[2022-07-06 07:32:31,526] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-06 07:32:31,526] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-06 07:32:31,526] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-06 07:32:31,527] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-06 07:32:31,527] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-06 07:32:31,527] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN7TMAFX3/merged [2022-07-06 07:32:32,289] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-06 07:32:32,289] multiqc [INFO ] This is MultiQC v1.9 [2022-07-06 07:32:32,289] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HN7TMAFX3/merged [2022-07-06 07:32:32,289] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HN7TMAFX3/merged [2022-07-06 07:32:32,289] multiqc [INFO ] Template : default [2022-07-06 07:32:32,289] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-06 07:32:32,289] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HN7TMAFX3/merged [2022-07-06 07:32:32,289] 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 [2022-07-06 07:32:32,290] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-21890283/tmpv5j6fg6q [2022-07-06 07:32:32,398] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-06 07:32:32,400] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-06 07:32:32,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-6_fastqc.html [2022-07-06 07:32:32,734] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-6_fastqc.html [2022-07-06 07:32:32,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_undetermined_fastqc.html [2022-07-06 07:32:32,781] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_undetermined_fastqc.html [2022-07-06 07:32:32,821] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-8_fastqc.html [2022-07-06 07:32:32,823] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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07:32:33,014] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-5_fastqc.html [2022-07-06 07:32:33,016] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-5_fastqc.html [2022-07-06 07:32:33,061] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-9_fastqc.html [2022-07-06 07:32:33,063] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-9_fastqc.html [2022-07-06 07:32:33,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-7_fastqc.html [2022-07-06 07:32:33,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-7_fastqc.html [2022-07-06 07:32:33,153] multiqc [DEBUG ] File ignored by 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pattern filesize limit: HN7TMAFX3_n01_as4-10_fastqc.html [2022-07-06 07:32:33,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-10_fastqc.html [2022-07-06 07:32:33,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-1_fastqc.html [2022-07-06 07:32:33,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-1_fastqc.html [2022-07-06 07:32:33,384] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-1_fastqc.html [2022-07-06 07:32:33,386] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-1_fastqc.html [2022-07-06 07:32:33,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-13_fastqc.html [2022-07-06 07:32:33,437] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-13_fastqc.html [2022-07-06 07:32:33,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-11_fastqc.html [2022-07-06 07:32:33,480] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-11_fastqc.html [2022-07-06 07:32:33,526] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-2_fastqc.html [2022-07-06 07:32:33,528] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-2_fastqc.html [2022-07-06 07:32:33,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-6_fastqc.html [2022-07-06 07:32:33,573] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-6_fastqc.html [2022-07-06 07:32:33,618] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-9_fastqc.html [2022-07-06 07:32:33,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-9_fastqc.html [2022-07-06 07:32:33,665] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-12_fastqc.html [2022-07-06 07:32:33,667] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-12_fastqc.html [2022-07-06 07:32:33,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-3_fastqc.html [2022-07-06 