[2021-11-18 23:29:42,049] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-18 23:29:42,049] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-18 23:29:42,049] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-18 23:29:42,050] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-18 23:29:42,050] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-18 23:29:42,050] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT2GDRXY/2 [2021-11-18 23:29:43,324] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-18 23:29:43,325] multiqc [INFO ] This is MultiQC v1.9 [2021-11-18 23:29:43,325] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT2GDRXY/2 [2021-11-18 23:29:43,325] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLT2GDRXY/2 [2021-11-18 23:29:43,325] multiqc [INFO ] Template : default [2021-11-18 23:29:43,325] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-18 23:29:43,325] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLT2GDRXY/2 [2021-11-18 23:29:43,325] 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 [2021-11-18 23:29:43,325] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12141232/tmpfzvqsihh [2021-11-18 23:29:43,415] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00001_fastqc.html [2021-11-18 23:29:43,418] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00001_fastqc.html [2021-11-18 23:29:43,461] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 23:29:43,463] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 23:29:43,491] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_undetermined_fastqc.html [2021-11-18 23:29:43,493] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_undetermined_fastqc.html [2021-11-18 23:29:43,531] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00004_fastqc.html [2021-11-18 23:29:43,533] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00004_fastqc.html [2021-11-18 23:29:43,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00001_fastqc.html [2021-11-18 23:29:43,577] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00001_fastqc.html [2021-11-18 23:29:43,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00003_fastqc.html [2021-11-18 23:29:43,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00003_fastqc.html [2021-11-18 23:29:43,661] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00003_fastqc.html [2021-11-18 23:29:43,663] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00003_fastqc.html [2021-11-18 23:29:43,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00002_fastqc.html [2021-11-18 23:29:43,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00002_fastqc.html [2021-11-18 23:29:43,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00004_fastqc.html [2021-11-18 23:29:43,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n02_WT_00004_fastqc.html [2021-11-18 23:29:43,789] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_undetermined_fastqc.html [2021-11-18 23:29:43,790] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_undetermined_fastqc.html [2021-11-18 23:29:43,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00002_fastqc.html [2021-11-18 23:29:43,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l02_n01_WT_00002_fastqc.html [2021-11-18 23:29:44,104] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 23:29:44,104] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 23:29:44,112] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 5 samples (table) [2021-11-18 23:29:44,121] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-18 23:29:44,123] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-18 23:29:44,126] multiqc [DEBUG ] No samples found: conpair [2021-11-18 23:29:44,129] multiqc [DEBUG ] No samples found: peddy [2021-11-18 23:29:44,131] multiqc [DEBUG ] No samples found: somalier [2021-11-18 23:29:44,134] multiqc [DEBUG ] No samples found: methylQA [2021-11-18 23:29:44,138] multiqc [DEBUG ] No samples found: mosdepth [2021-11-18 23:29:44,140] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-18 23:29:44,143] multiqc [DEBUG ] No samples found: qualimap [2021-11-18 23:29:44,146] multiqc [DEBUG ] No samples found: preseq [2021-11-18 23:29:44,148] multiqc [DEBUG ] No samples found: quast [2021-11-18 23:29:44,151] multiqc [DEBUG ] No samples found: qorts [2021-11-18 23:29:44,154] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-18 23:29:44,157] multiqc [DEBUG ] No samples found: rockhopper [2021-11-18 23:29:44,159] multiqc [DEBUG ] No samples found: rsem [2021-11-18 23:29:44,164] multiqc [DEBUG ] No samples found: rseqc [2021-11-18 23:29:44,166] multiqc [DEBUG ] No samples found: busco [2021-11-18 23:29:44,169] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-18 23:29:44,172] multiqc [DEBUG ] No samples found: disambiguate [2021-11-18 23:29:44,174] multiqc [DEBUG ] No samples found: supernova [2021-11-18 23:29:44,179] multiqc [DEBUG ] No samples found: deeptools [2021-11-18 23:29:44,182] multiqc [DEBUG ] No samples found: sargasso [2021-11-18 23:29:44,184] multiqc [DEBUG ] No samples found: verifybamid [2021-11-18 23:29:44,187] multiqc [DEBUG ] No samples found: mirtrace [2021-11-18 23:29:44,190] multiqc [DEBUG ] No samples found: happy [2021-11-18 23:29:44,193] multiqc [DEBUG ] No samples found: mirtop [2021-11-18 23:29:44,196] multiqc [DEBUG ] No samples found: homer [2021-11-18 23:29:44,198] multiqc [DEBUG ] No samples found: macs2 [2021-11-18 23:29:44,201] multiqc [DEBUG ] No samples found: theta2 [2021-11-18 23:29:44,204] multiqc [DEBUG ] No samples found: snpeff [2021-11-18 23:29:44,207] multiqc [DEBUG ] No samples found: gatk [2021-11-18 23:29:44,210] multiqc [DEBUG ] No samples found: htseq [2021-11-18 23:29:44,212] multiqc [DEBUG ] No samples found: bcftools [2021-11-18 23:29:44,215] multiqc [DEBUG ] No samples found: featureCounts [2021-11-18 23:29:44,218] multiqc [DEBUG ] No samples found: fgbio [2021-11-18 23:29:44,223] multiqc [DEBUG ] No samples found: dragen [2021-11-18 23:29:44,226] multiqc [DEBUG ] No samples found: dedup [2021-11-18 23:29:44,228] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-18 23:29:44,235] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-18 23:29:44,238] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-18 23:29:44,240] multiqc [DEBUG ] No samples found: picard [2021-11-18 23:29:44,243] multiqc [DEBUG ] No samples found: prokka [2021-11-18 23:29:44,246] multiqc [DEBUG ] No samples found: samblaster [2021-11-18 23:29:44,249] multiqc [DEBUG ] No samples found: samtools [2021-11-18 23:29:44,252] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-18 23:29:44,255] multiqc [DEBUG ] No samples found: bamtools [2021-11-18 23:29:44,257] multiqc [DEBUG ] No samples found: jellyfish [2021-11-18 23:29:44,261] multiqc [DEBUG ] No samples found: vcftools [2021-11-18 23:29:44,264] multiqc [DEBUG ] No samples found: longranger [2021-11-18 23:29:44,266] multiqc [DEBUG ] No samples found: stacks [2021-11-18 23:29:44,269] multiqc [DEBUG ] No samples found: varscan2 [2021-11-18 23:29:44,274] multiqc [DEBUG ] No samples found: bbmap [2021-11-18 23:29:44,277] multiqc [DEBUG ] No samples found: bismark [2021-11-18 23:29:44,279] multiqc [DEBUG ] No samples found: biscuit [2021-11-18 23:29:44,282] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-18 23:29:44,285] multiqc [DEBUG ] No samples found: hicup [2021-11-18 23:29:44,288] multiqc [DEBUG ] No samples found: hicpro [2021-11-18 23:29:44,290] multiqc [DEBUG ] No samples found: salmon [2021-11-18 23:29:44,293] multiqc [DEBUG ] No samples found: kallisto [2021-11-18 23:29:44,296] multiqc [DEBUG ] No samples found: slamdunk [2021-11-18 23:29:44,298] multiqc [DEBUG ] No samples found: star [2021-11-18 23:29:44,301] multiqc [DEBUG ] No samples found: hisat2 [2021-11-18 23:29:44,304] multiqc [DEBUG ] No samples found: tophat [2021-11-18 23:29:44,306] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-18 23:29:44,309] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-18 23:29:44,312] multiqc [DEBUG ] No samples found: snpsplit [2021-11-18 23:29:44,314] multiqc [DEBUG ] No samples found: kat [2021-11-18 23:29:44,317] multiqc [DEBUG ] No samples found: leehom [2021-11-18 23:29:44,319] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-18 23:29:44,322] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-18 23:29:44,325] multiqc [DEBUG ] No samples found: cutadapt [2021-11-18 23:29:44,327] multiqc [DEBUG ] No samples found: flexbar [2021-11-18 23:29:44,330] multiqc [DEBUG ] No samples found: kaiju [2021-11-18 23:29:44,333] multiqc [DEBUG ] No samples found: kraken [2021-11-18 23:29:44,335] multiqc [DEBUG ] No samples found: malt [2021-11-18 23:29:44,338] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-18 23:29:44,341] multiqc [DEBUG ] No samples found: sickle [2021-11-18 23:29:44,343] multiqc [DEBUG ] No samples found: skewer [2021-11-18 23:29:44,346] multiqc [DEBUG ] No samples found: sortmerna [2021-11-18 23:29:44,349] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-18 23:29:44,351] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-18 23:29:44,354] multiqc [DEBUG ] No samples found: afterqc [2021-11-18 23:29:44,357] multiqc [DEBUG ] No samples found: fastp [2021-11-18 23:29:44,590] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-11-18 23:29:44,683] multiqc [DEBUG ] No samples found: pycoqc [2021-11-18 23:29:44,685] multiqc [DEBUG ] No samples found: minionqc [2021-11-18 23:29:44,688] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-18 23:29:44,691] multiqc [DEBUG ] No samples found: clusterflow [2021-11-18 23:29:44,693] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-18 23:29:44,696] multiqc [DEBUG ] No samples found: interop [2021-11-18 23:29:44,699] multiqc [DEBUG ] No samples found: ivar [2021-11-18 23:29:44,701] multiqc [DEBUG ] No samples found: flash [2021-11-18 23:29:44,704] multiqc [DEBUG ] No samples found: seqyclean [2021-11-18 23:29:44,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-11-18 23:29:44,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2021-11-18 23:29:44,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-18 23:29:44,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-11-18 23:29:44,704] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-18 23:29:44,717] multiqc [INFO ] Compressing plot data [2021-11-18 23:29:44,888] multiqc [INFO ] Report : multiqc_report.html [2021-11-18 23:29:44,889] multiqc [INFO ] Data : multiqc_data [2021-11-18 23:29:44,889] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12141232/tmpfzvqsihh/multiqc_data' to '/scratch/gencore/logs/html/HLT2GDRXY/2/multiqc_data' [2021-11-18 23:29:45,006] multiqc [INFO ] MultiQC complete