[2022-04-04 09:24:18,091] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-04 09:24:18,091] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-04 09:24:18,091] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-04 09:24:18,092] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-04 09:24:18,092] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-04 09:24:18,092] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFMCGBGXL/merged [2022-04-04 09:24:18,767] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-04 09:24:18,767] multiqc [INFO ] This is MultiQC v1.9 [2022-04-04 09:24:18,767] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HFMCGBGXL/merged [2022-04-04 09:24:18,767] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HFMCGBGXL/merged [2022-04-04 09:24:18,767] multiqc [INFO ] Template : default [2022-04-04 09:24:18,767] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-04 09:24:18,767] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HFMCGBGXL/merged [2022-04-04 09:24:18,767] 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 [2022-04-04 09:24:18,768] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17215060/tmpukclg9sx [2022-04-04 09:24:18,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr584_fastqc.html [2022-04-04 09:24:18,878] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-04-04 09:24:24,123] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr561_fastqc.html [2022-04-04 09:24:24,170] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n02_dpr579_fastqc.html [2022-04-04 09:24:24,172] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n02_dpr579_fastqc.html [2022-04-04 09:24:24,217] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr583_fastqc.html [2022-04-04 09:24:24,219] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr583_fastqc.html [2022-04-04 09:24:24,260] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr565_fastqc.html [2022-04-04 09:24:24,262] multiqc [DEBUG 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filesize limit: HFMCGBGXL_n02_dpr564_fastqc.html [2022-04-04 09:24:24,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n02_dpr567_fastqc.html [2022-04-04 09:24:24,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n02_dpr567_fastqc.html [2022-04-04 09:24:24,623] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr574_fastqc.html [2022-04-04 09:24:24,625] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr574_fastqc.html [2022-04-04 09:24:24,668] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr570_fastqc.html [2022-04-04 09:24:24,670] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HFMCGBGXL_n01_dpr570_fastqc.html [2022-04-04 09:24:25,062] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-04 09:24:25,063] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-04 09:24:25,083] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 28 samples (table) [2022-04-04 09:24:25,093] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-04 09:24:25,094] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-04 09:24:25,100] multiqc [DEBUG ] No samples found: conpair [2022-04-04 09:24:25,105] multiqc [DEBUG ] No samples found: peddy [2022-04-04 09:24:25,111] multiqc [DEBUG ] No samples found: somalier [2022-04-04 09:24:25,115] multiqc [DEBUG ] No samples found: methylQA [2022-04-04 09:24:25,123] multiqc [DEBUG ] No samples found: mosdepth [2022-04-04 09:24:25,128] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-04 09:24:25,131] multiqc [DEBUG ] No samples found: qualimap [2022-04-04 09:24:25,135] multiqc [DEBUG ] No samples found: preseq [2022-04-04 09:24:25,140] multiqc [DEBUG ] No samples found: quast [2022-04-04 09:24:25,145] multiqc [DEBUG ] No samples found: qorts [2022-04-04 09:24:25,150] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-04 09:24:25,155] multiqc [DEBUG ] No samples found: rockhopper [2022-04-04 09:24:25,159] multiqc [DEBUG ] No samples found: rsem [2022-04-04 09:24:25,170] multiqc [DEBUG ] No samples found: rseqc [2022-04-04 09:24:25,174] multiqc [DEBUG ] No samples found: busco [2022-04-04 09:24:25,179] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-04 09:24:25,184] multiqc [DEBUG ] No samples found: disambiguate [2022-04-04 09:24:25,189] multiqc [DEBUG ] No samples found: supernova [2022-04-04 09:24:25,201] multiqc [DEBUG ] No samples found: deeptools [2022-04-04 09:24:25,206] multiqc [DEBUG ] No samples found: sargasso [2022-04-04 09:24:25,210] multiqc [DEBUG ] No samples found: verifybamid [2022-04-04 09:24:25,215] multiqc [DEBUG ] No samples found: mirtrace [2022-04-04 09:24:25,219] multiqc [DEBUG ] No samples found: happy [2022-04-04 09:24:25,224] multiqc [DEBUG ] No samples found: mirtop [2022-04-04 09:24:25,230] multiqc [DEBUG ] No samples found: homer [2022-04-04 09:24:25,235] multiqc [DEBUG ] No samples found: macs2 [2022-04-04 09:24:25,240] multiqc [DEBUG ] No samples found: theta2 [2022-04-04 09:24:25,245] multiqc [DEBUG ] No samples found: snpeff [2022-04-04 09:24:25,251] multiqc [DEBUG ] No samples