[2022-11-30 20:04:46,908] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-30 20:04:46,908] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-30 20:04:46,908] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-30 20:04:46,909] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-30 20:04:46,909] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-30 20:04:46,910] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-30 20:04:47,464] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-30 20:04:47,464] multiqc [INFO ] This is MultiQC v1.9 [2022-11-30 20:04:47,464] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-30 20:04:47,464] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-30 20:04:47,464] multiqc [INFO ] Template : default [2022-11-30 20:04:47,464] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-30 20:04:47,464] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLJKYDRX2/merged [2022-11-30 20:04:47,465] 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 [2022-11-30 20:04:47,465] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27528781/tmpqtb_0jr7 [2022-11-30 20:04:47,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO11_2_fastqc.html [2022-11-30 20:04:47,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-11-30 20:04:49,525] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO35_fastqc.html [2022-11-30 20:04:49,573] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO11_2_fastqc.html [2022-11-30 20:04:49,575] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO11_2_fastqc.html [2022-11-30 20:04:49,626] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO49_fastqc.html [2022-11-30 20:04:49,628] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n01_DO49_fastqc.html [2022-11-30 20:04:49,674] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n01_undetermined_fastqc.html [2022-11-30 20:04:49,676] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n01_undetermined_fastqc.html [2022-11-30 20:04:49,715] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO40_fastqc.html [2022-11-30 20:04:49,718] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLJKYDRX2_n02_DO40_fastqc.html [2022-11-30 20:04:50,108] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-30 20:04:50,110] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-30 20:04:50,127] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2022-11-30 20:04:50,137] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-30 20:04:50,139] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-30 20:04:50,144] multiqc [DEBUG ] No samples found: conpair [2022-11-30 20:04:50,149] multiqc [DEBUG ] No samples found: peddy [2022-11-30 20:04:50,154] multiqc [DEBUG ] No samples found: somalier [2022-11-30 20:04:50,159] multiqc [DEBUG ] No samples found: methylQA [2022-11-30 20:04:50,167] multiqc [DEBUG ] No samples found: mosdepth [2022-11-30 20:04:50,172] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-30 20:04:50,175] multiqc [DEBUG ] No samples found: qualimap [2022-11-30 20:04:50,180] multiqc [DEBUG ] No samples found: preseq [2022-11-30 20:04:50,185] multiqc [DEBUG ] No samples found: quast [2022-11-30 20:04:50,190] multiqc [DEBUG ] No samples found: qorts [2022-11-30 20:04:50,195] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-30 20:04:50,200] multiqc [DEBUG ] No samples found: rockhopper [2022-11-30 20:04:50,205] multiqc [DEBUG ] No samples found: rsem [2022-11-30 20:04:50,217] multiqc [DEBUG ] No samples found: rseqc [2022-11-30 20:04:50,222] multiqc [DEBUG ] No samples found: busco [2022-11-30 20:04:50,227] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-30 20:04:50,231] multiqc [DEBUG ] No samples found: disambiguate [2022-11-30 20:04:50,236] multiqc [DEBUG ] No samples found: supernova [2022-11-30 20:04:50,249] multiqc [DEBUG ] No samples found: deeptools [2022-11-30 20:04:50,254] multiqc [DEBUG ] No samples found: sargasso [2022-11-30 20:04:50,258] multiqc [DEBUG ] No samples found: verifybamid [2022-11-30 20:04:50,263] multiqc [DEBUG ] No samples found: mirtrace [2022-11-30 20:04:50,268] multiqc [DEBUG ] No samples found: happy [2022-11-30 20:04:50,272] multiqc [DEBUG ] No samples found: mirtop [2022-11-30 20:04:50,279] multiqc [DEBUG ] No samples found: homer [2022-11-30 20:04:50,283] multiqc [DEBUG ] No samples found: macs2 [2022-11-30 20:04:50,289] multiqc [DEBUG ] No samples found: theta2 [2022-11-30 20:04:50,294] multiqc [DEBUG ] No samples found: snpeff [2022-11-30 20:04:50,300] multiqc [DEBUG ] No samples found: gatk [2022-11-30 20:04:50,305] multiqc [DEBUG ] No samples found: htseq [2022-11-30 20:04:50,310] multiqc [DEBUG ] No samples found: bcftools [2022-11-30 20:04:50,315] multiqc [DEBUG ] No samples found: featureCounts [2022-11-30 20:04:50,321] multiqc [DEBUG ] No samples found: fgbio [2022-11-30 20:04:50,333] multiqc [DEBUG ] No samples found: dragen [2022-11-30 20:04:50,337] multiqc [DEBUG ] No samples found: dedup [2022-11-30 20:04:50,342] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-30 20:04:50,368] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-30 20:04:50,372] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-30 20:04:50,375] multiqc [DEBUG ] No samples found: picard [2022-11-30 20:04:50,379] multiqc [DEBUG ] No samples found: prokka [2022-11-30 20:04:50,383] multiqc [DEBUG ] No samples found: samblaster [2022-11-30 20:04:50,392] multiqc [DEBUG ] No samples found: samtools [2022-11-30 20:04:50,398] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-30 20:04:50,403] multiqc [DEBUG ] No samples found: bamtools [2022-11-30 20:04:50,407] multiqc [DEBUG ] No samples found: jellyfish [2022-11-30 20:04:50,415] multiqc [DEBUG ] No samples found: vcftools [2022-11-30 20:04:50,421] multiqc [DEBUG ] No samples found: longranger [2022-11-30 20:04:50,426] multiqc [DEBUG ] No samples found: stacks [2022-11-30 20:04:50,431] multiqc [DEBUG ] No samples found: varscan2 [2022-11-30 20:04:50,445] multiqc [DEBUG ] No samples found: bbmap [2022-11-30 20:04:50,450] multiqc [DEBUG ] No samples found: bismark [2022-11-30 20:04:50,454] multiqc [DEBUG ] No samples found: biscuit [2022-11-30 20:04:50,459] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-30 20:04:50,464] multiqc [DEBUG ] No samples found: hicup [2022-11-30 20:04:50,468] multiqc [DEBUG ] No samples found: hicpro [2022-11-30 20:04:50,473] multiqc [DEBUG ] No samples found: salmon [2022-11-30 20:04:50,478] multiqc [DEBUG ] No samples found: kallisto [2022-11-30 20:04:50,484] multiqc [DEBUG ] No samples found: slamdunk [2022-11-30 20:04:50,489] multiqc [DEBUG ] No samples found: star [2022-11-30 20:04:50,494] multiqc [DEBUG ] No samples found: hisat2 [2022-11-30 20:04:50,499] multiqc [DEBUG ] No samples found: tophat [2022-11-30 20:04:50,503] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-30 20:04:50,508] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-30 20:04:50,513] multiqc [DEBUG ] No samples found: snpsplit [2022-11-30 20:04:50,517] multiqc [DEBUG ] No samples found: kat [2022-11-30 20:04:50,521] multiqc [DEBUG ] No samples found: leehom [2022-11-30 20:04:50,526] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-30 20:04:50,530] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-30 20:04:50,535] multiqc [DEBUG ] No samples found: cutadapt [2022-11-30 20:04:50,539] multiqc [DEBUG ] No samples found: flexbar [2022-11-30 20:04:50,544] multiqc [DEBUG ] No samples found: kaiju [2022-11-30 20:04:50,549] multiqc [DEBUG ] No samples found: kraken [2022-11-30 20:04:50,553] multiqc [DEBUG ] No samples found: malt [2022-11-30 20:04:50,558] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-30 20:04:50,566] multiqc [DEBUG ] No samples found: sickle [2022-11-30 20:04:50,570] multiqc [DEBUG ] No samples found: skewer [2022-11-30 20:04:50,574] multiqc [DEBUG ] No samples found: sortmerna [2022-11-30 20:04:50,579] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-30 20:04:50,583] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-30 20:04:50,588] multiqc [DEBUG ] No samples found: afterqc [2022-11-30 20:04:50,592] multiqc [DEBUG ] No samples found: fastp [2022-11-30 20:04:52,477] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2022-11-30 20:04:52,845] multiqc [DEBUG ] No samples found: pycoqc [2022-11-30 20:04:52,850] multiqc [DEBUG ] No samples found: minionqc [2022-11-30 20:04:52,855] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-30 20:04:52,859] multiqc [DEBUG ] No samples found: clusterflow [2022-11-30 20:04:52,864] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-30 20:04:52,869] multiqc [DEBUG ] No samples found: interop [2022-11-30 20:04:52,873] multiqc [DEBUG ] No samples found: ivar [2022-11-30 20:04:52,878] multiqc [DEBUG ] No samples found: flash [2022-11-30 20:04:52,883] multiqc [DEBUG ] No samples found: seqyclean [2022-11-30 20:04:52,883] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-30 20:04:52,883] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-30 20:04:52,883] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-30 20:04:52,883] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-30 20:04:52,933] multiqc [INFO ] Compressing plot data [2022-11-30 20:04:53,637] multiqc [INFO ] Report : multiqc_report.html [2022-11-30 20:04:53,637] multiqc [INFO ] Data : multiqc_data [2022-11-30 20:04:53,638] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27528781/tmpqtb_0jr7/multiqc_data' to '/scratch/gencore/logs/html/HLJKYDRX2/merged/multiqc_data' [2022-11-30 20:04:53,766] multiqc [INFO ] MultiQC complete