[2021-04-28 12:49:11,869] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-04-28 12:49:11,869] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-04-28 12:49:11,869] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-04-28 12:49:11,870] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-04-28 12:49:11,870] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-04-28 12:49:11,870] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5CYGDRXY/merged [2021-04-28 12:49:13,329] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-04-28 12:49:13,330] multiqc [INFO ] This is MultiQC v1.9 [2021-04-28 12:49:13,330] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5CYGDRXY/merged [2021-04-28 12:49:13,330] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5CYGDRXY/merged [2021-04-28 12:49:13,330] multiqc [INFO ] Template : default [2021-04-28 12:49:13,330] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-04-28 12:49:13,330] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5CYGDRXY/merged [2021-04-28 12:49:13,330] 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 [2021-04-28 12:49:13,330] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6063466/tmplxlqgp2p [2021-04-28 12:49:13,461] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g37_fastqc.html [2021-04-28 12:49:13,464] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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filesize limit: H5CYGDRXY_n01_bc02_g37_fastqc.html [2021-04-28 12:49:13,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g149_fastqc.html [2021-04-28 12:49:13,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g149_fastqc.html [2021-04-28 12:49:13,801] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g149_fastqc.html [2021-04-28 12:49:13,801] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g149_fastqc.html [2021-04-28 12:49:13,801] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g149_fastqc.html [2021-04-28 12:49:13,801] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: 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H5CYGDRXY_n01_bc04_g62_fastqc.html [2021-04-28 12:49:14,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g62_fastqc.html [2021-04-28 12:49:14,129] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g99_fastqc.html [2021-04-28 12:49:14,130] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g99_fastqc.html [2021-04-28 12:49:14,218] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g5_fastqc.html [2021-04-28 12:49:14,220] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g5_fastqc.html [2021-04-28 12:49:14,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g124_fastqc.html [2021-04-28 12:49:14,312] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g124_fastqc.html [2021-04-28 12:49:14,403] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g149_fastqc.html [2021-04-28 12:49:14,405] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g149_fastqc.html [2021-04-28 12:49:14,492] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g149_fastqc.html [2021-04-28 12:49:14,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g149_fastqc.html [2021-04-28 12:49:14,577] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g124_fastqc.html [2021-04-28 12:49:14,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g124_fastqc.html [2021-04-28 12:49:14,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g99_fastqc.html [2021-04-28 12:49:14,666] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g99_fastqc.html [2021-04-28 12:49:14,749] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g99_fastqc.html [2021-04-28 12:49:14,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g99_fastqc.html [2021-04-28 12:49:14,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g62_fastqc.html [2021-04-28 12:49:14,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g62_fastqc.html [2021-04-28 12:49:14,913] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g37_fastqc.html [2021-04-28 12:49:14,914] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc04_g37_fastqc.html [2021-04-28 12:49:14,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g5_fastqc.html [2021-04-28 12:49:14,998] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g5_fastqc.html [2021-04-28 12:49:15,081] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g5_fastqc.html [2021-04-28 