[2022-11-20 04:24:08,058] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-20 04:24:08,058] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-20 04:24:08,058] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-20 04:24:08,059] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-20 04:24:08,059] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-20 04:24:08,059] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KKT88/1 [2022-11-20 04:24:08,553] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-20 04:24:08,553] multiqc [INFO ] This is MultiQC v1.9 [2022-11-20 04:24:08,553] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KKT88/1 [2022-11-20 04:24:08,553] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KKT88/1 [2022-11-20 04:24:08,553] multiqc [INFO ] Template : default [2022-11-20 04:24:08,553] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-20 04:24:08,553] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KKT88/1 [2022-11-20 04:24:08,554] 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 [2022-11-20 04:24:08,554] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27160640/tmpcg2jgnx1 [2022-11-20 04:24:08,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S0-2022_fastqc.html [2022-11-20 04:24:08,705] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S0-2022_fastqc.html [2022-11-20 04:24:08,750] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_undetermined_fastqc.html [2022-11-20 04:24:08,752] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_undetermined_fastqc.html [2022-11-20 04:24:08,791] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-20 04:24:08,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-11-20 04:24:08,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S6-2022_fastqc.html [2022-11-20 04:24:08,876] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S6-2022_fastqc.html [2022-11-20 04:24:08,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S0-2022_fastqc.html [2022-11-20 04:24:08,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S0-2022_fastqc.html [2022-11-20 04:24:08,965] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S7-2022_fastqc.html [2022-11-20 04:24:08,967] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S7-2022_fastqc.html [2022-11-20 04:24:09,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S8-2022_fastqc.html [2022-11-20 04:24:09,011] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n01_S8-2022_fastqc.html [2022-11-20 04:24:09,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_undetermined_fastqc.html [2022-11-20 04:24:09,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_undetermined_fastqc.html [2022-11-20 04:24:09,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S8-2022_fastqc.html [2022-11-20 04:24:09,095] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S8-2022_fastqc.html [2022-11-20 04:24:09,135] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S6-2022_fastqc.html [2022-11-20 04:24:09,137] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S6-2022_fastqc.html [2022-11-20 04:24:09,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S7-2022_fastqc.html [2022-11-20 04:24:09,181] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KKT88_l01_n02_S7-2022_fastqc.html [2022-11-20 04:24:09,590] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-20 04:24:09,595] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-20 04:24:09,606] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-20 04:24:09,609] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 5 samples (table) [2022-11-20 04:24:09,618] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-20 04:24:09,625] multiqc [DEBUG ] No samples found: conpair [2022-11-20 04:24:09,633] multiqc [DEBUG ] No samples found: peddy [2022-11-20 04:24:09,643] multiqc [DEBUG ] No samples found: somalier [2022-11-20 04:24:09,651] multiqc [DEBUG ] No samples found: methylQA [2022-11-20 04:24:09,666] multiqc [DEBUG ] No samples found: mosdepth [2022-11-20 04:24:09,673] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-20 04:24:09,680] multiqc [DEBUG ] No samples found: qualimap [2022-11-20 04:24:09,689] multiqc [DEBUG ] No samples found: preseq [2022-11-20 04:24:09,696] multiqc [DEBUG ] No samples found: quast [2022-11-20 04:24:09,706] multiqc [DEBUG ] No samples found: qorts [2022-11-20 04:24:09,714] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-20 04:24:09,723] multiqc [DEBUG ] No samples found: rockhopper [2022-11-20 04:24:09,731] multiqc [DEBUG ] No samples found: rsem [2022-11-20 04:24:09,754] multiqc [DEBUG ] No samples found: rseqc [2022-11-20 04:24:09,761] multiqc [DEBUG ] No samples found: busco [2022-11-20 04:24:09,771] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-20 04:24:09,778] multiqc [DEBUG ] No samples found: disambiguate [2022-11-20 04:24:09,788] multiqc [DEBUG ] No samples found: supernova [2022-11-20 04:24:09,824] multiqc [DEBUG ] No samples found: deeptools [2022-11-20 04:24:09,834] multiqc [DEBUG ] No samples found: sargasso [2022-11-20 04:24:09,842] multiqc [DEBUG ] No samples found: verifybamid [2022-11-20 04:24:09,851] multiqc [DEBUG ] No samples found: mirtrace [2022-11-20 04:24:09,859] multiqc [DEBUG ] No samples found: happy [2022-11-20 04:24:09,868] multiqc [DEBUG ] No samples found: mirtop [2022-11-20 04:24:09,880] multiqc [DEBUG ] No samples