[2022-07-13 06:35:02,880] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-13 06:35:02,880] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-13 06:35:02,880] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-13 06:35:02,881] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-13 06:35:02,881] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-13 06:35:02,881] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT2N7AFX3/merged [2022-07-13 06:35:03,621] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-13 06:35:03,621] multiqc [INFO ] This is MultiQC v1.9 [2022-07-13 06:35:03,621] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HT2N7AFX3/merged [2022-07-13 06:35:03,621] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HT2N7AFX3/merged [2022-07-13 06:35:03,621] multiqc [INFO ] Template : default [2022-07-13 06:35:03,621] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-13 06:35:03,621] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HT2N7AFX3/merged [2022-07-13 06:35:03,622] 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 [2022-07-13 06:35:03,622] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-22137071/tmpmn40byfj [2022-07-13 06:35:03,727] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Bot10plusIFNyR1_ETPR1_fastqc.html [2022-07-13 06:35:03,730] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Bot10plusIFNyR1_ETPR1_fastqc.html [2022-07-13 06:35:03,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortnoIFNyR1_Top10noIFNyR2_fastqc.html [2022-07-13 06:35:03,783] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortnoIFNyR1_Top10noIFNyR2_fastqc.html [2022-07-13 06:35:03,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-13 06:35:03,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-13 06:35:04,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortnoIFNyR2_fastqc.html [2022-07-13 06:35:04,233] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortnoIFNyR2_fastqc.html [2022-07-13 06:35:04,288] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Top10plusIFNyR1_Bot10plusIFNyR2_fastqc.html [2022-07-13 06:35:04,290] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Top10plusIFNyR1_Bot10plusIFNyR2_fastqc.html [2022-07-13 06:35:04,339] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Top10noIFNyR1_Bot10noIFNyR2_fastqc.html [2022-07-13 06:35:04,341] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Top10noIFNyR1_Bot10noIFNyR2_fastqc.html [2022-07-13 06:35:04,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Bot10noIFNyR1_PresortplusIFNyR2_fastqc.html [2022-07-13 06:35:04,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_Bot10noIFNyR1_PresortplusIFNyR2_fastqc.html [2022-07-13 06:35:04,439] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_undetermined_fastqc.html [2022-07-13 06:35:04,441] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_undetermined_fastqc.html [2022-07-13 06:35:04,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortplusIFNyR1_Top10plusIFNyR2_fastqc.html [2022-07-13 06:35:04,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2N7AFX3_n01_PresortplusIFNyR1_Top10plusIFNyR2_fastqc.html [2022-07-13 06:35:05,021] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-13 06:35:05,022] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-13 06:35:05,030] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-13 06:35:05,034] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2022-07-13 06:35:05,044] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-13 06:35:05,049] multiqc [DEBUG ] No samples found: conpair [2022-07-13 06:35:05,054] multiqc [DEBUG ] No samples found: peddy [2022-07-13 06:35:05,059] multiqc [DEBUG ] No samples found: somalier [2022-07-13 06:35:05,063] multiqc [DEBUG ] No samples found: methylQA [2022-07-13 06:35:05,072] multiqc [DEBUG ] No samples found: mosdepth [2022-07-13 06:35:05,076] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-13 06:35:05,080] multiqc [DEBUG ] No samples found: qualimap [2022-07-13 06:35:05,084] multiqc [DEBUG ] No samples found: preseq [2022-07-13 06:35:05,089] multiqc [DEBUG ] No samples found: quast [2022-07-13 06:35:05,094] multiqc [DEBUG ] No samples found: qorts [2022-07-13 06:35:05,099] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-13 06:35:05,104] multiqc [DEBUG ] No samples found: rockhopper [2022-07-13 06:35:05,109] multiqc [DEBUG ] No samples found: rsem [2022-07-13 06:35:05,122] multiqc [DEBUG ] No samples found: rseqc [2022-07-13 06:35:05,126] multiqc [DEBUG ] No samples found: busco [2022-07-13 06:35:05,131] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-13 06:35:05,136] multiqc [DEBUG ] No samples found: disambiguate [2022-07-13 06:35:05,141] multiqc [DEBUG ] No samples found: supernova [2022-07-13 06:35:05,154] multiqc [DEBUG ] No samples found: deeptools [2022-07-13 06:35:05,158] multiqc [DEBUG ] No samples found: sargasso [2022-07-13 06:35:05,163] multiqc [DEBUG ] No samples found: verifybamid [2022-07-13 06:35:05,168] multiqc [DEBUG ] No samples found: mirtrace [2022-07-13 06:35:05,173] multiqc [DEBUG ] No samples found: happy [2022-07-13 06:35:05,178] multiqc [DEBUG ] No samples found: mirtop [2022-07-13 06:35:05,184] multiqc [DEBUG ] No samples found: homer [2022-07-13 06:35:05,189] multiqc [DEBUG ] No samples found: macs2 [2022-07-13 06:35:05,194] multiqc [DEBUG ] No samples found: theta2 [2022-07-13 06:35:05,199] multiqc [DEBUG ] No samples found: snpeff [2022-07-13 06:35:05,206] multiqc [DEBUG ] No samples found: gatk [2022-07-13 06:35:05,210] multiqc [DEBUG ] No samples found: htseq [2022-07-13 06:35:05,216] multiqc [DEBUG ] No samples found: bcftools [2022-07-13 06:35:05,221] multiqc [DEBUG ] No samples found: featureCounts [2022-07-13 06:35:05,227] multiqc [DEBUG ] No samples found: fgbio [2022-07-13 06:35:05,240] multiqc [DEBUG ] No samples found: dragen [2022-07-13 06:35:05,245] multiqc [DEBUG ] No samples found: dedup [2022-07-13 06:35:05,250] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-13 06:35:05,275] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-13 06:35:05,279] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-13 06:35:05,281] multiqc [DEBUG ] No samples found: picard [2022-07-13 06:35:05,286] multiqc [DEBUG ] No samples found: prokka [2022-07-13 06:35:05,290] multiqc [DEBUG ] No samples found: samblaster [2022-07-13 06:35:05,299] multiqc [DEBUG ] No samples found: samtools [2022-07-13 06:35:05,304] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-13 06:35:05,309] multiqc [DEBUG ] No samples found: bamtools [2022-07-13 06:35:05,313] multiqc [DEBUG ] No samples found: jellyfish [2022-07-13 06:35:05,321] multiqc [DEBUG ] No samples found: vcftools [2022-07-13 06:35:05,326] multiqc [DEBUG ] No samples found: longranger [2022-07-13 06:35:05,331] multiqc [DEBUG ] No samples found: stacks [2022-07-13 06:35:05,335] multiqc [DEBUG ] No samples found: varscan2 [2022-07-13 06:35:05,349] multiqc [DEBUG ] No samples found: bbmap [2022-07-13 06:35:05,354] multiqc [DEBUG ] No samples found: bismark [2022-07-13 06:35:05,359] multiqc [DEBUG ] No samples found: biscuit [2022-07-13 06:35:05,364] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-13 06:35:05,369] multiqc [DEBUG ] No samples found: hicup [2022-07-13 06:35:05,374] multiqc [DEBUG ] No samples found: hicpro [2022-07-13 06:35:05,378] multiqc [DEBUG ] No samples found: salmon [2022-07-13 06:35:05,383] multiqc [DEBUG ] No samples found: kallisto [2022-07-13 06:35:05,387] multiqc [DEBUG ] No samples found: slamdunk [2022-07-13 06:35:05,392] multiqc [DEBUG ] No samples found: star [2022-07-13 06:35:05,397] multiqc [DEBUG ] No samples found: hisat2 [2022-07-13 06:35:05,402] multiqc [DEBUG ] No samples found: tophat [2022-07-13 06:35:05,406] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-13 06:35:05,411] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-13 06:35:05,416] multiqc [DEBUG ] No samples found: snpsplit [2022-07-13 06:35:05,420] multiqc [DEBUG ] No samples found: kat [2022-07-13 06:35:05,424] multiqc [DEBUG ] No samples found: leehom [2022-07-13 06:35:05,429] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-13 06:35:05,433] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-13 06:35:05,438] multiqc [DEBUG ] No samples found: cutadapt [2022-07-13 06:35:05,442] multiqc [DEBUG ] No samples found: flexbar [2022-07-13 06:35:05,447] multiqc [DEBUG ] No samples found: kaiju [2022-07-13 06:35:05,452] multiqc [DEBUG ] No samples found: kraken [2022-07-13 06:35:05,457] multiqc [DEBUG ] No samples found: malt [2022-07-13 06:35:05,461] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-13 06:35:05,466] multiqc [DEBUG ] No samples found: sickle [2022-07-13 06:35:05,470] multiqc [DEBUG ] No samples found: skewer [2022-07-13 06:35:05,475] multiqc [DEBUG ] No samples found: sortmerna [2022-07-13 06:35:05,479] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-13 06:35:05,484] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-13 06:35:05,488] multiqc [DEBUG ] No samples found: afterqc [2022-07-13 06:35:05,493] multiqc [DEBUG ] No samples found: fastp [2022-07-13 06:35:05,670] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2022-07-13 06:35:05,755] multiqc [DEBUG ] No samples found: pycoqc [2022-07-13 06:35:05,759] multiqc [DEBUG ] No samples found: minionqc [2022-07-13 06:35:05,764] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-13 06:35:05,769] multiqc [DEBUG ] No samples found: clusterflow [2022-07-13 06:35:05,774] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-13 06:35:05,778] multiqc [DEBUG ] No samples found: interop [2022-07-13 06:35:05,783] multiqc [DEBUG ] No samples found: ivar [2022-07-13 06:35:05,788] multiqc [DEBUG ] No samples found: flash [2022-07-13 06:35:05,792] multiqc [DEBUG ] No samples found: seqyclean [2022-07-13 06:35:05,792] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-13 06:35:05,792] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-13 06:35:05,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-13 06:35:05,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-13 06:35:05,803] multiqc [INFO ] Compressing plot data [2022-07-13 06:35:05,933] multiqc [INFO ] Report : multiqc_report.html [2022-07-13 06:35:05,933] multiqc [INFO ] Data : multiqc_data [2022-07-13 06:35:05,933] multiqc [DEBUG ] Moving data file from '/state/partition1/job-22137071/tmpmn40byfj/multiqc_data' to '/scratch/gencore/logs/html/HT2N7AFX3/merged/multiqc_data' [2022-07-13 06:35:15,084] multiqc [INFO ] MultiQC complete