[2022-04-08 12:20:07,985] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-08 12:20:07,985] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-08 12:20:07,985] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-08 12:20:07,986] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-08 12:20:07,986] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-08 12:20:07,986] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVCF2DRXY/2 [2022-04-08 12:20:08,732] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-08 12:20:08,732] multiqc [INFO ] This is MultiQC v1.9 [2022-04-08 12:20:08,732] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVCF2DRXY/2 [2022-04-08 12:20:08,732] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVCF2DRXY/2 [2022-04-08 12:20:08,732] multiqc [INFO ] Template : default [2022-04-08 12:20:08,732] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-08 12:20:08,732] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVCF2DRXY/2 [2022-04-08 12:20:08,733] 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 [2022-04-08 12:20:08,733] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17452572/tmpkg0tu0x8 [2022-04-08 12:20:08,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW179_fastqc.html [2022-04-08 12:20:08,844] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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HVCF2DRXY_l02_n01_2hS2_N_fastqc.html [2022-04-08 12:20:12,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_2hS2_N_fastqc.html [2022-04-08 12:20:12,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW267_fastqc.html [2022-04-08 12:20:12,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW267_fastqc.html [2022-04-08 12:20:12,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW308_fastqc.html [2022-04-08 12:20:12,811] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW308_fastqc.html [2022-04-08 12:20:12,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HVCF2DRXY_l02_n01_2hR3_KCl_fastqc.html [2022-04-08 12:20:13,243] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_2hR3_KCl_fastqc.html [2022-04-08 12:20:13,297] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW261_fastqc.html [2022-04-08 12:20:13,299] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW261_fastqc.html [2022-04-08 12:20:13,369] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW189_fastqc.html [2022-04-08 12:20:13,370] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW189_fastqc.html [2022-04-08 12:20:13,432] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW200_fastqc.html [2022-04-08 12:20:13,434] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW200_fastqc.html [2022-04-08 12:20:13,491] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW242_fastqc.html [2022-04-08 12:20:13,493] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW242_fastqc.html [2022-04-08 12:20:13,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW176_fastqc.html [2022-04-08 12:20:13,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW176_fastqc.html [2022-04-08 12:20:13,611] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW184_fastqc.html [2022-04-08 12:20:13,613] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW184_fastqc.html [2022-04-08 12:20:13,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_RS32_re_fastqc.html [2022-04-08 12:20:13,682] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_RS32_re_fastqc.html [2022-04-08 12:20:13,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW180_fastqc.html [2022-04-08 12:20:13,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVCF2DRXY_l02_n01_WW180_fastqc.html [2022-04-08 12:20:14,084] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 12:20:14,085] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-08 12:20:14,092] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-08 12:20:14,128] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 78 samples (table) [2022-04-08 12:20:14,137] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-08 12:20:14,140] multiqc [DEBUG ] No samples found: conpair [2022-04-08 12:20:14,143] multiqc [DEBUG ] No samples found: peddy [2022-04-08 12:20:14,146] multiqc [DEBUG ] No samples found: somalier [2022-04-08 12:20:14,149] multiqc [DEBUG ] No samples found: methylQA [2022-04-08 12:20:14,153] multiqc [DEBUG ] No samples found: mosdepth [2022-04-08 12:20:14,156] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-08 12:20:14,159] multiqc [DEBUG ] No samples found: qualimap [2022-04-08 12:20:14,162] multiqc [DEBUG ] No samples found: preseq [2022-04-08 12:20:14,165] multiqc [DEBUG ] No samples found: quast [2022-04-08 12:20:14,168] multiqc [DEBUG ] No samples found: qorts [2022-04-08 12:20:14,171] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-08 12:20:14,174] multiqc [DEBUG ] No samples found: rockhopper [2022-04-08 12:20:14,177] multiqc [DEBUG ] No samples found: rsem [2022-04-08 12:20:14,182] multiqc [DEBUG ] No samples found: rseqc [2022-04-08 12:20:14,185] multiqc [DEBUG ] No samples found: busco [2022-04-08 12:20:14,188] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-08 12:20:14,191] multiqc [DEBUG ] No samples found: disambiguate [2022-04-08 12:20:14,194] multiqc [DEBUG ] No samples found: supernova [2022-04-08 12:20:14,199] multiqc [DEBUG ] No samples found: deeptools [2022-04-08 12:20:14,202] multiqc [DEBUG ] No samples found: sargasso [2022-04-08 12:20:14,205] multiqc [DEBUG ] No samples found: verifybamid [2022-04-08 12:20:14,209] multiqc [DEBUG ] No samples found: mirtrace [2022-04-08 