[2022-03-09 16:50:30,781] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-09 16:50:30,781] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-09 16:50:30,781] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-09 16:50:30,782] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-09 16:50:30,782] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-09 16:50:30,782] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H75NHBGXL/merged [2022-03-09 16:50:31,420] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-09 16:50:31,420] multiqc [INFO ] This is MultiQC v1.9 [2022-03-09 16:50:31,420] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H75NHBGXL/merged [2022-03-09 16:50:31,420] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H75NHBGXL/merged [2022-03-09 16:50:31,420] multiqc [INFO ] Template : default [2022-03-09 16:50:31,420] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-09 16:50:31,420] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H75NHBGXL/merged [2022-03-09 16:50:31,421] 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 [2022-03-09 16:50:31,421] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15811218/tmp7p_ilbqx [2022-03-09 16:50:31,534] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-09 16:50:31,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-09 16:50:31,692] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO19_fastqc.html [2022-03-09 16:50:31,694] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO19_fastqc.html [2022-03-09 16:50:31,738] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA53_fastqc.html [2022-03-09 16:50:31,740] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA53_fastqc.html [2022-03-09 16:50:31,780] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA49_fastqc.html [2022-03-09 16:50:31,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA49_fastqc.html [2022-03-09 16:50:31,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO12_fastqc.html [2022-03-09 16:50:31,825] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO12_fastqc.html [2022-03-09 16:50:31,865] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA54_fastqc.html [2022-03-09 16:50:31,867] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA54_fastqc.html [2022-03-09 16:50:31,938] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO15_fastqc.html [2022-03-09 16:50:31,940] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO15_fastqc.html [2022-03-09 16:50:31,985] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA50_fastqc.html [2022-03-09 16:50:31,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA50_fastqc.html [2022-03-09 16:50:32,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO17_fastqc.html [2022-03-09 16:50:32,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO17_fastqc.html [2022-03-09 16:50:32,103] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO16_fastqc.html [2022-03-09 16:50:32,105] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO16_fastqc.html [2022-03-09 16:50:32,148] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO18_fastqc.html [2022-03-09 16:50:32,150] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO18_fastqc.html [2022-03-09 16:50:32,192] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM307_fastqc.html [2022-03-09 16:50:32,194] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM307_fastqc.html [2022-03-09 16:50:32,235] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA47_fastqc.html [2022-03-09 16:50:32,237] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA47_fastqc.html [2022-03-09 16:50:32,278] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM306_fastqc.html [2022-03-09 16:50:32,279] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM306_fastqc.html [2022-03-09 16:50:32,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA55_fastqc.html [2022-03-09 16:50:32,323] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA55_fastqc.html [2022-03-09 16:50:32,373] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO21_fastqc.html [2022-03-09 16:50:32,375] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO21_fastqc.html [2022-03-09 16:50:32,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM313_fastqc.html [2022-03-09 16:50:32,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM313_fastqc.html [2022-03-09 16:50:32,463] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO20_fastqc.html [2022-03-09 16:50:32,465] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO20_fastqc.html [2022-03-09 16:50:32,508] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM305_fastqc.html [2022-03-09 16:50:32,510] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AKM305_fastqc.html [2022-03-09 16:50:32,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_undetermined_fastqc.html [2022-03-09 16:50:32,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_undetermined_fastqc.html [2022-03-09 16:50:32,594] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA48_fastqc.html [2022-03-09 16:50:32,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA48_fastqc.html [2022-03-09 16:50:32,636] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA46_fastqc.html [2022-03-09 16:50:32,638] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA46_fastqc.html [2022-03-09 16:50:32,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA52_fastqc.html [2022-03-09 16:50:32,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA52_fastqc.html [2022-03-09 16:50:32,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA51_fastqc.html [2022-03-09 16:50:32,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_AA51_fastqc.html [2022-03-09 16:50:32,782] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO14_fastqc.html [2022-03-09 16:50:32,784] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO14_fastqc.html [2022-03-09 16:50:32,827] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO13_fastqc.html [2022-03-09 16:50:32,829] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75NHBGXL_n01_DO13_fastqc.html [2022-03-09 16:50:33,471] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-09 16:50:33,473] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-09 16:50:33,492] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2022-03-09 16:50:33,493] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-09 16:50:33,504] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-09 16:50:33,509] multiqc [DEBUG ] No samples found: conpair [2022-03-09 16:50:33,515] multiqc [DEBUG ] No samples found: peddy [2022-03-09 16:50:33,521] multiqc [DEBUG ] No samples found: somalier [2022-03-09 16:50:33,527] multiqc [DEBUG ] No samples found: methylQA [2022-03-09 16:50:33,537] multiqc [DEBUG ] No samples found: mosdepth [2022-03-09 16:50:33,542] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-09 16:50:33,545] multiqc [DEBUG ] No samples found: qualimap [2022-03-09 16:50:33,551] multiqc [DEBUG ] No samples found: preseq [2022-03-09 16:50:33,557] multiqc [DEBUG ] No samples found: quast [2022-03-09 16:50:33,562] multiqc [DEBUG ] No samples found: qorts [2022-03-09 16:50:33,568] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-09 16:50:33,575] multiqc [DEBUG ] No samples found: rockhopper [2022-03-09 16:50:33,581] multiqc [DEBUG ] No samples found: rsem [2022-03-09 16:50:33,594] multiqc [DEBUG ] No samples found: rseqc [2022-03-09 16:50:33,599] multiqc [DEBUG ] No samples found: busco [2022-03-09 16:50:33,605] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-09 16:50:33,609] multiqc [DEBUG ] No samples found: disambiguate [2022-03-09 16:50:33,617] multiqc [DEBUG ] No samples found: supernova [2022-03-09 16:50:33,633] multiqc [DEBUG ] No samples found: deeptools [2022-03-09 16:50:33,639] multiqc [DEBUG ] No samples found: sargasso [2022-03-09 16:50:33,645] multiqc [DEBUG ] No samples found: verifybamid [2022-03-09 16:50:33,651] multiqc [DEBUG ] No samples found: mirtrace [2022-03-09 16:50:33,656] multiqc [DEBUG ] No samples found: happy [2022-03-09 16:50:33,662] multiqc [DEBUG ] No samples found: mirtop [2022-03-09 16:50:33,669] multiqc [DEBUG ] No samples found: homer [2022-03-09 16:50:33,675] multiqc [DEBUG ] No samples found: macs2 [2022-03-09 16:50:33,680] multiqc [DEBUG ] No samples found: theta2 [2022-03-09 16:50:33,686] multiqc [DEBUG ] No samples found: snpeff [2022-03-09 16:50:33,694] multiqc [DEBUG ] No samples found: gatk [2022-03-09 16:50:33,699] multiqc [DEBUG ] No samples found: htseq [2022-03-09 16:50:33,707] multiqc [DEBUG ] No samples found: bcftools [2022-03-09 16:50:33,712] multiqc [DEBUG ] No samples found: featureCounts [2022-03-09 16:50:33,722] multiqc [DEBUG ] No samples found: fgbio [2022-03-09 16:50:33,738] multiqc [DEBUG ] No samples found: dragen [2022-03-09 16:50:33,743] multiqc [DEBUG ] No samples found: dedup [2022-03-09 16:50:33,751] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-09 16:50:33,777] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-09 