[2022-03-22 16:33:11,310] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-22 16:33:11,310] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-22 16:33:11,310] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-22 16:33:11,311] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-22 16:33:11,311] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-22 16:33:11,311] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKLCKAFX3/merged [2022-03-22 16:33:11,704] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-22 16:33:11,704] multiqc [INFO ] This is MultiQC v1.9 [2022-03-22 16:33:11,704] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKLCKAFX3/merged [2022-03-22 16:33:11,704] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKLCKAFX3/merged [2022-03-22 16:33:11,704] multiqc [INFO ] Template : default [2022-03-22 16:33:11,704] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-22 16:33:11,704] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKLCKAFX3/merged [2022-03-22 16:33:11,705] 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 [2022-03-22 16:33:11,705] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16513182/tmp5rfky2rt [2022-03-22 16:33:11,815] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr560_fastqc.html [2022-03-22 16:33:11,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr560_fastqc.html [2022-03-22 16:33:11,862] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,864] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:11,908] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-03-22 16:33:13,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr557_fastqc.html [2022-03-22 16:33:13,787] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr557_fastqc.html [2022-03-22 16:33:13,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr551_fastqc.html [2022-03-22 16:33:13,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr551_fastqc.html [2022-03-22 16:33:13,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr558_fastqc.html [2022-03-22 16:33:13,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr558_fastqc.html [2022-03-22 16:33:13,915] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr552_fastqc.html [2022-03-22 16:33:13,917] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr552_fastqc.html [2022-03-22 16:33:13,959] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr557_fastqc.html [2022-03-22 16:33:13,961] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr557_fastqc.html [2022-03-22 16:33:14,003] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr560_fastqc.html [2022-03-22 16:33:14,005] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr560_fastqc.html [2022-03-22 16:33:14,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_undetermined_fastqc.html [2022-03-22 16:33:14,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_undetermined_fastqc.html [2022-03-22 16:33:14,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr553_fastqc.html [2022-03-22 16:33:14,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr553_fastqc.html [2022-03-22 16:33:14,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr558_fastqc.html [2022-03-22 16:33:14,133] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr558_fastqc.html [2022-03-22 16:33:14,176] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr553_fastqc.html [2022-03-22 16:33:14,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr553_fastqc.html [2022-03-22 16:33:14,219] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr552_fastqc.html [2022-03-22 16:33:14,221] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr552_fastqc.html [2022-03-22 16:33:14,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr559_fastqc.html [2022-03-22 16:33:14,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr559_fastqc.html [2022-03-22 16:33:14,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr555_fastqc.html [2022-03-22 16:33:14,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr555_fastqc.html [2022-03-22 16:33:14,350] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr555_fastqc.html [2022-03-22 16:33:14,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr555_fastqc.html [2022-03-22 16:33:14,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr554_fastqc.html [2022-03-22 