[2022-03-11 08:00:22,203] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-11 08:00:22,203] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-11 08:00:22,203] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-11 08:00:22,204] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-11 08:00:22,204] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-11 08:00:22,205] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJHWJAFX3/merged [2022-03-11 08:00:22,959] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-11 08:00:22,959] multiqc [INFO ] This is MultiQC v1.9 [2022-03-11 08:00:22,960] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HJHWJAFX3/merged [2022-03-11 08:00:22,960] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HJHWJAFX3/merged [2022-03-11 08:00:22,960] multiqc [INFO ] Template : default [2022-03-11 08:00:22,960] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-11 08:00:22,960] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HJHWJAFX3/merged [2022-03-11 08:00:22,961] 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 [2022-03-11 08:00:22,961] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15935244/tmpir2k5key [2022-03-11 08:00:23,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep2_fastqc.html [2022-03-11 08:00:23,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep2_fastqc.html [2022-03-11 08:00:23,135] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep2_fastqc.html [2022-03-11 08:00:23,137] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep2_fastqc.html [2022-03-11 08:00:23,181] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep3_fastqc.html [2022-03-11 08:00:23,183] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep3_fastqc.html [2022-03-11 08:00:23,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:23,230] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-11 08:00:28,488] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep3_fastqc.html [2022-03-11 08:00:28,490] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep3_fastqc.html [2022-03-11 08:00:28,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep2_fastqc.html [2022-03-11 08:00:28,535] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep2_fastqc.html [2022-03-11 08:00:28,576] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep3_fastqc.html [2022-03-11 08:00:28,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep3_fastqc.html [2022-03-11 08:00:28,620] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_undetermined_fastqc.html [2022-03-11 08:00:28,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_undetermined_fastqc.html [2022-03-11 08:00:28,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep3_fastqc.html [2022-03-11 08:00:28,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep3_fastqc.html [2022-03-11 08:00:28,715] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep1_fastqc.html [2022-03-11 08:00:28,717] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep1_fastqc.html [2022-03-11 08:00:28,761] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep1_fastqc.html [2022-03-11 08:00:28,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep1_fastqc.html [2022-03-11 08:00:28,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep1_fastqc.html [2022-03-11 08:00:28,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep1_fastqc.html [2022-03-11 08:00:28,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep3_fastqc.html [2022-03-11 08:00:28,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep3_fastqc.html [2022-03-11 08:00:28,909] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_undetermined_fastqc.html [2022-03-11 08:00:28,911] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_undetermined_fastqc.html [2022-03-11 08:00:28,963] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep2_fastqc.html [2022-03-11 08:00:28,964] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep2_fastqc.html [2022-03-11 08:00:29,014] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep1_fastqc.html [2022-03-11 08:00:29,015] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3688_rep1_fastqc.html [2022-03-11 