[2022-05-09 10:57:34,631] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-09 10:57:34,631] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-09 10:57:34,631] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-09 10:57:34,632] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-09 10:57:34,632] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-09 10:57:34,633] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMWN5BGXL/merged [2022-05-09 10:57:35,249] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-09 10:57:35,249] multiqc [INFO ] This is MultiQC v1.9 [2022-05-09 10:57:35,249] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMWN5BGXL/merged [2022-05-09 10:57:35,249] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMWN5BGXL/merged [2022-05-09 10:57:35,249] multiqc [INFO ] Template : default [2022-05-09 10:57:35,250] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-09 10:57:35,250] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMWN5BGXL/merged [2022-05-09 10:57:35,250] 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 [2022-05-09 10:57:35,250] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19322885/tmp5m86nn6i [2022-05-09 10:57:35,356] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHB7_2_fastqc.html [2022-05-09 10:57:35,359] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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10:57:37,951] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_GR_1_fastqc.html [2022-05-09 10:57:37,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_GR_1_fastqc.html [2022-05-09 10:57:37,999] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_DAM_GR_3_fastqc.html [2022-05-09 10:57:38,001] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_DAM_GR_3_fastqc.html [2022-05-09 10:57:38,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP2_1_fastqc.html [2022-05-09 10:57:38,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP2_1_fastqc.html [2022-05-09 10:57:38,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aTGA1_P1_fastqc.html [2022-05-09 10:57:38,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aTGA1_P1_fastqc.html [2022-05-09 10:57:38,142] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_P3_fastqc.html [2022-05-09 10:57:38,144] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_P3_fastqc.html [2022-05-09 10:57:38,189] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHB7_3_fastqc.html [2022-05-09 10:57:38,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHB7_3_fastqc.html [2022-05-09 10:57:38,237] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_DAM_GR_1_fastqc.html [2022-05-09 10:57:38,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_DAM_GR_1_fastqc.html [2022-05-09 10:57:38,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP1_1_fastqc.html [2022-05-09 10:57:38,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP1_1_fastqc.html [2022-05-09 10:57:38,332] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_3_fastqc.html [2022-05-09 10:57:38,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1_3_fastqc.html [2022-05-09 10:57:38,380] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aCOL4_1_3_fastqc.html [2022-05-09 10:57:38,382] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aCOL4_1_3_fastqc.html [2022-05-09 10:57:38,428] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHB7_1_fastqc.html [2022-05-09 10:57:38,430] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHB7_1_fastqc.html [2022-05-09 10:57:38,476] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP1_2_fastqc.html [2022-05-09 10:57:38,478] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aEV_RFP1_2_fastqc.html [2022-05-09 10:57:38,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aDAM_Only_2_fastqc.html [2022-05-09 10:57:38,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aDAM_Only_2_fastqc.html [2022-05-09 10:57:38,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_N2_fastqc.html [2022-05-09 10:57:38,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_N2_fastqc.html [2022-05-09 10:57:38,619] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aCOL4_2_1_fastqc.html [2022-05-09 10:57:38,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aCOL4_2_1_fastqc.html [2022-05-09 10:57:38,667] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1y11_3_fastqc.html [2022-05-09 10:57:38,668] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1y11_3_fastqc.html [2022-05-09 10:57:38,715] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1y11_1_fastqc.html [2022-05-09 10:57:38,717] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aBZIP1y11_1_fastqc.html [2022-05-09 10:57:38,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_N1_fastqc.html [2022-05-09 10:57:38,767] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aHHO3_N1_fastqc.html [2022-05-09 10:57:38,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aNLP7_DAM_GR_1_fastqc.html [2022-05-09 10:57:38,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMWN5BGXL_n01_aNLP7_DAM_GR_1_fastqc.html [2022-05-09 10:57:39,152] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-09 10:57:39,153] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-09 10:57:39,162] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-09 10:57:39,194] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 70 samples (table) [2022-05-09 10:57:39,204] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-09 10:57:39,209] multiqc [DEBUG ] No samples found: conpair [2022-05-09 10:57:39,215] multiqc [DEBUG ] No samples found: peddy [2022-05-09 10:57:39,220] multiqc [DEBUG ] No samples found: somalier [2022-05-09 10:57:39,225] multiqc [DEBUG ] No samples found: methylQA [2022-05-09 10:57:39,234] multiqc [DEBUG ] No samples found: mosdepth [2022-05-09 10:57:39,239] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-09 10:57:39,242] multiqc [DEBUG ] No samples found: qualimap [2022-05-09 10:57:39,248] multiqc [DEBUG ] No samples found: preseq [2022-05-09 10:57:39,253] multiqc [DEBUG ] No samples found: quast [2022-05-09 10:57:39,258] multiqc [DEBUG ] No samples found: qorts [2022-05-09 10:57:39,263] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-09 10:57:39,268] multiqc [DEBUG ] No samples found: rockhopper [2022-05-09 10:57:39,273] multiqc [DEBUG ] No samples found: rsem [2022-05-09 10:57:39,284] multiqc [DEBUG ] No samples found: rseqc [2022-05-09 10:57:39,289] multiqc [DEBUG ] No samples found: busco [2022-05-09 10:57:39,294] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-09 10:57:39,299] multiqc [DEBUG ] No samples found: disambiguate [2022-05-09 10:57:39,304] multiqc [DEBUG ] No samples found: supernova [2022-05-09 10:57:39,318] multiqc [DEBUG ] No samples found: deeptools [2022-05-09 10:57:39,323] multiqc [DEBUG ] No samples found: sargasso [2022-05-09 10:57:39,328] multiqc [DEBUG ] No samples found: verifybamid [2022-05-09 10:57:39,333] multiqc [DEBUG ] No samples found: mirtrace [2022-05-09 10:57:39,339] multiqc [DEBUG ] No samples found: happy [2022-05-09 10:57:39,344] multiqc [DEBUG ] No samples found: mirtop [2022-05-09 10:57:39,351] multiqc [DEBUG ] No samples found: homer [2022-05-09 10:57:39,356] multiqc [DEBUG ] No samples found: macs2 [2022-05-09 10:57:39,361] multiqc [DEBUG ] No samples found: theta2 [2022-05-09 10:57:39,366] multiqc [DEBUG ] No samples found: snpeff [2022-05-09 10:57:39,373] multiqc [DEBUG ] No samples found: gatk [2022-05-09 10:57:39,378] multiqc [DEBUG ] No samples found: htseq [2022-05-09 10:57:39,384] multiqc [DEBUG ] No samples found: bcftools [2022-05-09 10:57:39,389] multiqc [DEBUG ] No samples found: featureCounts [2022-05-09 10:57:39,396] multiqc [DEBUG ] No samples found: fgbio [2022-05-09 10:57:39,411] multiqc [DEBUG ] No samples found: dragen [2022-05-09 10:57:39,416] multiqc [DEBUG ] No samples found: dedup [2022-05-09 10:57:39,421] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-09 10:57:39,446] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-09 10:57:39,451] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-09 10:57:39,453] multiqc [DEBUG ] No samples found: picard [2022-05-09 10:57:39,458] multiqc [DEBUG ] No samples found: prokka [2022-05-09 10:57:39,462] multiqc [DEBUG ] No samples found: samblaster [2022-05-09 10:57:39,471] multiqc [DEBUG ] No samples found: samtools [2022-05-09 10:57:39,476] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-09 10:57:39,482] multiqc [DEBUG ] No samples found: bamtools [2022-05-09 10:57:39,487] multiqc [DEBUG ] No samples found: jellyfish [2022-05-09 10:57:39,495] multiqc [DEBUG ] No samples found: vcftools [2022-05-09 10:57:39,500] multiqc [DEBUG ] No samples found: longranger [2022-05-09 10:57:39,505] multiqc [DEBUG ] No samples found: stacks [2022-05-09 10:57:39,510] multiqc [DEBUG ] No samples found: varscan2 [2022-05-09 10:57:39,525] multiqc [DEBUG ] No samples found: bbmap [2022-05-09 10:57:39,530] multiqc [DEBUG ] No samples found: bismark [2022-05-09 10:57:39,536] multiqc [DEBUG ] No samples found: biscuit [2022-05-09 10:57:39,541] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-09 10:57:39,546] multiqc [DEBUG ] No samples found: hicup [2022-05-09 10:57:39,551] multiqc [DEBUG ] No samples found: hicpro [2022-05-09 10:57:39,556] multiqc [DEBUG ] No samples found: salmon [2022-05-09 10:57:39,562] multiqc [DEBUG ] No samples found: kallisto [2022-05-09 10:57:39,567] multiqc [DEBUG ] No samples found: slamdunk [2022-05-09 10:57:39,572] multiqc [DEBUG ] No samples found: star [2022-05-09 10:57:39,576] multiqc [DEBUG ] No samples found: hisat2 [2022-05-09 10:57:39,581] multiqc [DEBUG ] No samples found: tophat [2022-05-09 10:57:39,586] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-09 10:57:39,591] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-09 10:57:39,596] multiqc [DEBUG ] No samples found: snpsplit [2022-05-09 10:57:39,601] multiqc [DEBUG ] No samples found: kat [2022-05-09 10:57:39,605] multiqc [DEBUG ] No samples found: leehom [2022-05-09 10:57:39,610] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-09 10:57:39,615] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-09 10:57:39,620] multiqc [DEBUG ] No samples found: cutadapt [2022-05-09 10:57:39,625] multiqc [DEBUG ] No samples found: flexbar [2022-05-09 10:57:39,630] multiqc [DEBUG ] No samples found: kaiju [2022-05-09 10:57:39,635] multiqc [DEBUG ] No samples found: kraken [2022-05-09 10:57:39,640] multiqc [DEBUG ] No samples found: malt [2022-05-09 10:57:39,645] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-09 10:57:39,650] multiqc [DEBUG ] No samples found: sickle [2022-05-09 10:57:39,655] multiqc [DEBUG ] No samples found: skewer [2022-05-09 10:57:39,659] multiqc [DEBUG ] No samples found: sortmerna [2022-05-09 10:57:39,664] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-09 10:57:39,669] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-09 10:57:39,675] multiqc [DEBUG ] No samples found: afterqc [2022-05-09 10:57:39,680] multiqc [DEBUG ] No samples found: fastp [2022-05-09 10:57:44,442] multiqc.modules.fastqc.fastqc [INFO ] Found 70 reports [2022-05-09 10:57:45,821] multiqc [DEBUG ] No samples found: pycoqc [2022-05-09 10:57:45,826] multiqc [DEBUG ] No samples found: minionqc [2022-05-09 10:57:45,831] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-09 10:57:45,836] multiqc [DEBUG ] No samples found: clusterflow [2022-05-09 10:57:45,841] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-09 10:57:45,847] multiqc [DEBUG ] No samples found: interop [2022-05-09 10:57:45,852] multiqc [DEBUG ] No samples found: ivar [2022-05-09 10:57:45,857] multiqc [DEBUG ] No samples found: flash [2022-05-09 10:57:45,862] multiqc [DEBUG ] No samples found: seqyclean [2022-05-09 10:57:45,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-09 10:57:45,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-09 10:57:45,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-09 10:57:45,862] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-09 10:57:45,943] multiqc [INFO ] Compressing plot data [2022-05-09 10:57:47,145] multiqc [INFO ] Report : multiqc_report.html [2022-05-09 10:57:47,145] multiqc [INFO ] Data : multiqc_data [2022-05-09 10:57:47,145] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19322885/tmp5m86nn6i/multiqc_data' to '/scratch/gencore/logs/html/HMWN5BGXL/merged/multiqc_data' [2022-05-09 10:57:47,275] multiqc [INFO ] MultiQC complete