[2021-07-09 12:42:25,738] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-09 12:42:25,739] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-09 12:42:25,739] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-09 12:42:25,740] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-09 12:42:25,740] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-09 12:42:25,740] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCVAFX2/merged [2021-07-09 12:42:28,480] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-09 12:42:28,481] multiqc [INFO ] This is MultiQC v1.9 [2021-07-09 12:42:28,481] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCVAFX2/merged [2021-07-09 12:42:28,481] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTHCVAFX2/merged [2021-07-09 12:42:28,481] multiqc [INFO ] Template : default [2021-07-09 12:42:28,481] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-09 12:42:28,481] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTHCVAFX2/merged [2021-07-09 12:42:28,481] 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 [2021-07-09 12:42:28,481] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8523027/tmppqq6wkv6 [2021-07-09 12:42:28,588] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_7797-input-_fastqc.html [2021-07-09 12:42:28,590] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_7797-antiPHD_fastqc.html [2021-07-09 12:42:29,558] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH9120-antiHop1-NH_fastqc.html [2021-07-09 12:42:29,559] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH9120-antiHop1-NH_fastqc.html [2021-07-09 12:42:29,598] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9251-antiPHD_fastqc.html [2021-07-09 12:42:29,599] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9251-antiPHD_fastqc.html [2021-07-09 12:42:29,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH10517-antiHop1-NH_fastqc.html [2021-07-09 12:42:29,641] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH10517-antiHop1-NH_fastqc.html [2021-07-09 12:42:29,678] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-noprotein-input_fastqc.html [2021-07-09 12:42:29,680] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-noprotein-input_fastqc.html [2021-07-09 12:42:29,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH10517-input_fastqc.html [2021-07-09 12:42:29,724] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH10517-input_fastqc.html [2021-07-09 12:42:29,762] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH9120-input_fastqc.html [2021-07-09 12:42:29,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH9120-input_fastqc.html [2021-07-09 12:42:29,801] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-input-_fastqc.html [2021-07-09 12:42:29,803] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-input-_fastqc.html [2021-07-09 12:42:29,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9120-input_fastqc.html [2021-07-09 12:42:29,846] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9120-input_fastqc.html [2021-07-09 12:42:29,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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limit: HTHCVAFX2_n02_AH7797-antiHop1NH_fastqc.html [2021-07-09 12:42:30,014] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH7797-antiHop1NH_fastqc.html [2021-07-09 12:42:30,051] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH9251-input_fastqc.html [2021-07-09 12:42:30,053] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH9251-input_fastqc.html [2021-07-09 12:42:30,091] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH5187-antiHop1-NH_fastqc.html [2021-07-09 12:42:30,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH5187-antiHop1-NH_fastqc.html [2021-07-09 12:42:30,133] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH7797-input-_fastqc.html [2021-07-09 12:42:30,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH7797-input-_fastqc.html [2021-07-09 12:42:30,174] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-noprotein-antiPHD_fastqc.html [2021-07-09 12:42:30,175] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_7797-noprotein-antiPHD_fastqc.html [2021-07-09 