08:00:29,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep2_fastqc.html [2022-03-11 08:00:29,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_67192_rep2_fastqc.html [2022-03-11 08:00:29,108] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep1_fastqc.html [2022-03-11 08:00:29,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_67192_rep1_fastqc.html [2022-03-11 08:00:29,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep1_fastqc.html [2022-03-11 08:00:29,154] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3694_rep1_fastqc.html [2022-03-11 08:00:29,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep2_fastqc.html [2022-03-11 08:00:29,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n02_3688_rep2_fastqc.html [2022-03-11 08:00:29,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep3_fastqc.html [2022-03-11 08:00:29,246] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJHWJAFX3_n01_3694_rep3_fastqc.html [2022-03-11 08:00:29,824] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-11 08:00:29,826] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-11 08:00:29,838] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 10 samples (table) [2022-03-11 08:00:29,840] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-11 08:00:29,848] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-11 08:00:29,855] multiqc [DEBUG ] No samples found: conpair [2022-03-11 08:00:29,862] multiqc [DEBUG ] No samples found: peddy [2022-03-11 08:00:29,872] multiqc [DEBUG ] No samples found: somalier [2022-03-11 08:00:29,878] multiqc [DEBUG ] No samples found: methylQA [2022-03-11 08:00:29,890] multiqc [DEBUG ] No samples found: mosdepth [2022-03-11 08:00:29,896] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-11 08:00:29,900] multiqc [DEBUG ] No samples found: qualimap [2022-03-11 08:00:29,907] multiqc [DEBUG ] No samples found: preseq [2022-03-11 08:00:29,913] multiqc [DEBUG ] No samples found: quast [2022-03-11 08:00:29,920] multiqc [DEBUG ] No samples found: qorts [2022-03-11 08:00:29,927] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-11 08:00:29,932] multiqc [DEBUG ] No samples found: rockhopper [2022-03-11 08:00:29,938] multiqc [DEBUG ] No samples found: rsem [2022-03-11 08:00:29,961] multiqc [DEBUG ] No samples found: rseqc [2022-03-11 08:00:29,972] multiqc [DEBUG ] No samples found: busco [2022-03-11 08:00:29,980] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-11 08:00:29,986] multiqc [DEBUG ] No samples found: disambiguate [2022-03-11 08:00:29,993] multiqc [DEBUG ] No samples found: supernova [2022-03-11 08:00:30,013] multiqc [DEBUG ] No samples found: deeptools [2022-03-11 08:00:30,022] multiqc [DEBUG ] No samples found: sargasso [2022-03-11 08:00:30,028] multiqc [DEBUG ] No samples found: verifybamid [2022-03-11 08:00:30,034] multiqc [DEBUG ] No samples found: mirtrace [2022-03-11 08:00:30,041] multiqc [DEBUG ] No samples found: happy [2022-03-11 08:00:30,048] multiqc [DEBUG ] No samples found: mirtop [2022-03-11 08:00:30,061] multiqc [DEBUG ] No samples found: homer [2022-03-11 08:00:30,069] multiqc [DEBUG ] No samples found: macs2 [2022-03-11 08:00:30,075] multiqc [DEBUG ] No samples found: theta2 [2022-03-11 08:00:30,082] multiqc [DEBUG ] No samples found: snpeff [2022-03-11 08:00:30,093] multiqc [DEBUG ] No samples found: gatk [2022-03-11 08:00:30,101] multiqc [DEBUG ] No samples found: htseq [2022-03-11 08:00:30,109] multiqc [DEBUG ] No samples found: bcftools [2022-03-11 08:00:30,116] multiqc [DEBUG ] No samples found: featureCounts [2022-03-11 08:00:30,125] multiqc [DEBUG ] No samples found: fgbio [2022-03-11 08:00:30,155] multiqc [DEBUG ] No samples found: dragen [2022-03-11 08:00:30,164] multiqc [DEBUG ] No samples found: dedup [2022-03-11 08:00:30,171] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-11 08:00:30,212] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-11 08:00:30,219] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-11 08:00:30,222] multiqc [DEBUG ] No samples found: picard [2022-03-11 08:00:30,228] multiqc [DEBUG ] No samples found: prokka [2022-03-11 08:00:30,234] multiqc [DEBUG ] No samples found: samblaster [2022-03-11 