16:50:33,783] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-09 16:50:33,786] multiqc [DEBUG ] No samples found: picard [2022-03-09 16:50:33,793] multiqc [DEBUG ] No samples found: prokka [2022-03-09 16:50:33,798] multiqc [DEBUG ] No samples found: samblaster [2022-03-09 16:50:33,809] multiqc [DEBUG ] No samples found: samtools [2022-03-09 16:50:33,815] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-09 16:50:33,821] multiqc [DEBUG ] No samples found: bamtools [2022-03-09 16:50:33,826] multiqc [DEBUG ] No samples found: jellyfish [2022-03-09 16:50:33,835] multiqc [DEBUG ] No samples found: vcftools [2022-03-09 16:50:33,843] multiqc [DEBUG ] No samples found: longranger [2022-03-09 16:50:33,848] multiqc [DEBUG ] No samples found: stacks [2022-03-09 16:50:33,853] multiqc [DEBUG ] No samples found: varscan2 [2022-03-09 16:50:33,869] multiqc [DEBUG ] No samples found: bbmap [2022-03-09 16:50:33,874] multiqc [DEBUG ] No samples found: bismark [2022-03-09 16:50:33,879] multiqc [DEBUG ] No samples found: biscuit [2022-03-09 16:50:33,885] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-09 16:50:33,890] multiqc [DEBUG ] No samples found: hicup [2022-03-09 16:50:33,895] multiqc [DEBUG ] No samples found: hicpro [2022-03-09 16:50:33,900] multiqc [DEBUG ] No samples found: salmon [2022-03-09 16:50:33,905] multiqc [DEBUG ] No samples found: kallisto [2022-03-09 16:50:33,911] multiqc [DEBUG ] No samples found: slamdunk [2022-03-09 16:50:33,915] multiqc [DEBUG ] No samples found: star [2022-03-09 16:50:33,920] multiqc [DEBUG ] No samples found: hisat2 [2022-03-09 16:50:33,925] multiqc [DEBUG ] No samples found: tophat [2022-03-09 16:50:33,930] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-09 16:50:33,935] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-09 16:50:33,940] multiqc [DEBUG ] No samples found: snpsplit [2022-03-09 16:50:33,945] multiqc [DEBUG ] No samples found: kat [2022-03-09 16:50:33,951] multiqc [DEBUG ] No samples found: leehom [2022-03-09 16:50:33,956] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-09 16:50:33,961] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-09 16:50:33,966] multiqc [DEBUG ] No samples found: cutadapt [2022-03-09 16:50:33,972] multiqc [DEBUG ] No samples found: flexbar [2022-03-09 16:50:33,977] multiqc [DEBUG ] No samples found: kaiju [2022-03-09 16:50:33,982] multiqc [DEBUG ] No samples found: kraken [2022-03-09 16:50:33,987] multiqc [DEBUG ] No samples found: malt [2022-03-09 16:50:33,992] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-09 16:50:33,997] multiqc [DEBUG ] No samples found: sickle [2022-03-09 16:50:34,002] multiqc [DEBUG ] No samples found: skewer [2022-03-09 16:50:34,007] multiqc [DEBUG ] No samples found: sortmerna [2022-03-09 16:50:34,012] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-09 16:50:34,017] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-09 16:50:34,022] multiqc [DEBUG ] No samples found: afterqc [2022-03-09 16:50:34,028] multiqc [DEBUG ] No samples found: fastp [2022-03-09 16:50:36,298] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2022-03-09 16:50:36,868] multiqc [DEBUG ] No samples found: pycoqc [2022-03-09 16:50:36,873] multiqc [DEBUG ] No samples found: minionqc [2022-03-09 16:50:36,878] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-09 16:50:36,884] multiqc [DEBUG ] No samples found: clusterflow [2022-03-09 16:50:36,890] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-09 16:50:36,895] multiqc [DEBUG ] No samples found: interop [2022-03-09 16:50:36,900] multiqc [DEBUG ] No samples found: ivar [2022-03-09 16:50:36,905] multiqc [DEBUG ] No samples found: flash [2022-03-09 16:50:36,910] multiqc [DEBUG ] No samples found: seqyclean [2022-03-09 16:50:36,910] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-09 16:50:36,910] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-09 16:50:36,910] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-09 16:50:36,910] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-09 16:50:36,941] multiqc [INFO ] Compressing plot data [2022-03-09 16:50:37,384] multiqc [INFO ] Report : multiqc_report.html [2022-03-09 16:50:37,384] multiqc [INFO ] Data : multiqc_data [2022-03-09 16:50:37,384] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15811218/tmp7p_ilbqx/multiqc_data' to '/scratch/gencore/logs/html/H75NHBGXL/merged/multiqc_data' [2022-03-09 16:50:37,543] multiqc [INFO ] MultiQC complete