[2022-10-05 17:08:30,032] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-05 17:08:30,032] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-05 17:08:30,032] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-05 17:08:30,033] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-05 17:08:30,033] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-05 17:08:30,033] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2CMNAFX5/merged [2022-10-05 17:08:31,447] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-05 17:08:31,447] multiqc [INFO ] This is MultiQC v1.9 [2022-10-05 17:08:31,447] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2CMNAFX5/merged [2022-10-05 17:08:31,447] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2CMNAFX5/merged [2022-10-05 17:08:31,447] multiqc [INFO ] Template : default [2022-10-05 17:08:31,447] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-05 17:08:31,447] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2CMNAFX5/merged [2022-10-05 17:08:31,448] 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 [2022-10-05 17:08:31,448] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-25681638/tmp_46a88wl [2022-10-05 17:08:31,555] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n02_Oct_sp11644hop1_fastqc.html [2022-10-05 17:08:31,558] multiqc [DEBUG ] File ignored by longranger/invocation because it 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exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp11757hop1_fastqc.html [2022-10-05 17:08:32,499] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11757in_fastqc.html [2022-10-05 17:08:32,500] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11757in_fastqc.html [2022-10-05 17:08:32,539] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11644in_fastqc.html [2022-10-05 17:08:32,541] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11644in_fastqc.html [2022-10-05 17:08:32,581] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp7797hop1_fastqc.html [2022-10-05 17:08:32,583] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp7797hop1_fastqc.html [2022-10-05 17:08:32,622] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n02_undetermined_fastqc.html [2022-10-05 17:08:32,624] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n02_undetermined_fastqc.html [2022-10-05 17:08:32,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp11757in_fastqc.html [2022-10-05 17:08:32,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp11757in_fastqc.html [2022-10-05 17:08:32,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp11758hop1_fastqc.html [2022-10-05 17:08:32,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_sp11758hop1_fastqc.html [2022-10-05 17:08:32,742] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n02_Oct_11644hop1_fastqc.html [2022-10-05 17:08:32,744] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n02_Oct_11644hop1_fastqc.html [2022-10-05 17:08:32,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11644hop1_fastqc.html [2022-10-05 17:08:32,787] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n01_Oct_11644hop1_fastqc.html [2022-10-05 17:08:32,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2CMNAFX5_n02_Oct_11758in_fastqc.html [2022-10-05 17:08:32,828] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2CMNAFX5_n02_Oct_11758in_fastqc.html [2022-10-05 17:08:33,160] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-05 17:08:33,161] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-05 17:08:33,175] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 15 samples (table) [2022-10-05 17:08:33,176] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-05 17:08:33,186] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-05 17:08:33,191] multiqc [DEBUG ] No samples found: conpair [2022-10-05 17:08:33,197] multiqc [DEBUG ] No samples found: peddy [2022-10-05 17:08:33,203] multiqc [DEBUG ] No samples found: somalier [2022-10-05 17:08:33,209] multiqc [DEBUG ] No samples found: methylQA [2022-10-05 17:08:33,219] multiqc [DEBUG ] No samples found: mosdepth [2022-10-05 17:08:33,224] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-05 17:08:33,227] multiqc [DEBUG ] No samples found: qualimap [2022-10-05 17:08:33,233] multiqc [DEBUG ] No samples found: preseq [2022-10-05 17:08:33,239] multiqc [DEBUG ] No samples found: quast [2022-10-05 17:08:33,245] multiqc [DEBUG ] No samples found: qorts [2022-10-05 17:08:33,250] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-05 17:08:33,256] multiqc [DEBUG ] No samples found: rockhopper [2022-10-05 17:08:33,262] multiqc [DEBUG ] No samples found: rsem [2022-10-05 17:08:33,273] multiqc [DEBUG ] No samples found: rseqc [2022-10-05 17:08:33,278] multiqc [DEBUG ] No samples found: busco [2022-10-05 17:08:33,284] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-05 17:08:33,288] multiqc [DEBUG ] No samples found: disambiguate [2022-10-05 17:08:33,294] multiqc [DEBUG ] No samples found: supernova [2022-10-05 17:08:33,307] multiqc [DEBUG ] No samples found: deeptools [2022-10-05 17:08:33,312] multiqc [DEBUG ] No samples found: sargasso [2022-10-05 17:08:33,317] multiqc [DEBUG ] No samples found: verifybamid [2022-10-05 17:08:33,323] multiqc [DEBUG ] No samples found: mirtrace [2022-10-05 17:08:33,328] multiqc [DEBUG ] No samples found: happy [2022-10-05 17:08:33,333] multiqc [DEBUG ] No samples