found: homer [2022-11-20 04:24:09,889] multiqc [DEBUG ] No samples found: macs2 [2022-11-20 04:24:09,894] multiqc [DEBUG ] No samples found: theta2 [2022-11-20 04:24:09,903] multiqc [DEBUG ] No samples found: snpeff [2022-11-20 04:24:09,921] multiqc [DEBUG ] No samples found: gatk [2022-11-20 04:24:09,929] multiqc [DEBUG ] No samples found: htseq [2022-11-20 04:24:09,940] multiqc [DEBUG ] No samples found: bcftools [2022-11-20 04:24:09,950] multiqc [DEBUG ] No samples found: featureCounts [2022-11-20 04:24:09,963] multiqc [DEBUG ] No samples found: fgbio [2022-11-20 04:24:09,999] multiqc [DEBUG ] No samples found: dragen [2022-11-20 04:24:10,008] multiqc [DEBUG ] No samples found: dedup [2022-11-20 04:24:10,017] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-20 04:24:10,081] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-20 04:24:10,087] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-20 04:24:10,090] multiqc [DEBUG ] No samples found: picard [2022-11-20 04:24:10,099] multiqc [DEBUG ] No samples found: prokka [2022-11-20 04:24:10,104] multiqc [DEBUG ] No samples found: samblaster [2022-11-20 04:24:10,125] multiqc [DEBUG ] No samples found: samtools [2022-11-20 04:24:10,134] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-20 04:24:10,143] multiqc [DEBUG ] No samples found: bamtools [2022-11-20 04:24:10,149] multiqc [DEBUG ] No samples found: jellyfish [2022-11-20 04:24:10,164] multiqc [DEBUG ] No samples found: vcftools [2022-11-20 04:24:10,173] multiqc [DEBUG ] No samples found: longranger [2022-11-20 04:24:10,181] multiqc [DEBUG ] No samples found: stacks [2022-11-20 04:24:10,190] multiqc [DEBUG ] No samples found: varscan2 [2022-11-20 04:24:10,222] multiqc [DEBUG ] No samples found: bbmap [2022-11-20 04:24:10,232] multiqc [DEBUG ] No samples found: bismark [2022-11-20 04:24:10,241] multiqc [DEBUG ] No samples found: biscuit [2022-11-20 04:24:10,249] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-20 04:24:10,256] multiqc [DEBUG ] No samples found: hicup [2022-11-20 04:24:10,265] multiqc [DEBUG ] No samples found: hicpro [2022-11-20 04:24:10,271] multiqc [DEBUG ] No samples found: salmon [2022-11-20 04:24:10,281] multiqc [DEBUG ] No samples found: kallisto [2022-11-20 04:24:10,289] multiqc [DEBUG ] No samples found: slamdunk [2022-11-20 04:24:10,300] multiqc [DEBUG ] No samples found: star [2022-11-20 04:24:10,309] multiqc [DEBUG ] No samples found: hisat2 [2022-11-20 04:24:10,319] multiqc [DEBUG ] No samples found: tophat [2022-11-20 04:24:10,328] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-20 04:24:10,336] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-20 04:24:10,346] multiqc [DEBUG ] No samples found: snpsplit [2022-11-20 04:24:10,353] multiqc [DEBUG ] No samples found: kat [2022-11-20 04:24:10,359] multiqc [DEBUG ] No samples found: leehom [2022-11-20 04:24:10,369] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-20 04:24:10,376] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-20 04:24:10,386] multiqc [DEBUG ] No samples found: cutadapt [2022-11-20 04:24:10,393] multiqc [DEBUG ] No samples found: flexbar [2022-11-20 04:24:10,402] multiqc [DEBUG ] No samples found: kaiju [2022-11-20 04:24:10,410] multiqc [DEBUG ] No samples found: kraken [2022-11-20 04:24:10,418] multiqc [DEBUG ] No samples found: malt [2022-11-20 04:24:10,425] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-20 04:24:10,434] multiqc [DEBUG ] No samples found: sickle [2022-11-20 04:24:10,442] multiqc [DEBUG ] No samples found: skewer [2022-11-20 04:24:10,447] multiqc [DEBUG ] No samples found: sortmerna [2022-11-20 04:24:10,453] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-20 04:24:10,461] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-20 04:24:10,468] multiqc [DEBUG ] No samples found: afterqc [2022-11-20 04:24:10,476] multiqc [DEBUG ] No samples found: fastp [2022-11-20 04:24:10,566] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2022-11-20 04:24:10,753] multiqc [DEBUG ] No samples found: pycoqc [2022-11-20 04:24:10,763] multiqc [DEBUG ] No samples found: minionqc [2022-11-20 04:24:10,772] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-20 04:24:10,782] multiqc [DEBUG ] No samples found: clusterflow [2022-11-20 04:24:10,791] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-20 04:24:10,800] multiqc [DEBUG ] No samples found: interop [2022-11-20 04:24:10,809] multiqc [DEBUG ] No samples found: ivar [2022-11-20 04:24:10,818] multiqc [DEBUG ] No samples found: flash [2022-11-20 04:24:10,826] multiqc [DEBUG ] No samples found: seqyclean [2022-11-20 04:24:10,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-20 04:24:10,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-20 04:24:10,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-11-20 04:24:10,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-20 04:24:10,827] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-20 04:24:10,840] multiqc [INFO ] Compressing plot data [2022-11-20 04:24:11,048] multiqc [INFO ] Report : multiqc_report.html [2022-11-20 04:24:11,049] multiqc [INFO ] Data : multiqc_data [2022-11-20 04:24:11,049] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27160640/tmpcg2jgnx1/multiqc_data' to '/scratch/gencore/logs/html/000000000-KKT88/1/multiqc_data' [2022-11-20 04:24:42,288] multiqc [INFO ] MultiQC complete