[2022-12-07 16:43:35,190] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-07 16:43:35,190] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-07 16:43:35,190] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-07 16:43:35,191] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-07 16:43:35,191] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-07 16:43:35,191] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLTC3DRX2/merged [2022-12-07 16:43:35,708] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-07 16:43:35,708] multiqc [INFO ] This is MultiQC v1.9 [2022-12-07 16:43:35,708] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLTC3DRX2/merged [2022-12-07 16:43:35,708] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLTC3DRX2/merged [2022-12-07 16:43:35,708] multiqc [INFO ] Template : default [2022-12-07 16:43:35,708] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-07 16:43:35,708] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLTC3DRX2/merged [2022-12-07 16:43:35,709] 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 [2022-12-07 16:43:35,709] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27735228/tmp4r11tq1a [2022-12-07 16:43:35,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLTC3DRX2_2_fastqc.html [2022-12-07 16:43:35,829] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLTC3DRX2_2_fastqc.html [2022-12-07 16:43:35,877] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLTC3DRX2_1_fastqc.html [2022-12-07 16:43:35,879] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLTC3DRX2_1_fastqc.html [2022-12-07 16:43:35,921] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLTC3DRX2_4_fastqc.html [2022-12-07 16:43:35,922] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLTC3DRX2_4_fastqc.html [2022-12-07 16:43:35,964] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLTC3DRX2_3_fastqc.html [2022-12-07 16:43:35,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLTC3DRX2_3_fastqc.html [2022-12-07 16:43:36,511] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-07 16:43:36,512] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-07 16:43:36,516] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-12-07 16:43:36,518] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-07 16:43:36,523] multiqc [DEBUG ] No samples found: conpair [2022-12-07 16:43:36,527] multiqc [DEBUG ] No samples found: peddy [2022-12-07 16:43:36,532] multiqc [DEBUG ] No samples found: somalier [2022-12-07 16:43:36,538] multiqc [DEBUG ] No samples found: methylQA [2022-12-07 16:43:36,546] multiqc [DEBUG ] No samples found: mosdepth [2022-12-07 16:43:36,550] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-07 16:43:36,554] multiqc [DEBUG ] No samples found: qualimap [2022-12-07 16:43:36,558] multiqc [DEBUG ] No samples found: preseq [2022-12-07 16:43:36,563] multiqc [DEBUG ] No samples found: quast [2022-12-07 16:43:36,568] multiqc [DEBUG ] No samples found: qorts [2022-12-07 16:43:36,572] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-07 16:43:36,577] multiqc [DEBUG ] No samples found: rockhopper [2022-12-07 16:43:36,582] multiqc [DEBUG ] No samples found: rsem [2022-12-07 16:43:36,594] multiqc [DEBUG ] No samples found: rseqc [2022-12-07 16:43:36,600] multiqc [DEBUG ] No samples found: busco [2022-12-07 16:43:36,605] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-07 16:43:36,609] multiqc [DEBUG ] No samples found: disambiguate [2022-12-07 16:43:36,614] multiqc [DEBUG ] No samples found: supernova [2022-12-07 16:43:36,628] multiqc [DEBUG ] No samples found: deeptools [2022-12-07 16:43:36,633] multiqc [DEBUG ] No samples found: sargasso [2022-12-07 16:43:36,637] multiqc [DEBUG ] No samples found: verifybamid [2022-12-07 16:43:36,642] multiqc [DEBUG ] No samples found: mirtrace [2022-12-07 16:43:36,648] multiqc [DEBUG ] No samples found: happy [2022-12-07 16:43:36,652] multiqc [DEBUG ] No samples found: mirtop [2022-12-07 16:43:36,659] multiqc [DEBUG ] No samples found: homer [2022-12-07 16:43:36,664] multiqc [DEBUG ] No samples found: macs2 [2022-12-07 16:43:36,668] multiqc [DEBUG ] No samples found: theta2 [2022-12-07 16:43:36,673] multiqc [DEBUG ] No samples found: snpeff [2022-12-07 16:43:36,680] multiqc [DEBUG ] No samples found: gatk [2022-12-07 16:43:36,685] multiqc [DEBUG ] No samples found: htseq [2022-12-07 16:43:36,690] multiqc [DEBUG ] No samples found: bcftools [2022-12-07 16:43:36,695] multiqc [DEBUG ] No samples found: featureCounts [2022-12-07 16:43:36,701] multiqc [DEBUG ] No samples found: fgbio [2022-12-07 16:43:36,714] multiqc [DEBUG ] No samples