[2022-07-20 23:56:31,246] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-20 23:56:31,246] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-20 23:56:31,246] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-20 23:56:31,247] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-20 23:56:31,247] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-20 23:56:31,247] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCNNBGXM/merged [2022-07-20 23:56:31,982] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-20 23:56:31,982] multiqc [INFO ] This is MultiQC v1.9 [2022-07-20 23:56:31,982] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCNNBGXM/merged [2022-07-20 23:56:31,982] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGCNNBGXM/merged [2022-07-20 23:56:31,982] multiqc [INFO ] Template : default [2022-07-20 23:56:31,982] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-20 23:56:31,982] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGCNNBGXM/merged [2022-07-20 23:56:31,983] 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 [2022-07-20 23:56:31,983] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22603394/tmp1weduyd6 [2022-07-20 23:56:32,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12267_DNA_fastqc.html [2022-07-20 23:56:32,098] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HGCNNBGXM_n02_12270_totalRNA_fastqc.html [2022-07-20 23:56:33,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12270_DNA_fastqc.html [2022-07-20 23:56:33,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12270_DNA_fastqc.html [2022-07-20 23:56:33,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12272_DNA_fastqc.html [2022-07-20 23:56:33,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12272_DNA_fastqc.html [2022-07-20 23:56:33,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12275_DNA_fastqc.html [2022-07-20 23:56:33,241] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12275_DNA_fastqc.html [2022-07-20 23:56:33,280] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12269_DNA_fastqc.html [2022-07-20 23:56:33,282] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12269_DNA_fastqc.html [2022-07-20 23:56:33,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12267_totalRNA_fastqc.html [2022-07-20 23:56:33,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12267_totalRNA_fastqc.html [2022-07-20 23:56:33,368] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12269_DNA_fastqc.html [2022-07-20 23:56:33,370] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12269_DNA_fastqc.html [2022-07-20 23:56:33,410] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_undetermined_fastqc.html [2022-07-20 23:56:33,412] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_undetermined_fastqc.html [2022-07-20 23:56:33,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12270_totalRNA_fastqc.html [2022-07-20 23:56:33,453] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12270_totalRNA_fastqc.html [2022-07-20 23:56:33,498] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12272_totalRNA_fastqc.html [2022-07-20 23:56:33,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12272_totalRNA_fastqc.html [2022-07-20 23:56:33,543] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12275_DNA_fastqc.html [2022-07-20 23:56:33,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12275_DNA_fastqc.html [2022-07-20 23:56:33,584] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12268_DNA_fastqc.html [2022-07-20 23:56:33,586] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12268_DNA_fastqc.html [2022-07-20 23:56:33,626] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12271_DNA_fastqc.html [2022-07-20 23:56:33,628] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12271_DNA_fastqc.html [2022-07-20 23:56:33,668] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12272_DNA_fastqc.html [2022-07-20 23:56:33,670] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12272_DNA_fastqc.html [2022-07-20 23:56:33,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12274_DNA_fastqc.html [2022-07-20 23:56:33,710] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12274_DNA_fastqc.html [2022-07-20 23:56:33,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_undetermined_fastqc.html [2022-07-20 23:56:33,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_undetermined_fastqc.html [2022-07-20 23:56:33,791] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12273_totalRNA_fastqc.html [2022-07-20 23:56:33,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n02_12273_totalRNA_fastqc.html [2022-07-20 23:56:33,836] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12269_totalRNA_fastqc.html [2022-07-20 23:56:33,838] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCNNBGXM_n01_12269_totalRNA_fastqc.html [2022-07-20 23:56:34,188] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-20 23:56:34,190] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-20 23:56:34,197] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-20 23:56:34,207] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 19 samples (table) [2022-07-20 23:56:34,217] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-20 23:56:34,222] multiqc [DEBUG ] No samples found: conpair [2022-07-20 23:56:34,227] multiqc [DEBUG ] No samples found: peddy [2022-07-20 23:56:34,233] multiqc [DEBUG ] No samples found: somalier [2022-07-20 23:56:34,237] multiqc [DEBUG ] No samples found: methylQA [2022-07-20 23:56:34,250] multiqc [DEBUG ] No samples found: mosdepth [2022-07-20 23:56:34,255] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-20 23:56:34,258] multiqc [DEBUG ] No samples found: qualimap [2022-07-20 23:56:34,263] multiqc [DEBUG ] No samples found: preseq [2022-07-20 23:56:34,269] multiqc [DEBUG ] No samples found: quast [2022-07-20 23:56:34,275] multiqc [DEBUG ] No samples found: qorts [2022-07-20 23:56:34,280] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-20 23:56:34,287] multiqc [DEBUG ] No samples found: rockhopper [2022-07-20 23:56:34,292] multiqc [DEBUG ] No samples found: rsem [2022-07-20 23:56:34,304] multiqc [DEBUG ] No samples found: rseqc [2022-07-20 23:56:34,308] multiqc [DEBUG ] No samples found: busco [2022-07-20 23:56:34,313] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-20 23:56:34,319] multiqc [DEBUG ] No samples found: disambiguate [2022-07-20 23:56:34,324] multiqc [DEBUG ] No samples found: supernova [2022-07-20 23:56:34,340] multiqc [DEBUG ] No samples found: deeptools [2022-07-20 23:56:34,345] multiqc [DEBUG ] No samples found: sargasso [2022-07-20 23:56:34,350] multiqc [DEBUG ] No samples found: verifybamid [2022-07-20 23:56:34,354] multiqc [DEBUG ] No samples found: mirtrace [2022-07-20 23:56:34,359] multiqc [DEBUG ] No samples found: happy [2022-07-20 23:56:34,365] multiqc [DEBUG ] No samples found: mirtop [2022-07-20 23:56:34,371] multiqc [DEBUG ] No samples found: homer [2022-07-20 23:56:34,376] multiqc [DEBUG ] No samples found: macs2 [2022-07-20 23:56:34,380] multiqc [DEBUG ] No samples found: theta2 [2022-07-20 23:56:34,385] multiqc [DEBUG ] No samples found: snpeff [2022-07-20 23:56:34,396] multiqc [DEBUG ] No samples found: gatk [2022-07-20 23:56:34,400] multiqc [DEBUG ] No samples found: htseq [2022-07-20 23:56:34,406] multiqc [DEBUG ] No samples found: bcftools [2022-07-20 23:56:34,414] multiqc [DEBUG ] No samples found: featureCounts [2022-07-20 23:56:34,422] multiqc [DEBUG ] No samples found: fgbio [2022-07-20 23:56:34,436] multiqc [DEBUG ] No samples found: dragen [2022-07-20 23:56:34,440] multiqc [DEBUG ] No samples found: dedup [2022-07-20 23:56:34,445] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-20 23:56:34,473] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-20 23:56:34,477] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-20 23:56:34,479] multiqc [DEBUG ] No samples found: picard [2022-07-20 23:56:34,487] multiqc [DEBUG ] No samples found: prokka [2022-07-20 23:56:34,492] multiqc [DEBUG ] No samples found: samblaster [2022-07-20 23:56:34,505] multiqc [DEBUG ] No samples found: samtools [2022-07-20 