[2022-12-07 17:47:41,259] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-12-07 17:47:41,259] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-12-07 17:47:41,259] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-12-07 17:47:41,260] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-12-07 17:47:41,260] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-12-07 17:47:41,260] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMTK2DRX2/merged [2022-12-07 17:47:41,966] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-12-07 17:47:41,966] multiqc [INFO ] This is MultiQC v1.9 [2022-12-07 17:47:41,966] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HMTK2DRX2/merged [2022-12-07 17:47:41,966] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HMTK2DRX2/merged [2022-12-07 17:47:41,966] multiqc [INFO ] Template : default [2022-12-07 17:47:41,966] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-12-07 17:47:41,966] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HMTK2DRX2/merged [2022-12-07 17:47:41,967] 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 [2022-12-07 17:47:41,967] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27764204/tmpc6jyrz5m [2022-12-07 17:47:42,060] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br193_fastqc.html [2022-12-07 17:47:42,063] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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17:47:44,471] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br183_fastqc.html [2022-12-07 17:47:44,473] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br183_fastqc.html [2022-12-07 17:47:44,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br205_fastqc.html [2022-12-07 17:47:44,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br205_fastqc.html [2022-12-07 17:47:44,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br186_fastqc.html [2022-12-07 17:47:44,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br186_fastqc.html [2022-12-07 17:47:44,589] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br178_fastqc.html [2022-12-07 17:47:44,591] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br178_fastqc.html [2022-12-07 17:47:44,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br185_fastqc.html [2022-12-07 17:47:44,641] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br185_fastqc.html [2022-12-07 17:47:44,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br203_fastqc.html [2022-12-07 17:47:44,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br203_fastqc.html [2022-12-07 17:47:44,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br184_fastqc.html [2022-12-07 17:47:44,738] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br184_fastqc.html [2022-12-07 17:47:44,783] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n02_undetermined_fastqc.html [2022-12-07 17:47:44,785] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n02_undetermined_fastqc.html [2022-12-07 17:47:44,824] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br186_fastqc.html [2022-12-07 17:47:44,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br186_fastqc.html [2022-12-07 17:47:44,847] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br196_fastqc.html [2022-12-07 17:47:44,849] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br196_fastqc.html [2022-12-07 17:47:44,893] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br200_fastqc.html [2022-12-07 17:47:44,895] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br200_fastqc.html [2022-12-07 17:47:44,938] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br207_fastqc.html [2022-12-07 17:47:44,939] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br207_fastqc.html [2022-12-07 17:47:44,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br185_fastqc.html [2022-12-07 17:47:44,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n02_br185_fastqc.html [2022-12-07 17:47:45,033] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_undetermined_fastqc.html [2022-12-07 17:47:45,035] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_undetermined_fastqc.html [2022-12-07 17:47:45,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br208_fastqc.html [2022-12-07 17:47:45,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br208_fastqc.html [2022-12-07 17:47:45,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br201_fastqc.html [2022-12-07 17:47:45,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br201_fastqc.html [2022-12-07 17:47:45,170] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br204_fastqc.html [2022-12-07 17:47:45,172] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HMTK2DRX2_n01_br204_fastqc.html [2022-12-07 17:47:45,496] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-07 17:47:45,496] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-12-07 17:47:45,512] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-12-07 17:47:45,513] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-12-07 17:47:45,531] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2022-12-07 17:47:45,534] multiqc [DEBUG ] No samples found: conpair [2022-12-07 17:47:45,537] multiqc [DEBUG ] No samples found: peddy [2022-12-07 17:47:45,541] multiqc [DEBUG ] No samples found: somalier [2022-12-07 17:47:45,544] multiqc [DEBUG ] No samples found: methylQA [2022-12-07 17:47:45,548] multiqc [DEBUG ] No samples found: mosdepth [2022-12-07 17:47:45,551] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-12-07 17:47:45,554] multiqc [DEBUG ] No samples found: qualimap [2022-12-07 17:47:45,557] multiqc [DEBUG ] No samples found: preseq [2022-12-07 17:47:45,560] multiqc [DEBUG ] No samples found: quast [2022-12-07 17:47:45,563] multiqc [DEBUG ] No samples found: qorts [2022-12-07 17:47:45,566] multiqc [DEBUG ] No samples found: rna_seqc [2022-12-07 17:47:45,569] multiqc [DEBUG ] No samples found: rockhopper [2022-12-07 17:47:45,572] multiqc [DEBUG ] No samples found: rsem [2022-12-07 17:47:45,578] multiqc [DEBUG ] No samples found: rseqc [2022-12-07 17:47:45,581] multiqc [DEBUG ] No samples found: busco [2022-12-07 17:47:45,584] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-12-07 17:47:45,587] multiqc [DEBUG ] No samples found: disambiguate [2022-12-07 17:47:45,591] multiqc [DEBUG ] No samples found: supernova [2022-12-07 17:47:45,596] multiqc [DEBUG ] No samples found: deeptools [2022-12-07 17:47:45,599] multiqc [DEBUG ] No samples found: sargasso [2022-12-07 17:47:45,602] multiqc [DEBUG ] No samples found: verifybamid [2022-12-07 17:47:45,606] multiqc [DEBUG ] No samples found: mirtrace [2022-12-07 17:47:45,609] multiqc [DEBUG ] No samples found: happy [2022-12-07 17:47:45,612] multiqc [DEBUG ] No samples found: mirtop [2022-12-07 17:47:45,615] multiqc [DEBUG ] No samples found: homer [2022-12-07 17:47:45,618] multiqc [DEBUG ] No samples found: macs2 [2022-12-07 17:47:45,621] multiqc [DEBUG ] No samples found: theta2 [2022-12-07 17:47:45,624] multiqc [DEBUG ] No samples found: snpeff [2022-12-07 17:47:45,628] multiqc [DEBUG ] No samples found: gatk [2022-12-07 17:47:45,631] multiqc [DEBUG ] No samples found: htseq [2022-12-07 17:47:45,634] multiqc [DEBUG ] No samples found: bcftools [2022-12-07 17:47:45,637] multiqc [DEBUG ] No samples found: featureCounts [2022-12-07 17:47:45,641] multiqc [DEBUG ] No samples found: fgbio [2022-12-07 17:47:45,647] multiqc [DEBUG ] No samples found: dragen [2022-12-07 17:47:45,650] multiqc [DEBUG ] No samples found: dedup [2022-12-07 17:47:45,653] multiqc [DEBUG ] No samples found: damageprofiler [2022-12-07 17:47:45,663] multiqc [DEBUG ] No samples found: biobambam2 [2022-12-07 17:47:45,666] multiqc [DEBUG ] No samples found: mtnucratio [2022-12-07 17:47:45,668] multiqc [DEBUG ] No samples found: picard [2022-12-07 17:47:45,672] multiqc [DEBUG ] No samples found: prokka [2022-12-07 17:47:45,675] multiqc [DEBUG ] No samples found: samblaster [2022-12-07 17:47:45,679] multiqc [DEBUG ] No samples found: samtools [2022-12-07 17:47:45,682] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-12-07 17:47:45,685] multiqc [DEBUG ] No samples found: bamtools [2022-12-07 17:47:45,688] multiqc [DEBUG ] No samples found: jellyfish [2022-12-07 17:47:45,692] multiqc [DEBUG ] No samples found: vcftools [2022-12-07 17:47:45,695] multiqc [DEBUG ] No samples found: longranger [2022-12-07 17:47:45,698] multiqc [DEBUG ] No samples found: stacks [2022-12-07 17:47:45,701] multiqc [DEBUG ] No samples found: varscan2 [2022-12-07 17:47:45,708] multiqc [DEBUG ] No samples found: bbmap [2022-12-07 17:47:45,711] multiqc [DEBUG ] No samples found: bismark [2022-12-07 17:47:45,714] multiqc [DEBUG ] No samples found: biscuit [2022-12-07 