[2021-08-09 22:33:25,815] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-09 22:33:25,815] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-09 22:33:25,815] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-09 22:33:25,816] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-09 22:33:25,816] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-09 22:33:25,817] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHWGYBGXJ/merged [2021-08-09 22:33:27,251] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-09 22:33:27,251] multiqc [INFO ] This is MultiQC v1.9 [2021-08-09 22:33:27,251] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHWGYBGXJ/merged [2021-08-09 22:33:27,251] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHWGYBGXJ/merged [2021-08-09 22:33:27,251] multiqc [INFO ] Template : default [2021-08-09 22:33:27,251] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-09 22:33:27,251] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHWGYBGXJ/merged [2021-08-09 22:33:27,252] 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 [2021-08-09 22:33:27,252] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9282583/tmpuycpca3n [2021-08-09 22:33:27,393] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-09 22:33:27,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-09 22:33:27,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr323_fastqc.html [2021-08-09 22:33:27,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr323_fastqc.html [2021-08-09 22:33:27,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr320_fastqc.html [2021-08-09 22:33:27,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr320_fastqc.html [2021-08-09 22:33:27,621] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_undetermined_fastqc.html [2021-08-09 22:33:27,623] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_undetermined_fastqc.html [2021-08-09 22:33:27,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr319_fastqc.html [2021-08-09 22:33:27,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr319_fastqc.html [2021-08-09 22:33:27,710] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr315_fastqc.html [2021-08-09 22:33:27,712] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr315_fastqc.html [2021-08-09 22:33:27,755] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr317_fastqc.html [2021-08-09 22:33:27,757] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr317_fastqc.html [2021-08-09 22:33:27,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr324_fastqc.html [2021-08-09 22:33:27,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr324_fastqc.html [2021-08-09 22:33:27,846] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr322_fastqc.html [2021-08-09 22:33:27,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr322_fastqc.html [2021-08-09 22:33:27,891] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr318_fastqc.html [2021-08-09 22:33:27,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr318_fastqc.html [2021-08-09 22:33:27,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr316_fastqc.html [2021-08-09 22:33:27,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWGYBGXJ_n01_dpr316_fastqc.html [2021-08-09 22:33:28,501] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-09 22:33:28,502] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-09 22:33:28,514] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2021-08-09 22:33:28,515] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-09 22:33:28,525] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-09 22:33:28,530] multiqc [DEBUG ] No samples found: conpair [2021-08-09 22:33:28,536] multiqc [DEBUG ] No samples found: peddy [2021-08-09 22:33:28,544] multiqc [DEBUG ] No samples found: somalier [2021-08-09 22:33:28,549] multiqc [DEBUG ] No samples found: methylQA [2021-08-09 22:33:28,558] multiqc [DEBUG ] No samples found: mosdepth [2021-08-09 22:33:28,562] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-09 22:33:28,566] multiqc [DEBUG ] No samples found: qualimap [2021-08-09 22:33:28,572] multiqc [DEBUG ] No samples found: preseq [2021-08-09 22:33:28,580] multiqc [DEBUG ] No samples found: quast [2021-08-09 22:33:28,586] multiqc [DEBUG ] No samples found: qorts [2021-08-09 22:33:28,593] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-09 22:33:28,602] multiqc [DEBUG ] No samples found: rockhopper [2021-08-09 22:33:28,608] multiqc [DEBUG ] No samples found: rsem [2021-08-09 22:33:28,624] multiqc [DEBUG ] No samples found: rseqc [2021-08-09 22:33:28,632] multiqc [DEBUG ] No samples found: busco [2021-08-09 22:33:28,640] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-09 22:33:28,645] multiqc [DEBUG ] No samples found: disambiguate [2021-08-09 22:33:28,652] multiqc [DEBUG ] No samples found: supernova [2021-08-09 22:33:28,669] multiqc [DEBUG ] No samples found: deeptools [2021-08-09 22:33:28,675] multiqc [DEBUG ] No samples found: sargasso [2021-08-09 22:33:28,683] multiqc [DEBUG ] No samples found: verifybamid [2021-08-09 22:33:28,693] multiqc [DEBUG ] No samples found: mirtrace [2021-08-09 22:33:28,711] multiqc [DEBUG ] No samples found: happy [2021-08-09 22:33:28,720] multiqc [DEBUG ] No samples found: mirtop [2021-08-09 22:33:28,731] multiqc [DEBUG ] No samples found: