[2021-11-08 19:46:08,804] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-08 19:46:08,804] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-08 19:46:08,804] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-08 19:46:08,805] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-08 19:46:08,805] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-08 19:46:08,805] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMY5DRXY/merged [2021-11-08 19:46:10,308] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-08 19:46:10,308] multiqc [INFO ] This is MultiQC v1.9 [2021-11-08 19:46:10,308] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJMY5DRXY/merged [2021-11-08 19:46:10,308] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJMY5DRXY/merged [2021-11-08 19:46:10,308] multiqc [INFO ] Template : default [2021-11-08 19:46:10,309] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-08 19:46:10,309] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJMY5DRXY/merged [2021-11-08 19:46:10,309] 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 [2021-11-08 19:46:10,309] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11715586/tmpm8rczfwh [2021-11-08 19:46:10,429] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr448_fastqc.html [2021-11-08 19:46:10,431] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2021-11-08 19:46:14,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr409_fastqc.html [2021-11-08 19:46:14,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr409_fastqc.html [2021-11-08 19:46:14,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr413_fastqc.html [2021-11-08 19:46:14,315] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr413_fastqc.html [2021-11-08 19:46:14,378] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr449_fastqc.html [2021-11-08 19:46:14,379] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr449_fastqc.html [2021-11-08 19:46:14,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr473_fastqc.html [2021-11-08 19:46:14,436] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr473_fastqc.html [2021-11-08 19:46:14,507] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr414_fastqc.html [2021-11-08 19:46:14,509] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr414_fastqc.html [2021-11-08 19:46:14,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr454_fastqc.html [2021-11-08 19:46:14,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr454_fastqc.html [2021-11-08 19:46:14,628] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr402_fastqc.html [2021-11-08 19:46:14,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr402_fastqc.html [2021-11-08 19:46:14,683] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr438_fastqc.html [2021-11-08 19:46:14,685] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr438_fastqc.html [2021-11-08 19:46:14,745] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr468_fastqc.html [2021-11-08 19:46:14,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr468_fastqc.html [2021-11-08 19:46:14,807] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr434_fastqc.html [2021-11-08 19:46:14,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr434_fastqc.html [2021-11-08 19:46:14,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr431_fastqc.html [2021-11-08 19:46:14,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr431_fastqc.html [2021-11-08 19:46:14,907] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr467_fastqc.html [2021-11-08 19:46:14,909] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr467_fastqc.html [2021-11-08 19:46:14,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr471_fastqc.html [2021-11-08 19:46:14,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr471_fastqc.html [2021-11-08 19:46:15,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr465_fastqc.html [2021-11-08 19:46:15,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr465_fastqc.html [2021-11-08 19:46:15,103] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr457_fastqc.html [2021-11-08 19:46:15,104] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMY5DRXY_n01_dpr457_fastqc.html [2021-11-08 19:46:15,523] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-08 19:46:15,525] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-08 19:46:15,566] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 78 samples (table) [2021-11-08 19:46:15,568] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-08 19:46:15,577] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-08 19:46:15,582] multiqc [DEBUG ] No samples found: conpair [2021-11-08 19:46:15,586] multiqc [DEBUG ] No samples found: peddy [2021-11-08 19:46:15,591] multiqc [DEBUG ] No samples found: somalier [2021-11-08 19:46:15,596] multiqc [DEBUG ] No samples found: methylQA [2021-11-08 19:46:15,604] multiqc [DEBUG ] No samples found: mosdepth [2021-11-08 19:46:15,608] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-08 19:46:15,611] multiqc [DEBUG ] No samples found: qualimap [2021-11-08 19:46:15,616] multiqc [DEBUG ] No samples found: preseq [2021-11-08 19:46:15,620] multiqc [DEBUG ] No samples found: quast [2021-11-08 19:46:15,625] multiqc [DEBUG ] No samples found: qorts [2021-11-08 19:46:15,630] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-08 19:46:15,634] multiqc [DEBUG ] No samples found: rockhopper [2021-11-08 19:46:15,638] multiqc [DEBUG ] No samples found: rsem [2021-11-08 19:46:15,649] multiqc [DEBUG ] No samples found: rseqc [2021-11-08 19:46:15,653] multiqc [DEBUG ] No samples found: busco [2021-11-08 19:46:15,658] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-08 19:46:15,662] multiqc [DEBUG ] No samples found: disambiguate [2021-11-08 19:46:15,666] multiqc [DEBUG ] No samples found: supernova [2021-11-08 19:46:15,679] multiqc [DEBUG ] No samples found: deeptools [2021-11-08 19:46:15,684] multiqc [DEBUG ] No samples found: sargasso [2021-11-08 19:46:15,688] multiqc [DEBUG ] No samples found: verifybamid [2021-11-08 19:46:15,693] multiqc [DEBUG ] No samples found: mirtrace [2021-11-08 19:46:15,698] multiqc [DEBUG ] No samples found: happy [2021-11-08 19:46:15,703] multiqc [DEBUG ] No samples found: mirtop [2021-11-08 19:46:15,710] multiqc [DEBUG ] No samples found: homer [2021-11-08 19:46:15,714] multiqc [DEBUG ] No samples found: macs2 [2021-11-08 19:46:15,718] multiqc [DEBUG ] No samples found: theta2 [2021-11-08 19:46:15,722] multiqc [DEBUG ] No samples found: snpeff [2021-11-08 19:46:15,729] multiqc [DEBUG ] No samples found: gatk [2021-11-08 19:46:15,733] multiqc [DEBUG ] No samples found: htseq [2021-11-08 19:46:15,738] multiqc [DEBUG ] No samples found: bcftools [2021-11-08 19:46:15,742] multiqc [DEBUG ] No samples found: featureCounts [2021-11-08 19:46:15,748] multiqc [DEBUG ] No samples found: fgbio [2021-11-08 19:46:15,766] multiqc [DEBUG ] No samples found: dragen [2021-11-08 19:46:15,770] multiqc [DEBUG ] No samples found: dedup [2021-11-08 19:46:15,774] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-08 19:46:15,793] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-08 19:46:15,796] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-08 19:46:15,799] multiqc [DEBUG ] No samples found: picard [2021-11-08 19:46:15,803] multiqc [DEBUG ] No samples found: prokka [2021-11-08 19:46:15,807] multiqc [DEBUG ] No samples found: samblaster [2021-11-08 19:46:15,814] multiqc [DEBUG ] No samples found: samtools [2021-11-08 19:46:15,819] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-08 19:46:15,824] multiqc [DEBUG ] No samples found: bamtools [2021-11-08 19:46:15,828] multiqc [DEBUG ] No samples found: jellyfish [2021-11-08 19:46:15,834] multiqc [DEBUG ] No samples found: vcftools [2021-11-08 19:46:15,839] multiqc [DEBUG ] No samples found: longranger [2021-11-08 19:46:15,843] multiqc [DEBUG ] No samples found: stacks [2021-11-08 19:46:15,847] multiqc [DEBUG ] No samples found: varscan2 [2021-11-08 19:46:15,860] multiqc [DEBUG ] No samples found: bbmap [2021-11-08 19:46:15,864] multiqc [DEBUG ] No samples found: bismark [2021-11-08 19:46:15,869] multiqc [DEBUG ] No samples found: biscuit [2021-11-08 19:46:15,874] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-08 19:46:15,879] multiqc [DEBUG ] No samples found: hicup [2021-11-08 19:46:15,884] multiqc [DEBUG ] No samples found: hicpro [2021-11-08 19:46:15,888] multiqc [DEBUG ] No samples found: salmon [2021-11-08 19:46:15,892] multiqc [DEBUG ] No samples found: kallisto [2021-11-08 19:46:15,897] multiqc [DEBUG ] No samples found: slamdunk [2021-11-08 19:46:15,901] multiqc [DEBUG ] No samples found: star [2021-11-08 19:46:15,906] multiqc [DEBUG ] No samples found: hisat2 [2021-11-08 19:46:15,910] multiqc [DEBUG ] No samples found: tophat [2021-11-08 19:46:15,915] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-08 19:46:15,919] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-08 19:46:15,924] multiqc [DEBUG ] No samples found: snpsplit [2021-11-08 19:46:15,928] multiqc [DEBUG ] No samples found: kat [2021-11-08 19:46:15,932] multiqc [DEBUG ] No samples found: leehom [2021-11-08 19:46:15,936] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-08 19:46:15,940] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-08 19:46:15,944] multiqc [DEBUG ] No samples found: cutadapt [2021-11-08 19:46:15,948] multiqc [DEBUG ] No samples found: flexbar [2021-11-08 19:46:15,952] multiqc [DEBUG ] No samples found: kaiju [2021-11-08 19:46:15,957] multiqc [DEBUG ] No samples found: kraken [2021-11-08 19:46:15,961] multiqc [DEBUG ] No samples found: malt [2021-11-08 19:46:15,966] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-08 19:46:15,969] multiqc [DEBUG ] No samples found: sickle [2021-11-08 19:46:15,974] multiqc [DEBUG ] No samples found: skewer [2021-11-08 19:46:15,977] multiqc [DEBUG ] No samples found: sortmerna [2021-11-08 19:46:15,981] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-08 19:46:15,986] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-08 19:46:15,990] multiqc [DEBUG ] No samples found: afterqc [2021-11-08 19:46:15,994] multiqc [DEBUG ] No samples found: fastp [2021-11-08 19:46:23,282] multiqc.modules.fastqc.fastqc [INFO ] Found 78 reports [2021-11-08 19:46:24,287] multiqc [DEBUG ] No samples found: pycoqc [2021-11-08 19:46:24,291] multiqc [DEBUG ] No samples found: minionqc [2021-11-08 19:46:24,295] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-08 19:46:24,300] multiqc [DEBUG ] No samples found: clusterflow [2021-11-08 19:46:24,305] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-08 19:46:24,310] multiqc [DEBUG ] No samples found: interop [2021-11-08 19:46:24,315] multiqc [DEBUG ] No samples found: ivar [2021-11-08 19:46:24,319] multiqc [DEBUG ] No samples found: flash [2021-11-08 19:46:24,323] multiqc [DEBUG ] No samples found: seqyclean [2021-11-08 19:46:24,323] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-08 19:46:24,323] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-08 19:46:24,323] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-08 19:46:24,323] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-08 19:46:24,413] multiqc [INFO ] Compressing plot data [2021-11-08 19:46:25,736] multiqc [INFO ] Report : multiqc_report.html [2021-11-08 19:46:25,736] multiqc [INFO ] Data : multiqc_data [2021-11-08 19:46:25,736] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11715586/tmpm8rczfwh/multiqc_data' to '/scratch/gencore/logs/html/HJMY5DRXY/merged/multiqc_data' [2021-11-08 19:46:25,852] multiqc [INFO ] MultiQC complete