found: dragen [2022-12-07 16:43:36,719] multiqc [DEBUG ] No samples found: dedup [2022-12-07 16:43:36,725] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-07 16:43:36,751] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-07 16:43:36,757] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-07 16:43:36,759] multiqc [DEBUG ] No samples found: picard [2022-12-07 16:43:36,764] multiqc [DEBUG ] No samples found: prokka [2022-12-07 16:43:36,769] multiqc [DEBUG ] No samples found: samblaster [2022-12-07 16:43:36,777] multiqc [DEBUG ] No samples found: samtools [2022-12-07 16:43:36,782] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-07 16:43:36,788] multiqc [DEBUG ] No samples found: bamtools [2022-12-07 16:43:36,794] multiqc [DEBUG ] No samples found: jellyfish [2022-12-07 16:43:36,802] multiqc [DEBUG ] No samples found: vcftools [2022-12-07 16:43:36,808] multiqc [DEBUG ] No samples found: longranger [2022-12-07 16:43:36,813] multiqc [DEBUG ] No samples found: stacks [2022-12-07 16:43:36,817] multiqc [DEBUG ] No samples found: varscan2 [2022-12-07 16:43:36,833] multiqc [DEBUG ] No samples found: bbmap [2022-12-07 16:43:36,838] multiqc [DEBUG ] No samples found: bismark [2022-12-07 16:43:36,843] multiqc [DEBUG ] No samples found: biscuit [2022-12-07 16:43:36,847] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-07 16:43:36,852] multiqc [DEBUG ] No samples found: hicup [2022-12-07 16:43:36,858] multiqc [DEBUG ] No samples found: hicpro [2022-12-07 16:43:36,862] multiqc [DEBUG ] No samples found: salmon [2022-12-07 16:43:36,867] multiqc [DEBUG ] No samples found: kallisto [2022-12-07 16:43:36,871] multiqc [DEBUG ] No samples found: slamdunk [2022-12-07 16:43:36,876] multiqc [DEBUG ] No samples found: star [2022-12-07 16:43:36,880] multiqc [DEBUG ] No samples found: hisat2 [2022-12-07 16:43:36,885] multiqc [DEBUG ] No samples found: tophat [2022-12-07 16:43:36,890] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-07 16:43:36,895] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-07 16:43:36,900] multiqc [DEBUG ] No samples found: snpsplit [2022-12-07 16:43:36,904] multiqc [DEBUG ] No samples found: kat [2022-12-07 16:43:36,908] multiqc [DEBUG ] No samples found: leehom [2022-12-07 16:43:36,913] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-07 16:43:36,918] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-07 16:43:36,923] multiqc [DEBUG ] No samples found: cutadapt [2022-12-07 16:43:36,927] multiqc [DEBUG ] No samples found: flexbar [2022-12-07 16:43:36,932] multiqc [DEBUG ] No samples found: kaiju [2022-12-07 16:43:36,937] multiqc [DEBUG ] No samples found: kraken [2022-12-07 16:43:36,942] multiqc [DEBUG ] No samples found: malt [2022-12-07 16:43:36,946] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-07 16:43:36,950] multiqc [DEBUG ] No samples found: sickle [2022-12-07 16:43:36,955] multiqc [DEBUG ] No samples found: skewer [2022-12-07 16:43:36,959] multiqc [DEBUG ] No samples found: sortmerna [2022-12-07 16:43:36,963] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-07 16:43:36,967] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-07 16:43:36,972] multiqc [DEBUG ] No samples found: afterqc [2022-12-07 16:43:36,977] multiqc [DEBUG ] No samples found: fastp [2022-12-07 16:43:37,140] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-12-07 16:43:37,188] multiqc [DEBUG ] No samples found: pycoqc [2022-12-07 16:43:37,192] multiqc [DEBUG ] No samples found: minionqc [2022-12-07 16:43:37,197] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-07 16:43:37,201] multiqc [DEBUG ] No samples found: clusterflow [2022-12-07 16:43:37,206] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-07 16:43:37,211] multiqc [DEBUG ] No samples found: interop [2022-12-07 16:43:37,216] multiqc [DEBUG ] No samples found: ivar [2022-12-07 16:43:37,220] multiqc [DEBUG ] No samples found: flash [2022-12-07 16:43:37,226] multiqc [DEBUG ] No samples found: seqyclean [2022-12-07 16:43:37,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-12-07 16:43:37,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-12-07 16:43:37,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-07 16:43:37,232] multiqc [INFO ] Compressing plot data [2022-12-07 16:43:37,306] multiqc [INFO ] Report : multiqc_report.html [2022-12-07 16:43:37,306] multiqc [INFO ] Data : multiqc_data [2022-12-07 16:43:37,306] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27735228/tmp4r11tq1a/multiqc_data' to '/scratch/gencore/logs/html/HLTC3DRX2/merged/multiqc_data' [2022-12-07 16:43:37,431] multiqc [INFO ] MultiQC complete