[2022-03-23 05:50:28,248] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-23 05:50:28,248] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-23 05:50:28,249] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-23 05:50:28,249] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-23 05:50:28,249] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-23 05:50:28,250] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMYYNDRXY/1 [2022-03-23 05:50:28,843] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-23 05:50:28,843] multiqc [INFO ] This is MultiQC v1.9 [2022-03-23 05:50:28,843] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMYYNDRXY/1 [2022-03-23 05:50:28,843] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMYYNDRXY/1 [2022-03-23 05:50:28,843] multiqc [INFO ] Template : default [2022-03-23 05:50:28,843] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-23 05:50:28,843] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMYYNDRXY/1 [2022-03-23 05:50:28,844] 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 [2022-03-23 05:50:28,844] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16535732/tmpcwkj1nz8 [2022-03-23 05:50:28,955] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS133J2_fastqc.html [2022-03-23 05:50:28,958] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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HMYYNDRXY_l01_n01_RS116J2_fastqc.html [2022-03-23 05:50:33,426] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS66J2_fastqc.html [2022-03-23 05:50:33,427] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS66J2_fastqc.html [2022-03-23 05:50:33,472] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS97J2_fastqc.html [2022-03-23 05:50:33,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS97J2_fastqc.html [2022-03-23 05:50:33,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS60J2_fastqc.html [2022-03-23 05:50:33,522] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS60J2_fastqc.html [2022-03-23 05:50:33,567] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS107J2_fastqc.html [2022-03-23 05:50:33,569] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMYYNDRXY_l01_n01_RS107J2_fastqc.html [2022-03-23 05:50:33,941] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-23 05:50:33,943] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-23 05:50:33,995] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 97 samples (table) [2022-03-23 05:50:34,004] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-23 05:50:34,006] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-23 05:50:34,012] multiqc [DEBUG ] No samples found: conpair [2022-03-23 05:50:34,017] multiqc [DEBUG ] No samples found: peddy [2022-03-23 05:50:34,022] multiqc [DEBUG ] No samples found: somalier [2022-03-23 05:50:34,027] multiqc [DEBUG ] No samples found: methylQA [2022-03-23 05:50:34,035] multiqc [DEBUG ] No samples found: mosdepth [2022-03-23 05:50:34,040] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-23 05:50:34,043] multiqc [DEBUG ] No samples found: qualimap [2022-03-23 05:50:34,048] multiqc [DEBUG ] No samples found: preseq [2022-03-23 05:50:34,053] multiqc [DEBUG ] No samples found: quast [2022-03-23 05:50:34,057] multiqc [DEBUG ] No samples found: qorts [2022-03-23 05:50:34,062] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-23 05:50:34,066] multiqc [DEBUG ] No samples found: rockhopper [2022-03-23 05:50:34,070] multiqc [DEBUG ] No samples found: rsem [2022-03-23 05:50:34,081] multiqc [DEBUG ] No samples found: rseqc [2022-03-23 05:50:34,085] multiqc [DEBUG ] No samples found: busco [2022-03-23 05:50:34,089] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-23 05:50:34,094] multiqc [DEBUG ] No samples found: disambiguate [2022-03-23 05:50:34,098] multiqc [DEBUG ] No samples found: supernova [2022-03-23 05:50:34,110] multiqc [DEBUG ] No samples found: deeptools [2022-03-23 05:50:34,115] multiqc [DEBUG ] No samples found: sargasso [2022-03-23 05:50:34,119] multiqc [DEBUG ] No samples found: verifybamid [2022-03-23 05:50:34,124] multiqc [DEBUG ] No samples found: mirtrace [2022-03-23 05:50:34,128] multiqc [DEBUG ] No samples found: happy [2022-03-23 05:50:34,133] multiqc [DEBUG ] No samples found: mirtop [2022-03-23 05:50:34,139] multiqc [DEBUG ] No samples found: homer [2022-03-23 05:50:34,143] multiqc [DEBUG ] No samples found: macs2 [2022-03-23 05:50:34,148] multiqc [DEBUG ] No samples found: theta2 [2022-03-23 05:50:34,152] multiqc [DEBUG ] No samples found: snpeff [2022-03-23 05:50:34,159] multiqc [DEBUG ] No samples found: gatk [2022-03-23 05:50:34,163] multiqc [DEBUG ] No samples found: htseq [2022-03-23 05:50:34,168] multiqc [DEBUG ] No samples found: bcftools [2022-03-23 05:50:34,173] multiqc [DEBUG ] No samples found: featureCounts [2022-03-23 05:50:34,179] multiqc [DEBUG ] No samples found: fgbio [2022-03-23 05:50:34,197] multiqc [DEBUG ] No samples found: dragen [2022-03-23 05:50:34,202] multiqc [DEBUG ] No samples found: dedup [2022-03-23 05:50:34,206] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-23 05:50:34,230] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-23 05:50:34,234] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-23 05:50:34,236] multiqc [DEBUG ] No samples found: picard [2022-03-23 05:50:34,241] multiqc [DEBUG ] No samples found: prokka [2022-03-23 05:50:34,245] multiqc [DEBUG ] No samples found: samblaster [2022-03-23 05:50:34,253] multiqc [DEBUG ] No samples found: samtools [2022-03-23 05:50:34,257] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-23 05:50:34,262] multiqc [DEBUG ] No samples found: bamtools [2022-03-23 05:50:34,266] multiqc [DEBUG ] No samples found: jellyfish [2022-03-23 05:50:34,274] multiqc [DEBUG ] No samples found: vcftools [2022-03-23 05:50:34,278] multiqc [DEBUG ] No samples found: longranger [2022-03-23 05:50:34,283] multiqc [DEBUG ] No samples found: stacks [2022-03-23 05:50:34,288] multiqc [DEBUG ] No samples found: varscan2 [2022-03-23 05:50:34,300] multiqc [DEBUG ] No samples found: bbmap [2022-03-23 05:50:34,305] multiqc [DEBUG ] No samples found: bismark [2022-03-23 05:50:34,310] multiqc [DEBUG ] No samples found: biscuit [2022-03-23 05:50:34,315] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-23 05:50:34,320] multiqc [DEBUG ] No samples found: hicup [2022-03-23 05:50:34,324] multiqc [DEBUG ] No samples found: hicpro [2022-03-23 05:50:34,328] multiqc [DEBUG ] No samples found: salmon [2022-03-23 05:50:34,333] multiqc [DEBUG ] No samples found: kallisto [2022-03-23 05:50:34,338] multiqc [DEBUG ] No samples found: slamdunk [2022-03-23 05:50:34,342] multiqc [DEBUG ] No samples found: star [2022-03-23 05:50:34,346] multiqc [DEBUG ] No samples found: hisat2 [2022-03-23 05:50:34,351] multiqc [DEBUG ] No samples found: tophat [2022-03-23 05:50:34,355] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-23 05:50:34,360] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-23 05:50:34,364] multiqc [DEBUG ] No samples found: snpsplit [2022-03-23 05:50:34,369] multiqc [DEBUG ] No samples found: kat [2022-03-23 05:50:34,373] multiqc [DEBUG ] No samples found: leehom [2022-03-23 05:50:34,378] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-23 05:50:34,381] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-23 05:50:34,386] multiqc [DEBUG ] No samples found: cutadapt [2022-03-23 05:50:34,390] multiqc [DEBUG ] No samples found: flexbar [2022-03-23 05:50:34,394] multiqc [DEBUG ] No samples found: kaiju [2022-03-23 05:50:34,399] multiqc [DEBUG ] No samples found: kraken [2022-03-23 05:50:34,403] multiqc [DEBUG ] No samples found: malt [2022-03-23 05:50:34,407] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-23 05:50:34,412] multiqc [DEBUG ] No samples found: sickle [2022-03-23 05:50:34,416] multiqc [DEBUG ] No samples found: skewer [2022-03-23 05:50:34,420] multiqc [DEBUG ] No samples found: sortmerna [2022-03-23 05:50:34,424] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-23 05:50:34,430] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-23 05:50:34,435] multiqc [DEBUG ] No samples found: afterqc [2022-03-23 05:50:34,439] multiqc [DEBUG ] No samples found: fastp [2022-03-23 05:50:40,734] multiqc.modules.fastqc.fastqc [INFO ] Found 97 reports [2022-03-23 05:50:41,990] multiqc [DEBUG ] No samples found: pycoqc [2022-03-23 05:50:41,994] multiqc [DEBUG ] No samples found: minionqc [2022-03-23 05:50:41,999] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-23 05:50:42,004] multiqc [DEBUG ] No samples found: clusterflow [2022-03-23 05:50:42,008] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-23 05:50:42,013] multiqc [DEBUG ] No samples found: interop [2022-03-23 05:50:42,017] multiqc [DEBUG ] No samples found: ivar [2022-03-23 05:50:42,022] multiqc [DEBUG ] No samples found: flash [2022-03-23 05:50:42,026] multiqc [DEBUG ] No samples found: seqyclean [2022-03-23 05:50:42,026] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-03-23 05:50:42,026] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-03-23 05:50:42,026] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-23 05:50:42,026] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-03-23 05:50:42,026] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-23 05:50:42,137] multiqc [INFO ] Compressing plot data [2022-03-23 05:50:43,856] multiqc [INFO ] Report : multiqc_report.html [2022-03-23 05:50:43,856] multiqc [INFO ] Data : multiqc_data [2022-03-23 05:50:43,856] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16535732/tmpcwkj1nz8/multiqc_data' to '/scratch/gencore/logs/html/HMYYNDRXY/1/multiqc_data' [2022-03-23 05:50:43,990] multiqc [INFO ] MultiQC complete