[2021-10-09 04:41:04,047] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-09 04:41:04,047] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-09 04:41:04,047] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-09 04:41:04,048] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-09 04:41:04,048] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-09 04:41:04,048] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3KVFAFX3/merged [2021-10-09 04:41:05,401] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-09 04:41:05,401] multiqc [INFO ] This is MultiQC v1.9 [2021-10-09 04:41:05,401] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H3KVFAFX3/merged [2021-10-09 04:41:05,401] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H3KVFAFX3/merged [2021-10-09 04:41:05,401] multiqc [INFO ] Template : default [2021-10-09 04:41:05,401] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-09 04:41:05,401] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H3KVFAFX3/merged [2021-10-09 04:41:05,402] 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 [2021-10-09 04:41:05,402] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10687082/tmpc1ph7kn7 [2021-10-09 04:41:05,509] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-9_fastqc.html [2021-10-09 04:41:05,512] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H3KVFAFX3_n01_dad1-3_fastqc.html [2021-10-09 04:41:05,938] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-8_fastqc.html [2021-10-09 04:41:05,939] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-8_fastqc.html [2021-10-09 04:41:05,978] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-7_fastqc.html [2021-10-09 04:41:05,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-7_fastqc.html [2021-10-09 04:41:06,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-8_fastqc.html [2021-10-09 04:41:06,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-8_fastqc.html [2021-10-09 04:41:06,060] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-2_fastqc.html [2021-10-09 04:41:06,062] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-2_fastqc.html [2021-10-09 04:41:06,102] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-1_fastqc.html [2021-10-09 04:41:06,104] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-1_fastqc.html [2021-10-09 04:41:06,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-1_fastqc.html [2021-10-09 04:41:06,145] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-1_fastqc.html [2021-10-09 04:41:06,184] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-6_fastqc.html [2021-10-09 04:41:06,185] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-6_fastqc.html [2021-10-09 04:41:06,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-6_fastqc.html [2021-10-09 04:41:06,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-6_fastqc.html [2021-10-09 04:41:06,265] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-10_fastqc.html [2021-10-09 04:41:06,267] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-10_fastqc.html [2021-10-09 04:41:06,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-4_fastqc.html [2021-10-09 04:41:06,307] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-4_fastqc.html [2021-10-09 04:41:06,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-3_fastqc.html [2021-10-09 04:41:06,347] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-3_fastqc.html [2021-10-09 04:41:06,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-2_fastqc.html [2021-10-09 04:41:06,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-2_fastqc.html [2021-10-09 04:41:06,431] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-5_fastqc.html [2021-10-09 04:41:06,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-5_fastqc.html [2021-10-09 04:41:06,474] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_undetermined_fastqc.html [2021-10-09 04:41:06,476] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_undetermined_fastqc.html [2021-10-09 04:41:06,513] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_undetermined_fastqc.html [2021-10-09 04:41:06,515] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_undetermined_fastqc.html [2021-10-09 04:41:06,553] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-10_fastqc.html [2021-10-09 04:41:06,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-10_fastqc.html [2021-10-09 04:41:06,592] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-4_fastqc.html [2021-10-09 04:41:06,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-4_fastqc.html [2021-10-09 04:41:06,634] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-5_fastqc.html [2021-10-09 04:41:06,636] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n01_dad1-5_fastqc.html [2021-10-09 04:41:06,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-9_fastqc.html [2021-10-09 04:41:06,677] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3KVFAFX3_n02_dad1-9_fastqc.html [2021-10-09 04:41:07,037] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-09 04:41:07,039] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-09 04:41:07,050] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2021-10-09 04:41:07,052] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-09 04:41:07,061] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-09 04:41:07,065] multiqc [DEBUG ] No samples found: conpair [2021-10-09 04:41:07,070] multiqc [DEBUG ] No samples found: peddy [2021-10-09 04:41:07,075] multiqc [DEBUG ] No samples found: somalier [2021-10-09 04:41:07,080] multiqc [DEBUG ] No samples found: methylQA [2021-10-09 04:41:07,087] multiqc [DEBUG ] No samples found: mosdepth [2021-10-09 04:41:07,092] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-09 04:41:07,095] multiqc [DEBUG ] No samples found: qualimap [2021-10-09 04:41:07,100] multiqc [DEBUG ] No samples found: preseq [2021-10-09 04:41:07,105] multiqc [DEBUG ] No samples found: quast [2021-10-09 04:41:07,109] multiqc [DEBUG ] No samples found: qorts [2021-10-09 04:41:07,114] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-09 04:41:07,119] multiqc [DEBUG ] No samples found: rockhopper [2021-10-09 04:41:07,124] multiqc [DEBUG ] No samples found: rsem [2021-10-09 04:41:07,134] multiqc [DEBUG ] No samples found: rseqc [2021-10-09 04:41:07,138] multiqc [DEBUG ] No samples found: busco [2021-10-09 04:41:07,143] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-09 04:41:07,147] multiqc [DEBUG ] No samples found: disambiguate [2021-10-09 04:41:07,152] multiqc [DEBUG ] No samples found: supernova [2021-10-09 04:41:07,164] multiqc [DEBUG ] No samples found: deeptools [2021-10-09 04:41:07,168] multiqc [DEBUG ] No samples found: sargasso [2021-10-09 04:41:07,173] multiqc [DEBUG ] No samples found: verifybamid [2021-10-09 04:41:07,178] multiqc [DEBUG ] No samples found: mirtrace [2021-10-09 04:41:07,183] multiqc [DEBUG ] No samples found: happy [2021-10-09 04:41:07,188] multiqc [DEBUG ] No samples found: mirtop [2021-10-09 04:41:07,194] multiqc [DEBUG ] No samples found: homer [2021-10-09 04:41:07,198] multiqc [DEBUG ] No samples found: macs2 [2021-10-09 04:41:07,203] multiqc [DEBUG ] No samples found: theta2 [2021-10-09 04:41:07,207] multiqc [DEBUG ] No samples found: snpeff [2021-10-09 04:41:07,214] multiqc [DEBUG ] No samples found: gatk [2021-10-09 04:41:07,219] multiqc [DEBUG ] No samples found: htseq [2021-10-09 04:41:07,225] multiqc [DEBUG ] No samples found: bcftools [2021-10-09 04:41:07,229] multiqc [DEBUG ] No samples found: featureCounts [2021-10-09 04:41:07,235] multiqc [DEBUG ] No samples found: fgbio [2021-10-09 04:41:07,247] multiqc [DEBUG ] No samples found: dragen [2021-10-09 04:41:07,252] multiqc [DEBUG ] No samples found: dedup [2021-10-09 04:41:07,256] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-09 04:41:07,279] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-09 04:41:07,284] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-09 04:41:07,286] multiqc [DEBUG ] No samples found: picard [2021-10-09 04:41:07,291] multiqc [DEBUG ] No samples found: prokka [2021-10-09 04:41:07,295] multiqc [DEBUG ] No samples found: samblaster [2021-10-09 04:41:07,303] multiqc [DEBUG ] No samples found: samtools [2021-10-09 04:41:07,308] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-09 04:41:07,313] multiqc [DEBUG ] No samples found: bamtools [2021-10-09 04:41:07,317] multiqc [DEBUG ] No samples found: jellyfish [2021-10-09 04:41:07,324] multiqc [DEBUG ] No samples found: vcftools [2021-10-09 04:41:07,328] multiqc [DEBUG ] No samples found: longranger [2021-10-09 04:41:07,333] multiqc [DEBUG ] No samples found: stacks [2021-10-09 04:41:07,337] multiqc [DEBUG ] No samples found: varscan2 [2021-10-09 04:41:07,351] multiqc [DEBUG ] No samples found: bbmap [2021-10-09 04:41:07,356] multiqc [DEBUG ] No samples found: bismark [2021-10-09 04:41:07,361] multiqc [DEBUG ] No samples found: biscuit [2021-10-09 04:41:07,366] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-09 04:41:07,370] multiqc [DEBUG ] No samples found: hicup [2021-10-09 04:41:07,375] multiqc [DEBUG ] No samples found: hicpro [2021-10-09 04:41:07,379] multiqc [DEBUG ] No samples found: salmon [2021-10-09 04:41:07,383] multiqc [DEBUG ] No samples found: kallisto [2021-10-09 04:41:07,388] multiqc [DEBUG ] No samples found: slamdunk [2021-10-09 04:41:07,393] multiqc [DEBUG ] No samples found: star [2021-10-09 04:41:07,397] multiqc [DEBUG ] No samples found: hisat2 [2021-10-09 04:41:07,402] multiqc [DEBUG ] No samples found: tophat [2021-10-09 04:41:07,406] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-09 04:41:07,411] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-09 04:41:07,416] multiqc [DEBUG ] No samples found: snpsplit [2021-10-09 04:41:07,420] multiqc [DEBUG ] No samples found: kat [2021-10-09 04:41:07,424] multiqc [DEBUG ] No samples found: leehom [2021-10-09 04:41:07,428] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-09 04:41:07,433] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-09 04:41:07,437] multiqc [DEBUG ] No samples found: cutadapt [2021-10-09 04:41:07,441] multiqc [DEBUG ] No samples found: flexbar [2021-10-09 04:41:07,446] multiqc [DEBUG ] No samples found: kaiju [2021-10-09 04:41:07,450] multiqc [DEBUG ] No samples found: kraken [2021-10-09 04:41:07,455] multiqc [DEBUG ] No samples found: malt [2021-10-09 04:41:07,459] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-09 04:41:07,464] multiqc [DEBUG ] No samples found: sickle [2021-10-09 04:41:07,468] multiqc [DEBUG ] No samples found: skewer [2021-10-09 04:41:07,472] multiqc [DEBUG ] No samples found: sortmerna [2021-10-09 04:41:07,476] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-09 04:41:07,481] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-09 04:41:07,486] multiqc [DEBUG ] No samples found: afterqc [2021-10-09 04:41:07,490] multiqc [DEBUG ] No samples found: fastp [2021-10-09 04:41:08,024] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2021-10-09 04:41:08,490] multiqc [DEBUG ] No samples found: pycoqc [2021-10-09 04:41:08,495] multiqc [DEBUG ] No samples found: minionqc [2021-10-09 04:41:08,499] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-09 04:41:08,504] multiqc [DEBUG ] No samples found: clusterflow [2021-10-09 04:41:08,510] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-09 04:41:08,514] multiqc [DEBUG ] No samples found: interop [2021-10-09 04:41:08,519] multiqc [DEBUG ] No samples found: ivar [2021-10-09 04:41:08,523] multiqc [DEBUG ] No samples found: flash [2021-10-09 04:41:08,528] multiqc [DEBUG ] No samples found: seqyclean [2021-10-09 04:41:08,528] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-09 04:41:08,528] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-09 04:41:08,528] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-09 04:41:08,528] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-09 04:41:08,554] multiqc [INFO ] Compressing plot data [2021-10-09 04:41:08,949] multiqc [INFO ] Report : multiqc_report.html [2021-10-09 04:41:08,949] multiqc [INFO ] Data : multiqc_data [2021-10-09 04:41:08,949] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10687082/tmpc1ph7kn7/multiqc_data' to '/scratch/gencore/logs/html/H3KVFAFX3/merged/multiqc_data' [2021-10-09 04:41:09,072] multiqc [INFO ] MultiQC complete