homer [2021-08-09 22:33:28,736] multiqc [DEBUG ] No samples found: macs2 [2021-08-09 22:33:28,745] multiqc [DEBUG ] No samples found: theta2 [2021-08-09 22:33:28,750] multiqc [DEBUG ] No samples found: snpeff [2021-08-09 22:33:28,758] multiqc [DEBUG ] No samples found: gatk [2021-08-09 22:33:28,763] multiqc [DEBUG ] No samples found: htseq [2021-08-09 22:33:28,770] multiqc [DEBUG ] No samples found: bcftools [2021-08-09 22:33:28,776] multiqc [DEBUG ] No samples found: featureCounts [2021-08-09 22:33:28,784] multiqc [DEBUG ] No samples found: fgbio [2021-08-09 22:33:28,804] multiqc [DEBUG ] No samples found: dragen [2021-08-09 22:33:28,810] multiqc [DEBUG ] No samples found: dedup [2021-08-09 22:33:28,816] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-09 22:33:28,855] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-09 22:33:28,862] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-09 22:33:28,864] multiqc [DEBUG ] No samples found: picard [2021-08-09 22:33:28,870] multiqc [DEBUG ] No samples found: prokka [2021-08-09 22:33:28,876] multiqc [DEBUG ] No samples found: samblaster [2021-08-09 22:33:28,893] multiqc [DEBUG ] No samples found: samtools [2021-08-09 22:33:28,901] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-09 22:33:28,908] multiqc [DEBUG ] No samples found: bamtools [2021-08-09 22:33:28,915] multiqc [DEBUG ] No samples found: jellyfish [2021-08-09 22:33:28,926] multiqc [DEBUG ] No samples found: vcftools [2021-08-09 22:33:28,932] multiqc [DEBUG ] No samples found: longranger [2021-08-09 22:33:28,937] multiqc [DEBUG ] No samples found: stacks [2021-08-09 22:33:28,943] multiqc [DEBUG ] No samples found: varscan2 [2021-08-09 22:33:28,959] multiqc [DEBUG ] No samples found: bbmap [2021-08-09 22:33:28,965] multiqc [DEBUG ] No samples found: bismark [2021-08-09 22:33:28,972] multiqc [DEBUG ] No samples found: biscuit [2021-08-09 22:33:28,979] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-09 22:33:28,985] multiqc [DEBUG ] No samples found: hicup [2021-08-09 22:33:28,991] multiqc [DEBUG ] No samples found: hicpro [2021-08-09 22:33:28,997] multiqc [DEBUG ] No samples found: salmon [2021-08-09 22:33:29,003] multiqc [DEBUG ] No samples found: kallisto [2021-08-09 22:33:29,009] multiqc [DEBUG ] No samples found: slamdunk [2021-08-09 22:33:29,015] multiqc [DEBUG ] No samples found: star [2021-08-09 22:33:29,020] multiqc [DEBUG ] No samples found: hisat2 [2021-08-09 22:33:29,026] multiqc [DEBUG ] No samples found: tophat [2021-08-09 22:33:29,033] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-09 22:33:29,038] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-09 22:33:29,044] multiqc [DEBUG ] No samples found: snpsplit [2021-08-09 22:33:29,050] multiqc [DEBUG ] No samples found: kat [2021-08-09 22:33:29,056] multiqc [DEBUG ] No samples found: leehom [2021-08-09 22:33:29,063] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-09 22:33:29,068] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-09 22:33:29,074] multiqc [DEBUG ] No samples found: cutadapt [2021-08-09 22:33:29,079] multiqc [DEBUG ] No samples found: flexbar [2021-08-09 22:33:29,086] multiqc [DEBUG ] No samples found: kaiju [2021-08-09 22:33:29,092] multiqc [DEBUG ] No samples found: kraken [2021-08-09 22:33:29,098] multiqc [DEBUG ] No samples found: malt [2021-08-09 22:33:29,107] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-09 22:33:29,116] multiqc [DEBUG ] No samples found: sickle [2021-08-09 22:33:29,123] multiqc [DEBUG ] No samples found: skewer [2021-08-09 22:33:29,133] multiqc [DEBUG ] No samples found: sortmerna [2021-08-09 22:33:29,139] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-09 22:33:29,146] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-09 22:33:29,151] multiqc [DEBUG ] No samples found: afterqc [2021-08-09 22:33:29,158] multiqc [DEBUG ] No samples found: fastp [2021-08-09 22:33:30,000] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-08-09 22:33:30,230] multiqc [DEBUG ] No samples found: pycoqc [2021-08-09 22:33:30,236] multiqc [DEBUG ] No samples found: minionqc [2021-08-09 22:33:30,241] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-09 22:33:30,246] multiqc [DEBUG ] No samples found: clusterflow [2021-08-09 22:33:30,252] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-09 22:33:30,258] multiqc [DEBUG ] No samples found: interop [2021-08-09 22:33:30,264] multiqc [DEBUG ] No samples found: ivar [2021-08-09 22:33:30,271] multiqc [DEBUG ] No samples found: flash [2021-08-09 22:33:30,276] multiqc [DEBUG ] No samples found: seqyclean [2021-08-09 22:33:30,276] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-09 22:33:30,276] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-09 22:33:30,276] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-09 22:33:30,276] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-09 22:33:30,290] multiqc [INFO ] Compressing plot data [2021-08-09 22:33:30,452] multiqc [INFO ] Report : multiqc_report.html [2021-08-09 22:33:30,452] multiqc [INFO ] Data : multiqc_data [2021-08-09 22:33:30,452] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9282583/tmpuycpca3n/multiqc_data' to '/scratch/gencore/logs/html/HHWGYBGXJ/merged/multiqc_data' [2021-08-09 22:33:30,654] multiqc [INFO ] MultiQC complete