[2022-11-23 21:25:05,922] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-23 21:25:05,922] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-23 21:25:05,922] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-23 21:25:05,923] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-23 21:25:05,923] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-23 21:25:05,923] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCJ57BGXN/merged [2022-11-23 21:25:06,778] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-23 21:25:06,779] multiqc [INFO ] This is MultiQC v1.9 [2022-11-23 21:25:06,779] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HCJ57BGXN/merged [2022-11-23 21:25:06,779] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HCJ57BGXN/merged [2022-11-23 21:25:06,779] multiqc [INFO ] Template : default [2022-11-23 21:25:06,779] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-23 21:25:06,779] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HCJ57BGXN/merged [2022-11-23 21:25:06,779] 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 [2022-11-23 21:25:06,779] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27282679/tmpvpaflqi6 [2022-11-23 21:25:06,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCJ57BGXN_2_fastqc.html [2022-11-23 21:25:06,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCJ57BGXN_2_fastqc.html [2022-11-23 21:25:06,943] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HCJ57BGXN_1_fastqc.html [2022-11-23 21:25:06,945] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HCJ57BGXN_1_fastqc.html [2022-11-23 21:25:07,323] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-23 21:25:07,325] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-23 21:25:07,328] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-11-23 21:25:07,331] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-23 21:25:07,336] multiqc [DEBUG ] No samples found: conpair [2022-11-23 21:25:07,341] multiqc [DEBUG ] No samples found: peddy [2022-11-23 21:25:07,346] multiqc [DEBUG ] No samples found: somalier [2022-11-23 21:25:07,351] multiqc [DEBUG ] No samples found: methylQA [2022-11-23 21:25:07,360] multiqc [DEBUG ] No samples found: mosdepth [2022-11-23 21:25:07,366] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-23 21:25:07,370] multiqc [DEBUG ] No samples found: qualimap [2022-11-23 21:25:07,375] multiqc [DEBUG ] No samples found: preseq [2022-11-23 21:25:07,380] multiqc [DEBUG ] No samples found: quast [2022-11-23 21:25:07,386] multiqc [DEBUG ] No samples found: qorts [2022-11-23 21:25:07,391] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-23 21:25:07,396] multiqc [DEBUG ] No samples found: rockhopper [2022-11-23 21:25:07,402] multiqc [DEBUG ] No samples found: rsem [2022-11-23 21:25:07,417] multiqc [DEBUG ] No samples found: rseqc [2022-11-23 21:25:07,421] multiqc [DEBUG ] No samples found: busco [2022-11-23 21:25:07,426] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-23 21:25:07,430] multiqc [DEBUG ] No samples found: disambiguate [2022-11-23 21:25:07,436] multiqc [DEBUG ] No samples found: supernova [2022-11-23 21:25:07,450] multiqc [DEBUG ] No samples found: deeptools [2022-11-23 21:25:07,455] multiqc [DEBUG ] No samples found: sargasso [2022-11-23 21:25:07,459] multiqc [DEBUG ] No samples found: verifybamid [2022-11-23 21:25:07,464] multiqc [DEBUG ] No samples found: mirtrace [2022-11-23 21:25:07,469] multiqc [DEBUG ] No samples found: happy [2022-11-23 21:25:07,476] multiqc [DEBUG ] No samples found: mirtop [2022-11-23 21:25:07,483] multiqc [DEBUG ] No samples found: homer [2022-11-23 21:25:07,488] multiqc [DEBUG ] No samples found: macs2 [2022-11-23 21:25:07,493] multiqc [DEBUG ] No samples found: theta2 [2022-11-23 21:25:07,498] multiqc [DEBUG ] No samples found: snpeff [2022-11-23 21:25:07,505] multiqc [DEBUG ] No samples found: gatk [2022-11-23 21:25:07,509] multiqc [DEBUG ] No samples found: htseq [2022-11-23 21:25:07,515] multiqc [DEBUG ] No samples found: bcftools [2022-11-23 21:25:07,522] multiqc [DEBUG ] No samples found: featureCounts [2022-11-23 21:25:07,528] multiqc [DEBUG ] No samples found: fgbio [2022-11-23 21:25:07,542] multiqc [DEBUG ] No samples found: dragen [2022-11-23 21:25:07,547] multiqc [DEBUG ] No samples found: dedup [2022-11-23 21:25:07,552] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-23 21:25:07,577] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-23 