[2023-05-04 17:03:15,939] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-04 17:03:15,939] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-04 17:03:15,939] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-04 17:03:15,942] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-04 17:03:15,942] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2023-05-04 17:03:15,942] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2WN3BGXT/merged [2023-05-04 17:03:16,108] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-04 17:03:16,108] multiqc [INFO ] This is MultiQC v1.9 [2023-05-04 17:03:16,108] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H2WN3BGXT/merged [2023-05-04 17:03:16,108] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H2WN3BGXT/merged [2023-05-04 17:03:16,108] multiqc [INFO ] Template : default [2023-05-04 17:03:16,108] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-04 17:03:16,108] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H2WN3BGXT/merged [2023-05-04 17:03:16,109] 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 [2023-05-04 17:03:16,109] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33035909/tmpd7utuhfk [2023-05-04 17:03:16,252] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br332a_fastqc.html [2023-05-04 17:03:16,255] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2023-05-04 17:03:17,357] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br326a_fastqc.html [2023-05-04 17:03:17,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br338a_fastqc.html [2023-05-04 17:03:17,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br338a_fastqc.html [2023-05-04 17:03:17,528] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br338a_fastqc.html [2023-05-04 17:03:17,530] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br338a_fastqc.html [2023-05-04 17:03:17,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br333a_fastqc.html [2023-05-04 17:03:17,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br333a_fastqc.html [2023-05-04 17:03:17,685] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br326a_fastqc.html [2023-05-04 17:03:17,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br326a_fastqc.html [2023-05-04 17:03:17,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_undetermined_fastqc.html [2023-05-04 17:03:17,731] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_undetermined_fastqc.html [2023-05-04 17:03:17,772] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br325a_fastqc.html [2023-05-04 17:03:17,774] multiqc [DEBUG ] File ignored by 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exceeded search pattern filesize limit: H2WN3BGXT_n02_br334a_fastqc.html [2023-05-04 17:03:18,024] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_undetermined_fastqc.html [2023-05-04 17:03:18,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_undetermined_fastqc.html [2023-05-04 17:03:18,068] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br335a_fastqc.html [2023-05-04 17:03:18,070] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br335a_fastqc.html [2023-05-04 17:03:18,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br321a_fastqc.html [2023-05-04 17:03:18,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br321a_fastqc.html [2023-05-04 17:03:18,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br331a_fastqc.html [2023-05-04 17:03:18,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br331a_fastqc.html [2023-05-04 17:03:18,241] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br328a_fastqc.html [2023-05-04 17:03:18,243] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br328a_fastqc.html [2023-05-04 17:03:18,284] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br336a_fastqc.html [2023-05-04 17:03:18,286] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br336a_fastqc.html [2023-05-04 17:03:18,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br337a_fastqc.html [2023-05-04 17:03:18,329] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br337a_fastqc.html [2023-05-04 17:03:18,369] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br330a_fastqc.html [2023-05-04 17:03:18,371] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br330a_fastqc.html [2023-05-04 17:03:18,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br320a_fastqc.html [2023-05-04 17:03:18,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br320a_fastqc.html [2023-05-04 17:03:18,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br327a_fastqc.html [2023-05-04 17:03:18,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n02_br327a_fastqc.html [2023-05-04 17:03:18,535] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br324a_fastqc.html [2023-05-04 17:03:18,537] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H2WN3BGXT_n01_br324a_fastqc.html [2023-05-04 17:03:18,884] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-04 17:03:18,886] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-04 17:03:18,894] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-04 17:03:18,903] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 20 samples (table) [2023-05-04 17:03:18,913] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-04 17:03:18,918] multiqc [DEBUG ] No samples found: conpair [2023-05-04 17:03:18,924] multiqc [DEBUG ] No samples found: peddy [2023-05-04 17:03:18,929] multiqc [DEBUG ] No samples found: somalier [2023-05-04 17:03:18,933] multiqc [DEBUG ] No samples found: methylQA [2023-05-04 17:03:18,941] multiqc [DEBUG ] No samples found: mosdepth [2023-05-04 17:03:18,951] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-04 17:03:18,954] multiqc [DEBUG ] No samples found: qualimap [2023-05-04 17:03:18,959] multiqc [DEBUG ] No samples found: preseq [2023-05-04 17:03:18,963] multiqc [DEBUG ] No samples found: quast [2023-05-04 17:03:18,968] multiqc [DEBUG ] No samples found: qorts [2023-05-04 17:03:18,973] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-04 17:03:18,984] multiqc [DEBUG ] No samples found: rockhopper [2023-05-04 