07:32:33,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-3_fastqc.html [2022-07-06 07:32:33,766] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-2_fastqc.html [2022-07-06 07:32:33,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-2_fastqc.html [2022-07-06 07:32:33,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-10_fastqc.html [2022-07-06 07:32:33,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-10_fastqc.html [2022-07-06 07:32:33,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_undetermined_fastqc.html [2022-07-06 07:32:33,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_undetermined_fastqc.html [2022-07-06 07:32:33,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-8_fastqc.html [2022-07-06 07:32:33,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n01_as4-8_fastqc.html [2022-07-06 07:32:33,946] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-5_fastqc.html [2022-07-06 07:32:33,947] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-5_fastqc.html [2022-07-06 07:32:33,994] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-11_fastqc.html [2022-07-06 07:32:33,996] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN7TMAFX3_n02_as4-11_fastqc.html [2022-07-06 07:32:34,335] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-06 07:32:34,337] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-06 07:32:34,350] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-06 07:32:34,360] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-06 07:32:34,366] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 14 samples (table) [2022-07-06 07:32:34,373] multiqc [DEBUG ] No samples found: conpair [2022-07-06 07:32:34,381] multiqc [DEBUG ] No samples found: peddy [2022-07-06 07:32:34,387] multiqc [DEBUG ] No samples found: somalier [2022-07-06 07:32:34,394] multiqc [DEBUG ] No samples found: methylQA [2022-07-06 07:32:34,405] multiqc [DEBUG ] No samples found: mosdepth [2022-07-06 07:32:34,412] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-06 07:32:34,416] multiqc [DEBUG ] No samples found: qualimap [2022-07-06 07:32:34,423] multiqc [DEBUG ] No samples found: preseq [2022-07-06 07:32:34,429] multiqc [DEBUG ] No samples found: quast [2022-07-06 07:32:34,434] multiqc [DEBUG ] No samples found: qorts [2022-07-06 07:32:34,441] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-06 07:32:34,446] multiqc [DEBUG ] No samples found: rockhopper [2022-07-06 07:32:34,452] multiqc [DEBUG ] No samples found: rsem [2022-07-06 07:32:34,470] multiqc [DEBUG ] No samples found: rseqc [2022-07-06 07:32:34,476] multiqc [DEBUG ] No samples found: busco [2022-07-06 07:32:34,483] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-06 07:32:34,490] multiqc [DEBUG ] No samples found: disambiguate [2022-07-06 07:32:34,495] multiqc [DEBUG ] No samples found: supernova [2022-07-06 07:32:34,516] multiqc [DEBUG ] No samples found: deeptools [2022-07-06 07:32:34,520] multiqc [DEBUG ] No samples found: sargasso [2022-07-06 07:32:34,525] multiqc [DEBUG ] No samples found: verifybamid [2022-07-06 07:32:34,532] multiqc [DEBUG ] No samples found: mirtrace [2022-07-06 07:32:34,538] multiqc [DEBUG ] No samples found: happy [2022-07-06 07:32:34,543] multiqc [DEBUG ] No samples found: mirtop [2022-07-06 07:32:34,551] multiqc [DEBUG ] No samples found: homer [2022-07-06 07:32:34,558] multiqc [DEBUG ] No samples found: macs2 [2022-07-06 07:32:34,562] multiqc [DEBUG ] No samples found: theta2 [2022-07-06 07:32:34,567] multiqc [DEBUG ] No samples found: snpeff [2022-07-06 07:32:34,575] multiqc [DEBUG ] No samples found: gatk [2022-07-06 07:32:34,582] multiqc [DEBUG ] No samples found: htseq [2022-07-06 07:32:34,589] multiqc [DEBUG ] No samples found: bcftools [2022-07-06 07:32:34,593] multiqc [DEBUG ] No samples found: featureCounts [2022-07-06 07:32:34,603] multiqc [DEBUG ] No samples found: fgbio [2022-07-06 07:32:34,622] multiqc [DEBUG ] No samples found: dragen [2022-07-06 07:32:34,628] multiqc [DEBUG ] No samples found: dedup [2022-07-06 07:32:34,635] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-06 07:32:34,675] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-06 07:32:34,681] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-06 07:32:34,684] multiqc [DEBUG ] No samples found: picard [2022-07-06 