16:33:14,395] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr554_fastqc.html [2022-03-22 16:33:14,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr551_fastqc.html [2022-03-22 16:33:14,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr551_fastqc.html [2022-03-22 16:33:14,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr554_fastqc.html [2022-03-22 16:33:14,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr554_fastqc.html [2022-03-22 16:33:14,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr556_fastqc.html [2022-03-22 16:33:14,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n02_dpr556_fastqc.html [2022-03-22 16:33:14,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr556_fastqc.html [2022-03-22 16:33:14,570] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr556_fastqc.html [2022-03-22 16:33:14,611] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_undetermined_fastqc.html [2022-03-22 16:33:14,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_undetermined_fastqc.html [2022-03-22 16:33:14,652] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr559_fastqc.html [2022-03-22 16:33:14,654] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKLCKAFX3_n01_dpr559_fastqc.html [2022-03-22 16:33:14,994] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-22 16:33:14,995] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-22 16:33:15,003] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-22 16:33:15,013] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-22 16:33:15,018] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-03-22 16:33:15,023] multiqc [DEBUG ] No samples found: conpair [2022-03-22 16:33:15,028] multiqc [DEBUG ] No samples found: peddy [2022-03-22 16:33:15,032] multiqc [DEBUG ] No samples found: somalier [2022-03-22 16:33:15,037] multiqc [DEBUG ] No samples found: methylQA [2022-03-22 16:33:15,044] multiqc [DEBUG ] No samples found: mosdepth [2022-03-22 16:33:15,049] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-22 16:33:15,052] multiqc [DEBUG ] No samples found: qualimap [2022-03-22 16:33:15,056] multiqc [DEBUG ] No samples found: preseq [2022-03-22 16:33:15,061] multiqc [DEBUG ] No samples found: quast [2022-03-22 16:33:15,066] multiqc [DEBUG ] No samples found: qorts [2022-03-22 16:33:15,070] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-22 16:33:15,074] multiqc [DEBUG ] No samples found: rockhopper [2022-03-22 16:33:15,079] multiqc [DEBUG ] No samples found: rsem [2022-03-22 16:33:15,089] multiqc [DEBUG ] No samples found: rseqc [2022-03-22 16:33:15,094] multiqc [DEBUG ] No samples found: busco [2022-03-22 16:33:15,098] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-22 16:33:15,102] multiqc [DEBUG ] No samples found: disambiguate [2022-03-22 16:33:15,107] multiqc [DEBUG ] No samples found: supernova [2022-03-22 16:33:15,119] multiqc [DEBUG ] No samples found: deeptools [2022-03-22 16:33:15,123] multiqc [DEBUG ] No samples found: sargasso [2022-03-22 16:33:15,127] multiqc [DEBUG ] No samples found: verifybamid [2022-03-22 16:33:15,132] multiqc [DEBUG ] No samples found: mirtrace [2022-03-22 16:33:15,136] multiqc [DEBUG ] No samples found: happy [2022-03-22 16:33:15,141] multiqc [DEBUG ] No samples found: mirtop [2022-03-22 16:33:15,147] multiqc [DEBUG ] No samples found: homer [2022-03-22 16:33:15,151] multiqc [DEBUG ] No samples found: macs2 [2022-03-22 16:33:15,155] multiqc [DEBUG ] No samples found: theta2 [2022-03-22 16:33:15,160] multiqc [DEBUG ] No samples found: snpeff [2022-03-22 16:33:15,166] multiqc [DEBUG ] No samples found: gatk [2022-03-22 16:33:15,172] multiqc [DEBUG ] No samples found: htseq [2022-03-22 16:33:15,177] multiqc [DEBUG ] No samples found: bcftools [2022-03-22 16:33:15,182] multiqc [DEBUG ] No samples found: featureCounts [2022-03-22 16:33:15,187] multiqc [DEBUG ] No samples found: fgbio [2022-03-22 16:33:15,199] multiqc [DEBUG ] No samples found: dragen [2022-03-22 16:33:15,204] multiqc [DEBUG ] No samples found: dedup [2022-03-22 16:33:15,208] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-22 16:33:15,228] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-22 16:33:15,233] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-22 16:33:15,236] multiqc [DEBUG ] No samples found: picard [2022-03-22 