[2021-08-23 11:45:52,175] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-23 11:45:52,175] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-23 11:45:52,175] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-23 11:45:52,176] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-23 11:45:52,176] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-23 11:45:52,176] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGVMYDRXY/merged [2021-08-23 11:45:53,921] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-23 11:45:53,921] multiqc [INFO ] This is MultiQC v1.9 [2021-08-23 11:45:53,921] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGVMYDRXY/merged [2021-08-23 11:45:53,921] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGVMYDRXY/merged [2021-08-23 11:45:53,922] multiqc [INFO ] Template : default [2021-08-23 11:45:53,922] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-23 11:45:53,922] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGVMYDRXY/merged [2021-08-23 11:45:53,922] 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 [2021-08-23 11:45:53,922] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9516306/tmp1fu_57nz [2021-08-23 11:45:54,084] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n01_CIVRCoV_P2_A05_U420_fastqc.html [2021-08-23 11:45:54,087] multiqc [DEBUG ] File ignored by longranger/invocation because it 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11:46:00,733] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_D01_C007_fastqc.html [2021-08-23 11:46:00,735] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_D01_C007_fastqc.html [2021-08-23 11:46:00,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_E01_U175_fastqc.html [2021-08-23 11:46:00,795] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_E01_U175_fastqc.html [2021-08-23 11:46:00,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_B01_C005_fastqc.html [2021-08-23 11:46:00,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_B01_C005_fastqc.html [2021-08-23 11:46:00,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_B04_C023_fastqc.html [2021-08-23 11:46:00,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_B04_C023_fastqc.html [2021-08-23 11:46:00,970] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n01_CIVRCoV_P2_B05_C010_fastqc.html [2021-08-23 11:46:00,971] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n01_CIVRCoV_P2_B05_C010_fastqc.html [2021-08-23 11:46:01,026] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P2_B06_U467_fastqc.html [2021-08-23 11:46:01,027] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P2_B06_U467_fastqc.html [2021-08-23 11:46:01,080] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_A01_C001_fastqc.html [2021-08-23 11:46:01,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P1_A01_C001_fastqc.html [2021-08-23 11:46:01,139] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P2_B05_C010_fastqc.html [2021-08-23 11:46:01,141] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGVMYDRXY_n02_CIVRCoV_P2_B05_C010_fastqc.html [2021-08-23 11:46:01,717] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-23 11:46:01,719] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-23 11:46:01,730] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-23 11:46:01,739] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-23 11:46:01,766] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 59 samples (table) [2021-08-23 11:46:01,773] multiqc [DEBUG ] No samples found: conpair [2021-08-23 11:46:01,782] multiqc [DEBUG ] No samples found: peddy [2021-08-23 11:46:01,788] multiqc [DEBUG ] No samples found: somalier [2021-08-23 11:46:01,798] multiqc [DEBUG ] No samples found: methylQA [2021-08-23 11:46:01,813] multiqc [DEBUG ] No samples found: mosdepth [2021-08-23 11:46:01,820] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-23 11:46:01,823] multiqc [DEBUG ] No samples found: qualimap [2021-08-23 11:46:01,830] multiqc [DEBUG ] No samples found: preseq [2021-08-23 11:46:01,841] multiqc [DEBUG ] No samples found: quast [2021-08-23 11:46:01,847] multiqc [DEBUG ] No samples found: qorts [2021-08-23 11:46:01,855] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-23 11:46:01,866] multiqc [DEBUG ] No samples found: rockhopper [2021-08-23 11:46:01,875] multiqc [DEBUG ] No samples found: rsem [2021-08-23 11:46:01,904] multiqc [DEBUG ] No samples found: rseqc [2021-08-23 11:46:01,910] multiqc [DEBUG ] No samples found: busco [2021-08-23 11:46:01,926] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-23 11:46:01,931] multiqc [DEBUG ] No samples found: disambiguate [2021-08-23 11:46:01,938] multiqc [DEBUG ] No samples found: supernova [2021-08-23 11:46:01,967] multiqc [DEBUG ] No samples found: deeptools [2021-08-23 11:46:01,975] multiqc [DEBUG ] No samples found: sargasso [2021-08-23 11:46:01,981] multiqc [DEBUG ] No samples found: verifybamid [2021-08-23 11:46:01,988] multiqc [DEBUG ] No samples found: mirtrace [2021-08-23 11:46:01,995] multiqc [DEBUG ] No samples found: happy [2021-08-23 11:46:02,002] multiqc [DEBUG ] No samples found: mirtop [2021-08-23 11:46:02,015] multiqc [DEBUG ] No samples found: homer [2021-08-23 11:46:02,024] multiqc [DEBUG ] No samples