[2021-12-18 14:21:49,613] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-12-18 14:21:49,614] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-12-18 14:21:49,614] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-12-18 14:21:49,614] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-12-18 14:21:49,615] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-12-18 14:21:49,615] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HM57KDRXY/merged [2021-12-18 14:21:50,968] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-12-18 14:21:50,968] multiqc [INFO ] This is MultiQC v1.9 [2021-12-18 14:21:50,968] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HM57KDRXY/merged [2021-12-18 14:21:50,968] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HM57KDRXY/merged [2021-12-18 14:21:50,968] multiqc [INFO ] Template : default [2021-12-18 14:21:50,968] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-12-18 14:21:50,968] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HM57KDRXY/merged [2021-12-18 14:21:50,969] 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 [2021-12-18 14:21:50,969] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13144296/tmp_mht9jnj [2021-12-18 14:21:51,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SC_DMSO_9_fastqc.html [2021-12-18 14:21:51,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HM57KDRXY_n01_3_SC_RAPA_0_fastqc.html [2021-12-18 14:21:54,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SC_RAPA_0_fastqc.html [2021-12-18 14:21:54,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SC_RAPA_0_fastqc.html [2021-12-18 14:21:54,667] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_3_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:54,668] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_3_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:54,711] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_undetermined_fastqc.html [2021-12-18 14:21:54,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_undetermined_fastqc.html [2021-12-18 14:21:54,773] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SOR_RAPA_6_fastqc.html [2021-12-18 14:21:54,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SOR_RAPA_6_fastqc.html [2021-12-18 14:21:54,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SOR_DMSO_3_fastqc.html [2021-12-18 14:21:54,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SOR_DMSO_3_fastqc.html [2021-12-18 14:21:54,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SC_RAPA_6_fastqc.html [2021-12-18 14:21:54,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SC_RAPA_6_fastqc.html [2021-12-18 14:21:54,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SC_DMSO_9_fastqc.html [2021-12-18 14:21:54,957] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SC_DMSO_9_fastqc.html [2021-12-18 14:21:55,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:55,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_2_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:55,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SC_RAPA_9_fastqc.html [2021-12-18 14:21:55,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_3_SC_RAPA_9_fastqc.html [2021-12-18 14:21:55,141] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_RAPA_9_fastqc.html [2021-12-18 14:21:55,143] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_RAPA_9_fastqc.html [2021-12-18 14:21:55,186] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_FY2_fastqc.html [2021-12-18 14:21:55,188] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_FY2_fastqc.html [2021-12-18 14:21:55,236] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:55,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_DMSO_9_fastqc.html [2021-12-18 14:21:55,281] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_3_SOR_RAPA_9_fastqc.html [2021-12-18 14:21:55,283] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_3_SOR_RAPA_9_fastqc.html [2021-12-18 14:21:55,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_DMSO_6_fastqc.html [2021-12-18 14:21:55,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n02_2_SOR_DMSO_6_fastqc.html [2021-12-18 14:21:55,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_O17_fastqc.html [2021-12-18 14:21:55,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_O17_fastqc.html [2021-12-18 14:21:55,433] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HM57KDRXY_n01_DGY2746_fastqc.html [2021-12-18 14:21:55,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HM57KDRXY_n01_DGY2746_fastqc.html [2021-12-18 14:21:55,755] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 14:21:55,756] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-12-18 14:21:55,764] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-12-18 14:21:55,782] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2021-12-18 14:21:55,792] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-12-18 14:21:55,796] multiqc [DEBUG ] No samples found: conpair [2021-12-18 14:21:55,800] multiqc [DEBUG ] No samples found: peddy [2021-12-18 14:21:55,806] multiqc [DEBUG ] No samples found: somalier [2021-12-18 14:21:55,811] multiqc [DEBUG ] No samples found: methylQA [2021-12-18 14:21:55,817] multiqc [DEBUG ] No samples found: mosdepth [2021-12-18 14:21:55,821] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-12-18 14:21:55,824] multiqc [DEBUG ] No samples found: qualimap [2021-12-18 14:21:55,828] multiqc [DEBUG ] No samples found: preseq [2021-12-18 14:21:55,832] multiqc [DEBUG ] No samples found: quast [2021-12-18 14:21:55,836] multiqc [DEBUG ] No samples found: qorts [2021-12-18 14:21:55,840] multiqc [DEBUG ] No samples found: rna_seqc [2021-12-18 14:21:55,844] multiqc [DEBUG ] No samples found: rockhopper [2021-12-18 14:21:55,848] multiqc [DEBUG ] No samples found: rsem [2021-12-18 14:21:55,860] multiqc [DEBUG ] No samples found: rseqc [2021-12-18 14:21:55,864] multiqc [DEBUG ] No samples found: busco [2021-12-18 14:21:55,868] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-12-18 14:21:55,872] multiqc [DEBUG ] No samples found: disambiguate [2021-12-18 14:21:55,876] multiqc [DEBUG ] No samples found: supernova [2021-12-18 14:21:55,884] multiqc [DEBUG ] No samples found: deeptools [2021-12-18 14:21:55,888] multiqc [DEBUG ] No samples found: sargasso [2021-12-18 14:21:55,893] multiqc [DEBUG ] No samples found: verifybamid [2021-12-18 14:21:55,897] multiqc [DEBUG ] No samples found: mirtrace [2021-12-18 14:21:55,902] multiqc [DEBUG ] No samples found: happy [2021-12-18 14:21:55,906] multiqc [DEBUG ] No samples found: mirtop [2021-12-18 14:21:55,911] multiqc [DEBUG ] No samples found: homer [2021-12-18 14:21:55,915] multiqc [DEBUG ] No samples found: macs2 [2021-12-18 14:21:55,919] multiqc [DEBUG ] No samples found: theta2 [2021-12-18 14:21:55,923] multiqc [DEBUG ] No samples found: snpeff [2021-12-18 14:21:55,928] multiqc [DEBUG ] No samples found: gatk [2021-12-18 14:21:55,932] multiqc [DEBUG ] No samples found: htseq [2021-12-18 14:21:55,936] multiqc [DEBUG ] No samples found: bcftools [2021-12-18 14:21:55,940] multiqc [DEBUG ] No samples found: featureCounts [2021-12-18 14:21:55,946] multiqc [DEBUG ] No samples found: fgbio [2021-12-18 14:21:55,954] multiqc [DEBUG ] No samples found: dragen [2021-12-18 14:21:55,958] multiqc [DEBUG ] No samples found: dedup [2021-12-18 14:21:55,962] multiqc [DEBUG ] No samples found: damageprofiler [2021-12-18 14:21:55,982] multiqc [DEBUG ] No samples found: biobambam2 [2021-12-18 14:21:55,986] multiqc [DEBUG ] No samples found: mtnucratio [2021-12-18 14:21:55,988] multiqc [DEBUG ] No samples found: picard [2021-12-18 14:21:55,992] multiqc [DEBUG ] No samples found: prokka [2021-12-18 14:21:55,996] multiqc [DEBUG ] No samples found: samblaster [2021-12-18 14:21:56,003] multiqc [DEBUG ] No samples found: samtools [2021-12-18 14:21:56,007] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-12-18 14:21:56,012] multiqc [DEBUG ] No samples found: bamtools [2021-12-18 