[2021-11-05 09:59:29,325] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-05 09:59:29,325] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-05 09:59:29,325] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-05 09:59:29,326] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-05 09:59:29,326] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-05 09:59:29,326] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF32FBGXK/merged [2021-11-05 09:59:30,937] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-05 09:59:30,937] multiqc [INFO ] This is MultiQC v1.9 [2021-11-05 09:59:30,937] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF32FBGXK/merged [2021-11-05 09:59:30,937] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF32FBGXK/merged [2021-11-05 09:59:30,937] multiqc [INFO ] Template : default [2021-11-05 09:59:30,937] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-05 09:59:30,937] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF32FBGXK/merged [2021-11-05 09:59:30,938] 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 [2021-11-05 09:59:30,938] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11573726/tmprbah7hi7 [2021-11-05 09:59:31,042] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3362_fastqc.html [2021-11-05 09:59:31,044] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HF32FBGXK_n01_5QG3181_fastqc.html [2021-11-05 09:59:40,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3181_fastqc.html [2021-11-05 09:59:40,319] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3221_fastqc.html [2021-11-05 09:59:40,321] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3221_fastqc.html [2021-11-05 09:59:40,360] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3494_fastqc.html [2021-11-05 09:59:40,362] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3494_fastqc.html [2021-11-05 09:59:40,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3391_fastqc.html [2021-11-05 09:59:40,403] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3391_fastqc.html [2021-11-05 09:59:40,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG336_fastqc.html [2021-11-05 09:59:40,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG336_fastqc.html [2021-11-05 09:59:40,505] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3195-2_fastqc.html [2021-11-05 09:59:40,507] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3195-2_fastqc.html [2021-11-05 09:59:40,573] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3157_fastqc.html [2021-11-05 09:59:40,574] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3157_fastqc.html [2021-11-05 09:59:40,613] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3367_fastqc.html [2021-11-05 09:59:40,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3367_fastqc.html [2021-11-05 09:59:40,653] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3429_fastqc.html [2021-11-05 09:59:40,655] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3429_fastqc.html [2021-11-05 09:59:40,694] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG329_fastqc.html [2021-11-05 09:59:40,696] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG329_fastqc.html [2021-11-05 09:59:40,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3242_fastqc.html [2021-11-05 09:59:40,757] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3242_fastqc.html [2021-11-05 09:59:40,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG328_fastqc.html [2021-11-05 09:59:40,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG328_fastqc.html [2021-11-05 09:59:40,868] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3153_fastqc.html [2021-11-05 09:59:40,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3153_fastqc.html [2021-11-05 09:59:40,909] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3384_fastqc.html [2021-11-05 09:59:40,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3384_fastqc.html [2021-11-05 09:59:40,987] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3325_fastqc.html [2021-11-05 09:59:40,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n01_5QG3325_fastqc.html [2021-11-05 09:59:41,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3228_fastqc.html [2021-11-05 09:59:41,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF32FBGXK_n02_5QG3228_fastqc.html [2021-11-05 09:59:41,355] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-05 09:59:41,356] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-05 09:59:41,406] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 96 samples (table) [2021-11-05 09:59:41,408] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-05 09:59:41,417] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-05 09:59:41,422] multiqc [DEBUG ] No samples found: conpair [2021-11-05 09:59:41,427] multiqc [DEBUG ] No samples found: peddy [2021-11-05 09:59:41,432] multiqc [DEBUG ] No samples found: somalier [2021-11-05 09:59:41,437] multiqc [DEBUG ] No samples found: methylQA [2021-11-05 09:59:41,446] multiqc [DEBUG ] No samples found: mosdepth [2021-11-05 09:59:41,451] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-05 09:59:41,455] multiqc [DEBUG ] No samples found: qualimap [2021-11-05 09:59:41,460] multiqc [DEBUG ] No samples found: preseq [2021-11-05 09:59:41,466] multiqc [DEBUG ] No samples found: quast [2021-11-05 09:59:41,471] multiqc [DEBUG ] No samples found: qorts [2021-11-05 09:59:41,476] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-05 09:59:41,481] multiqc [DEBUG ] No samples found: rockhopper [2021-11-05 09:59:41,485] multiqc [DEBUG ] No samples found: rsem [2021-11-05 09:59:41,496] multiqc [DEBUG ] No samples found: rseqc [2021-11-05 09:59:41,500] multiqc [DEBUG ] No samples found: busco [2021-11-05 09:59:41,505] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-05 09:59:41,511] multiqc [DEBUG ] No samples found: disambiguate [2021-11-05 09:59:41,516] multiqc [DEBUG ] No samples found: supernova [2021-11-05 09:59:41,529] multiqc [DEBUG ] No samples found: deeptools [2021-11-05 09:59:41,536] multiqc [DEBUG ] No samples found: sargasso [2021-11-05 09:59:41,542] multiqc [DEBUG ] No samples found: verifybamid [2021-11-05 09:59:41,547] multiqc [DEBUG ] No samples found: mirtrace [2021-11-05 09:59:41,552] multiqc [DEBUG ] No samples found: happy [2021-11-05 09:59:41,557] multiqc [DEBUG ] No samples found: mirtop [2021-11-05 09:59:41,564] multiqc [DEBUG ] No samples found: homer [2021-11-05 09:59:41,569] multiqc [DEBUG ] No samples found: macs2 [2021-11-05 09:59:41,573] multiqc [DEBUG ] No samples found: theta2 [2021-11-05 09:59:41,578] multiqc [DEBUG ] No samples found: snpeff [2021-11-05 09:59:41,587] multiqc [DEBUG ] No samples found: gatk [2021-11-05 09:59:41,592] multiqc [DEBUG ] No samples found: htseq [2021-11-05 09:59:41,598] multiqc [DEBUG ] No samples found: bcftools [2021-11-05 09:59:41,602] multiqc [DEBUG ] No samples found: featureCounts [2021-11-05 09:59:41,609] multiqc [DEBUG ] No samples found: fgbio [2021-11-05 09:59:41,621] multiqc [DEBUG ] No samples found: dragen [2021-11-05 09:59:41,626] multiqc [DEBUG ] No samples found: dedup [2021-11-05 09:59:41,632] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-05 09:59:41,656] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-05 09:59:41,660] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-05 09:59:41,662] multiqc [DEBUG ] No samples found: picard [2021-11-05 09:59:41,669] multiqc [DEBUG ] No samples found: prokka [2021-11-05 09:59:41,674] multiqc [DEBUG ] No samples found: samblaster [2021-11-05 09:59:41,685] multiqc [DEBUG ] No samples found: samtools [2021-11-05 09:59:41,693] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-05 09:59:41,699] multiqc [DEBUG ] No samples found: bamtools [2021-11-05 09:59:41,704] multiqc [DEBUG ] No samples found: jellyfish [2021-11-05 09:59:41,714] multiqc [DEBUG ] No samples found: vcftools [2021-11-05 09:59:41,719] multiqc [DEBUG ] No samples found: longranger [2021-11-05 09:59:41,724] multiqc [DEBUG ] No samples found: stacks [2021-11-05 09:59:41,729] multiqc [DEBUG ] No samples found: varscan2 [2021-11-05 09:59:41,741] multiqc [DEBUG ] No samples found: bbmap [2021-11-05 09:59:41,746] multiqc [DEBUG ] No samples found: bismark [2021-11-05 09:59:41,752] multiqc [DEBUG ] No samples found: biscuit [2021-11-05 09:59:41,757] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-05 09:59:41,762] multiqc [DEBUG ] No samples found: hicup [2021-11-05 09:59:41,767] multiqc [DEBUG ] No samples found: hicpro [2021-11-05 09:59:41,771] multiqc [DEBUG ] No samples found: salmon [2021-11-05 09:59:41,776] multiqc [DEBUG ] No samples found: kallisto [2021-11-05 09:59:41,781] multiqc [DEBUG ] No samples found: slamdunk [2021-11-05 09:59:41,786] multiqc [DEBUG ] No samples found: star [2021-11-05 09:59:41,790] multiqc [DEBUG ] No samples found: hisat2 [2021-11-05 09:59:41,795] multiqc [DEBUG ] No samples found: tophat [2021-11-05 09:59:41,799] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-05 09:59:41,804] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-05 09:59:41,809] multiqc [DEBUG ] No samples found: snpsplit [2021-11-05 09:59:41,814] multiqc [DEBUG ] No samples found: kat [2021-11-05 09:59:41,818] multiqc [DEBUG ] No samples found: leehom [2021-11-05 09:59:41,823] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-05 09:59:41,827] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-05 09:59:41,832] multiqc [DEBUG ] No samples found: cutadapt [2021-11-05 09:59:41,837] multiqc [DEBUG ] No samples found: flexbar [2021-11-05 09:59:41,842] multiqc [DEBUG ] No samples found: kaiju [2021-11-05 09:59:41,847] multiqc [DEBUG ] No samples found: kraken [2021-11-05 09:59:41,852] multiqc [DEBUG ] No samples found: malt [2021-11-05 09:59:41,857] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-05 09:59:41,861] multiqc [DEBUG ] No samples found: sickle [2021-11-05 09:59:41,866] multiqc [DEBUG ] No samples found: skewer [2021-11-05 09:59:41,870] multiqc [DEBUG ] No samples found: sortmerna [2021-11-05 09:59:41,874] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-05 09:59:41,879] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-05 09:59:41,884] multiqc [DEBUG ] No samples found: afterqc [2021-11-05 09:59:41,889] multiqc [DEBUG ] No samples found: fastp [2021-11-05 09:59:57,350] multiqc.modules.fastqc.fastqc [INFO ] Found 192 reports [2021-11-05 10:00:18,345] multiqc [DEBUG ] No samples found: pycoqc [2021-11-05 10:00:18,350] multiqc [DEBUG ] No samples found: minionqc [2021-11-05 10:00:18,355] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-05 10:00:18,359] multiqc [DEBUG ] No samples found: clusterflow [2021-11-05 10:00:18,365] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-05 10:00:18,370] multiqc [DEBUG ] No samples found: interop [2021-11-05 10:00:18,375] multiqc [DEBUG ] No samples found: ivar [2021-11-05 10:00:18,380] multiqc [DEBUG ] No samples found: flash [2021-11-05 10:00:18,384] multiqc [DEBUG ] No samples found: seqyclean [2021-11-05 10:00:18,384] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-05 10:00:18,384] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-05 10:00:18,384] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-05 10:00:18,384] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-05 10:00:18,600] multiqc [INFO ] Compressing plot data [2021-11-05 10:00:18,664] multiqc [INFO ] Report : multiqc_report.html [2021-11-05 10:00:18,664] multiqc [INFO ] Data : multiqc_data [2021-11-05 10:00:18,664] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11573726/tmprbah7hi7/multiqc_data' to '/scratch/gencore/logs/html/HF32FBGXK/merged/multiqc_data' [2021-11-05 10:00:18,792] multiqc [INFO ] MultiQC complete