] multiqc [DEBUG ] No samples found: afterqc [2021-12-21 03:40:01,452] multiqc [DEBUG ] No samples found: fastp [2021-12-21 03:40:02,369] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2021-12-21 03:40:03,135] multiqc [DEBUG ] No samples found: pycoqc [2021-12-21 03:40:03,140] multiqc [DEBUG ] No samples found: minionqc [2021-12-21 03:40:03,143] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-21 03:40:03,147] multiqc [DEBUG ] No samples found: clusterflow [2021-12-21 03:40:03,152] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-21 03:40:03,157] multiqc [DEBUG ] No samples found: interop [2021-12-21 03:40:03,161] multiqc [DEBUG ] No samples found: ivar [2021-12-21 03:40:03,164] multiqc [DEBUG ] No samples found: flash [2021-12-21 03:40:03,170] multiqc [DEBUG ] No samples found: seqyclean [2021-12-21 03:40:03,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-21 03:40:03,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-21 03:40:03,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-21 03:40:03,170] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-21 03:40:03,214] multiqc [INFO ] Compressing plot data [2021-12-21 03:40:03,906] multiqc [INFO ] Report : multiqc_report.html [2021-12-21 03:40:03,906] multiqc [INFO ] Data : multiqc_data [2021-12-21 03:40:03,906] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13227763/tmpcxa5ou4y/multiqc_data' to '/scratch/gencore/logs/html/HGL5JAFX3/merged/multiqc_data' [2021-12-21 03:40:04,016] multiqc [INFO ] MultiQC complete