14:21:56,015] multiqc [DEBUG ] No samples found: jellyfish [2021-12-18 14:21:56,021] multiqc [DEBUG ] No samples found: vcftools [2021-12-18 14:21:56,025] multiqc [DEBUG ] No samples found: longranger [2021-12-18 14:21:56,029] multiqc [DEBUG ] No samples found: stacks [2021-12-18 14:21:56,033] multiqc [DEBUG ] No samples found: varscan2 [2021-12-18 14:21:56,042] multiqc [DEBUG ] No samples found: bbmap [2021-12-18 14:21:56,046] multiqc [DEBUG ] No samples found: bismark [2021-12-18 14:21:56,050] multiqc [DEBUG ] No samples found: biscuit [2021-12-18 14:21:56,053] multiqc [DEBUG ] No samples found: hicexplorer [2021-12-18 14:21:56,057] multiqc [DEBUG ] No samples found: hicup [2021-12-18 14:21:56,063] multiqc [DEBUG ] No samples found: hicpro [2021-12-18 14:21:56,067] multiqc [DEBUG ] No samples found: salmon [2021-12-18 14:21:56,071] multiqc [DEBUG ] No samples found: kallisto [2021-12-18 14:21:56,075] multiqc [DEBUG ] No samples found: slamdunk [2021-12-18 14:21:56,081] multiqc [DEBUG ] No samples found: star [2021-12-18 14:21:56,085] multiqc [DEBUG ] No samples found: hisat2 [2021-12-18 14:21:56,089] multiqc [DEBUG ] No samples found: tophat [2021-12-18 14:21:56,092] multiqc [DEBUG ] No samples found: bowtie2 [2021-12-18 14:21:56,096] multiqc [DEBUG ] No samples found: bowtie1 [2021-12-18 14:21:56,100] multiqc [DEBUG ] No samples found: snpsplit [2021-12-18 14:21:56,104] multiqc [DEBUG ] No samples found: kat [2021-12-18 14:21:56,108] multiqc [DEBUG ] No samples found: leehom [2021-12-18 14:21:56,112] multiqc [DEBUG ] No samples found: adapterRemoval [2021-12-18 14:21:56,115] multiqc [DEBUG ] No samples found: clipandmerge [2021-12-18 14:21:56,119] multiqc [DEBUG ] No samples found: cutadapt [2021-12-18 14:21:56,123] multiqc [DEBUG ] No samples found: flexbar [2021-12-18 14:21:56,127] multiqc [DEBUG ] No samples found: kaiju [2021-12-18 14:21:56,131] multiqc [DEBUG ] No samples found: kraken [2021-12-18 14:21:56,134] multiqc [DEBUG ] No samples found: malt [2021-12-18 14:21:56,138] multiqc [DEBUG ] No samples found: trimmomatic [2021-12-18 14:21:56,142] multiqc [DEBUG ] No samples found: sickle [2021-12-18 14:21:56,146] multiqc [DEBUG ] No samples found: skewer [2021-12-18 14:21:56,150] multiqc [DEBUG ] No samples found: sortmerna [2021-12-18 14:21:56,154] multiqc [DEBUG ] No samples found: biobloomtools [2021-12-18 14:21:56,158] multiqc [DEBUG ] No samples found: fastq_screen [2021-12-18 14:21:56,162] multiqc [DEBUG ] No samples found: afterqc [2021-12-18 14:21:56,166] multiqc [DEBUG ] No samples found: fastp [2021-12-18 14:22:00,277] multiqc.modules.fastqc.fastqc [INFO ] Found 74 reports [2021-12-18 14:22:01,232] multiqc [DEBUG ] No samples found: pycoqc [2021-12-18 14:22:01,236] multiqc [DEBUG ] No samples found: minionqc [2021-12-18 14:22:01,240] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-12-18 14:22:01,244] multiqc [DEBUG ] No samples found: clusterflow [2021-12-18 14:22:01,249] multiqc [DEBUG ] No samples found: bcl2fastq [2021-12-18 14:22:01,253] multiqc [DEBUG ] No samples found: interop [2021-12-18 14:22:01,257] multiqc [DEBUG ] No samples found: ivar [2021-12-18 14:22:01,261] multiqc [DEBUG ] No samples found: flash [2021-12-18 14:22:01,265] multiqc [DEBUG ] No samples found: seqyclean [2021-12-18 14:22:01,265] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-12-18 14:22:01,265] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-12-18 14:22:01,265] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-12-18 14:22:01,265] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-12-18 14:22:01,354] multiqc [INFO ] Compressing plot data [2021-12-18 14:22:02,715] multiqc [INFO ] Report : multiqc_report.html [2021-12-18 14:22:02,715] multiqc [INFO ] Data : multiqc_data [2021-12-18 14:22:02,715] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13144296/tmp_mht9jnj/multiqc_data' to '/scratch/gencore/logs/html/HM57KDRXY/merged/multiqc_data' [2021-12-18 14:22:02,822] multiqc [INFO ] MultiQC complete