[2022-07-25 21:51:19,956] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-25 21:51:19,957] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-25 21:51:19,957] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-25 21:51:19,958] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-25 21:51:19,958] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-25 21:51:19,958] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF5FLDRX2/merged [2022-07-25 21:51:20,511] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-25 21:51:20,512] multiqc [INFO ] This is MultiQC v1.9 [2022-07-25 21:51:20,512] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HF5FLDRX2/merged [2022-07-25 21:51:20,512] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HF5FLDRX2/merged [2022-07-25 21:51:20,512] multiqc [INFO ] Template : default [2022-07-25 21:51:20,512] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-25 21:51:20,512] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HF5FLDRX2/merged [2022-07-25 21:51:20,512] 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 [2022-07-25 21:51:20,512] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22775668/tmprbc2azdf [2022-07-25 21:51:20,631] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br107_fastqc.html [2022-07-25 21:51:20,634] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HF5FLDRX2_n01_br110_fastqc.html [2022-07-25 21:51:24,102] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br97_fastqc.html [2022-07-25 21:51:24,104] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br97_fastqc.html [2022-07-25 21:51:24,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br115_fastqc.html [2022-07-25 21:51:24,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br115_fastqc.html [2022-07-25 21:51:24,187] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br125_fastqc.html [2022-07-25 21:51:24,189] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br125_fastqc.html [2022-07-25 21:51:24,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br117_fastqc.html [2022-07-25 21:51:24,231] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br117_fastqc.html [2022-07-25 21:51:24,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br97_fastqc.html [2022-07-25 21:51:24,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br97_fastqc.html [2022-07-25 21:51:24,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br107_fastqc.html [2022-07-25 21:51:24,316] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br107_fastqc.html [2022-07-25 21:51:24,356] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ03_fastqc.html [2022-07-25 21:51:24,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ03_fastqc.html [2022-07-25 21:51:24,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ03_fastqc.html [2022-07-25 21:51:24,403] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ03_fastqc.html [2022-07-25 21:51:24,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br103_fastqc.html [2022-07-25 21:51:24,446] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br103_fastqc.html [2022-07-25 21:51:24,487] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br124_fastqc.html [2022-07-25 21:51:24,489] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br124_fastqc.html [2022-07-25 21:51:24,530] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ07_fastqc.html [2022-07-25 21:51:24,532] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ07_fastqc.html [2022-07-25 21:51:24,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ02_fastqc.html [2022-07-25 21:51:24,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_OQ02_fastqc.html [2022-07-25 21:51:24,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ06_fastqc.html [2022-07-25 21:51:24,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ06_fastqc.html [2022-07-25 21:51:24,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br87_fastqc.html [2022-07-25 21:51:24,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br87_fastqc.html [2022-07-25 21:51:24,706] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br90_fastqc.html [2022-07-25 21:51:24,707] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br90_fastqc.html [2022-07-25 