[2022-10-27 14:29:12,712] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-27 14:29:12,712] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-27 14:29:12,712] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-27 14:29:12,713] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-27 14:29:12,713] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-27 14:29:12,713] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2F5LAFX5/merged [2022-10-27 14:29:13,192] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-27 14:29:13,193] multiqc [INFO ] This is MultiQC v1.9 [2022-10-27 14:29:13,193] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2F5LAFX5/merged [2022-10-27 14:29:13,193] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2F5LAFX5/merged [2022-10-27 14:29:13,193] multiqc [INFO ] Template : default [2022-10-27 14:29:13,193] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-27 14:29:13,193] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2F5LAFX5/merged [2022-10-27 14:29:13,193] 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 [2022-10-27 14:29:13,193] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26335730/tmp11f4ka4j [2022-10-27 14:29:13,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_8098-in_fastqc.html [2022-10-27 14:29:13,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H2F5LAFX5_n01_11617-input_fastqc.html [2022-10-27 14:29:14,274] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_BAM_fastqc.html [2022-10-27 14:29:14,276] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_BAM_fastqc.html [2022-10-27 14:29:14,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_11617-input_fastqc.html [2022-10-27 14:29:14,318] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n02_11617-input_fastqc.html [2022-10-27 14:29:14,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_9531-in_fastqc.html [2022-10-27 14:29:14,359] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_9531-in_fastqc.html [2022-10-27 14:29:14,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_7797a-in_fastqc.html [2022-10-27 14:29:14,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n02_7797a-in_fastqc.html [2022-10-27 14:29:14,441] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_9531-in_fastqc.html [2022-10-27 14:29:14,443] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n02_9531-in_fastqc.html [2022-10-27 14:29:14,483] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_5187-in_fastqc.html [2022-10-27 14:29:14,484] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n02_5187-in_fastqc.html [2022-10-27 14:29:14,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_7797b-in_fastqc.html [2022-10-27 14:29:14,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_7797b-in_fastqc.html [2022-10-27 14:29:14,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_8098-in_fastqc.html [2022-10-27 14:29:14,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_8098-in_fastqc.html [2022-10-27 14:29:14,608] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n02_11976-in_fastqc.html [2022-10-27 14:29:14,610] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n02_11976-in_fastqc.html [2022-10-27 14:29:14,650] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_5187-in_fastqc.html [2022-10-27 14:29:14,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_5187-in_fastqc.html [2022-10-27 14:29:14,691] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2F5LAFX5_n01_7797b-chp_fastqc.html [2022-10-27 14:29:14,693] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2F5LAFX5_n01_7797b-chp_fastqc.html [2022-10-27 14:29:15,029] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-27 14:29:15,031] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-27 14:29:15,044] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2022-10-27 14:29:15,046] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-27 14:29:15,055] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-27 14:29:15,062] multiqc [DEBUG ] No samples found: conpair [2022-10-27 14:29:15,068] multiqc [DEBUG ] No samples found: peddy [2022-10-27 14:29:15,077] multiqc [DEBUG ] No samples found: somalier [2022-10-27 14:29:15,082] multiqc [DEBUG ] No samples found: methylQA [2022-10-27 14:29:15,091] multiqc [DEBUG ] No samples found: mosdepth [2022-10-27 14:29:15,096] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-27 14:29:15,099] multiqc [DEBUG ] No samples found: qualimap [2022-10-27 14:29:15,105] multiqc [DEBUG ] No samples found: preseq [2022-10-27 14:29:15,110] multiqc [DEBUG ] No samples found: quast [2022-10-27 14:29:15,114] multiqc [DEBUG ] No samples found: qorts [2022-10-27 14:29:15,119] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-27 14:29:15,125] multiqc [DEBUG ] No samples found: rockhopper [2022-10-27 14:29:15,129] multiqc [DEBUG ] No samples found: rsem [2022-10-27 14:29:15,142] multiqc [DEBUG ] No samples found: rseqc [2022-10-27 14:29:15,147] multiqc [DEBUG ] No samples found: busco [2022-10-27 14:29:15,152] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-27 14:29:15,157] multiqc [DEBUG ] No samples found: disambiguate [2022-10-27 14:29:15,162] multiqc [DEBUG ] No samples found: supernova [2022-10-27 14:29:15,177] multiqc [DEBUG ] No samples found: deeptools [2022-10-27 14:29:15,181] multiqc [DEBUG ] No samples found: sargasso [2022-10-27 14:29:15,187] multiqc [DEBUG ] No samples found: verifybamid [2022-10-27 14:29:15,192] multiqc [DEBUG ] No samples found: mirtrace [2022-10-27 