[2021-11-07 09:29:15,022] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-07 09:29:15,022] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-07 09:29:15,022] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-07 09:29:15,023] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-07 09:29:15,023] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-07 09:29:15,023] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF7KYBGXK/merged [2021-11-07 09:29:16,607] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-07 09:29:16,607] multiqc [INFO ] This is MultiQC v1.9 [2021-11-07 09:29:16,607] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF7KYBGXK/merged [2021-11-07 09:29:16,607] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF7KYBGXK/merged [2021-11-07 09:29:16,607] multiqc [INFO ] Template : default [2021-11-07 09:29:16,607] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-07 09:29:16,607] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF7KYBGXK/merged [2021-11-07 09:29:16,608] 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 [2021-11-07 09:29:16,608] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11642121/tmpinoqr2ld [2021-11-07 09:29:16,752] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2876_d08_rep1_fastqc.html [2021-11-07 09:29:16,755] multiqc [DEBUG ] File ignored by longranger/invocation because it 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HF7KYBGXK_n01_2997_d02_rep1_fastqc.html [2021-11-07 09:29:36,111] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n01_2997_d02_rep1_fastqc.html [2021-11-07 09:29:36,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2859_d08_rep1_fastqc.html [2021-11-07 09:29:36,209] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2859_d08_rep1_fastqc.html [2021-11-07 09:29:36,260] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2890_d12_rep1_fastqc.html [2021-11-07 09:29:36,262] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2890_d12_rep1_fastqc.html [2021-11-07 09:29:36,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3020_d06_rep1_fastqc.html [2021-11-07 09:29:36,305] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3020_d06_rep1_fastqc.html [2021-11-07 09:29:36,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3000_d04_rep1_fastqc.html [2021-11-07 09:29:36,348] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3000_d04_rep1_fastqc.html [2021-11-07 09:29:36,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2853_d12_rep1_fastqc.html [2021-11-07 09:29:36,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2853_d12_rep1_fastqc.html [2021-11-07 09:29:36,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2877_d10_rep1_fastqc.html [2021-11-07 09:29:36,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2877_d10_rep1_fastqc.html [2021-11-07 09:29:36,510] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2878_d02_rep1_fastqc.html [2021-11-07 09:29:36,512] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2878_d02_rep1_fastqc.html [2021-11-07 09:29:36,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2856_d06_rep1_fastqc.html [2021-11-07 09:29:36,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2856_d06_rep1_fastqc.html [2021-11-07 09:29:36,630] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2858_d12_rep1_fastqc.html [2021-11-07 09:29:36,631] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2858_d12_rep1_fastqc.html [2021-11-07 09:29:36,688] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2855_d02_rep1_fastqc.html [2021-11-07 09:29:36,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_2855_d02_rep1_fastqc.html [2021-11-07 09:29:36,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3008_d06_rep1_fastqc.html [2021-11-07 09:29:36,737] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n02_3008_d06_rep1_fastqc.html [2021-11-07 09:29:36,820] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n01_3004_d02_rep1_fastqc.html [2021-11-07 09:29:36,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n01_3004_d02_rep1_fastqc.html [2021-11-07 09:29:36,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF7KYBGXK_n01_2854_d06_rep1_fastqc.html [2021-11-07 09:29:36,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF7KYBGXK_n01_2854_d06_rep1_fastqc.html [2021-11-07 09:29:37,373] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-07 09:29:37,375] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-07 09:29:37,464] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 181 samples (table) [2021-11-07 09:29:37,466] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-07 09:29:37,475] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-07 09:29:37,480] multiqc [DEBUG ] No samples found: conpair [2021-11-07 09:29:37,486] multiqc [DEBUG ] No samples found: peddy [2021-11-07 09:29:37,491] multiqc [DEBUG ] No samples found: somalier [2021-11-07 09:29:37,496] multiqc [DEBUG ] No samples found: methylQA [2021-11-07 09:29:37,504] multiqc [DEBUG ] No samples found: mosdepth [2021-11-07 09:29:37,508] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-07 09:29:37,512] multiqc [DEBUG ] No samples found: qualimap [2021-11-07 09:29:37,517] multiqc [DEBUG ] No samples found: preseq [2021-11-07 09:29:37,522] multiqc [DEBUG ] No samples found: quast [2021-11-07 09:29:37,527] multiqc [DEBUG ] No samples found: qorts [2021-11-07 09:29:37,532] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-07 09:29:37,537] multiqc [DEBUG ] No samples found: rockhopper [2021-11-07 09:29:37,542] multiqc [DEBUG ] No samples found: rsem [2021-11-07 09:29:37,552] multiqc [DEBUG ] No samples found: rseqc [2021-11-07 09:29:37,557] multiqc [DEBUG ] No samples found: busco [2021-11-07 09:29:37,562] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-07 09:29:37,567] multiqc [DEBUG ] No samples found: disambiguate [2021-11-07 