21:51:24,748] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br105_fastqc.html [2022-07-25 21:51:24,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br105_fastqc.html [2022-07-25 21:51:24,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br118_fastqc.html [2022-07-25 21:51:24,794] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br118_fastqc.html [2022-07-25 21:51:24,835] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br108_fastqc.html [2022-07-25 21:51:24,837] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_br108_fastqc.html [2022-07-25 21:51:24,878] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br88_fastqc.html [2022-07-25 21:51:24,880] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n02_br88_fastqc.html [2022-07-25 21:51:24,920] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ07_fastqc.html [2022-07-25 21:51:24,922] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF5FLDRX2_n01_OQ07_fastqc.html [2022-07-25 21:51:25,282] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-25 21:51:25,284] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-25 21:51:25,300] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-25 21:51:25,323] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 48 samples (table) [2022-07-25 21:51:25,325] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-25 21:51:25,329] multiqc [DEBUG ] No samples found: conpair [2022-07-25 21:51:25,334] multiqc [DEBUG ] No samples found: peddy [2022-07-25 21:51:25,343] multiqc [DEBUG ] No samples found: somalier [2022-07-25 21:51:25,348] multiqc [DEBUG ] No samples found: methylQA [2022-07-25 21:51:25,355] multiqc [DEBUG ] No samples found: mosdepth [2022-07-25 21:51:25,359] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-25 21:51:25,363] multiqc [DEBUG ] No samples found: qualimap [2022-07-25 21:51:25,367] multiqc [DEBUG ] No samples found: preseq [2022-07-25 21:51:25,372] multiqc [DEBUG ] No samples found: quast [2022-07-25 21:51:25,376] multiqc [DEBUG ] No samples found: qorts [2022-07-25 21:51:25,381] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-25 21:51:25,385] multiqc [DEBUG ] No samples found: rockhopper [2022-07-25 21:51:25,391] multiqc [DEBUG ] No samples found: rsem [2022-07-25 21:51:25,402] multiqc [DEBUG ] No samples found: rseqc [2022-07-25 21:51:25,406] multiqc [DEBUG ] No samples found: busco [2022-07-25 21:51:25,410] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-25 21:51:25,414] multiqc [DEBUG ] No samples found: disambiguate [2022-07-25 21:51:25,419] multiqc [DEBUG ] No samples found: supernova [2022-07-25 21:51:25,433] multiqc [DEBUG ] No samples found: deeptools [2022-07-25 21:51:25,437] multiqc [DEBUG ] No samples found: sargasso [2022-07-25 21:51:25,442] multiqc [DEBUG ] No samples found: verifybamid [2022-07-25 21:51:25,446] multiqc [DEBUG ] No samples found: mirtrace [2022-07-25 21:51:25,451] multiqc [DEBUG ] No samples found: happy [2022-07-25 21:51:25,455] multiqc [DEBUG ] No samples found: mirtop [2022-07-25 21:51:25,461] multiqc [DEBUG ] No samples found: homer [2022-07-25 21:51:25,466] multiqc [DEBUG ] No samples found: macs2 [2022-07-25 21:51:25,469] multiqc [DEBUG ] No samples found: theta2 [2022-07-25 21:51:25,474] multiqc [DEBUG ] No samples found: snpeff [2022-07-25 21:51:25,481] multiqc [DEBUG ] No samples found: gatk [2022-07-25 21:51:25,485] multiqc [DEBUG ] No samples found: htseq [2022-07-25 21:51:25,490] multiqc [DEBUG ] No samples found: bcftools [2022-07-25 21:51:25,496] multiqc [DEBUG ] No samples found: featureCounts [2022-07-25 21:51:25,502] multiqc [DEBUG ] No samples found: fgbio [2022-07-25 21:51:25,515] multiqc [DEBUG ] No samples found: dragen [2022-07-25 21:51:25,519] multiqc [DEBUG ] No samples found: dedup [2022-07-25 21:51:25,524] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-25 21:51:25,547] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-25 21:51:25,551] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-25 21:51:25,553] multiqc [DEBUG ] No samples found: picard [2022-07-25 21:51:25,559] multiqc [DEBUG ] No samples found: prokka [2022-07-25 21:51:25,563] multiqc [DEBUG ] No samples found: samblaster [2022-07-25 21:51:25,574] multiqc [DEBUG ] No samples found: samtools [2022-07-25 21:51:25,578] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-25 21:51:25,583] multiqc [DEBUG ] No samples found: bamtools [2022-07-25 21:51:25,587] multiqc [DEBUG ] No samples found: jellyfish [2022-07-25 21:51:25,596] multiqc [DEBUG ] No samples found: vcftools [2022-07-25 21:51:25,601] multiqc [DEBUG ] No samples found: longranger [2022-07-25 21:51:25,606] multiqc [DEBUG ] No samples found: stacks [2022-07-25 21:51:25,610] multiqc [DEBUG ] No samples found: varscan2 [2022-07-25 21:51:25,625] multiqc [DEBUG ] No samples found: bbmap [2022-07-25 21:51:25,629] multiqc [DEBUG ] No samples found: bismark [2022-07-25 21:51:25,636] multiqc [DEBUG ] No samples found: biscuit [2022-07-25 21:51:25,641] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-25 21:51:25,645] multiqc [DEBUG ] No samples found: hicup [2022-07-25 21:51:25,650] multiqc [DEBUG ] No samples found: hicpro [2022-07-25 21:51:25,654] multiqc [DEBUG ] No samples found: salmon [2022-07-25 21:51:25,658] multiqc [DEBUG ] No samples found: kallisto [2022-07-25 21:51:25,662] multiqc [DEBUG ] No samples found: slamdunk [2022-07-25 21:51:25,667] multiqc [DEBUG ] No samples found: star [2022-07-25 21:51:25,672] multiqc [DEBUG ] No samples found: hisat2 [2022-07-25 21:51:25,676] multiqc [DEBUG ] No samples found: tophat [2022-07-25 21:51:25,680] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-25 21:51:25,685] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-25 21:51:25,689] multiqc [DEBUG ] No samples found: snpsplit [2022-07-25 21:51:25,693] multiqc [DEBUG ] No samples found: kat [2022-07-25 21:51:25,697] multiqc [DEBUG ] No samples found: leehom [2022-07-25 21:51:25,701] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-25 21:51:25,705] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-25 21:51:25,709] multiqc [DEBUG ] No samples found: cutadapt [2022-07-25 21:51:25,713] multiqc [DEBUG ] No samples found: flexbar [2022-07-25 21:51:25,718] multiqc [DEBUG ] No samples found: kaiju [2022-07-25 21:51:25,722] multiqc [DEBUG ] No samples found: kraken [2022-07-25 21:51:25,726] multiqc [DEBUG ] No samples found: malt [2022-07-25 21:51:25,731] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-25 21:51:25,735] multiqc [DEBUG ] No samples found: sickle [2022-07-25 21:51:25,741] multiqc [DEBUG ] No samples found: skewer [2022-07-25 21:51:25,745] multiqc [DEBUG ] No samples found: sortmerna [2022-07-25 21:51:25,749] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-25 21:51:25,753] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-25 21:51:25,757] multiqc [DEBUG ] No samples found: afterqc [2022-07-25 21:51:25,762] multiqc [DEBUG ] No samples found: fastp [2022-07-25 21:51:30,514] multiqc.modules.fastqc.fastqc [INFO ] Found 96 reports [2022-07-25 21:51:31,248] multiqc [DEBUG ] No samples found: pycoqc [2022-07-25 21:51:31,254] multiqc [DEBUG ] No samples found: minionqc [2022-07-25 21:51:31,260] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-25 21:51:31,266] multiqc [DEBUG ] No samples found: clusterflow [2022-07-25 21:51:31,274] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-25 21:51:31,279] multiqc [DEBUG ] No samples found: interop [2022-07-25 21:51:31,284] multiqc [DEBUG ] No samples found: ivar [2022-07-25 21:51:31,291] multiqc [DEBUG ] No samples found: flash [2022-07-25 21:51:31,298] multiqc [DEBUG ] No samples found: seqyclean [2022-07-25 21:51:31,298] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-25 21:51:31,298] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-25 21:51:31,299] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-25 21:51:31,299] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-25 21:51:31,418] multiqc [INFO ] Compressing plot data [2022-07-25 21:51:32,981] multiqc [INFO ] Report : multiqc_report.html [2022-07-25 21:51:32,981] multiqc [INFO ] Data : multiqc_data [2022-07-25 21:51:32,982] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22775668/tmprbc2azdf/multiqc_data' to '/scratch/gencore/logs/html/HF5FLDRX2/merged/multiqc_data' [2022-07-25 21:51:58,418] multiqc [INFO ] MultiQC complete