[2022-04-19 05:11:42,510] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-19 05:11:42,510] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-19 05:11:42,510] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-19 05:11:42,511] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-19 05:11:42,511] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-19 05:11:42,511] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKMN3AFX3/merged [2022-04-19 05:11:43,006] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-19 05:11:43,006] multiqc [INFO ] This is MultiQC v1.9 [2022-04-19 05:11:43,006] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKMN3AFX3/merged [2022-04-19 05:11:43,006] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKMN3AFX3/merged [2022-04-19 05:11:43,006] multiqc [INFO ] Template : default [2022-04-19 05:11:43,007] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-19 05:11:43,007] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKMN3AFX3/merged [2022-04-19 05:11:43,007] 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 [2022-04-19 05:11:43,007] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-18268709/tmp543ukms8 [2022-04-19 05:11:43,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_C2_220412_fastqc.html [2022-04-19 05:11:43,124] multiqc [DEBUG ] File ignored by longranger/invocation because it 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ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_HTO_C_220412_fastqc.html [2022-04-19 05:11:44,297] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_C3_220412_fastqc.html [2022-04-19 05:11:44,298] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_C3_220412_fastqc.html [2022-04-19 05:11:44,342] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_HTO_A_220412_fastqc.html [2022-04-19 05:11:44,343] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_HTO_A_220412_fastqc.html [2022-04-19 05:11:44,410] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_A4_220412_fastqc.html [2022-04-19 05:11:44,412] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_A4_220412_fastqc.html [2022-04-19 05:11:44,451] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_HTO_C_220412_fastqc.html [2022-04-19 05:11:44,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_HTO_C_220412_fastqc.html [2022-04-19 05:11:44,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_HTO_B_220412_fastqc.html [2022-04-19 05:11:44,495] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_HTO_B_220412_fastqc.html [2022-04-19 05:11:44,563] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_B1_220412_fastqc.html [2022-04-19 05:11:44,564] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_B1_220412_fastqc.html [2022-04-19 05:11:44,606] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_B4_220412_fastqc.html [2022-04-19 05:11:44,608] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_B4_220412_fastqc.html [2022-04-19 05:11:44,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_HTO_A_220412_fastqc.html [2022-04-19 05:11:44,648] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_HTO_A_220412_fastqc.html [2022-04-19 05:11:44,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_B2_220412_fastqc.html [2022-04-19 05:11:44,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_B2_220412_fastqc.html [2022-04-19 05:11:44,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_A3_220412_fastqc.html [2022-04-19 05:11:44,731] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n02_cDNA_A3_220412_fastqc.html [2022-04-19 05:11:44,773] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_A1_220412_fastqc.html [2022-04-19 05:11:44,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKMN3AFX3_n01_cDNA_A1_220412_fastqc.html [2022-04-19 05:11:45,372] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-19 05:11:45,374] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-19 05:11:45,390] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-19 05:11:45,392] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-19 05:11:45,400] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2022-04-19 05:11:45,405] multiqc [DEBUG ] No samples found: conpair [2022-04-19 05:11:45,410] multiqc [DEBUG ] No samples found: peddy [2022-04-19 05:11:45,416] multiqc [DEBUG ] No samples found: somalier [2022-04-19 05:11:45,423] multiqc [DEBUG ] No samples found: methylQA [2022-04-19 05:11:45,436] multiqc [DEBUG ] No samples found: mosdepth [2022-04-19 05:11:45,441] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-19 05:11:45,444] multiqc [DEBUG ] No samples found: qualimap [2022-04-19 05:11:45,449] multiqc [DEBUG ] No samples found: preseq [2022-04-19 05:11:45,455] multiqc [DEBUG ] No samples found: quast [2022-04-19 05:11:45,460] multiqc [DEBUG ] No samples found: qorts [2022-04-19 05:11:45,465] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-19 05:11:45,470] multiqc [DEBUG ] No samples found: rockhopper [2022-04-19 05:11:45,479] multiqc [DEBUG ] No samples found: rsem [2022-04-19 05:11:45,495] multiqc [DEBUG ] No samples found: rseqc [2022-04-19 05:11:45,500] multiqc [DEBUG ] No samples found: busco [2022-04-19 05:11:45,505] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-19 05:11:45,510] multiqc [DEBUG ] No samples found: disambiguate [2022-04-19 05:11:45,515] multiqc [DEBUG ] No samples found: supernova [2022-04-19 05:11:45,533] multiqc [DEBUG ] No samples found: deeptools [2022-04-19 05:11:45,539] multiqc [DEBUG ] No samples found: sargasso [2022-04-19 05:11:45,545] multiqc [DEBUG ] No samples found: verifybamid [2022-04-19 05:11:45,549] multiqc [DEBUG ] No samples found: mirtrace [2022-04-19 05:11:45,555] multiqc [DEBUG ] No samples found: happy [2022-04-19 05:11:45,560] multiqc [DEBUG ] No samples found: mirtop [2022-04-19 05:11:45,568] multiqc [DEBUG ] No samples found: homer [2022-04-19 05:11:45,573] multiqc [DEBUG ] No samples found: macs2 [2022-04-19 05:11:45,577] multiqc [DEBUG ] No samples found: theta2 [2022-04-19 05:11:45,583] multiqc [DEBUG ] No samples found: snpeff [2022-04-19 05:11:45,591] multiqc [DEBUG ] No samples found: gatk [2022-04-19 05:11:45,596] multiqc [DEBUG ] No samples found: htseq [2022-04-19 05:11:45,601] multiqc [DEBUG ] No samples found: bcftools [2022-04-19 05:11:45,608] multiqc [DEBUG ] No samples found: featureCounts [2022-04-19 05:11:45,615] multiqc [DEBUG ] No samples found: fgbio [2022-04-19 05:11:45,635] multiqc [DEBUG ] No samples found: dragen [2022-04-19 05:11:45,640] multiqc [DEBUG ] No samples found: dedup [2022-04-19 05:11:45,646] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-19 05:11:45,671] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-19 05:11:45,676] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-19 05:11:45,679] multiqc [DEBUG ] No samples found: picard [2022-04-19 05:11:45,685] multiqc [DEBUG ] No samples found: prokka [2022-04-19 05:11:45,690] multiqc [DEBUG ] No samples found: samblaster [2022-04-19 05:11:45,702] multiqc [DEBUG ] No samples found: samtools [2022-04-19 05:11:45,707] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-19 05:11:45,712] multiqc [DEBUG ] No samples found: bamtools [2022-04-19 05:11:45,717] multiqc [DEBUG ] No samples found: jellyfish [2022-04-19 05:11:45,725] multiqc [DEBUG ] No samples found: vcftools [2022-04-19 05:11:45,731] multiqc [DEBUG ] No samples found: longranger [2022-04-19 05:11:45,736] multiqc [DEBUG ] No samples found: stacks [2022-04-19 05:11:45,741] multiqc [DEBUG ] No samples found: varscan2 [2022-04-19 05:11:45,759] multiqc [DEBUG ] No samples found: bbmap [2022-04-19 05:11:45,765] multiqc [DEBUG ] No samples found: bismark [2022-04-19 05:11:45,770] multiqc [DEBUG ] No samples found: biscuit [2022-04-19 05:11:45,775] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-19 05:11:45,780] multiqc [DEBUG ] No samples found: hicup [2022-04-19 05:11:45,785] multiqc [DEBUG ] No samples found: hicpro [2022-04-19 05:11:45,791] multiqc [DEBUG ] No samples found: salmon [2022-04-19 05:11:45,796] multiqc [DEBUG ] No samples found: kallisto [2022-04-19 05:11:45,802] multiqc [DEBUG ] No samples found: slamdunk [2022-04-19 05:11:45,808] multiqc [DEBUG ] No samples found: star [2022-04-19 05:11:45,814] multiqc [DEBUG ] No samples found: hisat2 [2022-04-19 05:11:45,818] multiqc [DEBUG ] No samples found: tophat [2022-04-19 05:11:45,824] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-19 05:11:45,830] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-19 05:11:45,835] multiqc [DEBUG ] No samples found: snpsplit [2022-04-19 05:11:45,841] multiqc [DEBUG ] No samples found: kat [2022-04-19 05:11:45,845] multiqc [DEBUG ] No samples found: leehom [2022-04-19 05:11:45,850] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-19 05:11:45,855] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-19 05:11:45,860] multiqc [DEBUG ] No samples found: cutadapt [2022-04-19 05:11:45,864] multiqc [DEBUG ] No samples found: flexbar [2022-04-19 05:11:45,869] multiqc [DEBUG ] No samples found: kaiju [2022-04-19 05:11:45,875] multiqc [DEBUG ] No samples found: kraken [2022-04-19 05:11:45,880] multiqc [DEBUG ] No samples found: malt [2022-04-19 05:11:45,885] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-19 05:11:45,891] multiqc [DEBUG ] No samples found: sickle [2022-04-19 05:11:45,896] multiqc [DEBUG ] No samples found: skewer [2022-04-19 05:11:45,901] multiqc [DEBUG ] No samples found: sortmerna [2022-04-19 05:11:45,906] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-19 05:11:45,911] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-19 05:11:45,916] multiqc [DEBUG ] No samples found: afterqc [2022-04-19 05:11:45,921] multiqc [DEBUG ] No samples found: fastp [2022-04-19 05:11:46,692] multiqc.modules.fastqc.fastqc [INFO ] Found 32 reports [2022-04-19 05:11:47,023] multiqc [DEBUG ] No samples found: pycoqc [2022-04-19 05:11:47,028] multiqc [DEBUG ] No samples found: minionqc [2022-04-19 05:11:47,033] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-19 05:11:47,038] multiqc [DEBUG ] No samples found: clusterflow [2022-04-19 05:11:47,044] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-19 05:11:47,050] multiqc [DEBUG ] No samples found: interop [2022-04-19 05:11:47,057] multiqc [DEBUG ] No samples found: ivar [2022-04-19 05:11:47,064] multiqc [DEBUG ] No samples found: flash [2022-04-19 05:11:47,071] multiqc [DEBUG ] No samples found: seqyclean [2022-04-19 05:11:47,071] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-19 05:11:47,071] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-19 05:11:47,071] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-19 05:11:47,071] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-19 05:11:47,109] multiqc [INFO ] Compressing plot data [2022-04-19 05:11:47,612] multiqc [INFO ] Report : multiqc_report.html [2022-04-19 05:11:47,612] multiqc [INFO ] Data : multiqc_data [2022-04-19 05:11:47,612] multiqc [DEBUG ] Moving data file from '/state/partition1/job-18268709/tmp543ukms8/multiqc_data' to '/scratch/gencore/logs/html/HKMN3AFX3/merged/multiqc_data' [2022-04-19 05:11:47,759] multiqc [INFO ] MultiQC complete