[2021-11-21 12:29:23,371] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-21 12:29:23,371] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-21 12:29:23,371] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-21 12:29:23,372] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-21 12:29:23,372] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-21 12:29:23,372] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTTCNDSX2/1 [2021-11-21 12:29:25,878] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-21 12:29:25,878] multiqc [INFO ] This is MultiQC v1.9 [2021-11-21 12:29:25,878] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTTCNDSX2/1 [2021-11-21 12:29:25,878] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTTCNDSX2/1 [2021-11-21 12:29:25,878] multiqc [INFO ] Template : default [2021-11-21 12:29:25,878] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-21 12:29:25,878] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTTCNDSX2/1 [2021-11-21 12:29:25,878] 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 [2021-11-21 12:29:25,878] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12141206/tmpz38ag0hu [2021-11-21 12:29:26,002] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA2d_fastqc.html [2021-11-21 12:29:26,004] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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[2021-11-21 12:29:26,220] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 12:29:27,025] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO1a_fastqc.html [2021-11-21 12:29:27,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO1a_fastqc.html [2021-11-21 12:29:27,095] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2a_fastqc.html [2021-11-21 12:29:27,097] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2a_fastqc.html [2021-11-21 12:29:27,177] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO1c_fastqc.html [2021-11-21 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12:29:27,806] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2a_fastqc.html [2021-11-21 12:29:27,884] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2c_fastqc.html [2021-11-21 12:29:27,886] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2c_fastqc.html [2021-11-21 12:29:27,949] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA2a_fastqc.html [2021-11-21 12:29:27,950] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA2a_fastqc.html [2021-11-21 12:29:28,005] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1d_fastqc.html [2021-11-21 12:29:28,007] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1d_fastqc.html [2021-11-21 12:29:28,072] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO1b_fastqc.html [2021-11-21 12:29:28,074] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO1b_fastqc.html [2021-11-21 12:29:28,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2d_fastqc.html [2021-11-21 12:29:28,155] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2d_fastqc.html [2021-11-21 12:29:28,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA2b_fastqc.html [2021-11-21 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12:29:28,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA2d_fastqc.html [2021-11-21 12:29:28,546] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA1c_fastqc.html [2021-11-21 12:29:28,548] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA1c_fastqc.html [2021-11-21 12:29:28,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1b_fastqc.html [2021-11-21 12:29:28,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1b_fastqc.html [2021-11-21 12:29:28,669] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_undetermined_fastqc.html [2021-11-21 12:29:28,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_undetermined_fastqc.html [2021-11-21 12:29:28,745] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_HTO2_fastqc.html [2021-11-21 12:29:28,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_HTO2_fastqc.html [2021-11-21 12:29:28,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA2b_fastqc.html [2021-11-21 12:29:28,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA2b_fastqc.html [2021-11-21 12:29:28,869] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO1b_fastqc.html [2021-11-21 12:29:28,871] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO1b_fastqc.html [2021-11-21 