[2022-04-09 21:58:54,460] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-04-09 21:58:54,460] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-04-09 21:58:54,460] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-09 21:58:54,462] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-04-09 21:58:54,462] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-04-09 21:58:54,462] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC33HDMXY/merged [2022-04-09 21:58:55,076] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-09 21:58:55,076] multiqc [INFO ] This is MultiQC v1.9 [2022-04-09 21:58:55,076] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HC33HDMXY/merged [2022-04-09 21:58:55,076] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HC33HDMXY/merged [2022-04-09 21:58:55,076] multiqc [INFO ] Template : default [2022-04-09 21:58:55,077] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-04-09 21:58:55,077] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HC33HDMXY/merged [2022-04-09 21:58:55,078] 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 [2022-04-09 21:58:55,078] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-17496352/tmpw3651j37 [2022-04-09 21:58:55,244] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T8_F09_fastqc.html [2022-04-09 21:58:55,248] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-04-09 21:59:09,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_C04_fastqc.html [2022-04-09 21:59:09,759] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_C04_fastqc.html [2022-04-09 21:59:09,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_H09_fastqc.html [2022-04-09 21:59:09,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_H09_fastqc.html [2022-04-09 21:59:09,928] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n02_T0_F09_fastqc.html [2022-04-09 21:59:09,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n02_T0_F09_fastqc.html [2022-04-09 21:59:10,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T0_A10_fastqc.html [2022-04-09 21:59:10,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n01_T0_A10_fastqc.html [2022-04-09 21:59:10,067] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T6_C10_fastqc.html [2022-04-09 21:59:10,071] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n01_T6_C10_fastqc.html [2022-04-09 21:59:10,152] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_A04_fastqc.html [2022-04-09 21:59:10,154] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n01_T4_A04_fastqc.html [2022-04-09 21:59:10,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HC33HDMXY_n02_T0_A10_fastqc.html [2022-04-09 21:59:10,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HC33HDMXY_n02_T0_A10_fastqc.html [2022-04-09 21:59:10,766] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-09 21:59:10,769] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-04-09 21:59:10,783] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-04-09 21:59:10,828] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 97 samples (table) [2022-04-09 21:59:10,837] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-04-09 21:59:10,844] multiqc [DEBUG ] No samples found: conpair [2022-04-09 21:59:10,851] multiqc [DEBUG ] No samples found: peddy [2022-04-09 21:59:10,861] multiqc [DEBUG ] No samples found: somalier [2022-04-09 21:59:10,869] multiqc [DEBUG ] No samples found: methylQA [2022-04-09 21:59:10,884] multiqc [DEBUG ] No samples found: mosdepth [2022-04-09 21:59:10,890] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-04-09 21:59:10,897] multiqc [DEBUG ] No samples found: qualimap [2022-04-09 21:59:10,905] multiqc [DEBUG ] No samples found: preseq [2022-04-09 21:59:10,915] multiqc [DEBUG ] No samples found: quast [2022-04-09 21:59:10,927] multiqc [DEBUG ] No samples found: qorts [2022-04-09 21:59:10,936] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-09 21:59:10,942] multiqc [DEBUG ] No samples found: rockhopper [2022-04-09 21:59:10,948] multiqc [DEBUG ] No samples found: rsem [2022-04-09 21:59:10,963] multiqc [DEBUG ] No samples found: rseqc [2022-04-09 21:59:10,969] multiqc [DEBUG ] No samples found: busco [2022-04-09 21:59:10,975] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-09 21:59:10,981] multiqc [DEBUG ] No samples found: disambiguate [2022-04-09 21:59:10,992] multiqc [DEBUG ] No samples found: supernova [2022-04-09 21:59:11,014] multiqc [DEBUG ] No samples found: deeptools [2022-04-09 21:59:11,021] multiqc [DEBUG ] No samples found: sargasso [2022-04-09 21:59:11,028] multiqc [DEBUG ] No samples found: verifybamid [2022-04-09 21:59:11,033] multiqc [DEBUG ] No samples found: mirtrace [2022-04-09 21:59:11,040] multiqc [DEBUG ] No samples found: happy [2022-04-09 21:59:11,046] multiqc [DEBUG ] No samples found: mirtop [2022-04-09 21:59:11,054] multiqc [DEBUG ] No samples found: homer [2022-04-09 21:59:11,060] multiqc [DEBUG ] No samples found: macs2 [2022-04-09 21:59:11,065] multiqc [DEBUG ] No samples found: theta2 [2022-04-09 21:59:11,071] multiqc [DEBUG ] No samples found: snpeff [2022-04-09 21:59:11,080] multiqc [DEBUG ] No samples found: gatk [2022-04-09 21:59:11,085] multiqc [DEBUG ] No samples found: htseq [2022-04-09 21:59:11,092] multiqc [DEBUG ] No samples found: bcftools [2022-04-09 21:59:11,099] multiqc [DEBUG ] No samples found: featureCounts [2022-04-09 21:59:11,113] multiqc [DEBUG ] No samples found: fgbio [2022-04-09 21:59:11,133] multiqc [DEBUG ] No samples found: dragen [2022-04-09 21:59:11,141] multiqc [DEBUG ] No samples found: dedup [2022-04-09 21:59:11,147] multiqc [DEBUG ] No samples found: damageprofiler [2022-04-09 21:59:11,182] multiqc [DEBUG ] No samples found: biobambam2 [2022-04-09 21:59:11,188] multiqc [DEBUG ] No samples found: mtnucratio [2022-04-09 21:59:11,191] multiqc [DEBUG ] No samples found: picard [2022-04-09 21:59:11,197] multiqc [DEBUG ] No samples found: prokka [2022-04-09 21:59:11,203] multiqc [DEBUG ] No samples found: samblaster [2022-04-09 21:59:11,216] multiqc [DEBUG ] No samples found: samtools [2022-04-09 21:59:11,223] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-04-09 21:59:11,229] multiqc [DEBUG ] No samples found: bamtools [2022-04-09 21:59:11,234] multiqc [DEBUG ] No samples found: jellyfish [2022-04-09 21:59:11,248] multiqc [DEBUG ] No samples found: vcftools [2022-04-09 21:59:11,254] multiqc [DEBUG ] No samples found: longranger [2022-04-09 21:59:11,260] multiqc [DEBUG ] No samples found: stacks [2022-04-09 21:59:11,267] multiqc [DEBUG ] No samples found: varscan2 [2022-04-09 21:59:11,284] multiqc [DEBUG ] No samples found: bbmap [2022-04-09 21:59:11,290] multiqc [DEBUG ] No samples found: bismark [2022-04-09 21:59:11,297] multiqc [DEBUG ] No samples found: biscuit [2022-04-09 21:59:11,303] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-09 21:59:11,309] multiqc [DEBUG ] No samples found: hicup [2022-04-09 21:59:11,315] multiqc [DEBUG ] No samples found: hicpro [2022-04-09 21:59:11,320] multiqc [DEBUG ] No samples found: salmon [2022-04-09 21:59:11,325] multiqc [DEBUG ] No samples found: kallisto [2022-04-09 21:59:11,331] multiqc [DEBUG ] No samples found: slamdunk [2022-04-09 21:59:11,337] multiqc [DEBUG ] No samples found: star [2022-04-09 21:59:11,343] multiqc [DEBUG ] No samples found: hisat2 [2022-04-09 21:59:11,348] multiqc [DEBUG ] No samples found: tophat [2022-04-09 21:59:11,354] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-09 21:59:11,359] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-09 21:59:11,365] multiqc [DEBUG ] No samples found: snpsplit [2022-04-09 21:59:11,370] multiqc [DEBUG ] No samples found: kat [2022-04-09 21:59:11,376] multiqc [DEBUG ] No samples found: leehom [2022-04-09 21:59:11,381] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-09 21:59:11,387] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-09 21:59:11,392] multiqc [DEBUG ] No samples found: cutadapt [2022-04-09 21:59:11,397] multiqc [DEBUG ] No samples found: flexbar [2022-04-09 21:59:11,403] multiqc [DEBUG ] No samples found: kaiju [2022-04-09 21:59:11,408] multiqc [DEBUG ] No samples found: kraken [2022-04-09 21:59:11,414] multiqc [DEBUG ] No samples found: malt [2022-04-09 21:59:11,419] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-09 21:59:11,424] multiqc [DEBUG ] No samples found: sickle [2022-04-09 21:59:11,430] multiqc [DEBUG ] No samples found: skewer [2022-04-09 21:59:11,435] multiqc [DEBUG ] No samples found: sortmerna [2022-04-09 21:59:11,440] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-09 21:59:11,446] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-09 21:59:11,453] multiqc [DEBUG ] No samples found: afterqc [2022-04-09 21:59:11,464] multiqc [DEBUG ] No samples found: fastp [2022-04-09 21:59:55,924] multiqc.modules.fastqc.fastqc [INFO ] Found 194 reports [2022-04-09 22:00:11,523] multiqc [DEBUG ] No samples found: pycoqc [2022-04-09 22:00:11,530] multiqc [DEBUG ] No samples found: minionqc [2022-04-09 22:00:11,536] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-04-09 22:00:11,542] multiqc [DEBUG ] No samples found: clusterflow [2022-04-09 22:00:11,551] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-09 22:00:11,560] multiqc [DEBUG ] No samples found: interop [2022-04-09 22:00:11,567] multiqc [DEBUG ] No samples found: ivar [2022-04-09 22:00:11,575] multiqc [DEBUG ] No samples found: flash [2022-04-09 22:00:11,584] multiqc [DEBUG ] No samples found: seqyclean [2022-04-09 22:00:11,584] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-04-09 22:00:11,584] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-04-09 22:00:11,584] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-04-09 22:00:11,584] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-04-09 22:00:11,803] multiqc [INFO ] Compressing plot data [2022-04-09 22:00:11,860] multiqc [INFO ] Report : multiqc_report.html [2022-04-09 22:00:11,860] multiqc [INFO ] Data : multiqc_data [2022-04-09 22:00:11,861] multiqc [DEBUG ] Moving data file from '/state/partition1/job-17496352/tmpw3651j37/multiqc_data' to '/scratch/gencore/logs/html/HC33HDMXY/merged/multiqc_data' [2022-04-09 22:00:12,040] multiqc [INFO ] MultiQC complete