[2022-07-09 13:40:19,465] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-09 13:40:19,465] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-09 13:40:19,465] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-09 13:40:19,466] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-09 13:40:19,466] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-09 13:40:19,467] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNCMNAFX3/merged [2022-07-09 13:40:20,025] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-09 13:40:20,025] multiqc [INFO ] This is MultiQC v1.9 [2022-07-09 13:40:20,025] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNCMNAFX3/merged [2022-07-09 13:40:20,025] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNCMNAFX3/merged [2022-07-09 13:40:20,025] multiqc [INFO ] Template : default [2022-07-09 13:40:20,025] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-09 13:40:20,025] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNCMNAFX3/merged [2022-07-09 13:40:20,025] 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 [2022-07-09 13:40:20,025] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22004841/tmpgcb4n8bi [2022-07-09 13:40:20,127] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMNAFX3_n02_NPB-43__fastqc.html [2022-07-09 13:40:20,129] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMNAFX3_n02_NPB-43__fastqc.html [2022-07-09 13:40:20,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMNAFX3_n01_NPB-43__fastqc.html [2022-07-09 13:40:20,172] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMNAFX3_n01_NPB-43__fastqc.html [2022-07-09 13:40:20,212] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMNAFX3_n02_undetermined_fastqc.html [2022-07-09 13:40:20,214] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMNAFX3_n02_undetermined_fastqc.html [2022-07-09 13:40:20,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNCMNAFX3_n01_undetermined_fastqc.html [2022-07-09 13:40:20,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNCMNAFX3_n01_undetermined_fastqc.html [2022-07-09 13:40:20,522] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-09 13:40:20,523] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-09 13:40:20,528] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-07-09 13:40:20,529] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 2 samples (table) [2022-07-09 13:40:20,531] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-09 13:40:20,534] multiqc [DEBUG ] No samples found: conpair [2022-07-09 13:40:20,537] multiqc [DEBUG ] No samples found: peddy [2022-07-09 13:40:20,540] multiqc [DEBUG ] No samples found: somalier [2022-07-09 13:40:20,543] multiqc [DEBUG ] No samples found: methylQA [2022-07-09 13:40:20,548] multiqc [DEBUG ] No samples found: mosdepth [2022-07-09 13:40:20,551] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-09 13:40:20,553] multiqc [DEBUG ] No samples found: qualimap [2022-07-09 13:40:20,556] multiqc [DEBUG ] No samples found: preseq [2022-07-09 13:40:20,559] multiqc [DEBUG ] No samples found: quast [2022-07-09 13:40:20,562] multiqc [DEBUG ] No samples found: qorts [2022-07-09 13:40:20,565] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-09 13:40:20,568] multiqc [DEBUG ] No samples found: rockhopper [2022-07-09 13:40:20,572] multiqc [DEBUG ] No samples found: rsem [2022-07-09 13:40:20,577] multiqc [DEBUG ] No samples found: rseqc [2022-07-09 13:40:20,580] multiqc [DEBUG ] No samples found: busco [2022-07-09 13:40:20,583] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-09 13:40:20,586] multiqc [DEBUG ] No samples found: disambiguate [2022-07-09 13:40:20,589] multiqc [DEBUG ] No samples found: supernova [2022-07-09 13:40:20,595] multiqc [DEBUG ] No samples found: deeptools [2022-07-09 13:40:20,598] multiqc [DEBUG ] No samples found: sargasso [2022-07-09 13:40:20,601] multiqc [DEBUG ] No samples found: verifybamid [2022-07-09 13:40:20,604] multiqc [DEBUG ] No samples found: mirtrace [2022-07-09 13:40:20,607] multiqc [DEBUG ] No samples found: happy [2022-07-09 13:40:20,610] multiqc [DEBUG ] No samples found: mirtop [2022-07-09 13:40:20,614] multiqc [DEBUG ] No samples found: homer [2022-07-09 13:40:20,617] multiqc [DEBUG ] No samples found: macs2 [2022-07-09 13:40:20,620] multiqc [DEBUG ] No samples found: theta2 [2022-07-09 13:40:20,623] multiqc [DEBUG ] No samples found: snpeff [2022-07-09 13:40:20,626] multiqc [DEBUG ] No samples found: gatk [2022-07-09 13:40:20,629] multiqc [DEBUG ] No samples found: htseq [2022-07-09 13:40:20,633] multiqc [DEBUG ] No samples found: bcftools [2022-07-09 13:40:20,636] multiqc [DEBUG ] No samples found: featureCounts [2022-07-09 13:40:20,639] multiqc [DEBUG ] No samples found: fgbio [2022-07-09 13:40:20,645] multiqc [DEBUG ] No samples found: dragen [2022-07-09 13:40:20,648] multiqc [DEBUG ] No samples found: dedup [2022-07-09 13:40:20,651] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-09 13:40:20,661] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-09 13:40:20,664] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-09 13:40:20,666] multiqc [DEBUG ] No samples found: picard [2022-07-09 13:40:20,669] multiqc [DEBUG ] No samples found: prokka [2022-07-09 13:40:20,672] multiqc [DEBUG ] No samples found: samblaster [2022-07-09 13:40:20,677] multiqc [DEBUG ] No samples found: samtools [2022-07-09 13:40:20,680] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-09 13:40:20,683] multiqc [DEBUG ] No samples found: bamtools [2022-07-09 13:40:20,686] multiqc [DEBUG ] No samples found: jellyfish [2022-07-09 13:40:20,690] multiqc [DEBUG ] No samples found: vcftools [2022-07-09 13:40:20,693] multiqc [DEBUG ] No samples found: longranger [2022-07-09 13:40:20,696] multiqc [DEBUG ] No samples found: stacks [2022-07-09 13:40:20,699] multiqc [DEBUG ] No samples found: varscan2 [2022-07-09 13:40:20,705] multiqc [DEBUG ] No samples found: bbmap [2022-07-09 13:40:20,708] multiqc [DEBUG ] No samples found: bismark [2022-07-09 13:40:20,712] multiqc [DEBUG ] No samples found: biscuit [2022-07-09 13:40:20,715] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-09 13:40:20,718] multiqc [DEBUG ] No samples found: hicup [2022-07-09 13:40:20,721] multiqc [DEBUG ] No samples found: hicpro [2022-07-09 13:40:20,724] multiqc [DEBUG ] No samples found: salmon [2022-07-09 13:40:20,727] multiqc [DEBUG ] No samples found: kallisto [2022-07-09 13:40:20,730] multiqc [DEBUG ] No samples found: slamdunk [2022-07-09 13:40:20,733] multiqc [DEBUG ] No samples found: star [2022-07-09 13:40:20,736] multiqc [DEBUG ] No samples found: hisat2 [2022-07-09 13:40:20,739] multiqc [DEBUG ] No samples found: tophat [2022-07-09 13:40:20,742] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-09 13:40:20,745] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-09 13:40:20,748] multiqc [DEBUG ] No samples found: snpsplit [2022-07-09 13:40:20,751] multiqc [DEBUG ] No samples found: kat [2022-07-09 13:40:20,754] multiqc [DEBUG ] No samples found: leehom [2022-07-09 13:40:20,757] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-09 13:40:20,760] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-09 13:40:20,763] multiqc [DEBUG ] No samples found: cutadapt [2022-07-09 13:40:20,766] multiqc [DEBUG ] No samples found: flexbar [2022-07-09 13:40:20,769] multiqc [DEBUG ] No samples found: kaiju [2022-07-09 13:40:20,772] multiqc [DEBUG ] No samples found: kraken [2022-07-09 13:40:20,775] multiqc [DEBUG ] No samples found: malt [2022-07-09 13:40:20,778] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-09 13:40:20,781] multiqc [DEBUG ] No samples found: sickle [2022-07-09 13:40:20,784] multiqc [DEBUG ] No samples found: skewer [2022-07-09 13:40:20,787] multiqc [DEBUG ] No samples found: sortmerna [2022-07-09 13:40:20,790] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-09 13:40:20,793] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-09 13:40:20,796] multiqc [DEBUG ] No samples found: afterqc [2022-07-09 13:40:20,799] multiqc [DEBUG ] No samples found: fastp [2022-07-09 13:40:20,848] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-07-09 13:40:20,848] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HNCMNAFX3_n02_undetermined' [2022-07-09 13:40:20,848] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HNCMNAFX3_n01_undetermined' [2022-07-09 13:40:20,890] multiqc [DEBUG ] No samples found: pycoqc [2022-07-09 13:40:20,894] multiqc [DEBUG ] No samples found: minionqc [2022-07-09 13:40:20,897] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-09 13:40:20,900] multiqc [DEBUG ] No samples found: clusterflow [2022-07-09 13:40:20,903] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-09 13:40:20,906] multiqc [DEBUG ] No samples found: interop [2022-07-09 13:40:20,909] multiqc [DEBUG ] No samples found: ivar [2022-07-09 13:40:20,912] multiqc [DEBUG ] No samples found: flash [2022-07-09 13:40:20,915] multiqc [DEBUG ] No samples found: seqyclean [2022-07-09 13:40:20,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-09 13:40:20,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-09 13:40:20,915] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-09 13:40:20,920] multiqc [INFO ] Compressing plot data [2022-07-09 13:40:20,976] multiqc [INFO ] Report : multiqc_report.html [2022-07-09 13:40:20,976] multiqc [INFO ] Data : multiqc_data [2022-07-09 13:40:20,980] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22004841/tmpgcb4n8bi/multiqc_data' to '/scratch/gencore/logs/html/HNCMNAFX3/merged/multiqc_data' [2022-07-09 13:40:21,076] multiqc [INFO ] MultiQC complete