09:29:37,573] multiqc [DEBUG ] No samples found: supernova [2021-11-07 09:29:37,585] multiqc [DEBUG ] No samples found: deeptools [2021-11-07 09:29:37,590] multiqc [DEBUG ] No samples found: sargasso [2021-11-07 09:29:37,596] multiqc [DEBUG ] No samples found: verifybamid [2021-11-07 09:29:37,601] multiqc [DEBUG ] No samples found: mirtrace [2021-11-07 09:29:37,606] multiqc [DEBUG ] No samples found: happy [2021-11-07 09:29:37,611] multiqc [DEBUG ] No samples found: mirtop [2021-11-07 09:29:37,618] multiqc [DEBUG ] No samples found: homer [2021-11-07 09:29:37,623] multiqc [DEBUG ] No samples found: macs2 [2021-11-07 09:29:37,628] multiqc [DEBUG ] No samples found: theta2 [2021-11-07 09:29:37,633] multiqc [DEBUG ] No samples found: snpeff [2021-11-07 09:29:37,640] multiqc [DEBUG ] No samples found: gatk [2021-11-07 09:29:37,645] multiqc [DEBUG ] No samples found: htseq [2021-11-07 09:29:37,650] multiqc [DEBUG ] No samples found: bcftools [2021-11-07 09:29:37,655] multiqc [DEBUG ] No samples found: featureCounts [2021-11-07 09:29:37,662] multiqc [DEBUG ] No samples found: fgbio [2021-11-07 09:29:37,675] multiqc [DEBUG ] No samples found: dragen [2021-11-07 09:29:37,679] multiqc [DEBUG ] No samples found: dedup [2021-11-07 09:29:37,684] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-07 09:29:37,707] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-07 09:29:37,711] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-07 09:29:37,714] multiqc [DEBUG ] No samples found: picard [2021-11-07 09:29:37,718] multiqc [DEBUG ] No samples found: prokka [2021-11-07 09:29:37,723] multiqc [DEBUG ] No samples found: samblaster [2021-11-07 09:29:37,730] multiqc [DEBUG ] No samples found: samtools [2021-11-07 09:29:37,736] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-07 09:29:37,741] multiqc [DEBUG ] No samples found: bamtools [2021-11-07 09:29:37,745] multiqc [DEBUG ] No samples found: jellyfish [2021-11-07 09:29:37,752] multiqc [DEBUG ] No samples found: vcftools [2021-11-07 09:29:37,757] multiqc [DEBUG ] No samples found: longranger [2021-11-07 09:29:37,762] multiqc [DEBUG ] No samples found: stacks [2021-11-07 09:29:37,767] multiqc [DEBUG ] No samples found: varscan2 [2021-11-07 09:29:37,780] multiqc [DEBUG ] No samples found: bbmap [2021-11-07 09:29:37,785] multiqc [DEBUG ] No samples found: bismark [2021-11-07 09:29:37,790] multiqc [DEBUG ] No samples found: biscuit [2021-11-07 09:29:37,795] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-07 09:29:37,800] multiqc [DEBUG ] No samples found: hicup [2021-11-07 09:29:37,805] multiqc [DEBUG ] No samples found: hicpro [2021-11-07 09:29:37,809] multiqc [DEBUG ] No samples found: salmon [2021-11-07 09:29:37,814] multiqc [DEBUG ] No samples found: kallisto [2021-11-07 09:29:37,819] multiqc [DEBUG ] No samples found: slamdunk [2021-11-07 09:29:37,823] multiqc [DEBUG ] No samples found: star [2021-11-07 09:29:37,828] multiqc [DEBUG ] No samples found: hisat2 [2021-11-07 09:29:37,832] multiqc [DEBUG ] No samples found: tophat [2021-11-07 09:29:37,837] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-07 09:29:37,841] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-07 09:29:37,846] multiqc [DEBUG ] No samples found: snpsplit [2021-11-07 09:29:37,851] multiqc [DEBUG ] No samples found: kat [2021-11-07 09:29:37,855] multiqc [DEBUG ] No samples found: leehom [2021-11-07 09:29:37,860] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-07 09:29:37,864] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-07 09:29:37,868] multiqc [DEBUG ] No samples found: cutadapt [2021-11-07 09:29:37,873] multiqc [DEBUG ] No samples found: flexbar [2021-11-07 09:29:37,878] multiqc [DEBUG ] No samples found: kaiju [2021-11-07 09:29:37,883] multiqc [DEBUG ] No samples found: kraken [2021-11-07 09:29:37,888] multiqc [DEBUG ] No samples found: malt [2021-11-07 09:29:37,892] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-07 09:29:37,897] multiqc [DEBUG ] No samples found: sickle [2021-11-07 09:29:37,901] multiqc [DEBUG ] No samples found: skewer [2021-11-07 09:29:37,906] multiqc [DEBUG ] No samples found: sortmerna [2021-11-07 09:29:37,910] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-07 09:29:37,915] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-07 09:29:37,921] multiqc [DEBUG ] No samples found: afterqc [2021-11-07 09:29:37,926] multiqc [DEBUG ] No samples found: fastp [2021-11-07 09:30:09,506] multiqc.modules.fastqc.fastqc [INFO ] Found 362 reports [2021-11-07 09:30:38,901] multiqc [DEBUG ] No samples found: pycoqc [2021-11-07 09:30:38,906] multiqc [DEBUG ] No samples found: minionqc [2021-11-07 09:30:38,910] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-07 09:30:38,915] multiqc [DEBUG ] No samples found: clusterflow [2021-11-07 09:30:38,920] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-07 09:30:38,926] multiqc [DEBUG ] No samples found: interop [2021-11-07 09:30:38,931] multiqc [DEBUG ] No samples found: ivar [2021-11-07 09:30:38,935] multiqc [DEBUG ] No samples found: flash [2021-11-07 09:30:38,939] multiqc [DEBUG ] No samples found: seqyclean [2021-11-07 09:30:38,940] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-07 09:30:38,940] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-07 09:30:38,940] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-07 09:30:38,940] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-07 09:30:39,355] multiqc [INFO ] Compressing plot data [2021-11-07 09:30:39,476] multiqc [INFO ] Report : multiqc_report.html [2021-11-07 09:30:39,476] multiqc [INFO ] Data : multiqc_data [2021-11-07 09:30:39,476] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11642121/tmpinoqr2ld/multiqc_data' to '/scratch/gencore/logs/html/HF7KYBGXK/merged/multiqc_data' [2021-11-07 09:30:39,620] multiqc [INFO ] MultiQC complete