23:56:34,512] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-20 23:56:34,520] multiqc [DEBUG ] No samples found: bamtools [2022-07-20 23:56:34,526] multiqc [DEBUG ] No samples found: jellyfish [2022-07-20 23:56:34,534] multiqc [DEBUG ] No samples found: vcftools [2022-07-20 23:56:34,540] multiqc [DEBUG ] No samples found: longranger [2022-07-20 23:56:34,545] multiqc [DEBUG ] No samples found: stacks [2022-07-20 23:56:34,550] multiqc [DEBUG ] No samples found: varscan2 [2022-07-20 23:56:34,565] multiqc [DEBUG ] No samples found: bbmap [2022-07-20 23:56:34,570] multiqc [DEBUG ] No samples found: bismark [2022-07-20 23:56:34,577] multiqc [DEBUG ] No samples found: biscuit [2022-07-20 23:56:34,582] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-20 23:56:34,587] multiqc [DEBUG ] No samples found: hicup [2022-07-20 23:56:34,592] multiqc [DEBUG ] No samples found: hicpro [2022-07-20 23:56:34,596] multiqc [DEBUG ] No samples found: salmon [2022-07-20 23:56:34,601] multiqc [DEBUG ] No samples found: kallisto [2022-07-20 23:56:34,606] multiqc [DEBUG ] No samples found: slamdunk [2022-07-20 23:56:34,611] multiqc [DEBUG ] No samples found: star [2022-07-20 23:56:34,618] multiqc [DEBUG ] No samples found: hisat2 [2022-07-20 23:56:34,623] multiqc [DEBUG ] No samples found: tophat [2022-07-20 23:56:34,627] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-20 23:56:34,632] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-20 23:56:34,637] multiqc [DEBUG ] No samples found: snpsplit [2022-07-20 23:56:34,642] multiqc [DEBUG ] No samples found: kat [2022-07-20 23:56:34,646] multiqc [DEBUG ] No samples found: leehom [2022-07-20 23:56:34,651] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-20 23:56:34,655] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-20 23:56:34,660] multiqc [DEBUG ] No samples found: cutadapt [2022-07-20 23:56:34,664] multiqc [DEBUG ] No samples found: flexbar [2022-07-20 23:56:34,669] multiqc [DEBUG ] No samples found: kaiju [2022-07-20 23:56:34,674] multiqc [DEBUG ] No samples found: kraken [2022-07-20 23:56:34,679] multiqc [DEBUG ] No samples found: malt [2022-07-20 23:56:34,683] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-20 23:56:34,687] multiqc [DEBUG ] No samples found: sickle [2022-07-20 23:56:34,695] multiqc [DEBUG ] No samples found: skewer [2022-07-20 23:56:34,700] multiqc [DEBUG ] No samples found: sortmerna [2022-07-20 23:56:34,704] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-20 23:56:34,711] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-20 23:56:34,716] multiqc [DEBUG ] No samples found: afterqc [2022-07-20 23:56:34,721] multiqc [DEBUG ] No samples found: fastp [2022-07-20 23:56:37,065] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2022-07-20 23:56:37,393] multiqc [DEBUG ] No samples found: pycoqc [2022-07-20 23:56:37,402] multiqc [DEBUG ] No samples found: minionqc [2022-07-20 23:56:37,407] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-20 23:56:37,411] multiqc [DEBUG ] No samples found: clusterflow [2022-07-20 23:56:37,417] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-20 23:56:37,422] multiqc [DEBUG ] No samples found: interop [2022-07-20 23:56:37,426] multiqc [DEBUG ] No samples found: ivar [2022-07-20 23:56:37,431] multiqc [DEBUG ] No samples found: flash [2022-07-20 23:56:37,437] multiqc [DEBUG ] No samples found: seqyclean [2022-07-20 23:56:37,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-20 23:56:37,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-20 23:56:37,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-20 23:56:37,437] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-20 23:56:37,483] multiqc [INFO ] Compressing plot data [2022-07-20 23:56:38,115] multiqc [INFO ] Report : multiqc_report.html [2022-07-20 23:56:38,115] multiqc [INFO ] Data : multiqc_data [2022-07-20 23:56:38,115] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22603394/tmp1weduyd6/multiqc_data' to '/scratch/gencore/logs/html/HGCNNBGXM/merged/multiqc_data' [2022-07-20 23:56:38,250] multiqc [INFO ] MultiQC complete