[2021-07-20 11:34:16,216] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-20 11:34:16,216] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-20 11:34:16,216] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-20 11:34:16,217] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-20 11:34:16,217] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-20 11:34:16,217] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGV55BGXJ/merged [2021-07-20 11:34:17,492] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-20 11:34:17,493] multiqc [INFO ] This is MultiQC v1.9 [2021-07-20 11:34:17,493] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGV55BGXJ/merged [2021-07-20 11:34:17,493] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGV55BGXJ/merged [2021-07-20 11:34:17,493] multiqc [INFO ] Template : default [2021-07-20 11:34:17,493] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-20 11:34:17,493] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGV55BGXJ/merged [2021-07-20 11:34:17,493] 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 [2021-07-20 11:34:17,493] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8807938/tmpf9a9evzt [2021-07-20 11:34:17,612] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3155_fastqc.html [2021-07-20 11:34:17,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-07-20 11:34:27,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_undetermined_fastqc.html [2021-07-20 11:34:27,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_undetermined_fastqc.html [2021-07-20 11:34:27,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3426_fastqc.html [2021-07-20 11:34:27,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3426_fastqc.html [2021-07-20 11:34:27,589] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3350_fastqc.html [2021-07-20 11:34:27,591] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3350_fastqc.html [2021-07-20 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File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3370_fastqc.html [2021-07-20 11:34:27,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3370_fastqc.html [2021-07-20 11:34:27,870] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3303_fastqc.html [2021-07-20 11:34:27,872] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3303_fastqc.html [2021-07-20 11:34:27,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3232_fastqc.html [2021-07-20 11:34:27,920] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3232_fastqc.html [2021-07-20 11:34:27,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3297_fastqc.html [2021-07-20 11:34:27,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3297_fastqc.html [2021-07-20 11:34:28,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3366_fastqc.html [2021-07-20 11:34:28,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3366_fastqc.html [2021-07-20 11:34:28,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3339_fastqc.html [2021-07-20 11:34:28,097] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3339_fastqc.html [2021-07-20 11:34:28,143] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3254_fastqc.html [2021-07-20 11:34:28,145] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3254_fastqc.html [2021-07-20 11:34:28,188] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3225_fastqc.html [2021-07-20 11:34:28,190] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3225_fastqc.html [2021-07-20 11:34:28,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3422_fastqc.html [2021-07-20 11:34:28,235] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3422_fastqc.html [2021-07-20 11:34:28,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3257_fastqc.html [2021-07-20 11:34:28,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3257_fastqc.html [2021-07-20 11:34:28,324] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3375_fastqc.html [2021-07-20 11:34:28,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3375_fastqc.html [2021-07-20 11:34:28,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3482_fastqc.html [2021-07-20 11:34:28,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3482_fastqc.html [2021-07-20 11:34:28,417] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3502_fastqc.html [2021-07-20 11:34:28,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n02_4QG3502_fastqc.html [2021-07-20 11:34:28,482] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3401_fastqc.html [2021-07-20 11:34:28,484] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGV55BGXJ_n01_4QG3401_fastqc.html [2021-07-20 11:34:28,886] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-20 11:34:28,887] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-20 11:34:28,941] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 95 samples (table) [2021-07-20 11:34:28,942] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-20 11:34:28,953] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-20 11:34:28,957] multiqc [DEBUG ] No samples found: conpair [2021-07-20 11:34:28,962] multiqc [DEBUG ] No samples found: peddy [2021-07-20 11:34:28,967] multiqc [DEBUG ] No samples found: somalier [2021-07-20 11:34:28,971] multiqc [DEBUG ] No samples found: methylQA [2021-07-20 11:34:28,979] multiqc [DEBUG ] No samples found: mosdepth [2021-07-20 11:34:28,983] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-20 11:34:28,987] multiqc [DEBUG ] No samples found: qualimap [2021-07-20 11:34:28,991] multiqc [DEBUG ] No samples found: preseq [2021-07-20 11:34:28,996] multiqc [DEBUG ] No samples found: quast [2021-07-20 11:34:29,001] multiqc [DEBUG ] No samples found: qorts [2021-07-20 11:34:29,005] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-20 11:34:29,010] multiqc [DEBUG ] No samples found: rockhopper [2021-07-20 11:34:29,015] multiqc [DEBUG ] No samples found: rsem [2021-07-20 11:34:29,024] multiqc [DEBUG ] No samples found: rseqc [2021-07-20 11:34:29,029] multiqc [DEBUG ] No samples