found: mirtop [2022-10-05 17:08:33,340] multiqc [DEBUG ] No samples found: homer [2022-10-05 17:08:33,345] multiqc [DEBUG ] No samples found: macs2 [2022-10-05 17:08:33,350] multiqc [DEBUG ] No samples found: theta2 [2022-10-05 17:08:33,355] multiqc [DEBUG ] No samples found: snpeff [2022-10-05 17:08:33,362] multiqc [DEBUG ] No samples found: gatk [2022-10-05 17:08:33,367] multiqc [DEBUG ] No samples found: htseq [2022-10-05 17:08:33,373] multiqc [DEBUG ] No samples found: bcftools [2022-10-05 17:08:33,379] multiqc [DEBUG ] No samples found: featureCounts [2022-10-05 17:08:33,385] multiqc [DEBUG ] No samples found: fgbio [2022-10-05 17:08:33,399] multiqc [DEBUG ] No samples found: dragen [2022-10-05 17:08:33,404] multiqc [DEBUG ] No samples found: dedup [2022-10-05 17:08:33,410] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-05 17:08:33,433] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-05 17:08:33,438] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-05 17:08:33,441] multiqc [DEBUG ] No samples found: picard [2022-10-05 17:08:33,446] multiqc [DEBUG ] No samples found: prokka [2022-10-05 17:08:33,450] multiqc [DEBUG ] No samples found: samblaster [2022-10-05 17:08:33,459] multiqc [DEBUG ] No samples found: samtools [2022-10-05 17:08:33,464] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-05 17:08:33,469] multiqc [DEBUG ] No samples found: bamtools [2022-10-05 17:08:33,474] multiqc [DEBUG ] No samples found: jellyfish [2022-10-05 17:08:33,481] multiqc [DEBUG ] No samples found: vcftools [2022-10-05 17:08:33,487] multiqc [DEBUG ] No samples found: longranger [2022-10-05 17:08:33,492] multiqc [DEBUG ] No samples found: stacks [2022-10-05 17:08:33,497] multiqc [DEBUG ] No samples found: varscan2 [2022-10-05 17:08:33,512] multiqc [DEBUG ] No samples found: bbmap [2022-10-05 17:08:33,517] multiqc [DEBUG ] No samples found: bismark [2022-10-05 17:08:33,522] multiqc [DEBUG ] No samples found: biscuit [2022-10-05 17:08:33,528] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-05 17:08:33,533] multiqc [DEBUG ] No samples found: hicup [2022-10-05 17:08:33,538] multiqc [DEBUG ] No samples found: hicpro [2022-10-05 17:08:33,543] multiqc [DEBUG ] No samples found: salmon [2022-10-05 17:08:33,548] multiqc [DEBUG ] No samples found: kallisto [2022-10-05 17:08:33,553] multiqc [DEBUG ] No samples found: slamdunk [2022-10-05 17:08:33,558] multiqc [DEBUG ] No samples found: star [2022-10-05 17:08:33,563] multiqc [DEBUG ] No samples found: hisat2 [2022-10-05 17:08:33,568] multiqc [DEBUG ] No samples found: tophat [2022-10-05 17:08:33,573] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-05 17:08:33,577] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-05 17:08:33,582] multiqc [DEBUG ] No samples found: snpsplit [2022-10-05 17:08:33,587] multiqc [DEBUG ] No samples found: kat [2022-10-05 17:08:33,591] multiqc [DEBUG ] No samples found: leehom [2022-10-05 17:08:33,596] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-05 17:08:33,601] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-05 17:08:33,606] multiqc [DEBUG ] No samples found: cutadapt [2022-10-05 17:08:33,611] multiqc [DEBUG ] No samples found: flexbar [2022-10-05 17:08:33,616] multiqc [DEBUG ] No samples found: kaiju [2022-10-05 17:08:33,621] multiqc [DEBUG ] No samples found: kraken [2022-10-05 17:08:33,626] multiqc [DEBUG ] No samples found: malt [2022-10-05 17:08:33,631] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-05 17:08:33,636] multiqc [DEBUG ] No samples found: sickle [2022-10-05 17:08:33,641] multiqc [DEBUG ] No samples found: skewer [2022-10-05 17:08:33,645] multiqc [DEBUG ] No samples found: sortmerna [2022-10-05 17:08:33,650] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-05 17:08:33,655] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-05 17:08:33,660] multiqc [DEBUG ] No samples found: afterqc [2022-10-05 17:08:33,665] multiqc [DEBUG ] No samples found: fastp [2022-10-05 17:08:34,310] multiqc.modules.fastqc.fastqc [INFO ] Found 30 reports [2022-10-05 17:08:34,569] multiqc [DEBUG ] No samples found: pycoqc [2022-10-05 17:08:34,574] multiqc [DEBUG ] No samples found: minionqc [2022-10-05 17:08:34,579] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-05 17:08:34,584] multiqc [DEBUG ] No samples found: clusterflow [2022-10-05 17:08:34,590] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-05 17:08:34,595] multiqc [DEBUG ] No samples found: interop [2022-10-05 17:08:34,600] multiqc [DEBUG ] No samples found: ivar [2022-10-05 17:08:34,605] multiqc [DEBUG ] No samples found: flash [2022-10-05 17:08:34,610] multiqc [DEBUG ] No samples found: seqyclean [2022-10-05 17:08:34,610] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-05 17:08:34,610] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-05 17:08:34,610] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-05 17:08:34,610] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-05 17:08:34,646] multiqc [INFO ] Compressing plot data [2022-10-05 17:08:35,143] multiqc [INFO ] Report : multiqc_report.html [2022-10-05 17:08:35,143] multiqc [INFO ] Data : multiqc_data [2022-10-05 17:08:35,143] multiqc [DEBUG ] Moving data file from '/state/partition1/job-25681638/tmp_46a88wl/multiqc_data' to '/scratch/gencore/logs/html/H2CMNAFX5/merged/multiqc_data' [2022-10-05 17:08:35,270] multiqc [INFO ] MultiQC complete