[2022-11-15 14:20:01,058] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-15 14:20:01,058] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-15 14:20:01,058] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-15 14:20:01,059] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-15 14:20:01,059] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-15 14:20:01,060] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVV2HAFX3/merged [2022-11-15 14:20:01,602] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-15 14:20:01,602] multiqc [INFO ] This is MultiQC v1.9 [2022-11-15 14:20:01,602] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HVV2HAFX3/merged [2022-11-15 14:20:01,602] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HVV2HAFX3/merged [2022-11-15 14:20:01,602] multiqc [INFO ] Template : default [2022-11-15 14:20:01,603] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-15 14:20:01,603] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HVV2HAFX3/merged [2022-11-15 14:20:01,603] 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 [2022-11-15 14:20:01,603] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27028449/tmpp11m05bm [2022-11-15 14:20:01,725] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_Dan_fastqc.html [2022-11-15 14:20:01,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_Wt-NF-Spike-input_fastqc.html [2022-11-15 14:20:02,614] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s1-NF-hop1_fastqc.html [2022-11-15 14:20:02,616] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s1-NF-hop1_fastqc.html [2022-11-15 14:20:02,659] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_9120-spike-chip_fastqc.html [2022-11-15 14:20:02,661] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_9120-spike-chip_fastqc.html [2022-11-15 14:20:02,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s-NF-Spike-hop1_fastqc.html [2022-11-15 14:20:02,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s-NF-Spike-hop1_fastqc.html [2022-11-15 14:20:02,748] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s-NF-Spike-hop1_fastqc.html [2022-11-15 14:20:02,750] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s-NF-Spike-hop1_fastqc.html [2022-11-15 14:20:02,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n01_Dan_fastqc.html [2022-11-15 14:20:02,795] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_Dan_fastqc.html [2022-11-15 14:20:02,837] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s1-NF-hop1_fastqc.html [2022-11-15 14:20:02,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s1-NF-hop1_fastqc.html [2022-11-15 14:20:02,883] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_undetermined_fastqc.html [2022-11-15 14:20:02,885] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_undetermined_fastqc.html [2022-11-15 14:20:02,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_11644-Spk-in_fastqc.html [2022-11-15 14:20:02,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_11644-Spk-in_fastqc.html [2022-11-15 14:20:02,973] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_Wt-NF-hop1_fastqc.html [2022-11-15 14:20:02,975] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_Wt-NF-hop1_fastqc.html [2022-11-15 14:20:03,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_7797-Spk-in_fastqc.html [2022-11-15 14:20:03,020] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_7797-Spk-in_fastqc.html [2022-11-15 14:20:03,062] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_11644-Spk-hop1_fastqc.html [2022-11-15 14:20:03,064] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_nov2022_11644-Spk-hop1_fastqc.html [2022-11-15 14:20:03,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n01_nov2022_11644-Spk-in_fastqc.html [2022-11-15 14:20:03,108] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_nov2022_11644-Spk-in_fastqc.html [2022-11-15 14:20:03,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s1-NF-input_fastqc.html [2022-11-15 14:20:03,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n01_2s1-NF-input_fastqc.html [2022-11-15 14:20:03,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s-NF-Spike-input_fastqc.html [2022-11-15 14:20:03,197] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVV2HAFX3_n02_2s-NF-Spike-input_fastqc.html [2022-11-15 14:20:03,567] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-15 14:20:03,569] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-15 14:20:03,584] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2022-11-15 14:20:03,593] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-15 14:20:03,595] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-15 14:20:03,601] multiqc [DEBUG ] No samples found: conpair [2022-11-15 14:20:03,607] multiqc [DEBUG ] No samples found: peddy [2022-11-15 14:20:03,613] multiqc [DEBUG ] No samples found: somalier [2022-11-15 14:20:03,620] multiqc [DEBUG ] No samples found: methylQA [2022-11-15 14:20:03,630] multiqc [DEBUG ] No samples found: mosdepth [2022-11-15 14:20:03,635] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-15 14:20:03,639] multiqc [DEBUG ] No samples found: qualimap [2022-11-15 14:20:03,645] multiqc [DEBUG ] No samples found: preseq [2022-11-15 14:20:03,651] multiqc [DEBUG ] No samples found: quast [2022-11-15 14:20:03,657] multiqc [DEBUG ] No samples found: qorts [2022-11-15 14:20:03,662] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-15 14:20:03,668] multiqc [DEBUG ] No samples found: rockhopper [2022-11-15 14:20:03,674] multiqc [DEBUG ] No samples found: rsem [2022-11-15 14:20:03,687] multiqc [DEBUG ] No samples found: rseqc [2022-11-15 14:20:03,692] multiqc [DEBUG ] No samples found: busco [2022-11-15 14:20:03,698] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-15 14:20:03,704] multiqc [DEBUG ] No samples found: disambiguate [2022-11-15 