17:47:45,717] multiqc [DEBUG ] No samples found: hicexplorer [2022-12-07 17:47:45,720] multiqc [DEBUG ] No samples found: hicup [2022-12-07 17:47:45,723] multiqc [DEBUG ] No samples found: hicpro [2022-12-07 17:47:45,726] multiqc [DEBUG ] No samples found: salmon [2022-12-07 17:47:45,729] multiqc [DEBUG ] No samples found: kallisto [2022-12-07 17:47:45,732] multiqc [DEBUG ] No samples found: slamdunk [2022-12-07 17:47:45,735] multiqc [DEBUG ] No samples found: star [2022-12-07 17:47:45,738] multiqc [DEBUG ] No samples found: hisat2 [2022-12-07 17:47:45,741] multiqc [DEBUG ] No samples found: tophat [2022-12-07 17:47:45,744] multiqc [DEBUG ] No samples found: bowtie2 [2022-12-07 17:47:45,747] multiqc [DEBUG ] No samples found: bowtie1 [2022-12-07 17:47:45,750] multiqc [DEBUG ] No samples found: snpsplit [2022-12-07 17:47:45,753] multiqc [DEBUG ] No samples found: kat [2022-12-07 17:47:45,756] multiqc [DEBUG ] No samples found: leehom [2022-12-07 17:47:45,759] multiqc [DEBUG ] No samples found: adapterRemoval [2022-12-07 17:47:45,762] multiqc [DEBUG ] No samples found: clipandmerge [2022-12-07 17:47:45,765] multiqc [DEBUG ] No samples found: cutadapt [2022-12-07 17:47:45,768] multiqc [DEBUG ] No samples found: flexbar [2022-12-07 17:47:45,771] multiqc [DEBUG ] No samples found: kaiju [2022-12-07 17:47:45,774] multiqc [DEBUG ] No samples found: kraken [2022-12-07 17:47:45,777] multiqc [DEBUG ] No samples found: malt [2022-12-07 17:47:45,780] multiqc [DEBUG ] No samples found: trimmomatic [2022-12-07 17:47:45,783] multiqc [DEBUG ] No samples found: sickle [2022-12-07 17:47:45,786] multiqc [DEBUG ] No samples found: skewer [2022-12-07 17:47:45,789] multiqc [DEBUG ] No samples found: sortmerna [2022-12-07 17:47:45,792] multiqc [DEBUG ] No samples found: biobloomtools [2022-12-07 17:47:45,795] multiqc [DEBUG ] No samples found: fastq_screen [2022-12-07 17:47:45,798] multiqc [DEBUG ] No samples found: afterqc [2022-12-07 17:47:45,801] multiqc [DEBUG ] No samples found: fastp [2022-12-07 17:47:46,205] multiqc.modules.fastqc.fastqc [INFO ] Found 74 reports [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br186' [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br198' [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br199' [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br197' [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br180' [2022-12-07 17:47:46,207] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br199' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br195' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n01_br189' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br186' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br189' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br197' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br198' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br195' [2022-12-07 17:47:46,208] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HMTK2DRX2_n02_br180' [2022-12-07 17:47:46,664] multiqc [DEBUG ] No samples found: pycoqc [2022-12-07 17:47:46,668] multiqc [DEBUG ] No samples found: minionqc [2022-12-07 17:47:46,671] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-12-07 17:47:46,674] multiqc [DEBUG ] No samples found: clusterflow [2022-12-07 17:47:46,677] multiqc [DEBUG ] No samples found: bcl2fastq [2022-12-07 17:47:46,680] multiqc [DEBUG ] No samples found: interop [2022-12-07 17:47:46,683] multiqc [DEBUG ] No samples found: ivar [2022-12-07 17:47:46,686] multiqc [DEBUG ] No samples found: flash [2022-12-07 17:47:46,689] multiqc [DEBUG ] No samples found: seqyclean [2022-12-07 17:47:46,689] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-12-07 17:47:46,689] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-12-07 17:47:46,689] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-12-07 17:47:46,689] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-12-07 17:47:46,775] multiqc [INFO ] Compressing plot data [2022-12-07 17:47:47,350] multiqc [INFO ] Report : multiqc_report.html [2022-12-07 17:47:47,350] multiqc [INFO ] Data : multiqc_data [2022-12-07 17:47:47,350] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27764204/tmpc6jyrz5m/multiqc_data' to '/scratch/gencore/logs/html/HMTK2DRX2/merged/multiqc_data' [2022-12-07 17:47:47,453] multiqc [INFO ] MultiQC complete