[2021-12-21 21:11:46,758] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-21 21:11:46,758] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-21 21:11:46,758] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-21 21:11:46,759] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-21 21:11:46,759] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-21 21:11:46,759] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWT3FBGXK/merged [2021-12-21 21:11:48,136] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-21 21:11:48,136] multiqc [INFO ] This is MultiQC v1.9 [2021-12-21 21:11:48,136] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWT3FBGXK/merged [2021-12-21 21:11:48,136] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWT3FBGXK/merged [2021-12-21 21:11:48,136] multiqc [INFO ] Template : default [2021-12-21 21:11:48,136] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-21 21:11:48,136] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWT3FBGXK/merged [2021-12-21 21:11:48,136] 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 [2021-12-21 21:11:48,137] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13245906/tmp5mpcryac [2021-12-21 21:11:48,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 21:11:48,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-12-21 21:11:48,368] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO02_fastqc.html [2021-12-21 21:11:48,370] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO02_fastqc.html [2021-12-21 21:11:48,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO08_fastqc.html [2021-12-21 21:11:48,437] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO08_fastqc.html [2021-12-21 21:11:48,503] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO05_fastqc.html [2021-12-21 21:11:48,505] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO05_fastqc.html [2021-12-21 21:11:48,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO06_fastqc.html [2021-12-21 21:11:48,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO06_fastqc.html [2021-12-21 21:11:48,615] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO11_fastqc.html [2021-12-21 21:11:48,617] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO11_fastqc.html [2021-12-21 21:11:48,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO09_fastqc.html [2021-12-21 21:11:48,679] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO09_fastqc.html [2021-12-21 21:11:48,726] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK75_fastqc.html [2021-12-21 21:11:48,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK75_fastqc.html [2021-12-21 21:11:48,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO04_fastqc.html [2021-12-21 21:11:48,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO04_fastqc.html [2021-12-21 21:11:48,833] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK82_fastqc.html [2021-12-21 21:11:48,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK82_fastqc.html [2021-12-21 21:11:48,885] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO10_fastqc.html [2021-12-21 21:11:48,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO10_fastqc.html [2021-12-21 21:11:48,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK79_fastqc.html [2021-12-21 21:11:48,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK79_fastqc.html [2021-12-21 21:11:48,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK81_fastqc.html [2021-12-21 21:11:48,982] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK81_fastqc.html [2021-12-21 21:11:49,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_undetermined_fastqc.html [2021-12-21 21:11:49,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_undetermined_fastqc.html [2021-12-21 21:11:49,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK74_fastqc.html [2021-12-21 21:11:49,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK74_fastqc.html [2021-12-21 21:11:49,126] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO07_fastqc.html [2021-12-21 21:11:49,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO07_fastqc.html [2021-12-21 21:11:49,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO03_fastqc.html [2021-12-21 21:11:49,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_DO03_fastqc.html [2021-12-21 21:11:49,234] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK80_fastqc.html [2021-12-21 21:11:49,236] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK80_fastqc.html [2021-12-21 21:11:49,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK78_fastqc.html [2021-12-21 21:11:49,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK78_fastqc.html [2021-12-21 21:11:49,320] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK77_fastqc.html [2021-12-21 21:11:49,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK77_fastqc.html [2021-12-21 21:11:49,362] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK76_fastqc.html [2021-12-21 21:11:49,363] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK76_fastqc.html [2021-12-21 21:11:49,423] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK83_fastqc.html [2021-12-21 21:11:49,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK83_fastqc.html [2021-12-21 21:11:49,466] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK84_fastqc.html [2021-12-21 21:11:49,468] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWT3FBGXK_n01_JK84_fastqc.html [2021-12-21 21:11:49,966] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 21:11:49,967] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-21 21:11:49,983] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 22 samples (table) [2021-12-21 21:11:49,993] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-21 21:11:49,994] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-21 21:11:50,000] multiqc [DEBUG ] No samples found: conpair [2021-12-21 21:11:50,005] multiqc [DEBUG ] No samples found: peddy [2021-12-21 21:11:50,011] multiqc [DEBUG ] No samples found: somalier [2021-12-21 21:11:50,015] multiqc [DEBUG ] No samples found: methylQA [2021-12-21 21:11:50,021] multiqc [DEBUG ] No samples found: mosdepth [2021-12-21 21:11:50,025] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-21 21:11:50,030] multiqc [DEBUG ] No samples found: qualimap [2021-12-21 21:11:50,034] multiqc [DEBUG ] No samples found: preseq [2021-12-21 21:11:50,038] multiqc [DEBUG ] No samples found: quast [2021-12-21 21:11:50,042] multiqc [DEBUG ] No samples found: qorts [2021-12-21 21:11:50,046] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-21 21:11:50,051] multiqc [DEBUG ] No samples found: rockhopper [2021-12-21 21:11:50,055] multiqc [DEBUG ] No samples found: rsem [2021-12-21 21:11:50,064] multiqc [DEBUG ] No samples found: rseqc [2021-12-21 21:11:50,067] multiqc [DEBUG ] No samples found: busco [2021-12-21 21:11:50,071] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-21 21:11:50,075] multiqc [DEBUG ] No samples found: disambiguate [2021-12-21 21:11:50,079] multiqc [DEBUG ] No samples found: supernova [2021-12-21 21:11:50,090] multiqc [DEBUG ] No samples found: deeptools [2021-12-21 21:11:50,094] multiqc [DEBUG ] No samples found: sargasso [2021-12-21 21:11:50,098] multiqc [DEBUG ] No samples found: verifybamid [2021-12-21 21:11:50,102] multiqc [DEBUG ] No samples found: mirtrace [2021-12-21 21:11:50,105] multiqc [DEBUG ] No samples found: happy [2021-12-21 21:11:50,109] multiqc [DEBUG ] No samples found: mirtop [2021-12-21 21:11:50,114] multiqc [DEBUG ] No samples found: homer [2021-12-21 21:11:50,118] multiqc [DEBUG ] No samples found: macs2 [2021-12-21 21:11:50,122] multiqc [DEBUG ] No samples found: theta2 [2021-12-21 21:11:50,126] multiqc [DEBUG ] No samples found: snpeff [2021-12-21 21:11:50,131] multiqc [DEBUG ] No samples found: gatk [2021-12-21 21:11:50,135] multiqc [DEBUG ] No samples found: htseq [2021-12-21 21:11:50,139] multiqc [DEBUG ] No samples found: bcftools [2021-12-21 21:11:50,143] multiqc [DEBUG ] No samples found: featureCounts [2021-12-21 21:11:50,147] multiqc [DEBUG ] No samples found: fgbio [2021-12-21 21:11:50,159] multiqc [DEBUG ] No samples found: dragen [2021-12-21 21:11:50,163] multiqc [DEBUG ] No samples found: dedup [2021-12-21 21:11:50,167] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-21 21:11:50,186] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-21 21:11:50,189] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-21 21:11:50,191] multiqc [DEBUG ] No samples found: picard [2021-12-21 21:11:50,195] multiqc [DEBUG ] No