21:25:07,582] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-23 21:25:07,585] multiqc [DEBUG ] No samples found: picard [2022-11-23 21:25:07,590] multiqc [DEBUG ] No samples found: prokka [2022-11-23 21:25:07,594] multiqc [DEBUG ] No samples found: samblaster [2022-11-23 21:25:07,605] multiqc [DEBUG ] No samples found: samtools [2022-11-23 21:25:07,610] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-23 21:25:07,615] multiqc [DEBUG ] No samples found: bamtools [2022-11-23 21:25:07,619] multiqc [DEBUG ] No samples found: jellyfish [2022-11-23 21:25:07,626] multiqc [DEBUG ] No samples found: vcftools [2022-11-23 21:25:07,631] multiqc [DEBUG ] No samples found: longranger [2022-11-23 21:25:07,636] multiqc [DEBUG ] No samples found: stacks [2022-11-23 21:25:07,641] multiqc [DEBUG ] No samples found: varscan2 [2022-11-23 21:25:07,655] multiqc [DEBUG ] No samples found: bbmap [2022-11-23 21:25:07,660] multiqc [DEBUG ] No samples found: bismark [2022-11-23 21:25:07,665] multiqc [DEBUG ] No samples found: biscuit [2022-11-23 21:25:07,670] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-23 21:25:07,675] multiqc [DEBUG ] No samples found: hicup [2022-11-23 21:25:07,681] multiqc [DEBUG ] No samples found: hicpro [2022-11-23 21:25:07,687] multiqc [DEBUG ] No samples found: salmon [2022-11-23 21:25:07,693] multiqc [DEBUG ] No samples found: kallisto [2022-11-23 21:25:07,698] multiqc [DEBUG ] No samples found: slamdunk [2022-11-23 21:25:07,704] multiqc [DEBUG ] No samples found: star [2022-11-23 21:25:07,710] multiqc [DEBUG ] No samples found: hisat2 [2022-11-23 21:25:07,715] multiqc [DEBUG ] No samples found: tophat [2022-11-23 21:25:07,720] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-23 21:25:07,725] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-23 21:25:07,730] multiqc [DEBUG ] No samples found: snpsplit [2022-11-23 21:25:07,734] multiqc [DEBUG ] No samples found: kat [2022-11-23 21:25:07,739] multiqc [DEBUG ] No samples found: leehom [2022-11-23 21:25:07,744] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-23 21:25:07,748] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-23 21:25:07,753] multiqc [DEBUG ] No samples found: cutadapt [2022-11-23 21:25:07,757] multiqc [DEBUG ] No samples found: flexbar [2022-11-23 21:25:07,762] multiqc [DEBUG ] No samples found: kaiju [2022-11-23 21:25:07,767] multiqc [DEBUG ] No samples found: kraken [2022-11-23 21:25:07,772] multiqc [DEBUG ] No samples found: malt [2022-11-23 21:25:07,777] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-23 21:25:07,781] multiqc [DEBUG ] No samples found: sickle [2022-11-23 21:25:07,786] multiqc [DEBUG ] No samples found: skewer [2022-11-23 21:25:07,790] multiqc [DEBUG ] No samples found: sortmerna [2022-11-23 21:25:07,794] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-23 21:25:07,799] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-23 21:25:07,805] multiqc [DEBUG ] No samples found: afterqc [2022-11-23 21:25:07,810] multiqc [DEBUG ] No samples found: fastp [2022-11-23 21:25:07,896] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2022-11-23 21:25:07,946] multiqc [DEBUG ] No samples found: pycoqc [2022-11-23 21:25:07,951] multiqc [DEBUG ] No samples found: minionqc [2022-11-23 21:25:07,958] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-23 21:25:07,963] multiqc [DEBUG ] No samples found: clusterflow [2022-11-23 21:25:07,968] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-23 21:25:07,973] multiqc [DEBUG ] No samples found: interop [2022-11-23 21:25:07,977] multiqc [DEBUG ] No samples found: ivar [2022-11-23 21:25:07,982] multiqc [DEBUG ] No samples found: flash [2022-11-23 21:25:07,986] multiqc [DEBUG ] No samples found: seqyclean [2022-11-23 21:25:07,987] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-23 21:25:07,987] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-23 21:25:07,987] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-23 21:25:07,990] multiqc [INFO ] Compressing plot data [2022-11-23 21:25:08,029] multiqc [INFO ] Report : multiqc_report.html [2022-11-23 21:25:08,029] multiqc [INFO ] Data : multiqc_data [2022-11-23 21:25:08,029] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27282679/tmpvpaflqi6/multiqc_data' to '/scratch/gencore/logs/html/HCJ57BGXN/merged/multiqc_data' [2022-11-23 21:25:08,590] multiqc [INFO ] MultiQC complete