found: busco [2021-07-20 11:34:29,033] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-20 11:34:29,038] multiqc [DEBUG ] No samples found: disambiguate [2021-07-20 11:34:29,043] multiqc [DEBUG ] No samples found: supernova [2021-07-20 11:34:29,054] multiqc [DEBUG ] No samples found: deeptools [2021-07-20 11:34:29,058] multiqc [DEBUG ] No samples found: sargasso [2021-07-20 11:34:29,063] multiqc [DEBUG ] No samples found: verifybamid [2021-07-20 11:34:29,068] multiqc [DEBUG ] No samples found: mirtrace [2021-07-20 11:34:29,073] multiqc [DEBUG ] No samples found: happy [2021-07-20 11:34:29,077] multiqc [DEBUG ] No samples found: mirtop [2021-07-20 11:34:29,083] multiqc [DEBUG ] No samples found: homer [2021-07-20 11:34:29,088] multiqc [DEBUG ] No samples found: macs2 [2021-07-20 11:34:29,092] multiqc [DEBUG ] No samples found: theta2 [2021-07-20 11:34:29,097] multiqc [DEBUG ] No samples found: snpeff [2021-07-20 11:34:29,103] multiqc [DEBUG ] No samples found: gatk [2021-07-20 11:34:29,108] multiqc [DEBUG ] No samples found: htseq [2021-07-20 11:34:29,113] multiqc [DEBUG ] No samples found: bcftools [2021-07-20 11:34:29,118] multiqc [DEBUG ] No samples found: featureCounts [2021-07-20 11:34:29,123] multiqc [DEBUG ] No samples found: fgbio [2021-07-20 11:34:29,135] multiqc [DEBUG ] No samples found: dragen [2021-07-20 11:34:29,139] multiqc [DEBUG ] No samples found: dedup [2021-07-20 11:34:29,144] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-20 11:34:29,164] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-20 11:34:29,168] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-20 11:34:29,171] multiqc [DEBUG ] No samples found: picard [2021-07-20 11:34:29,175] multiqc [DEBUG ] No samples found: prokka [2021-07-20 11:34:29,179] multiqc [DEBUG ] No samples found: samblaster [2021-07-20 11:34:29,187] multiqc [DEBUG ] No samples found: samtools [2021-07-20 11:34:29,192] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-20 11:34:29,197] multiqc [DEBUG ] No samples found: bamtools [2021-07-20 11:34:29,201] multiqc [DEBUG ] No samples found: jellyfish [2021-07-20 11:34:29,208] multiqc [DEBUG ] No samples found: vcftools [2021-07-20 11:34:29,213] multiqc [DEBUG ] No samples found: longranger [2021-07-20 11:34:29,218] multiqc [DEBUG ] No samples found: stacks [2021-07-20 11:34:29,222] multiqc [DEBUG ] No samples found: varscan2 [2021-07-20 11:34:29,235] multiqc [DEBUG ] No samples found: bbmap [2021-07-20 11:34:29,239] multiqc [DEBUG ] No samples found: bismark [2021-07-20 11:34:29,244] multiqc [DEBUG ] No samples found: biscuit [2021-07-20 11:34:29,249] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-20 11:34:29,253] multiqc [DEBUG ] No samples found: hicup [2021-07-20 11:34:29,258] multiqc [DEBUG ] No samples found: hicpro [2021-07-20 11:34:29,262] multiqc [DEBUG ] No samples found: salmon [2021-07-20 11:34:29,266] multiqc [DEBUG ] No samples found: kallisto [2021-07-20 11:34:29,271] multiqc [DEBUG ] No samples found: slamdunk [2021-07-20 11:34:29,275] multiqc [DEBUG ] No samples found: star [2021-07-20 11:34:29,280] multiqc [DEBUG ] No samples found: hisat2 [2021-07-20 11:34:29,284] multiqc [DEBUG ] No samples found: tophat [2021-07-20 11:34:29,288] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-20 11:34:29,293] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-20 11:34:29,297] multiqc [DEBUG ] No samples found: snpsplit [2021-07-20 11:34:29,301] multiqc [DEBUG ] No samples found: kat [2021-07-20 11:34:29,305] multiqc [DEBUG ] No samples found: leehom [2021-07-20 11:34:29,310] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-20 11:34:29,314] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-20 11:34:29,318] multiqc [DEBUG ] No samples found: cutadapt [2021-07-20 11:34:29,322] multiqc [DEBUG ] No samples found: flexbar [2021-07-20 11:34:29,326] multiqc [DEBUG ] No samples found: kaiju [2021-07-20 11:34:29,331] multiqc [DEBUG ] No samples found: kraken [2021-07-20 11:34:29,335] multiqc [DEBUG ] No samples found: malt [2021-07-20 11:34:29,340] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-20 11:34:29,344] multiqc [DEBUG ] No samples found: sickle [2021-07-20 11:34:29,348] multiqc [DEBUG ] No samples found: skewer [2021-07-20 11:34:29,353] multiqc [DEBUG ] No samples found: sortmerna [2021-07-20 11:34:29,357] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-20 11:34:29,361] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-20 11:34:29,365] multiqc [DEBUG ] No samples found: afterqc [2021-07-20 11:34:29,370] multiqc [DEBUG ] No samples found: fastp [2021-07-20 11:34:44,420] multiqc.modules.fastqc.fastqc [INFO ] Found 190 reports [2021-07-20 11:35:08,462] multiqc [DEBUG ] No samples found: pycoqc [2021-07-20 11:35:08,467] multiqc [DEBUG ] No samples found: minionqc [2021-07-20 11:35:08,471] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-20 11:35:08,476] multiqc [DEBUG ] No samples found: clusterflow [2021-07-20 11:35:08,481] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-20 11:35:08,485] multiqc [DEBUG ] No samples found: interop [2021-07-20 11:35:08,490] multiqc [DEBUG ] No samples found: ivar [2021-07-20 11:35:08,495] multiqc [DEBUG ] No samples found: flash [2021-07-20 11:35:08,499] multiqc [DEBUG ] No samples found: seqyclean [2021-07-20 11:35:08,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-20 11:35:08,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-20 11:35:08,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-20 11:35:08,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-20 11:35:08,730] multiqc [INFO ] Compressing plot data [2021-07-20 11:35:08,797] multiqc [INFO ] Report : multiqc_report.html [2021-07-20 11:35:08,797] multiqc [INFO ] Data : multiqc_data [2021-07-20 11:35:08,797] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8807938/tmpf9a9evzt/multiqc_data' to '/scratch/gencore/logs/html/HGV55BGXJ/merged/multiqc_data' [2021-07-20 11:35:08,931] multiqc [INFO ] MultiQC complete