samples found: prokka [2021-12-21 21:11:50,199] multiqc [DEBUG ] No samples found: samblaster [2021-12-21 21:11:50,207] multiqc [DEBUG ] No samples found: samtools [2021-12-21 21:11:50,211] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-21 21:11:50,215] multiqc [DEBUG ] No samples found: bamtools [2021-12-21 21:11:50,218] multiqc [DEBUG ] No samples found: jellyfish [2021-12-21 21:11:50,224] multiqc [DEBUG ] No samples found: vcftools [2021-12-21 21:11:50,228] multiqc [DEBUG ] No samples found: longranger [2021-12-21 21:11:50,232] multiqc [DEBUG ] No samples found: stacks [2021-12-21 21:11:50,236] multiqc [DEBUG ] No samples found: varscan2 [2021-12-21 21:11:50,248] multiqc [DEBUG ] No samples found: bbmap [2021-12-21 21:11:50,252] multiqc [DEBUG ] No samples found: bismark [2021-12-21 21:11:50,257] multiqc [DEBUG ] No samples found: biscuit [2021-12-21 21:11:50,261] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-21 21:11:50,265] multiqc [DEBUG ] No samples found: hicup [2021-12-21 21:11:50,269] multiqc [DEBUG ] No samples found: hicpro [2021-12-21 21:11:50,273] multiqc [DEBUG ] No samples found: salmon [2021-12-21 21:11:50,276] multiqc [DEBUG ] No samples found: kallisto [2021-12-21 21:11:50,280] multiqc [DEBUG ] No samples found: slamdunk [2021-12-21 21:11:50,284] multiqc [DEBUG ] No samples found: star [2021-12-21 21:11:50,288] multiqc [DEBUG ] No samples found: hisat2 [2021-12-21 21:11:50,292] multiqc [DEBUG ] No samples found: tophat [2021-12-21 21:11:50,297] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-21 21:11:50,301] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-21 21:11:50,304] multiqc [DEBUG ] No samples found: snpsplit [2021-12-21 21:11:50,308] multiqc [DEBUG ] No samples found: kat [2021-12-21 21:11:50,312] multiqc [DEBUG ] No samples found: leehom [2021-12-21 21:11:50,316] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-21 21:11:50,319] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-21 21:11:50,323] multiqc [DEBUG ] No samples found: cutadapt [2021-12-21 21:11:50,328] multiqc [DEBUG ] No samples found: flexbar [2021-12-21 21:11:50,332] multiqc [DEBUG ] No samples found: kaiju [2021-12-21 21:11:50,335] multiqc [DEBUG ] No samples found: kraken [2021-12-21 21:11:50,339] multiqc [DEBUG ] No samples found: malt [2021-12-21 21:11:50,343] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-21 21:11:50,347] multiqc [DEBUG ] No samples found: sickle [2021-12-21 21:11:50,351] multiqc [DEBUG ] No samples found: skewer [2021-12-21 21:11:50,356] multiqc [DEBUG ] No samples found: sortmerna [2021-12-21 21:11:50,359] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-21 21:11:50,365] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-21 21:11:50,369] multiqc [DEBUG ] No samples found: afterqc [2021-12-21 21:11:50,373] multiqc [DEBUG ] No samples found: fastp [2021-12-21 21:11:52,235] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2021-12-21 21:11:52,705] multiqc [DEBUG ] No samples found: pycoqc [2021-12-21 21:11:52,709] multiqc [DEBUG ] No samples found: minionqc [2021-12-21 21:11:52,714] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-21 21:11:52,718] multiqc [DEBUG ] No samples found: clusterflow [2021-12-21 21:11:52,722] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-21 21:11:52,726] multiqc [DEBUG ] No samples found: interop [2021-12-21 21:11:52,731] multiqc [DEBUG ] No samples found: ivar [2021-12-21 21:11:52,735] multiqc [DEBUG ] No samples found: flash [2021-12-21 21:11:52,740] multiqc [DEBUG ] No samples found: seqyclean [2021-12-21 21:11:52,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-21 21:11:52,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-21 21:11:52,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-21 21:11:52,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-21 21:11:52,767] multiqc [INFO ] Compressing plot data [2021-12-21 21:11:53,172] multiqc [INFO ] Report : multiqc_report.html [2021-12-21 21:11:53,172] multiqc [INFO ] Data : multiqc_data [2021-12-21 21:11:53,172] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13245906/tmp5mpcryac/multiqc_data' to '/scratch/gencore/logs/html/HWT3FBGXK/merged/multiqc_data' [2021-12-21 21:11:53,283] multiqc [INFO ] MultiQC complete