07:32:34,688] multiqc [DEBUG ] No samples found: prokka [2022-07-06 07:32:34,692] multiqc [DEBUG ] No samples found: samblaster [2022-07-06 07:32:34,702] multiqc [DEBUG ] No samples found: samtools [2022-07-06 07:32:34,709] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-06 07:32:34,717] multiqc [DEBUG ] No samples found: bamtools [2022-07-06 07:32:34,725] multiqc [DEBUG ] No samples found: jellyfish [2022-07-06 07:32:34,734] multiqc [DEBUG ] No samples found: vcftools [2022-07-06 07:32:34,739] multiqc [DEBUG ] No samples found: longranger [2022-07-06 07:32:34,744] multiqc [DEBUG ] No samples found: stacks [2022-07-06 07:32:34,749] multiqc [DEBUG ] No samples found: varscan2 [2022-07-06 07:32:34,772] multiqc [DEBUG ] No samples found: bbmap [2022-07-06 07:32:34,777] multiqc [DEBUG ] No samples found: bismark [2022-07-06 07:32:34,782] multiqc [DEBUG ] No samples found: biscuit [2022-07-06 07:32:34,787] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-06 07:32:34,792] multiqc [DEBUG ] No samples found: hicup [2022-07-06 07:32:34,797] multiqc [DEBUG ] No samples found: hicpro [2022-07-06 07:32:34,804] multiqc [DEBUG ] No samples found: salmon [2022-07-06 07:32:34,811] multiqc [DEBUG ] No samples found: kallisto [2022-07-06 07:32:34,816] multiqc [DEBUG ] No samples found: slamdunk [2022-07-06 07:32:34,820] multiqc [DEBUG ] No samples found: star [2022-07-06 07:32:34,825] multiqc [DEBUG ] No samples found: hisat2 [2022-07-06 07:32:34,830] multiqc [DEBUG ] No samples found: tophat [2022-07-06 07:32:34,836] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-06 07:32:34,840] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-06 07:32:34,845] multiqc [DEBUG ] No samples found: snpsplit [2022-07-06 07:32:34,850] multiqc [DEBUG ] No samples found: kat [2022-07-06 07:32:34,855] multiqc [DEBUG ] No samples found: leehom [2022-07-06 07:32:34,861] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-06 07:32:34,866] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-06 07:32:34,873] multiqc [DEBUG ] No samples found: cutadapt [2022-07-06 07:32:34,877] multiqc [DEBUG ] No samples found: flexbar [2022-07-06 07:32:34,882] multiqc [DEBUG ] No samples found: kaiju [2022-07-06 07:32:34,887] multiqc [DEBUG ] No samples found: kraken [2022-07-06 07:32:34,892] multiqc [DEBUG ] No samples found: malt [2022-07-06 07:32:34,897] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-06 07:32:34,902] multiqc [DEBUG ] No samples found: sickle [2022-07-06 07:32:34,908] multiqc [DEBUG ] No samples found: skewer [2022-07-06 07:32:34,912] multiqc [DEBUG ] No samples found: sortmerna [2022-07-06 07:32:34,917] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-06 07:32:34,923] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-06 07:32:34,929] multiqc [DEBUG ] No samples found: afterqc [2022-07-06 07:32:34,935] multiqc [DEBUG ] No samples found: fastp [2022-07-06 07:32:35,603] multiqc.modules.fastqc.fastqc [INFO ] Found 28 reports [2022-07-06 07:32:36,184] multiqc [DEBUG ] No samples found: pycoqc [2022-07-06 07:32:36,189] multiqc [DEBUG ] No samples found: minionqc [2022-07-06 07:32:36,196] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-06 07:32:36,203] multiqc [DEBUG ] No samples found: clusterflow [2022-07-06 07:32:36,210] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-06 07:32:36,216] multiqc [DEBUG ] No samples found: interop [2022-07-06 07:32:36,221] multiqc [DEBUG ] No samples found: ivar [2022-07-06 07:32:36,226] multiqc [DEBUG ] No samples found: flash [2022-07-06 07:32:36,233] multiqc [DEBUG ] No samples found: seqyclean [2022-07-06 07:32:36,233] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-06 07:32:36,233] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-06 07:32:36,233] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-06 07:32:36,233] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-06 07:32:36,266] multiqc [INFO ] Compressing plot data [2022-07-06 07:32:36,772] multiqc [INFO ] Report : multiqc_report.html [2022-07-06 07:32:36,772] multiqc [INFO ] Data : multiqc_data [2022-07-06 07:32:36,772] multiqc [DEBUG ] Moving data file from '/state/partition1/job-21890283/tmpv5j6fg6q/multiqc_data' to '/scratch/gencore/logs/html/HN7TMAFX3/merged/multiqc_data' [2022-07-06 07:32:36,900] multiqc [INFO ] MultiQC complete