12:29:28,937] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2b_fastqc.html [2021-11-21 12:29:28,939] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2b_fastqc.html [2021-11-21 12:29:29,014] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2c_fastqc.html [2021-11-21 12:29:29,015] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO2c_fastqc.html [2021-11-21 12:29:29,077] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_undetermined_fastqc.html [2021-11-21 12:29:29,079] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_undetermined_fastqc.html [2021-11-21 12:29:29,130] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2b_fastqc.html [2021-11-21 12:29:29,131] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_GDO2b_fastqc.html [2021-11-21 12:29:29,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA1b_fastqc.html [2021-11-21 12:29:29,186] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_cDNA1b_fastqc.html [2021-11-21 12:29:29,245] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO1a_fastqc.html [2021-11-21 12:29:29,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n02_EP_GDO1a_fastqc.html [2021-11-21 12:29:29,347] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1c_fastqc.html [2021-11-21 12:29:29,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l01_n01_EP_cDNA1c_fastqc.html [2021-11-21 12:29:29,678] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-21 12:29:29,680] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-21 12:29:29,695] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 19 samples (table) [2021-11-21 12:29:29,697] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-21 12:29:29,706] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-21 12:29:29,712] multiqc [DEBUG ] No samples found: conpair [2021-11-21 12:29:29,717] multiqc [DEBUG ] No samples found: peddy [2021-11-21 12:29:29,726] multiqc [DEBUG ] No samples found: somalier [2021-11-21 12:29:29,730] multiqc [DEBUG ] No samples found: methylQA [2021-11-21 12:29:29,739] multiqc [DEBUG ] No samples found: mosdepth [2021-11-21 12:29:29,743] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-21 12:29:29,746] multiqc [DEBUG ] No samples found: qualimap [2021-11-21 12:29:29,751] multiqc [DEBUG ] No samples found: preseq [2021-11-21 12:29:29,756] multiqc [DEBUG ] No samples found: quast [2021-11-21 12:29:29,761] multiqc [DEBUG ] No samples found: qorts [2021-11-21 12:29:29,766] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-21 12:29:29,772] multiqc [DEBUG ] No samples found: rockhopper [2021-11-21 12:29:29,776] multiqc [DEBUG ] No samples found: rsem [2021-11-21 12:29:29,788] multiqc [DEBUG ] No samples found: rseqc [2021-11-21 12:29:29,792] multiqc [DEBUG ] No samples found: busco [2021-11-21 12:29:29,797] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-21 12:29:29,802] multiqc [DEBUG ] No samples found: disambiguate [2021-11-21 12:29:29,809] multiqc [DEBUG ] No samples found: supernova [2021-11-21 12:29:29,822] multiqc [DEBUG ] No samples found: deeptools [2021-11-21 12:29:29,827] multiqc [DEBUG ] No samples found: sargasso [2021-11-21 12:29:29,832] multiqc [DEBUG ] No samples found: verifybamid [2021-11-21 12:29:29,837] multiqc [DEBUG ] No samples found: mirtrace [2021-11-21 12:29:29,841] multiqc [DEBUG ] No samples found: happy [2021-11-21 12:29:29,846] multiqc [DEBUG ] No samples found: mirtop [2021-11-21 12:29:29,853] multiqc [DEBUG ] No samples found: homer [2021-11-21 12:29:29,857] multiqc [DEBUG ] No samples found: macs2 [2021-11-21 12:29:29,862] multiqc [DEBUG ] No samples found: theta2 [2021-11-21 12:29:29,867] multiqc [DEBUG ] No samples found: snpeff [2021-11-21 12:29:29,873] multiqc [DEBUG ] No samples found: gatk [2021-11-21 12:29:29,878] multiqc [DEBUG ] No samples found: htseq [2021-11-21 12:29:29,884] multiqc [DEBUG ] No samples found: bcftools [2021-11-21 12:29:29,888] multiqc [DEBUG ] No samples found: featureCounts [2021-11-21 12:29:29,895] multiqc [DEBUG ] No samples found: fgbio [2021-11-21 12:29:29,909] multiqc [DEBUG ] No samples found: dragen [2021-11-21 12:29:29,913] multiqc [DEBUG ] No samples found: dedup [2021-11-21 12:29:29,918] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-21 12:29:29,941] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-21 12:29:29,945] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-21 12:29:29,947] multiqc [DEBUG ] No samples found: picard [2021-11-21 12:29:29,952] multiqc [DEBUG ] No samples found: prokka [2021-11-21 12:29:29,956] multiqc [DEBUG ] No samples found: samblaster [2021-11-21 12:29:29,965] multiqc [DEBUG ] No samples found: samtools [2021-11-21 12:29:29,970] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-21 12:29:29,975] multiqc [DEBUG ] No samples found: bamtools [2021-11-21 12:29:29,979] multiqc [DEBUG ] No samples found: jellyfish [2021-11-21 12:29:29,988] multiqc [DEBUG ] No samples found: vcftools [2021-11-21 12:29:29,993] multiqc [DEBUG ] No samples found: longranger [2021-11-21 12:29:29,998] multiqc [DEBUG ] No samples found: stacks [2021-11-21 12:29:30,002] multiqc [DEBUG ] No samples found: varscan2 [2021-11-21 12:29:30,017] multiqc [DEBUG ] No samples found: bbmap [2021-11-21 12:29:30,021] multiqc [DEBUG ] No samples found: bismark [2021-11-21 12:29:30,026] multiqc [DEBUG ] No samples found: biscuit [2021-11-21 12:29:30,031] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-21 12:29:30,036] multiqc [DEBUG ] No samples found: hicup [2021-11-21 12:29:30,041] multiqc [DEBUG ] No samples found: hicpro [2021-11-21 12:29:30,045] multiqc [DEBUG ] No samples found: salmon [2021-11-21 12:29:30,049] multiqc [DEBUG ] No samples found: kallisto [2021-11-21 12:29:30,054] multiqc [DEBUG ] No samples found: slamdunk [2021-11-21 12:29:30,059] multiqc [DEBUG ] No samples found: star [2021-11-21 12:29:30,063] multiqc [DEBUG ] No samples found: hisat2 [2021-11-21 12:29:30,067] multiqc [DEBUG ] No samples found: tophat [2021-11-21 12:29:30,071] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-21 12:29:30,076] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-21 12:29:30,080] multiqc [DEBUG ] No samples found: snpsplit [2021-11-21 12:29:30,085] multiqc [DEBUG ] No samples found: kat [2021-11-21 12:29:30,089] multiqc [DEBUG ] No samples found: leehom [2021-11-21 12:29:30,093] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-21 12:29:30,097] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-21 12:29:30,102] multiqc [DEBUG ] No samples found: cutadapt [2021-11-21 12:29:30,106] multiqc [DEBUG ] No samples found: flexbar [2021-11-21 12:29:30,110] multiqc [DEBUG ] No samples found: kaiju [2021-11-21 12:29:30,115] multiqc [DEBUG ] No samples found: kraken [2021-11-21 12:29:30,124] multiqc [DEBUG ] No samples found: malt [2021-11-21 12:29:30,128] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-21 12:29:30,133] multiqc [DEBUG ] No samples found: sickle [2021-11-21 12:29:30,137] multiqc [DEBUG ] No samples found: skewer [2021-11-21 12:29:30,141] multiqc [DEBUG ] No samples found: sortmerna [2021-11-21 12:29:30,145] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-21 12:29:30,150] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-21 12:29:30,154] multiqc [DEBUG ] No samples found: afterqc [2021-11-21 12:29:30,160] multiqc [DEBUG ] No samples found: fastp [2021-11-21 12:29:38,596] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2021-11-21 12:29:39,074] multiqc [DEBUG ] No samples found: pycoqc [2021-11-21 12:29:39,078] multiqc [DEBUG ] No samples found: minionqc [2021-11-21 12:29:39,082] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-21 12:29:39,087] multiqc [DEBUG ] No samples found: clusterflow [2021-11-21 12:29:39,092] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-21 12:29:39,097] multiqc [DEBUG ] No samples found: interop [2021-11-21 12:29:39,102] multiqc [DEBUG ] No samples found: ivar [2021-11-21 12:29:39,106] multiqc [DEBUG ] No samples found: flash [2021-11-21 12:29:39,110] multiqc [DEBUG ] No samples found: seqyclean [2021-11-21 12:29:39,110] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-11-21 12:29:39,110] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-11-21 12:29:39,110] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-11-21 12:29:39,111] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-21 12:29:39,111] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-21 12:29:39,154] multiqc [INFO ] Compressing plot data [2021-11-21 12:29:39,835] multiqc [INFO ] Report : multiqc_report.html [2021-11-21 12:29:39,835] multiqc [INFO ] Data : multiqc_data [2021-11-21 12:29:39,835] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12141206/tmpz38ag0hu/multiqc_data' to '/scratch/gencore/logs/html/HTTCNDSX2/1/multiqc_data' [2021-11-21 12:29:40,000] multiqc [INFO ] MultiQC complete