17:03:18,989] multiqc [DEBUG ] No samples found: rsem [2023-05-04 17:03:19,000] multiqc [DEBUG ] No samples found: rseqc [2023-05-04 17:03:19,005] multiqc [DEBUG ] No samples found: busco [2023-05-04 17:03:19,018] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-04 17:03:19,028] multiqc [DEBUG ] No samples found: disambiguate [2023-05-04 17:03:19,040] multiqc [DEBUG ] No samples found: supernova [2023-05-04 17:03:19,054] multiqc [DEBUG ] No samples found: deeptools [2023-05-04 17:03:19,059] multiqc [DEBUG ] No samples found: sargasso [2023-05-04 17:03:19,065] multiqc [DEBUG ] No samples found: verifybamid [2023-05-04 17:03:19,072] multiqc [DEBUG ] No samples found: mirtrace [2023-05-04 17:03:19,077] multiqc [DEBUG ] No samples found: happy [2023-05-04 17:03:19,083] multiqc [DEBUG ] No samples found: mirtop [2023-05-04 17:03:19,090] multiqc [DEBUG ] No samples found: homer [2023-05-04 17:03:19,094] multiqc [DEBUG ] No samples found: macs2 [2023-05-04 17:03:19,099] multiqc [DEBUG ] No samples found: theta2 [2023-05-04 17:03:19,103] multiqc [DEBUG ] No samples found: snpeff [2023-05-04 17:03:19,110] multiqc [DEBUG ] No samples found: gatk [2023-05-04 17:03:19,121] multiqc [DEBUG ] No samples found: htseq [2023-05-04 17:03:19,126] multiqc [DEBUG ] No samples found: bcftools [2023-05-04 17:03:19,131] multiqc [DEBUG ] No samples found: featureCounts [2023-05-04 17:03:19,138] multiqc [DEBUG ] No samples found: fgbio [2023-05-04 17:03:19,150] multiqc [DEBUG ] No samples found: dragen [2023-05-04 17:03:19,154] multiqc [DEBUG ] No samples found: dedup [2023-05-04 17:03:19,174] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-04 17:03:19,199] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-04 17:03:19,204] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-04 17:03:19,206] multiqc [DEBUG ] No samples found: picard [2023-05-04 17:03:19,211] multiqc [DEBUG ] No samples found: prokka [2023-05-04 17:03:19,216] multiqc [DEBUG ] No samples found: samblaster [2023-05-04 17:03:19,224] multiqc [DEBUG ] No samples found: samtools [2023-05-04 17:03:19,228] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-04 17:03:19,234] multiqc [DEBUG ] No samples found: bamtools [2023-05-04 17:03:19,239] multiqc [DEBUG ] No samples found: jellyfish [2023-05-04 17:03:19,246] multiqc [DEBUG ] No samples found: vcftools [2023-05-04 17:03:19,251] multiqc [DEBUG ] No samples found: longranger [2023-05-04 17:03:19,255] multiqc [DEBUG ] No samples found: stacks [2023-05-04 17:03:19,260] multiqc [DEBUG ] No samples found: varscan2 [2023-05-04 17:03:19,274] multiqc [DEBUG ] No samples found: bbmap [2023-05-04 17:03:19,279] multiqc [DEBUG ] No samples found: bismark [2023-05-04 17:03:19,284] multiqc [DEBUG ] No samples found: biscuit [2023-05-04 17:03:19,289] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-04 17:03:19,294] multiqc [DEBUG ] No samples found: hicup [2023-05-04 17:03:19,298] multiqc [DEBUG ] No samples found: hicpro [2023-05-04 17:03:19,302] multiqc [DEBUG ] No samples found: salmon [2023-05-04 17:03:19,307] multiqc [DEBUG ] No samples found: kallisto [2023-05-04 17:03:19,311] multiqc [DEBUG ] No samples found: slamdunk [2023-05-04 17:03:19,315] multiqc [DEBUG ] No samples found: star [2023-05-04 17:03:19,320] multiqc [DEBUG ] No samples found: hisat2 [2023-05-04 17:03:19,324] multiqc [DEBUG ] No samples found: tophat [2023-05-04 17:03:19,328] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-04 17:03:19,333] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-04 17:03:19,337] multiqc [DEBUG ] No samples found: snpsplit [2023-05-04 17:03:19,341] multiqc [DEBUG ] No samples found: kat [2023-05-04 17:03:19,345] multiqc [DEBUG ] No samples found: leehom [2023-05-04 17:03:19,350] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-04 17:03:19,354] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-04 17:03:19,359] multiqc [DEBUG ] No samples found: cutadapt [2023-05-04 17:03:19,363] multiqc [DEBUG ] No samples found: flexbar [2023-05-04 17:03:19,368] multiqc [DEBUG ] No samples found: kaiju [2023-05-04 17:03:19,372] multiqc [DEBUG ] No samples found: kraken [2023-05-04 17:03:19,376] multiqc [DEBUG ] No samples found: malt [2023-05-04 17:03:19,380] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-04 17:03:19,384] multiqc [DEBUG ] No samples found: sickle [2023-05-04 17:03:19,389] multiqc [DEBUG ] No samples found: skewer [2023-05-04 17:03:19,393] multiqc [DEBUG ] No samples found: sortmerna [2023-05-04 17:03:19,401] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-04 17:03:19,409] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-04 17:03:19,414] multiqc [DEBUG ] No samples found: afterqc [2023-05-04 17:03:19,420] multiqc [DEBUG ] No samples found: fastp [2023-05-04 17:03:22,811] multiqc.modules.fastqc.fastqc [INFO ] Found 40 reports [2023-05-04 17:03:23,177] multiqc [DEBUG ] No samples found: pycoqc [2023-05-04 17:03:23,182] multiqc [DEBUG ] No samples found: minionqc [2023-05-04 17:03:23,186] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-04 17:03:23,191] multiqc [DEBUG ] No samples found: clusterflow [2023-05-04 17:03:23,196] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-04 17:03:23,200] multiqc [DEBUG ] No samples found: interop [2023-05-04 17:03:23,205] multiqc [DEBUG ] No samples found: ivar [2023-05-04 17:03:23,209] multiqc [DEBUG ] No samples found: flash [2023-05-04 17:03:23,213] multiqc [DEBUG ] No samples found: seqyclean [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,213] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-04 17:03:23,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-04 17:03:23,260] multiqc [INFO ] Compressing plot data [2023-05-04 17:03:23,920] multiqc [INFO ] Report : multiqc_report.html [2023-05-04 17:03:23,921] multiqc [INFO ] Data : multiqc_data [2023-05-04 17:03:23,921] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33035909/tmpd7utuhfk/multiqc_data' to '/scratch/gencore/logs/html/H2WN3BGXT/merged/multiqc_data' [2023-05-04 17:03:24,049] multiqc [INFO ] MultiQC complete