found: macs2 [2021-08-23 11:46:02,032] multiqc [DEBUG ] No samples found: theta2 [2021-08-23 11:46:02,040] multiqc [DEBUG ] No samples found: snpeff [2021-08-23 11:46:02,050] multiqc [DEBUG ] No samples found: gatk [2021-08-23 11:46:02,060] multiqc [DEBUG ] No samples found: htseq [2021-08-23 11:46:02,073] multiqc [DEBUG ] No samples found: bcftools [2021-08-23 11:46:02,081] multiqc [DEBUG ] No samples found: featureCounts [2021-08-23 11:46:02,096] multiqc [DEBUG ] No samples found: fgbio [2021-08-23 11:46:02,135] multiqc [DEBUG ] No samples found: dragen [2021-08-23 11:46:02,143] multiqc [DEBUG ] No samples found: dedup [2021-08-23 11:46:02,155] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-23 11:46:02,211] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-23 11:46:02,220] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-23 11:46:02,222] multiqc [DEBUG ] No samples found: picard [2021-08-23 11:46:02,230] multiqc [DEBUG ] No samples found: prokka [2021-08-23 11:46:02,238] multiqc [DEBUG ] No samples found: samblaster [2021-08-23 11:46:02,249] multiqc [DEBUG ] No samples found: samtools [2021-08-23 11:46:02,262] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-23 11:46:02,270] multiqc [DEBUG ] No samples found: bamtools [2021-08-23 11:46:02,277] multiqc [DEBUG ] No samples found: jellyfish [2021-08-23 11:46:02,290] multiqc [DEBUG ] No samples found: vcftools [2021-08-23 11:46:02,295] multiqc [DEBUG ] No samples found: longranger [2021-08-23 11:46:02,301] multiqc [DEBUG ] No samples found: stacks [2021-08-23 11:46:02,309] multiqc [DEBUG ] No samples found: varscan2 [2021-08-23 11:46:02,341] multiqc [DEBUG ] No samples found: bbmap [2021-08-23 11:46:02,351] multiqc [DEBUG ] No samples found: bismark [2021-08-23 11:46:02,359] multiqc [DEBUG ] No samples found: biscuit [2021-08-23 11:46:02,366] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-23 11:46:02,372] multiqc [DEBUG ] No samples found: hicup [2021-08-23 11:46:02,384] multiqc [DEBUG ] No samples found: hicpro [2021-08-23 11:46:02,388] multiqc [DEBUG ] No samples found: salmon [2021-08-23 11:46:02,395] multiqc [DEBUG ] No samples found: kallisto [2021-08-23 11:46:02,401] multiqc [DEBUG ] No samples found: slamdunk [2021-08-23 11:46:02,405] multiqc [DEBUG ] No samples found: star [2021-08-23 11:46:02,411] multiqc [DEBUG ] No samples found: hisat2 [2021-08-23 11:46:02,420] multiqc [DEBUG ] No samples found: tophat [2021-08-23 11:46:02,426] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-23 11:46:02,434] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-23 11:46:02,440] multiqc [DEBUG ] No samples found: snpsplit [2021-08-23 11:46:02,445] multiqc [DEBUG ] No samples found: kat [2021-08-23 11:46:02,453] multiqc [DEBUG ] No samples found: leehom [2021-08-23 11:46:02,465] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-23 11:46:02,472] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-23 11:46:02,482] multiqc [DEBUG ] No samples found: cutadapt [2021-08-23 11:46:02,487] multiqc [DEBUG ] No samples found: flexbar [2021-08-23 11:46:02,496] multiqc [DEBUG ] No samples found: kaiju [2021-08-23 11:46:02,505] multiqc [DEBUG ] No samples found: kraken [2021-08-23 11:46:02,511] multiqc [DEBUG ] No samples found: malt [2021-08-23 11:46:02,516] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-23 11:46:02,524] multiqc [DEBUG ] No samples found: sickle [2021-08-23 11:46:02,530] multiqc [DEBUG ] No samples found: skewer [2021-08-23 11:46:02,535] multiqc [DEBUG ] No samples found: sortmerna [2021-08-23 11:46:02,540] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-23 11:46:02,551] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-23 11:46:02,565] multiqc [DEBUG ] No samples found: afterqc [2021-08-23 11:46:02,570] multiqc [DEBUG ] No samples found: fastp [2021-08-23 11:46:11,006] multiqc.modules.fastqc.fastqc [INFO ] Found 118 reports [2021-08-23 11:46:32,301] multiqc [DEBUG ] No samples found: pycoqc [2021-08-23 11:46:32,311] multiqc [DEBUG ] No samples found: minionqc [2021-08-23 11:46:32,317] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-23 11:46:32,326] multiqc [DEBUG ] No samples found: clusterflow [2021-08-23 11:46:32,333] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-23 11:46:32,339] multiqc [DEBUG ] No samples found: interop [2021-08-23 11:46:32,347] multiqc [DEBUG ] No samples found: ivar [2021-08-23 11:46:32,355] multiqc [DEBUG ] No samples found: flash [2021-08-23 11:46:32,362] multiqc [DEBUG ] No samples found: seqyclean [2021-08-23 11:46:32,362] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-23 11:46:32,362] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-23 11:46:32,362] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-23 11:46:32,362] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-23 11:46:32,496] multiqc [INFO ] Compressing plot data [2021-08-23 11:46:32,539] multiqc [INFO ] Report : multiqc_report.html [2021-08-23 11:46:32,540] multiqc [INFO ] Data : multiqc_data [2021-08-23 11:46:32,540] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9516306/tmp1fu_57nz/multiqc_data' to '/scratch/gencore/logs/html/HGVMYDRXY/merged/multiqc_data' [2021-08-23 11:46:32,709] multiqc [INFO ] MultiQC complete