14:20:03,710] multiqc [DEBUG ] No samples found: supernova [2022-11-15 14:20:03,726] multiqc [DEBUG ] No samples found: deeptools [2022-11-15 14:20:03,732] multiqc [DEBUG ] No samples found: sargasso [2022-11-15 14:20:03,738] multiqc [DEBUG ] No samples found: verifybamid [2022-11-15 14:20:03,743] multiqc [DEBUG ] No samples found: mirtrace [2022-11-15 14:20:03,749] multiqc [DEBUG ] No samples found: happy [2022-11-15 14:20:03,755] multiqc [DEBUG ] No samples found: mirtop [2022-11-15 14:20:03,763] multiqc [DEBUG ] No samples found: homer [2022-11-15 14:20:03,769] multiqc [DEBUG ] No samples found: macs2 [2022-11-15 14:20:03,774] multiqc [DEBUG ] No samples found: theta2 [2022-11-15 14:20:03,780] multiqc [DEBUG ] No samples found: snpeff [2022-11-15 14:20:03,788] multiqc [DEBUG ] No samples found: gatk [2022-11-15 14:20:03,793] multiqc [DEBUG ] No samples found: htseq [2022-11-15 14:20:03,800] multiqc [DEBUG ] No samples found: bcftools [2022-11-15 14:20:03,806] multiqc [DEBUG ] No samples found: featureCounts [2022-11-15 14:20:03,814] multiqc [DEBUG ] No samples found: fgbio [2022-11-15 14:20:03,833] multiqc [DEBUG ] No samples found: dragen [2022-11-15 14:20:03,839] multiqc [DEBUG ] No samples found: dedup [2022-11-15 14:20:03,845] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-15 14:20:03,874] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-15 14:20:03,881] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-15 14:20:03,884] multiqc [DEBUG ] No samples found: picard [2022-11-15 14:20:03,889] multiqc [DEBUG ] No samples found: prokka [2022-11-15 14:20:03,895] multiqc [DEBUG ] No samples found: samblaster [2022-11-15 14:20:03,904] multiqc [DEBUG ] No samples found: samtools [2022-11-15 14:20:03,910] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-15 14:20:03,916] multiqc [DEBUG ] No samples found: bamtools [2022-11-15 14:20:03,921] multiqc [DEBUG ] No samples found: jellyfish [2022-11-15 14:20:03,930] multiqc [DEBUG ] No samples found: vcftools [2022-11-15 14:20:03,936] multiqc [DEBUG ] No samples found: longranger [2022-11-15 14:20:03,942] multiqc [DEBUG ] No samples found: stacks [2022-11-15 14:20:03,948] multiqc [DEBUG ] No samples found: varscan2 [2022-11-15 14:20:03,966] multiqc [DEBUG ] No samples found: bbmap [2022-11-15 14:20:03,971] multiqc [DEBUG ] No samples found: bismark [2022-11-15 14:20:03,978] multiqc [DEBUG ] No samples found: biscuit [2022-11-15 14:20:03,984] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-15 14:20:03,990] multiqc [DEBUG ] No samples found: hicup [2022-11-15 14:20:03,996] multiqc [DEBUG ] No samples found: hicpro [2022-11-15 14:20:04,001] multiqc [DEBUG ] No samples found: salmon [2022-11-15 14:20:04,007] multiqc [DEBUG ] No samples found: kallisto [2022-11-15 14:20:04,013] multiqc [DEBUG ] No samples found: slamdunk [2022-11-15 14:20:04,018] multiqc [DEBUG ] No samples found: star [2022-11-15 14:20:04,024] multiqc [DEBUG ] No samples found: hisat2 [2022-11-15 14:20:04,029] multiqc [DEBUG ] No samples found: tophat [2022-11-15 14:20:04,034] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-15 14:20:04,040] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-15 14:20:04,045] multiqc [DEBUG ] No samples found: snpsplit [2022-11-15 14:20:04,050] multiqc [DEBUG ] No samples found: kat [2022-11-15 14:20:04,055] multiqc [DEBUG ] No samples found: leehom [2022-11-15 14:20:04,061] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-15 14:20:04,066] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-15 14:20:04,071] multiqc [DEBUG ] No samples found: cutadapt [2022-11-15 14:20:04,076] multiqc [DEBUG ] No samples found: flexbar [2022-11-15 14:20:04,082] multiqc [DEBUG ] No samples found: kaiju [2022-11-15 14:20:04,088] multiqc [DEBUG ] No samples found: kraken [2022-11-15 14:20:04,094] multiqc [DEBUG ] No samples found: malt [2022-11-15 14:20:04,099] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-15 14:20:04,105] multiqc [DEBUG ] No samples found: sickle [2022-11-15 14:20:04,111] multiqc [DEBUG ] No samples found: skewer [2022-11-15 14:20:04,116] multiqc [DEBUG ] No samples found: sortmerna [2022-11-15 14:20:04,121] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-15 14:20:04,127] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-15 14:20:04,133] multiqc [DEBUG ] No samples found: afterqc [2022-11-15 14:20:04,139] multiqc [DEBUG ] No samples found: fastp [2022-11-15 14:20:04,848] multiqc.modules.fastqc.fastqc [INFO ] Found 32 reports [2022-11-15 14:20:05,141] multiqc [DEBUG ] No samples found: pycoqc [2022-11-15 14:20:05,147] multiqc [DEBUG ] No samples found: minionqc [2022-11-15 14:20:05,153] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-15 14:20:05,159] multiqc [DEBUG ] No samples found: clusterflow [2022-11-15 14:20:05,165] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-15 14:20:05,171] multiqc [DEBUG ] No samples found: interop [2022-11-15 14:20:05,177] multiqc [DEBUG ] No samples found: ivar [2022-11-15 14:20:05,183] multiqc [DEBUG ] No samples found: flash [2022-11-15 14:20:05,188] multiqc [DEBUG ] No samples found: seqyclean [2022-11-15 14:20:05,188] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-15 14:20:05,188] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-11-15 14:20:05,188] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-11-15 14:20:05,189] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-15 14:20:05,227] multiqc [INFO ] Compressing plot data [2022-11-15 14:20:05,768] multiqc [INFO ] Report : multiqc_report.html [2022-11-15 14:20:05,769] multiqc [INFO ] Data : multiqc_data [2022-11-15 14:20:05,769] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27028449/tmpp11m05bm/multiqc_data' to '/scratch/gencore/logs/html/HVV2HAFX3/merged/multiqc_data' [2022-11-15 14:20:05,913] multiqc [INFO ] MultiQC complete