08:00:30,245] multiqc [DEBUG ] No samples found: samtools [2022-03-11 08:00:30,252] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-11 08:00:30,259] multiqc [DEBUG ] No samples found: bamtools [2022-03-11 08:00:30,265] multiqc [DEBUG ] No samples found: jellyfish [2022-03-11 08:00:30,275] multiqc [DEBUG ] No samples found: vcftools [2022-03-11 08:00:30,282] multiqc [DEBUG ] No samples found: longranger [2022-03-11 08:00:30,288] multiqc [DEBUG ] No samples found: stacks [2022-03-11 08:00:30,294] multiqc [DEBUG ] No samples found: varscan2 [2022-03-11 08:00:30,314] multiqc [DEBUG ] No samples found: bbmap [2022-03-11 08:00:30,321] multiqc [DEBUG ] No samples found: bismark [2022-03-11 08:00:30,337] multiqc [DEBUG ] No samples found: biscuit [2022-03-11 08:00:30,347] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-11 08:00:30,355] multiqc [DEBUG ] No samples found: hicup [2022-03-11 08:00:30,362] multiqc [DEBUG ] No samples found: hicpro [2022-03-11 08:00:30,368] multiqc [DEBUG ] No samples found: salmon [2022-03-11 08:00:30,375] multiqc [DEBUG ] No samples found: kallisto [2022-03-11 08:00:30,381] multiqc [DEBUG ] No samples found: slamdunk [2022-03-11 08:00:30,387] multiqc [DEBUG ] No samples found: star [2022-03-11 08:00:30,393] multiqc [DEBUG ] No samples found: hisat2 [2022-03-11 08:00:30,398] multiqc [DEBUG ] No samples found: tophat [2022-03-11 08:00:30,405] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-11 08:00:30,411] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-11 08:00:30,416] multiqc [DEBUG ] No samples found: snpsplit [2022-03-11 08:00:30,422] multiqc [DEBUG ] No samples found: kat [2022-03-11 08:00:30,428] multiqc [DEBUG ] No samples found: leehom [2022-03-11 08:00:30,434] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-11 08:00:30,440] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-11 08:00:30,446] multiqc [DEBUG ] No samples found: cutadapt [2022-03-11 08:00:30,453] multiqc [DEBUG ] No samples found: flexbar [2022-03-11 08:00:30,462] multiqc [DEBUG ] No samples found: kaiju [2022-03-11 08:00:30,470] multiqc [DEBUG ] No samples found: kraken [2022-03-11 08:00:30,477] multiqc [DEBUG ] No samples found: malt [2022-03-11 08:00:30,483] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-11 08:00:30,489] multiqc [DEBUG ] No samples found: sickle [2022-03-11 08:00:30,494] multiqc [DEBUG ] No samples found: skewer [2022-03-11 08:00:30,500] multiqc [DEBUG ] No samples found: sortmerna [2022-03-11 08:00:30,505] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-11 08:00:30,511] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-11 08:00:30,518] multiqc [DEBUG ] No samples found: afterqc [2022-03-11 08:00:30,524] multiqc [DEBUG ] No samples found: fastp [2022-03-11 08:00:31,164] multiqc.modules.fastqc.fastqc [INFO ] Found 20 reports [2022-03-11 08:00:31,544] multiqc [DEBUG ] No samples found: pycoqc [2022-03-11 08:00:31,549] multiqc [DEBUG ] No samples found: minionqc [2022-03-11 08:00:31,555] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-11 08:00:31,561] multiqc [DEBUG ] No samples found: clusterflow [2022-03-11 08:00:31,567] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-11 08:00:31,573] multiqc [DEBUG ] No samples found: interop [2022-03-11 08:00:31,579] multiqc [DEBUG ] No samples found: ivar [2022-03-11 08:00:31,585] multiqc [DEBUG ] No samples found: flash [2022-03-11 08:00:31,591] multiqc [DEBUG ] No samples found: seqyclean [2022-03-11 08:00:31,591] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-11 08:00:31,591] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-11 08:00:31,591] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-11 08:00:31,591] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-11 08:00:31,613] multiqc [INFO ] Compressing plot data [2022-03-11 08:00:31,997] multiqc [INFO ] Report : multiqc_report.html [2022-03-11 08:00:31,997] multiqc [INFO ] Data : multiqc_data [2022-03-11 08:00:31,997] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15935244/tmpir2k5key/multiqc_data' to '/scratch/gencore/logs/html/HJHWJAFX3/merged/multiqc_data' [2022-03-11 08:00:32,147] multiqc [INFO ] MultiQC complete