[2021-03-16 17:12:11,810] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-03-16 17:12:11,811] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-03-16 17:12:11,811] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-16 17:12:11,812] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-03-16 17:12:11,812] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-03-16 17:12:11,812] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNWF2AFX2/merged [2021-03-16 17:12:13,272] multiqc [WARNING] MultiQC Version v1.10 now available! [2021-03-16 17:12:13,272] multiqc [INFO ] This is MultiQC v1.9 [2021-03-16 17:12:13,272] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNWF2AFX2/merged [2021-03-16 17:12:13,272] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNWF2AFX2/merged [2021-03-16 17:12:13,272] multiqc [INFO ] Template : default [2021-03-16 17:12:13,272] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-03-16 17:12:13,272] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNWF2AFX2/merged [2021-03-16 17:12:13,272] 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 [2021-03-16 17:12:13,272] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-3820239/tmp49tffcbc [2021-03-16 17:12:13,387] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-16 17:12:13,390] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-03-16 17:12:13,479] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH9251-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,480] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH9251-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,519] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH7797-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,520] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH7797-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH10517-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,561] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH10517-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,599] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH7797-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,601] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH7797-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH5187-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,641] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH5187-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,679] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_undetermined_fastqc.html [2021-03-16 17:12:13,681] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_undetermined_fastqc.html [2021-03-16 17:12:13,719] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH9251-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,721] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH9251-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,760] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH10517-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH10517-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,800] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH10517-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,802] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH10517-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH9251-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,843] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH9251-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:13,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH5187-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH5187-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,923] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH9251-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH9251-3h-input-SNP_fastqc.html [2021-03-16 17:12:13,964] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_undetermined_fastqc.html [2021-03-16 17:12:13,966] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_undetermined_fastqc.html [2021-03-16 17:12:14,005] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH7797-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,007] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH7797-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH5187-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH5187-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH5187-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,089] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH5187-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,127] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH10517-3h-input-SNP_fastqc.html [2021-03-16 17:12:14,128] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n02_AH10517-3h-input-SNP_fastqc.html [2021-03-16 17:12:14,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH7797-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,168] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNWF2AFX2_n01_AH7797-3h-anti-Hop1-SNP_fastqc.html [2021-03-16 17:12:14,652] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-16 17:12:14,654] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-03-16 17:12:14,661] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-03-16 17:12:14,666] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 9 samples (table) [2021-03-16 17:12:14,676] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-03-16 17:12:14,681] multiqc [DEBUG ] No samples found: conpair [2021-03-16 17:12:14,687] multiqc [DEBUG ] No samples found: peddy [2021-03-16 17:12:14,695] multiqc [DEBUG ] No samples found: somalier [2021-03-16 17:12:14,699] multiqc [DEBUG ] No samples found: methylQA [2021-03-16 17:12:14,708] multiqc [DEBUG ] No samples found: mosdepth [2021-03-16 17:12:14,712] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-16 17:12:14,715] multiqc [DEBUG ] No samples found: qualimap [2021-03-16 17:12:14,720] multiqc [DEBUG ] No samples found: preseq [2021-03-16 17:12:14,725] multiqc [DEBUG ] No samples found: quast [2021-03-16 17:12:14,730] multiqc [DEBUG ] No samples found: qorts [2021-03-16 17:12:14,735] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-16 17:12:14,740] multiqc [DEBUG ] No samples found: rockhopper [2021-03-16 17:12:14,744] multiqc [DEBUG ] No samples found: rsem [2021-03-16 17:12:14,756] multiqc [DEBUG ] No samples found: rseqc [2021-03-16 17:12:14,760] multiqc [DEBUG ] No samples found: busco [2021-03-16 17:12:14,765] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-16 17:12:14,769] multiqc [DEBUG ] No samples found: disambiguate [2021-03-16 17:12:14,774] multiqc [DEBUG ] No samples found: supernova [2021-03-16 17:12:14,789] multiqc [DEBUG ] No samples found: deeptools [2021-03-16 17:12:14,794] multiqc [DEBUG ] No samples found: sargasso [2021-03-16 17:12:14,799] multiqc [DEBUG ] No samples found: verifybamid [2021-03-16 17:12:14,804] multiqc [DEBUG ] No samples found: mirtrace [2021-03-16 17:12:14,809] multiqc [DEBUG ] No samples found: happy [2021-03-16 17:12:14,813] multiqc [DEBUG ] No samples found: mirtop [2021-03-16 17:12:14,820] multiqc [DEBUG ] No samples found: homer [2021-03-16 17:12:14,825] multiqc [DEBUG ] No samples found: macs2 [2021-03-16 17:12:14,829] multiqc [DEBUG ] No samples found: theta2 [2021-03-16 17:12:14,833] multiqc [DEBUG ] No samples found: snpeff [2021-03-16 17:12:14,841] multiqc [DEBUG ] No samples found: gatk [2021-03-16 17:12:14,846] multiqc [DEBUG ] No samples found: htseq [2021-03-16 17:12:14,851] multiqc [DEBUG ] No samples found: bcftools [2021-03-16 17:12:14,856] multiqc [DEBUG ] No samples found: featureCounts [2021-03-16 17:12:14,863] multiqc [DEBUG ] No samples found: fgbio [2021-03-16 17:12:14,877] multiqc [DEBUG ] No samples found: dragen [2021-03-16 17:12:14,882] multiqc [DEBUG ] No samples found: dedup [2021-03-16 17:12:14,887] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-16 17:12:14,910] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-16 17:12:14,915] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-16 17:12:14,917] multiqc [DEBUG ] No samples found: picard [2021-03-16 17:12:14,922] multiqc [DEBUG ] No samples found: prokka [2021-03-16 17:12:14,926] multiqc [DEBUG ] No samples found: samblaster [2021-03-16 17:12:14,936] multiqc [DEBUG ] No samples found: samtools [2021-03-16 17:12:14,940] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-16 17:12:14,945] multiqc [DEBUG ] No samples found: bamtools [2021-03-16 17:12:14,949] multiqc [DEBUG ] No samples found: jellyfish [2021-03-16 17:12:14,958] multiqc [DEBUG ] No samples found: vcftools [2021-03-16 17:12:14,964] multiqc [DEBUG ] No samples found: longranger [2021-03-16 17:12:14,969] multiqc [DEBUG ] No samples found: stacks [2021-03-16 17:12:14,973] multiqc [DEBUG ] No samples found: varscan2 [2021-03-16 17:12:14,988] multiqc [DEBUG ] No samples found: bbmap [2021-03-16 17:12:14,994] multiqc [DEBUG ] No samples found: bismark [2021-03-16 17:12:14,999] multiqc [DEBUG ] No samples found: biscuit [2021-03-16 17:12:15,004] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-16 17:12:15,009] multiqc [DEBUG ] No samples found: hicup [2021-03-16 17:12:15,014] multiqc [DEBUG ] No samples found: hicpro [2021-03-16 17:12:15,018] multiqc [DEBUG ] No samples found: salmon [2021-03-16 17:12:15,022] multiqc [DEBUG ] No samples found: kallisto [2021-03-16 17:12:15,027] multiqc [DEBUG ] No samples found: slamdunk [2021-03-16 17:12:15,031] multiqc [DEBUG ] No samples found: star [2021-03-16 17:12:15,036] multiqc [DEBUG ] No samples found: hisat2 [2021-03-16 17:12:15,040] multiqc [DEBUG ] No samples found: tophat [2021-03-16 17:12:15,045] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-16 17:12:15,050] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-16 17:12:15,054] multiqc [DEBUG ] No samples found: snpsplit [2021-03-16 17:12:15,059] multiqc [DEBUG ] No samples found: kat [2021-03-16 17:12:15,063] multiqc [DEBUG ] No samples found: leehom [2021-03-16 17:12:15,068] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-16 17:12:15,072] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-16 17:12:15,077] multiqc [DEBUG ] No samples found: cutadapt [2021-03-16 17:12:15,081] multiqc [DEBUG ] No samples found: flexbar [2021-03-16 17:12:15,086] multiqc [DEBUG ] No samples found: kaiju [2021-03-16 17:12:15,091] multiqc [DEBUG ] No samples found: kraken [2021-03-16 17:12:15,096] multiqc [DEBUG ] No samples found: malt [2021-03-16 17:12:15,100] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-16 17:12:15,104] multiqc [DEBUG ] No samples found: sickle [2021-03-16 17:12:15,109] multiqc [DEBUG ] No samples found: skewer [2021-03-16 17:12:15,113] multiqc [DEBUG ] No samples found: sortmerna [2021-03-16 17:12:15,117] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-16 17:12:15,122] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-16 17:12:15,127] multiqc [DEBUG ] No samples found: afterqc [2021-03-16 17:12:15,132] multiqc [DEBUG ] No samples found: fastp [2021-03-16 17:12:15,520] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-03-16 17:12:15,705] multiqc [DEBUG ] No samples found: pycoqc [2021-03-16 17:12:15,709] multiqc [DEBUG ] No samples found: minionqc [2021-03-16 17:12:15,713] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-03-16 17:12:15,718] multiqc [DEBUG ] No samples found: clusterflow [2021-03-16 17:12:15,722] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-16 17:12:15,727] multiqc [DEBUG ] No samples found: interop [2021-03-16 17:12:15,732] multiqc [DEBUG ] No samples found: ivar [2021-03-16 17:12:15,736] multiqc [DEBUG ] No samples found: flash [2021-03-16 17:12:15,740] multiqc [DEBUG ] No samples found: seqyclean [2021-03-16 17:12:15,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-03-16 17:12:15,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-03-16 17:12:15,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-03-16 17:12:15,740] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-03-16 17:12:15,762] multiqc [INFO ] Compressing plot data [2021-03-16 17:12:16,078] multiqc [INFO ] Report : multiqc_report.html [2021-03-16 17:12:16,079] multiqc [INFO ] Data : multiqc_data [2021-03-16 17:12:16,079] multiqc [DEBUG ] Moving data file from '/state/partition1/job-3820239/tmp49tffcbc/multiqc_data' to '/scratch/gencore/logs/html/HNWF2AFX2/merged/multiqc_data' [2021-03-16 17:12:16,211] multiqc [INFO ] MultiQC complete