found: gatk [2022-04-04 09:24:25,256] multiqc [DEBUG ] No samples found: htseq [2022-04-04 09:24:25,263] multiqc [DEBUG ] No samples found: bcftools [2022-04-04 09:24:25,268] multiqc [DEBUG ] No samples found: featureCounts [2022-04-04 09:24:25,276] multiqc [DEBUG ] No samples found: fgbio [2022-04-04 09:24:25,288] multiqc [DEBUG ] No samples found: dragen [2022-04-04 09:24:25,293] multiqc [DEBUG ] No samples found: dedup [2022-04-04 09:24:25,297] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-04 09:24:25,321] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-04 09:24:25,326] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-04 09:24:25,329] multiqc [DEBUG ] No samples found: picard [2022-04-04 09:24:25,333] multiqc [DEBUG ] No samples found: prokka [2022-04-04 09:24:25,339] multiqc [DEBUG ] No samples found: samblaster [2022-04-04 09:24:25,347] multiqc [DEBUG ] No samples found: samtools [2022-04-04 09:24:25,352] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-04 09:24:25,357] multiqc [DEBUG ] No samples found: bamtools [2022-04-04 09:24:25,362] multiqc [DEBUG ] No samples found: jellyfish [2022-04-04 09:24:25,370] multiqc [DEBUG ] No samples found: vcftools [2022-04-04 09:24:25,375] multiqc [DEBUG ] No samples found: longranger [2022-04-04 09:24:25,379] multiqc [DEBUG ] No samples found: stacks [2022-04-04 09:24:25,384] multiqc [DEBUG ] No samples found: varscan2 [2022-04-04 09:24:25,396] multiqc [DEBUG ] No samples found: bbmap [2022-04-04 09:24:25,401] multiqc [DEBUG ] No samples found: bismark [2022-04-04 09:24:25,406] multiqc [DEBUG ] No samples found: biscuit [2022-04-04 09:24:25,411] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-04 09:24:25,416] multiqc [DEBUG ] No samples found: hicup [2022-04-04 09:24:25,420] multiqc [DEBUG ] No samples found: hicpro [2022-04-04 09:24:25,425] multiqc [DEBUG ] No samples found: salmon [2022-04-04 09:24:25,430] multiqc [DEBUG ] No samples found: kallisto [2022-04-04 09:24:25,434] multiqc [DEBUG ] No samples found: slamdunk [2022-04-04 09:24:25,439] multiqc [DEBUG ] No samples found: star [2022-04-04 09:24:25,444] multiqc [DEBUG ] No samples found: hisat2 [2022-04-04 09:24:25,448] multiqc [DEBUG ] No samples found: tophat [2022-04-04 09:24:25,453] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-04 09:24:25,458] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-04 09:24:25,463] multiqc [DEBUG ] No samples found: snpsplit [2022-04-04 09:24:25,467] multiqc [DEBUG ] No samples found: kat [2022-04-04 09:24:25,471] multiqc [DEBUG ] No samples found: leehom [2022-04-04 09:24:25,476] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-04 09:24:25,481] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-04 09:24:25,485] multiqc [DEBUG ] No samples found: cutadapt [2022-04-04 09:24:25,490] multiqc [DEBUG ] No samples found: flexbar [2022-04-04 09:24:25,495] multiqc [DEBUG ] No samples found: kaiju [2022-04-04 09:24:25,498] multiqc [DEBUG ] No samples found: kraken [2022-04-04 09:24:25,503] multiqc [DEBUG ] No samples found: malt [2022-04-04 09:24:25,508] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-04 09:24:25,512] multiqc [DEBUG ] No samples found: sickle [2022-04-04 09:24:25,517] multiqc [DEBUG ] No samples found: skewer [2022-04-04 09:24:25,521] multiqc [DEBUG ] No samples found: sortmerna [2022-04-04 09:24:25,525] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-04 09:24:25,530] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-04 09:24:25,535] multiqc [DEBUG ] No samples found: afterqc [2022-04-04 09:24:25,540] multiqc [DEBUG ] No samples found: fastp [2022-04-04 09:24:28,546] multiqc.modules.fastqc.fastqc [INFO ] Found 56 reports [2022-04-04 09:24:28,943] multiqc [DEBUG ] No samples found: pycoqc [2022-04-04 09:24:28,948] multiqc [DEBUG ] No samples found: minionqc [2022-04-04 09:24:28,954] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-04 09:24:28,959] multiqc [DEBUG ] No samples found: clusterflow [2022-04-04 09:24:28,963] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-04 09:24:28,968] multiqc [DEBUG ] No samples found: interop [2022-04-04 09:24:28,973] multiqc [DEBUG ] No samples found: ivar [2022-04-04 09:24:28,978] multiqc [DEBUG ] No samples found: flash [2022-04-04 09:24:28,983] multiqc [DEBUG ] No samples found: seqyclean [2022-04-04 09:24:28,983] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-04 09:24:28,983] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-04 09:24:28,984] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-04 09:24:28,984] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-04 09:24:29,049] multiqc [INFO ] Compressing plot data [2022-04-04 09:24:29,898] multiqc [INFO ] Report : multiqc_report.html [2022-04-04 09:24:29,899] multiqc [INFO ] Data : multiqc_data [2022-04-04 09:24:29,899] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17215060/tmpukclg9sx/multiqc_data' to '/scratch/gencore/logs/html/HFMCGBGXL/merged/multiqc_data' [2022-04-04 09:24:30,016] multiqc [INFO ] MultiQC complete