12:42:30,216] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_10517-antiPHD_fastqc.html [2021-07-09 12:42:30,218] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_10517-antiPHD_fastqc.html [2021-07-09 12:42:30,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_10517-input_fastqc.html [2021-07-09 12:42:30,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_10517-input_fastqc.html [2021-07-09 12:42:30,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH7797-input-_fastqc.html [2021-07-09 12:42:30,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n02_AH7797-input-_fastqc.html [2021-07-09 12:42:30,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH9251-input_fastqc.html [2021-07-09 12:42:30,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_AH9251-input_fastqc.html [2021-07-09 12:42:30,384] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9120-antiPHD_fastqc.html [2021-07-09 12:42:30,385] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCVAFX2_n01_9120-antiPHD_fastqc.html [2021-07-09 12:42:30,900] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-09 12:42:30,902] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-09 12:42:30,909] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-09 12:42:30,919] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-09 12:42:30,929] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2021-07-09 12:42:30,933] multiqc [DEBUG ] No samples found: conpair [2021-07-09 12:42:30,937] multiqc [DEBUG ] No samples found: peddy [2021-07-09 12:42:30,942] multiqc [DEBUG ] No samples found: somalier [2021-07-09 12:42:30,946] multiqc [DEBUG ] No samples found: methylQA [2021-07-09 12:42:30,953] multiqc [DEBUG ] No samples found: mosdepth [2021-07-09 12:42:30,957] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-09 12:42:30,960] multiqc [DEBUG ] No samples found: qualimap [2021-07-09 12:42:30,964] multiqc [DEBUG ] No samples found: preseq [2021-07-09 12:42:30,968] multiqc [DEBUG ] No samples found: quast [2021-07-09 12:42:30,972] multiqc [DEBUG ] No samples found: qorts [2021-07-09 12:42:30,976] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-09 12:42:30,981] multiqc [DEBUG ] No samples found: rockhopper [2021-07-09 12:42:30,985] multiqc [DEBUG ] No samples found: rsem [2021-07-09 12:42:30,994] multiqc [DEBUG ] No samples found: rseqc [2021-07-09 12:42:30,998] multiqc [DEBUG ] No samples found: busco [2021-07-09 12:42:31,003] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-09 12:42:31,008] multiqc [DEBUG ] No samples found: disambiguate [2021-07-09 12:42:31,013] multiqc [DEBUG ] No samples found: supernova [2021-07-09 12:42:31,023] multiqc [DEBUG ] No samples found: deeptools [2021-07-09 12:42:31,028] multiqc [DEBUG ] No samples found: sargasso [2021-07-09 12:42:31,032] multiqc [DEBUG ] No samples found: verifybamid [2021-07-09 12:42:31,036] multiqc [DEBUG ] No samples found: mirtrace [2021-07-09 12:42:31,040] multiqc [DEBUG ] No samples found: happy [2021-07-09 12:42:31,044] multiqc [DEBUG ] No samples found: mirtop [2021-07-09 12:42:31,050] multiqc [DEBUG ] No samples found: homer [2021-07-09 12:42:31,054] multiqc [DEBUG ] No samples found: macs2 [2021-07-09 12:42:31,058] multiqc [DEBUG ] No samples found: theta2 [2021-07-09 12:42:31,062] multiqc [DEBUG ] No samples found: snpeff [2021-07-09 12:42:31,068] multiqc [DEBUG ] No samples found: gatk [2021-07-09 12:42:31,072] multiqc [DEBUG ] No samples found: htseq [2021-07-09 12:42:31,077] multiqc [DEBUG ] No samples found: bcftools [2021-07-09 12:42:31,081] multiqc [DEBUG ] No samples found: featureCounts [2021-07-09 12:42:31,086] multiqc [DEBUG ] No samples found: fgbio [2021-07-09 12:42:31,099] multiqc [DEBUG ] No samples found: dragen [2021-07-09 12:42:31,103] multiqc [DEBUG ] No samples found: dedup [2021-07-09 12:42:31,107] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-09 12:42:31,126] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-09 12:42:31,130] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-09 12:42:31,133] multiqc [DEBUG ] No samples found: picard [2021-07-09 12:42:31,137] multiqc [DEBUG ] No samples found: prokka [2021-07-09 12:42:31,141] multiqc [DEBUG ] No samples found: samblaster [2021-07-09 12:42:31,148] multiqc [DEBUG ] No samples found: samtools [2021-07-09 12:42:31,152] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-09 12:42:31,157] multiqc [DEBUG ] No samples found: bamtools [2021-07-09 12:42:31,160] multiqc [DEBUG ] No samples found: jellyfish [2021-07-09 12:42:31,168] multiqc [DEBUG ] No samples found: vcftools [2021-07-09 12:42:31,174] multiqc [DEBUG ] No samples found: longranger [2021-07-09 12:42:31,180] multiqc [DEBUG ] No samples found: stacks [2021-07-09 12:42:31,184] multiqc [DEBUG ] No samples found: varscan2 [2021-07-09 12:42:31,198] multiqc [DEBUG ] No samples found: bbmap [2021-07-09 12:42:31,202] multiqc [DEBUG ] No samples found: bismark [2021-07-09 12:42:31,208] multiqc [DEBUG ] No samples found: biscuit [2021-07-09 12:42:31,213] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-09 12:42:31,217] multiqc [DEBUG ] No samples found: hicup [2021-07-09 12:42:31,222] multiqc [DEBUG ] No samples found: hicpro [2021-07-09 12:42:31,226] multiqc [DEBUG ] No samples found: salmon [2021-07-09 12:42:31,230] multiqc [DEBUG ] No samples found: kallisto [2021-07-09 12:42:31,235] multiqc [DEBUG ] No samples found: slamdunk [2021-07-09 12:42:31,239] multiqc [DEBUG ] No samples found: star [2021-07-09 12:42:31,243] multiqc [DEBUG ] No samples found: hisat2 [2021-07-09 12:42:31,247] multiqc [DEBUG ] No samples found: tophat [2021-07-09 12:42:31,253] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-09 12:42:31,259] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-09 12:42:31,263] multiqc [DEBUG ] No samples found: snpsplit [2021-07-09 12:42:31,268] multiqc [DEBUG ] No samples found: kat [2021-07-09 12:42:31,272] multiqc [DEBUG ] No samples found: leehom [2021-07-09 12:42:31,276] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-09 12:42:31,280] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-09 12:42:31,284] multiqc [DEBUG ] No samples found: cutadapt [2021-07-09 12:42:31,288] multiqc [DEBUG ] No samples found: flexbar [2021-07-09 12:42:31,292] multiqc [DEBUG ] No samples found: kaiju [2021-07-09 12:42:31,296] multiqc [DEBUG ] No samples found: kraken [2021-07-09 12:42:31,300] multiqc [DEBUG ] No samples found: malt [2021-07-09 12:42:31,304] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-09 12:42:31,309] multiqc [DEBUG ] No samples found: sickle [2021-07-09 12:42:31,313] multiqc [DEBUG ] No samples found: skewer [2021-07-09 12:42:31,316] multiqc [DEBUG ] No samples found: sortmerna [2021-07-09 12:42:31,320] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-09 12:42:31,324] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-09 12:42:31,328] multiqc [DEBUG ] No samples found: afterqc [2021-07-09 12:42:31,332] multiqc [DEBUG ] No samples found: fastp [2021-07-09 12:42:32,312] multiqc.modules.fastqc.fastqc [INFO ] Found 42 reports [2021-07-09 12:42:32,647] multiqc [DEBUG ] No samples found: pycoqc [2021-07-09 12:42:32,651] multiqc [DEBUG ] No samples found: minionqc [2021-07-09 12:42:32,656] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-09 12:42:32,660] multiqc [DEBUG ] No samples found: clusterflow [2021-07-09 12:42:32,664] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-09 12:42:32,669] multiqc [DEBUG ] No samples found: interop [2021-07-09 12:42:32,673] multiqc [DEBUG ] No samples found: ivar [2021-07-09 12:42:32,677] multiqc [DEBUG ] No samples found: flash [2021-07-09 12:42:32,684] multiqc [DEBUG ] No samples found: seqyclean [2021-07-09 12:42:32,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-09 12:42:32,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-09 12:42:32,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-09 12:42:32,684] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-09 12:42:32,733] multiqc [INFO ] Compressing plot data [2021-07-09 12:42:33,405] multiqc [INFO ] Report : multiqc_report.html [2021-07-09 12:42:33,405] multiqc [INFO ] Data : multiqc_data [2021-07-09 12:42:33,405] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8523027/tmppqq6wkv6/multiqc_data' to '/scratch/gencore/logs/html/HTHCVAFX2/merged/multiqc_data' [2021-07-09 12:42:33,535] multiqc [INFO ] MultiQC complete