[2022-12-20 23:55:17,199] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-20 23:55:17,199] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-20 23:55:17,199] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-20 23:55:17,201] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-20 23:55:17,201] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-20 23:55:17,201] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC3N3BGXN/merged [2022-12-20 23:55:17,820] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-20 23:55:17,820] multiqc [INFO ] This is MultiQC v1.9 [2022-12-20 23:55:17,820] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC3N3BGXN/merged [2022-12-20 23:55:17,820] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HC3N3BGXN/merged [2022-12-20 23:55:17,820] multiqc [INFO ] Template : default [2022-12-20 23:55:17,821] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-20 23:55:17,821] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HC3N3BGXN/merged [2022-12-20 23:55:17,822] 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 [2022-12-20 23:55:17,822] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-28496870/tmpy9htvjg0 [2022-12-20 23:55:18,005] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO60_fastqc.html [2022-12-20 23:55:18,008] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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HC3N3BGXN_n01_DO59_fastqc.html [2022-12-20 23:55:18,584] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO59_fastqc.html [2022-12-20 23:55:18,619] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO58_fastqc.html [2022-12-20 23:55:18,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO58_fastqc.html [2022-12-20 23:55:18,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO61_fastqc.html [2022-12-20 23:55:18,658] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO61_fastqc.html [2022-12-20 23:55:18,694] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ23_fastqc.html [2022-12-20 23:55:18,695] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ23_fastqc.html [2022-12-20 23:55:18,731] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ29_fastqc.html [2022-12-20 23:55:18,733] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ29_fastqc.html [2022-12-20 23:55:18,769] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA71_fastqc.html [2022-12-20 23:55:18,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA71_fastqc.html [2022-12-20 23:55:18,807] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ24_fastqc.html [2022-12-20 23:55:18,809] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ24_fastqc.html [2022-12-20 23:55:18,850] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA76_fastqc.html [2022-12-20 23:55:18,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA76_fastqc.html [2022-12-20 23:55:18,887] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO62_fastqc.html [2022-12-20 23:55:18,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_DO62_fastqc.html [2022-12-20 23:55:18,925] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA73_fastqc.html [2022-12-20 23:55:18,926] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_AA73_fastqc.html [2022-12-20 23:55:18,962] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ22_fastqc.html [2022-12-20 23:55:18,963] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC3N3BGXN_n01_YZ22_fastqc.html [2022-12-20 23:55:19,433] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-20 23:55:19,438] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-20 23:55:19,465] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2022-12-20 23:55:19,466] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-20 23:55:19,475] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-12-20 23:55:19,487] multiqc [DEBUG ] No samples found: conpair [2022-12-20 23:55:19,500] multiqc [DEBUG ] No samples found: peddy [2022-12-20 23:55:19,521] multiqc [DEBUG ] No samples found: somalier [2022-12-20 23:55:19,539] multiqc [DEBUG ] No samples found: methylQA [2022-12-20 23:55:19,575] multiqc [DEBUG ] No samples found: mosdepth [2022-12-20 23:55:19,592] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-20 23:55:19,603] multiqc [DEBUG ] No samples found: qualimap [2022-12-20 23:55:19,617] multiqc [DEBUG ] No samples found: preseq [2022-12-20 23:55:19,636] multiqc [DEBUG ] No samples found: quast [2022-12-20 23:55:19,654] multiqc [DEBUG ] No samples found: qorts [2022-12-20 23:55:19,674] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-20 23:55:19,694] multiqc [DEBUG ] No samples found: rockhopper [2022-12-20 23:55:19,718] multiqc [DEBUG ] No samples found: rsem [2022-12-20 23:55:19,762] multiqc [DEBUG ] No samples found: rseqc [2022-12-20 23:55:19,778] multiqc [DEBUG ] No samples found: busco [2022-12-20 23:55:19,794] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-20 23:55:19,809] multiqc [DEBUG ] No samples found: disambiguate [2022-12-20 23:55:19,829] multiqc [DEBUG ] No samples found: supernova [2022-12-20 23:55:19,885] multiqc [DEBUG ] No samples found: deeptools [2022-12-20 23:55:19,907] multiqc [DEBUG ] No samples found: sargasso [2022-12-20 23:55:19,923] multiqc [DEBUG ] No samples found: verifybamid [2022-12-20 23:55:19,940] multiqc [DEBUG ] No samples found: mirtrace [2022-12-20 23:55:19,953] multiqc [DEBUG ] No samples found: happy [2022-12-20 23:55:19,973] multiqc [DEBUG ] No samples found: mirtop [2022-12-20 23:55:19,999] multiqc [DEBUG ] No samples found: homer [2022-12-20 23:55:20,012] multiqc [DEBUG ] No samples found: macs2 [2022-12-20 23:55:20,028] multiqc [DEBUG ] No samples found: theta2 [2022-12-20 23:55:20,054] multiqc [DEBUG ] No samples found: snpeff [2022-12-20 23:55:20,079] multiqc [DEBUG ] No samples found: gatk [2022-12-20 23:55:20,097] multiqc [DEBUG ] No samples found: htseq [2022-12-20 23:55:20,124] multiqc [DEBUG ] No samples found: bcftools [2022-12-20 23:55:20,142] multiqc [DEBUG ] No samples found: featureCounts [2022-12-20 23:55:20,168] multiqc [DEBUG ] No samples found: fgbio [2022-12-20 23:55:20,218] multiqc [DEBUG ] No samples found: dragen [2022-12-20 23:55:20,237] multiqc [DEBUG ] No samples found: dedup [2022-12-20 23:55:20,258] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-20 23:55:20,375] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-20 23:55:20,392] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-20 23:55:20,398] multiqc [DEBUG ] No samples found: picard [2022-12-20 23:55:20,421] multiqc [DEBUG ] No samples found: prokka [2022-12-20 23:55:20,440] multiqc [DEBUG ] No samples found: samblaster [2022-12-20 23:55:20,472] multiqc [DEBUG ] No samples found: samtools [2022-12-20 23:55:20,493] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-20 23:55:20,512] multiqc [DEBUG ] No samples found: bamtools [2022-12-20 23:55:20,529] multiqc [DEBUG ] No samples found: jellyfish [2022-12-20 23:55:20,561] multiqc [DEBUG ] No samples found: vcftools [2022-12-20 23:55:20,580] multiqc [DEBUG ] No samples found: longranger [2022-12-20 23:55:20,595] multiqc [DEBUG ] No samples found: stacks [2022-12-20 23:55:20,610] multiqc [DEBUG ] No samples found: varscan2 [2022-12-20 23:55:20,656] multiqc [DEBUG ] No samples found: bbmap [2022-12-20 23:55:20,673] multiqc [DEBUG ] No samples found: bismark [2022-12-20 23:55:20,691] multiqc [DEBUG ] No samples found: biscuit [2022-12-20 23:55:20,707] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-20 23:55:20,729] multiqc [DEBUG ] No samples found: hicup [2022-12-20 23:55:20,746] multiqc [DEBUG ] No samples found: hicpro [2022-12-20 23:55:20,765] multiqc [DEBUG ] No samples found: salmon [2022-12-20 23:55:20,781] multiqc [DEBUG ] No samples found: kallisto [2022-12-20 23:55:20,796] multiqc [DEBUG ] No samples found: slamdunk [2022-12-20 23:55:20,810] multiqc [DEBUG ] No samples found: star [2022-12-20 23:55:20,826] multiqc [DEBUG ] No samples found: hisat2 [2022-12-20 23:55:20,847] multiqc [DEBUG ] No samples found: tophat [2022-12-20 23:55:20,865] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-20 23:55:20,880] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-20 23:55:20,903] multiqc [DEBUG ] No samples found: snpsplit [2022-12-20 23:55:20,921] multiqc [DEBUG ] No samples found: kat [2022-12-20 23:55:20,938] multiqc [DEBUG ] No samples found: leehom [2022-12-20 23:55:20,961] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-20 23:55:20,978] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-20 23:55:20,991] multiqc [DEBUG ] No samples found: cutadapt [2022-12-20 23:55:21,008] multiqc [DEBUG ] No samples found: flexbar [2022-12-20 23:55:21,026] multiqc [DEBUG ] No samples found: kaiju [2022-12-20 23:55:21,045] multiqc [DEBUG ] No samples found: kraken [2022-12-20 23:55:21,064] multiqc [DEBUG ] No samples found: malt [2022-12-20 23:55:21,081] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-20 23:55:21,100] multiqc [DEBUG ] No samples found: sickle [2022-12-20 23:55:21,118] multiqc [DEBUG ] No samples found: skewer [2022-12-20 23:55:21,135] multiqc [DEBUG ] No samples found: sortmerna [2022-12-20 23:55:21,155] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-20 23:55:21,174] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-20 23:55:21,193] multiqc [DEBUG ] No samples found: afterqc [2022-12-20 23:55:21,216] multiqc [DEBUG ] No samples found: fastp [2022-12-20 23:55:22,660] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2022-12-20 23:55:23,126] multiqc [DEBUG ] No samples found: pycoqc [2022-12-20 23:55:23,147] multiqc [DEBUG ] No samples found: minionqc [2022-12-20 23:55:23,164] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-20 23:55:23,185] multiqc [DEBUG ] No samples found: clusterflow [2022-12-20 23:55:23,204] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-20 23:55:23,223] multiqc [DEBUG ] No samples found: interop [2022-12-20 23:55:23,243] multiqc [DEBUG ] No samples found: ivar [2022-12-20 23:55:23,265] multiqc [DEBUG ] No samples found: flash [2022-12-20 23:55:23,281] multiqc [DEBUG ] No samples found: seqyclean [2022-12-20 23:55:23,281] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-12-20 23:55:23,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-12-20 23:55:23,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-12-20 23:55:23,282] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-20 23:55:23,312] multiqc [INFO ] Compressing plot data [2022-12-20 23:55:23,683] multiqc [INFO ] Report : multiqc_report.html [2022-12-20 23:55:23,683] multiqc [INFO ] Data : multiqc_data [2022-12-20 23:55:23,683] multiqc [DEBUG ] Moving data file from '/state/partition1/job-28496870/tmpy9htvjg0/multiqc_data' to '/scratch/gencore/logs/html/HC3N3BGXN/merged/multiqc_data' [2022-12-20 23:55:23,966] multiqc [INFO ] MultiQC complete