16:33:15,240] multiqc [DEBUG ] No samples found: prokka [2022-03-22 16:33:15,244] multiqc [DEBUG ] No samples found: samblaster [2022-03-22 16:33:15,252] multiqc [DEBUG ] No samples found: samtools [2022-03-22 16:33:15,256] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-22 16:33:15,262] multiqc [DEBUG ] No samples found: bamtools [2022-03-22 16:33:15,266] multiqc [DEBUG ] No samples found: jellyfish [2022-03-22 16:33:15,273] multiqc [DEBUG ] No samples found: vcftools [2022-03-22 16:33:15,277] multiqc [DEBUG ] No samples found: longranger [2022-03-22 16:33:15,282] multiqc [DEBUG ] No samples found: stacks [2022-03-22 16:33:15,287] multiqc [DEBUG ] No samples found: varscan2 [2022-03-22 16:33:15,301] multiqc [DEBUG ] No samples found: bbmap [2022-03-22 16:33:15,306] multiqc [DEBUG ] No samples found: bismark [2022-03-22 16:33:15,310] multiqc [DEBUG ] No samples found: biscuit [2022-03-22 16:33:15,315] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-22 16:33:15,319] multiqc [DEBUG ] No samples found: hicup [2022-03-22 16:33:15,324] multiqc [DEBUG ] No samples found: hicpro [2022-03-22 16:33:15,328] multiqc [DEBUG ] No samples found: salmon [2022-03-22 16:33:15,332] multiqc [DEBUG ] No samples found: kallisto [2022-03-22 16:33:15,337] multiqc [DEBUG ] No samples found: slamdunk [2022-03-22 16:33:15,341] multiqc [DEBUG ] No samples found: star [2022-03-22 16:33:15,346] multiqc [DEBUG ] No samples found: hisat2 [2022-03-22 16:33:15,350] multiqc [DEBUG ] No samples found: tophat [2022-03-22 16:33:15,355] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-22 16:33:15,359] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-22 16:33:15,364] multiqc [DEBUG ] No samples found: snpsplit [2022-03-22 16:33:15,368] multiqc [DEBUG ] No samples found: kat [2022-03-22 16:33:15,372] multiqc [DEBUG ] No samples found: leehom [2022-03-22 16:33:15,377] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-22 16:33:15,381] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-22 16:33:15,385] multiqc [DEBUG ] No samples found: cutadapt [2022-03-22 16:33:15,389] multiqc [DEBUG ] No samples found: flexbar [2022-03-22 16:33:15,394] multiqc [DEBUG ] No samples found: kaiju [2022-03-22 16:33:15,398] multiqc [DEBUG ] No samples found: kraken [2022-03-22 16:33:15,403] multiqc [DEBUG ] No samples found: malt [2022-03-22 16:33:15,407] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-22 16:33:15,411] multiqc [DEBUG ] No samples found: sickle [2022-03-22 16:33:15,416] multiqc [DEBUG ] No samples found: skewer [2022-03-22 16:33:15,420] multiqc [DEBUG ] No samples found: sortmerna [2022-03-22 16:33:15,426] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-22 16:33:15,431] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-22 16:33:15,435] multiqc [DEBUG ] No samples found: afterqc [2022-03-22 16:33:15,439] multiqc [DEBUG ] No samples found: fastp [2022-03-22 16:33:15,973] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-03-22 16:33:16,444] multiqc [DEBUG ] No samples found: pycoqc [2022-03-22 16:33:16,449] multiqc [DEBUG ] No samples found: minionqc [2022-03-22 16:33:16,453] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-22 16:33:16,458] multiqc [DEBUG ] No samples found: clusterflow [2022-03-22 16:33:16,462] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-22 16:33:16,467] multiqc [DEBUG ] No samples found: interop [2022-03-22 16:33:16,471] multiqc [DEBUG ] No samples found: ivar [2022-03-22 16:33:16,475] multiqc [DEBUG ] No samples found: flash [2022-03-22 16:33:16,480] multiqc [DEBUG ] No samples found: seqyclean [2022-03-22 16:33:16,480] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-22 16:33:16,480] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-22 16:33:16,480] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-22 16:33:16,480] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-22 16:33:16,507] multiqc [INFO ] Compressing plot data [2022-03-22 16:33:16,920] multiqc [INFO ] Report : multiqc_report.html [2022-03-22 16:33:16,921] multiqc [INFO ] Data : multiqc_data [2022-03-22 16:33:16,921] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16513182/tmp5rfky2rt/multiqc_data' to '/scratch/gencore/logs/html/HKLCKAFX3/merged/multiqc_data' [2022-03-22 16:33:17,042] multiqc [INFO ] MultiQC complete