12:49:15,082] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_bc02_g5_fastqc.html [2021-04-28 12:49:15,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g124_fastqc.html [2021-04-28 12:49:15,171] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g124_fastqc.html [2021-04-28 12:49:15,253] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g62_fastqc.html [2021-04-28 12:49:15,254] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g62_fastqc.html [2021-04-28 12:49:15,345] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g62_fastqc.html [2021-04-28 12:49:15,346] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g62_fastqc.html [2021-04-28 12:49:15,428] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g37_fastqc.html [2021-04-28 12:49:15,430] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc02_g37_fastqc.html [2021-04-28 12:49:15,513] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,515] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: H5CYGDRXY_n02_bc04_g5_fastqc.html [2021-04-28 12:49:15,588] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5CYGDRXY_n01_undetermined_fastqc.html [2021-04-28 12:49:15,590] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5CYGDRXY_n01_undetermined_fastqc.html [2021-04-28 12:49:16,046] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-28 12:49:16,047] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-28 12:49:16,061] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2021-04-28 12:49:16,063] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-04-28 12:49:16,072] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-04-28 12:49:16,078] multiqc [DEBUG ] No samples found: conpair [2021-04-28 12:49:16,084] multiqc [DEBUG ] No samples found: peddy [2021-04-28 12:49:16,089] multiqc [DEBUG ] No samples found: somalier [2021-04-28 12:49:16,095] multiqc [DEBUG ] No samples found: methylQA [2021-04-28 12:49:16,105] multiqc [DEBUG ] No samples found: mosdepth [2021-04-28 12:49:16,109] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-04-28 12:49:16,113] multiqc [DEBUG ] No samples found: qualimap [2021-04-28 12:49:16,119] multiqc [DEBUG ] No samples found: preseq [2021-04-28 12:49:16,125] multiqc [DEBUG ] No samples found: quast [2021-04-28 12:49:16,130] multiqc [DEBUG ] No samples found: qorts [2021-04-28 12:49:16,136] multiqc [DEBUG ] No samples found: rna_seqc [2021-04-28 12:49:16,141] multiqc [DEBUG ] No samples found: rockhopper [2021-04-28 12:49:16,146] multiqc [DEBUG ] No samples found: rsem [2021-04-28 12:49:16,159] multiqc [DEBUG ] No samples found: rseqc [2021-04-28 12:49:16,163] multiqc [DEBUG ] No samples found: busco [2021-04-28 12:49:16,169] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-04-28 12:49:16,174] multiqc [DEBUG ] No samples found: disambiguate [2021-04-28 12:49:16,180] multiqc [DEBUG ] No samples found: supernova [2021-04-28 12:49:16,203] multiqc [DEBUG ] No samples found: deeptools [2021-04-28 12:49:16,209] multiqc [DEBUG ] No samples found: sargasso [2021-04-28 12:49:16,214] multiqc [DEBUG ] No samples found: verifybamid [2021-04-28 12:49:16,220] multiqc [DEBUG ] No samples found: mirtrace [2021-04-28 12:49:16,225] multiqc [DEBUG ] No samples found: happy [2021-04-28 12:49:16,234] multiqc [DEBUG ] No samples found: mirtop [2021-04-28 12:49:16,242] multiqc [DEBUG ] No samples found: homer [2021-04-28 12:49:16,247] multiqc [DEBUG ] No samples found: macs2 [2021-04-28 12:49:16,253] multiqc [DEBUG ] No samples found: theta2 [2021-04-28 12:49:16,259] multiqc [DEBUG ] No samples found: snpeff [2021-04-28 12:49:16,267] multiqc [DEBUG ] No samples found: gatk [2021-04-28 12:49:16,272] multiqc [DEBUG ] No samples found: htseq [2021-04-28 12:49:16,278] multiqc [DEBUG ] No samples found: bcftools [2021-04-28 12:49:16,283] multiqc [DEBUG ] No samples found: featureCounts [2021-04-28 12:49:16,290] multiqc [DEBUG ] No samples found: fgbio [2021-04-28 12:49:16,305] multiqc [DEBUG ] No samples found: dragen [2021-04-28 12:49:16,310] multiqc [DEBUG ] No samples found: dedup [2021-04-28 12:49:16,316] multiqc [DEBUG ] No samples found: damageprofiler [2021-04-28 12:49:16,337] multiqc [DEBUG ] No samples found: biobambam2 [2021-04-28 12:49:16,342] multiqc [DEBUG ] No samples found: mtnucratio [2021-04-28 12:49:16,344] multiqc [DEBUG ] No samples found: picard [2021-04-28 