12:20:14,212] multiqc [DEBUG ] No samples found: happy [2022-04-08 12:20:14,215] multiqc [DEBUG ] No samples found: mirtop [2022-04-08 12:20:14,219] multiqc [DEBUG ] No samples found: homer [2022-04-08 12:20:14,222] multiqc [DEBUG ] No samples found: macs2 [2022-04-08 12:20:14,224] multiqc [DEBUG ] No samples found: theta2 [2022-04-08 12:20:14,227] multiqc [DEBUG ] No samples found: snpeff [2022-04-08 12:20:14,231] multiqc [DEBUG ] No samples found: gatk [2022-04-08 12:20:14,234] multiqc [DEBUG ] No samples found: htseq [2022-04-08 12:20:14,237] multiqc [DEBUG ] No samples found: bcftools [2022-04-08 12:20:14,240] multiqc [DEBUG ] No samples found: featureCounts [2022-04-08 12:20:14,244] multiqc [DEBUG ] No samples found: fgbio [2022-04-08 12:20:14,249] multiqc [DEBUG ] No samples found: dragen [2022-04-08 12:20:14,252] multiqc [DEBUG ] No samples found: dedup [2022-04-08 12:20:14,255] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-08 12:20:14,264] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-08 12:20:14,267] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-08 12:20:14,270] multiqc [DEBUG ] No samples found: picard [2022-04-08 12:20:14,273] multiqc [DEBUG ] No samples found: prokka [2022-04-08 12:20:14,275] multiqc [DEBUG ] No samples found: samblaster [2022-04-08 12:20:14,280] multiqc [DEBUG ] No samples found: samtools [2022-04-08 12:20:14,282] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-08 12:20:14,286] multiqc [DEBUG ] No samples found: bamtools [2022-04-08 12:20:14,288] multiqc [DEBUG ] No samples found: jellyfish [2022-04-08 12:20:14,293] multiqc [DEBUG ] No samples found: vcftools [2022-04-08 12:20:14,296] multiqc [DEBUG ] No samples found: longranger [2022-04-08 12:20:14,299] multiqc [DEBUG ] No samples found: stacks [2022-04-08 12:20:14,301] multiqc [DEBUG ] No samples found: varscan2 [2022-04-08 12:20:14,307] multiqc [DEBUG ] No samples found: bbmap [2022-04-08 12:20:14,311] multiqc [DEBUG ] No samples found: bismark [2022-04-08 12:20:14,314] multiqc [DEBUG ] No samples found: biscuit [2022-04-08 12:20:14,317] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-08 12:20:14,320] multiqc [DEBUG ] No samples found: hicup [2022-04-08 12:20:14,323] multiqc [DEBUG ] No samples found: hicpro [2022-04-08 12:20:14,325] multiqc [DEBUG ] No samples found: salmon [2022-04-08 12:20:14,328] multiqc [DEBUG ] No samples found: kallisto [2022-04-08 12:20:14,331] multiqc [DEBUG ] No samples found: slamdunk [2022-04-08 12:20:14,334] multiqc [DEBUG ] No samples found: star [2022-04-08 12:20:14,337] multiqc [DEBUG ] No samples found: hisat2 [2022-04-08 12:20:14,340] multiqc [DEBUG ] No samples found: tophat [2022-04-08 12:20:14,343] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-08 12:20:14,346] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-08 12:20:14,349] multiqc [DEBUG ] No samples found: snpsplit [2022-04-08 12:20:14,352] multiqc [DEBUG ] No samples found: kat [2022-04-08 12:20:14,355] multiqc [DEBUG ] No samples found: leehom [2022-04-08 12:20:14,358] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-08 12:20:14,361] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-08 12:20:14,364] multiqc [DEBUG ] No samples found: cutadapt [2022-04-08 12:20:14,366] multiqc [DEBUG ] No samples found: flexbar [2022-04-08 12:20:14,369] multiqc [DEBUG ] No samples found: kaiju [2022-04-08 12:20:14,372] multiqc [DEBUG ] No samples found: kraken [2022-04-08 12:20:14,375] multiqc [DEBUG ] No samples found: malt [2022-04-08 12:20:14,378] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-08 12:20:14,381] multiqc [DEBUG ] No samples found: sickle [2022-04-08 12:20:14,384] multiqc [DEBUG ] No samples found: skewer [2022-04-08 12:20:14,387] multiqc [DEBUG ] No samples found: sortmerna [2022-04-08 12:20:14,390] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-08 12:20:14,393] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-08 12:20:14,396] multiqc [DEBUG ] No samples found: afterqc [2022-04-08 12:20:14,399] multiqc [DEBUG ] No samples found: fastp [2022-04-08 12:20:21,931] multiqc.modules.fastqc.fastqc [INFO ] Found 78 reports [2022-04-08 12:20:22,948] multiqc [DEBUG ] No samples found: pycoqc [2022-04-08 12:20:22,951] multiqc [DEBUG ] No samples found: minionqc [2022-04-08 12:20:22,954] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-08 12:20:22,957] multiqc [DEBUG ] No samples found: clusterflow [2022-04-08 12:20:22,960] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-08 12:20:22,963] multiqc [DEBUG ] No samples found: interop [2022-04-08 12:20:22,966] multiqc [DEBUG ] No samples found: ivar [2022-04-08 12:20:22,969] multiqc [DEBUG ] No samples found: flash [2022-04-08 12:20:22,972] multiqc [DEBUG ] No samples found: seqyclean [2022-04-08 12:20:22,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-04-08 12:20:22,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-04-08 12:20:22,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-04-08 12:20:22,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-08 12:20:22,972] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-08 12:20:23,061] multiqc [INFO ] Compressing plot data [2022-04-08 12:20:24,422] multiqc [INFO ] Report : multiqc_report.html [2022-04-08 12:20:24,422] multiqc [INFO ] Data : multiqc_data [2022-04-08 12:20:24,422] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17452572/tmpkg0tu0x8/multiqc_data' to '/scratch/gencore/logs/html/HVCF2DRXY/2/multiqc_data' [2022-04-08 12:20:24,523] multiqc [INFO ] MultiQC complete