14:29:15,197] multiqc [DEBUG ] No samples found: happy [2022-10-27 14:29:15,203] multiqc [DEBUG ] No samples found: mirtop [2022-10-27 14:29:15,210] multiqc [DEBUG ] No samples found: homer [2022-10-27 14:29:15,216] multiqc [DEBUG ] No samples found: macs2 [2022-10-27 14:29:15,221] multiqc [DEBUG ] No samples found: theta2 [2022-10-27 14:29:15,226] multiqc [DEBUG ] No samples found: snpeff [2022-10-27 14:29:15,233] multiqc [DEBUG ] No samples found: gatk [2022-10-27 14:29:15,238] multiqc [DEBUG ] No samples found: htseq [2022-10-27 14:29:15,244] multiqc [DEBUG ] No samples found: bcftools [2022-10-27 14:29:15,248] multiqc [DEBUG ] No samples found: featureCounts [2022-10-27 14:29:15,255] multiqc [DEBUG ] No samples found: fgbio [2022-10-27 14:29:15,272] multiqc [DEBUG ] No samples found: dragen [2022-10-27 14:29:15,277] multiqc [DEBUG ] No samples found: dedup [2022-10-27 14:29:15,282] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-27 14:29:15,308] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-27 14:29:15,314] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-27 14:29:15,316] multiqc [DEBUG ] No samples found: picard [2022-10-27 14:29:15,322] multiqc [DEBUG ] No samples found: prokka [2022-10-27 14:29:15,327] multiqc [DEBUG ] No samples found: samblaster [2022-10-27 14:29:15,339] multiqc [DEBUG ] No samples found: samtools [2022-10-27 14:29:15,344] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-27 14:29:15,350] multiqc [DEBUG ] No samples found: bamtools [2022-10-27 14:29:15,355] multiqc [DEBUG ] No samples found: jellyfish [2022-10-27 14:29:15,367] multiqc [DEBUG ] No samples found: vcftools [2022-10-27 14:29:15,372] multiqc [DEBUG ] No samples found: longranger [2022-10-27 14:29:15,378] multiqc [DEBUG ] No samples found: stacks [2022-10-27 14:29:15,384] multiqc [DEBUG ] No samples found: varscan2 [2022-10-27 14:29:15,399] multiqc [DEBUG ] No samples found: bbmap [2022-10-27 14:29:15,405] multiqc [DEBUG ] No samples found: bismark [2022-10-27 14:29:15,410] multiqc [DEBUG ] No samples found: biscuit [2022-10-27 14:29:15,418] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-27 14:29:15,423] multiqc [DEBUG ] No samples found: hicup [2022-10-27 14:29:15,429] multiqc [DEBUG ] No samples found: hicpro [2022-10-27 14:29:15,434] multiqc [DEBUG ] No samples found: salmon [2022-10-27 14:29:15,439] multiqc [DEBUG ] No samples found: kallisto [2022-10-27 14:29:15,445] multiqc [DEBUG ] No samples found: slamdunk [2022-10-27 14:29:15,450] multiqc [DEBUG ] No samples found: star [2022-10-27 14:29:15,456] multiqc [DEBUG ] No samples found: hisat2 [2022-10-27 14:29:15,460] multiqc [DEBUG ] No samples found: tophat [2022-10-27 14:29:15,466] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-27 14:29:15,471] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-27 14:29:15,477] multiqc [DEBUG ] No samples found: snpsplit [2022-10-27 14:29:15,481] multiqc [DEBUG ] No samples found: kat [2022-10-27 14:29:15,486] multiqc [DEBUG ] No samples found: leehom [2022-10-27 14:29:15,491] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-27 14:29:15,496] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-27 14:29:15,501] multiqc [DEBUG ] No samples found: cutadapt [2022-10-27 14:29:15,505] multiqc [DEBUG ] No samples found: flexbar [2022-10-27 14:29:15,511] multiqc [DEBUG ] No samples found: kaiju [2022-10-27 14:29:15,522] multiqc [DEBUG ] No samples found: kraken [2022-10-27 14:29:15,528] multiqc [DEBUG ] No samples found: malt [2022-10-27 14:29:15,533] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-27 14:29:15,538] multiqc [DEBUG ] No samples found: sickle [2022-10-27 14:29:15,544] multiqc [DEBUG ] No samples found: skewer [2022-10-27 14:29:15,549] multiqc [DEBUG ] No samples found: sortmerna [2022-10-27 14:29:15,554] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-27 14:29:15,559] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-27 14:29:15,565] multiqc [DEBUG ] No samples found: afterqc [2022-10-27 14:29:15,570] multiqc [DEBUG ] No samples found: fastp [2022-10-27 14:29:16,255] multiqc.modules.fastqc.fastqc [INFO ] Found 32 reports [2022-10-27 14:29:16,539] multiqc [DEBUG ] No samples found: pycoqc [2022-10-27 14:29:16,544] multiqc [DEBUG ] No samples found: minionqc [2022-10-27 14:29:16,550] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-27 14:29:16,555] multiqc [DEBUG ] No samples found: clusterflow [2022-10-27 14:29:16,561] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-27 14:29:16,566] multiqc [DEBUG ] No samples found: interop [2022-10-27 14:29:16,572] multiqc [DEBUG ] No samples found: ivar [2022-10-27 14:29:16,577] multiqc [DEBUG ] No samples found: flash [2022-10-27 14:29:16,582] multiqc [DEBUG ] No samples found: seqyclean [2022-10-27 14:29:16,582] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-27 14:29:16,582] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-27 14:29:16,582] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-27 14:29:16,582] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-27 14:29:16,620] multiqc [INFO ] Compressing plot data [2022-10-27 14:29:17,150] multiqc [INFO ] Report : multiqc_report.html [2022-10-27 14:29:17,150] multiqc [INFO ] Data : multiqc_data [2022-10-27 14:29:17,150] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26335730/tmp11f4ka4j/multiqc_data' to '/scratch/gencore/logs/html/H2F5LAFX5/merged/multiqc_data' [2022-10-27 14:29:17,289] multiqc [INFO ] MultiQC complete