12:49:16,349] multiqc [DEBUG ] No samples found: prokka [2021-04-28 12:49:16,354] multiqc [DEBUG ] No samples found: samblaster [2021-04-28 12:49:16,362] multiqc [DEBUG ] No samples found: samtools [2021-04-28 12:49:16,368] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-04-28 12:49:16,373] multiqc [DEBUG ] No samples found: bamtools [2021-04-28 12:49:16,378] multiqc [DEBUG ] No samples found: jellyfish [2021-04-28 12:49:16,387] multiqc [DEBUG ] No samples found: vcftools [2021-04-28 12:49:16,392] multiqc [DEBUG ] No samples found: longranger [2021-04-28 12:49:16,397] multiqc [DEBUG ] No samples found: stacks [2021-04-28 12:49:16,402] multiqc [DEBUG ] No samples found: varscan2 [2021-04-28 12:49:16,417] multiqc [DEBUG ] No samples found: bbmap [2021-04-28 12:49:16,422] multiqc [DEBUG ] No samples found: bismark [2021-04-28 12:49:16,428] multiqc [DEBUG ] No samples found: biscuit [2021-04-28 12:49:16,434] multiqc [DEBUG ] No samples found: hicexplorer [2021-04-28 12:49:16,440] multiqc [DEBUG ] No samples found: hicup [2021-04-28 12:49:16,445] multiqc [DEBUG ] No samples found: hicpro [2021-04-28 12:49:16,450] multiqc [DEBUG ] No samples found: salmon [2021-04-28 12:49:16,456] multiqc [DEBUG ] No samples found: kallisto [2021-04-28 12:49:16,461] multiqc [DEBUG ] No samples found: slamdunk [2021-04-28 12:49:16,466] multiqc [DEBUG ] No samples found: star [2021-04-28 12:49:16,471] multiqc [DEBUG ] No samples found: hisat2 [2021-04-28 12:49:16,476] multiqc [DEBUG ] No samples found: tophat [2021-04-28 12:49:16,481] multiqc [DEBUG ] No samples found: bowtie2 [2021-04-28 12:49:16,486] multiqc [DEBUG ] No samples found: bowtie1 [2021-04-28 12:49:16,491] multiqc [DEBUG ] No samples found: snpsplit [2021-04-28 12:49:16,497] multiqc [DEBUG ] No samples found: kat [2021-04-28 12:49:16,501] multiqc [DEBUG ] No samples found: leehom [2021-04-28 12:49:16,507] multiqc [DEBUG ] No samples found: adapterRemoval [2021-04-28 12:49:16,512] multiqc [DEBUG ] No samples found: clipandmerge [2021-04-28 12:49:16,517] multiqc [DEBUG ] No samples found: cutadapt [2021-04-28 12:49:16,522] multiqc [DEBUG ] No samples found: flexbar [2021-04-28 12:49:16,527] multiqc [DEBUG ] No samples found: kaiju [2021-04-28 12:49:16,532] multiqc [DEBUG ] No samples found: kraken [2021-04-28 12:49:16,537] multiqc [DEBUG ] No samples found: malt [2021-04-28 12:49:16,542] multiqc [DEBUG ] No samples found: trimmomatic [2021-04-28 12:49:16,547] multiqc [DEBUG ] No samples found: sickle [2021-04-28 12:49:16,552] multiqc [DEBUG ] No samples found: skewer [2021-04-28 12:49:16,556] multiqc [DEBUG ] No samples found: sortmerna [2021-04-28 12:49:16,561] multiqc [DEBUG ] No samples found: biobloomtools [2021-04-28 12:49:16,566] multiqc [DEBUG ] No samples found: fastq_screen [2021-04-28 12:49:16,572] multiqc [DEBUG ] No samples found: afterqc [2021-04-28 12:49:16,577] multiqc [DEBUG ] No samples found: fastp [2021-04-28 12:49:18,210] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2021-04-28 12:49:18,580] multiqc [DEBUG ] No samples found: pycoqc [2021-04-28 12:49:18,585] multiqc [DEBUG ] No samples found: minionqc [2021-04-28 12:49:18,590] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-04-28 12:49:18,596] multiqc [DEBUG ] No samples found: clusterflow [2021-04-28 12:49:18,601] multiqc [DEBUG ] No samples found: bcl2fastq [2021-04-28 12:49:18,607] multiqc [DEBUG ] No samples found: interop [2021-04-28 12:49:18,613] multiqc [DEBUG ] No samples found: ivar [2021-04-28 12:49:18,617] multiqc [DEBUG ] No samples found: flash [2021-04-28 12:49:18,622] multiqc [DEBUG ] No samples found: seqyclean [2021-04-28 12:49:18,622] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-04-28 12:49:18,622] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-04-28 12:49:18,622] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-04-28 12:49:18,622] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-04-28 12:49:18,655] multiqc [INFO ] Compressing plot data [2021-04-28 12:49:19,083] multiqc [INFO ] Report : multiqc_report.html [2021-04-28 12:49:19,083] multiqc [INFO ] Data : multiqc_data [2021-04-28 12:49:19,083] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6063466/tmplxlqgp2p/multiqc_data' to '/scratch/gencore/logs/html/H5CYGDRXY/merged/multiqc_data' [2021-04-28 12:49:19,209] multiqc [INFO ] MultiQC complete