[2022-06-03 07:44:39,265] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-03 07:44:39,265] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-03 07:44:39,265] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-03 07:44:39,266] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-03 07:44:39,266] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-03 07:44:39,267] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLMCVAFX3/merged [2022-06-03 07:44:39,738] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-03 07:44:39,738] multiqc [INFO ] This is MultiQC v1.9 [2022-06-03 07:44:39,738] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLMCVAFX3/merged [2022-06-03 07:44:39,738] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLMCVAFX3/merged [2022-06-03 07:44:39,738] multiqc [INFO ] Template : default [2022-06-03 07:44:39,738] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-03 07:44:39,738] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLMCVAFX3/merged [2022-06-03 07:44:39,738] 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 [2022-06-03 07:44:39,738] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20486911/tmpy4yid8i2 [2022-06-03 07:44:39,849] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_1_fastqc.html [2022-06-03 07:44:39,851] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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undetermined_barcodes.txt [2022-06-03 07:44:40,311] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_3_fastqc.html [2022-06-03 07:44:40,312] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_3_fastqc.html [2022-06-03 07:44:40,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_11_fastqc.html [2022-06-03 07:44:40,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_11_fastqc.html [2022-06-03 07:44:40,393] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_6_fastqc.html [2022-06-03 07:44:40,394] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_6_fastqc.html [2022-06-03 07:44:40,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_1_fastqc.html [2022-06-03 07:44:40,437] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_1_fastqc.html [2022-06-03 07:44:40,479] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_4_fastqc.html [2022-06-03 07:44:40,481] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_4_fastqc.html [2022-06-03 07:44:40,522] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_5_fastqc.html [2022-06-03 07:44:40,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_5_fastqc.html [2022-06-03 07:44:40,566] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_2_fastqc.html [2022-06-03 07:44:40,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_2_fastqc.html [2022-06-03 07:44:40,607] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_13_fastqc.html [2022-06-03 07:44:40,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_13_fastqc.html [2022-06-03 07:44:40,647] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_7_fastqc.html [2022-06-03 07:44:40,649] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_7_fastqc.html [2022-06-03 07:44:40,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_undetermined_fastqc.html [2022-06-03 07:44:40,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_undetermined_fastqc.html [2022-06-03 07:44:40,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_5_fastqc.html [2022-06-03 07:44:40,731] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_5_fastqc.html [2022-06-03 07:44:40,773] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_9_fastqc.html [2022-06-03 07:44:40,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_9_fastqc.html [2022-06-03 07:44:40,814] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_10_fastqc.html [2022-06-03 07:44:40,816] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_10_fastqc.html [2022-06-03 07:44:40,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_8_fastqc.html [2022-06-03 07:44:40,859] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_8_fastqc.html [2022-06-03 07:44:40,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_6_fastqc.html [2022-06-03 07:44:40,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_6_fastqc.html [2022-06-03 07:44:40,944] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_12_fastqc.html [2022-06-03 07:44:40,946] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_12_fastqc.html [2022-06-03 07:44:40,985] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_11_fastqc.html [2022-06-03 07:44:40,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_11_fastqc.html [2022-06-03 07:44:41,027] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_13_fastqc.html [2022-06-03 07:44:41,028] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_13_fastqc.html [2022-06-03 07:44:41,069] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_4_fastqc.html [2022-06-03 07:44:41,070] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_4_fastqc.html [2022-06-03 07:44:41,111] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_2_fastqc.html [2022-06-03 07:44:41,113] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_2_fastqc.html [2022-06-03 07:44:41,153] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_undetermined_fastqc.html [2022-06-03 07:44:41,155] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_undetermined_fastqc.html [2022-06-03 07:44:41,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_8_fastqc.html [2022-06-03 07:44:41,197] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_8_fastqc.html [2022-06-03 07:44:41,236] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_7_fastqc.html [2022-06-03 07:44:41,238] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_7_fastqc.html [2022-06-03 07:44:41,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_9_fastqc.html [2022-06-03 07:44:41,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n02_dad3a_9_fastqc.html [2022-06-03 07:44:41,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_10_fastqc.html [2022-06-03 07:44:41,324] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLMCVAFX3_n01_dad3a_10_fastqc.html [2022-06-03 07:44:41,886] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-03 07:44:41,887] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-03 07:44:41,903] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-03 07:44:41,910] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 14 samples (table) [2022-06-03 07:44:41,911] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-03 07:44:41,919] multiqc [DEBUG ] No samples found: conpair [2022-06-03 07:44:41,925] multiqc [DEBUG ] No samples found: peddy [2022-06-03 07:44:41,931] multiqc [DEBUG ] No samples found: somalier [2022-06-03 07:44:41,937] multiqc [DEBUG ] No samples found: methylQA [2022-06-03 07:44:41,948] multiqc [DEBUG ] No samples found: mosdepth [2022-06-03 07:44:41,953] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-03 07:44:41,957] multiqc [DEBUG ] No samples found: qualimap [2022-06-03 07:44:41,963] multiqc [DEBUG ] No samples found: preseq [2022-06-03 07:44:41,968] multiqc [DEBUG ] No samples found: quast [2022-06-03 07:44:41,975] multiqc [DEBUG ] No samples found: qorts [2022-06-03 07:44:41,981] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-03 07:44:41,987] multiqc [DEBUG ] No samples found: rockhopper [2022-06-03 07:44:41,994] multiqc [DEBUG ] No samples found: rsem [2022-06-03 07:44:42,009] multiqc [DEBUG ] No samples found: rseqc [2022-06-03 07:44:42,016] multiqc [DEBUG ] No samples found: busco [2022-06-03 07:44:42,023] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-03 07:44:42,029] multiqc [DEBUG ] No samples found: disambiguate [2022-06-03 07:44:42,034] multiqc [DEBUG ] No samples found: supernova [2022-06-03 07:44:42,064] multiqc [DEBUG ] No samples found: deeptools [2022-06-03 07:44:42,069] multiqc [DEBUG ] No samples found: sargasso [2022-06-03 07:44:42,075] multiqc [DEBUG ] No samples found: verifybamid [2022-06-03 07:44:42,080] multiqc [DEBUG ] No samples found: mirtrace [2022-06-03 07:44:42,087] multiqc [DEBUG ] No samples found: happy [2022-06-03 07:44:42,094] multiqc [DEBUG ] No samples found: mirtop [2022-06-03 07:44:42,102] multiqc [DEBUG ] No samples found: homer [2022-06-03 07:44:42,107] multiqc [DEBUG ] No samples found: macs2 [2022-06-03 07:44:42,114] multiqc [DEBUG ] No samples found: theta2 [2022-06-03 07:44:42,119] multiqc [DEBUG ] No samples found: snpeff [2022-06-03 07:44:42,127] multiqc [DEBUG ] No samples found: gatk [2022-06-03 07:44:42,132] multiqc [DEBUG ] No samples found: htseq [2022-06-03 07:44:42,139] multiqc [DEBUG ] No samples found: bcftools [2022-06-03 07:44:42,146] multiqc [DEBUG ] No samples found: featureCounts [2022-06-03 07:44:42,154] multiqc [DEBUG ] No samples found: fgbio [2022-06-03 07:44:42,173] multiqc [DEBUG ] No samples found: dragen [2022-06-03 07:44:42,178] multiqc [DEBUG ] No samples found: dedup [2022-06-03 07:44:42,186] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-03 07:44:42,211] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-03 07:44:42,218] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-03 07:44:42,220] multiqc [DEBUG ] No samples found: picard [2022-06-03 07:44:42,226] multiqc [DEBUG ] No samples found: prokka [2022-06-03 07:44:42,233] multiqc [DEBUG ] No samples found: samblaster [2022-06-03 07:44:42,244] multiqc [DEBUG ] No samples found: samtools [2022-06-03 07:44:42,249] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-03 07:44:42,255] multiqc [DEBUG ] No samples found: bamtools [2022-06-03 07:44:42,263] multiqc [DEBUG ] No samples found: jellyfish [2022-06-03 07:44:42,273] multiqc [DEBUG ] No samples found: vcftools [2022-06-03 07:44:42,278] multiqc [DEBUG ] No samples found: longranger [2022-06-03 07:44:42,284] multiqc [DEBUG ] No samples found: stacks [2022-06-03 07:44:42,290] multiqc [DEBUG ] No samples found: varscan2 [2022-06-03 07:44:42,309] multiqc [DEBUG ] No samples found: bbmap [2022-06-03 07:44:42,314] multiqc [DEBUG ] No samples found: bismark [2022-06-03 07:44:42,320] multiqc [DEBUG ] No samples found: biscuit [2022-06-03 07:44:42,326] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-03 07:44:42,333] multiqc [DEBUG ] No samples found: hicup [2022-06-03 07:44:42,338] multiqc [DEBUG ] No samples found: hicpro [2022-06-03 07:44:42,344] multiqc [DEBUG ] No samples found: salmon [2022-06-03 07:44:42,349] multiqc [DEBUG ] No samples found: kallisto [2022-06-03 07:44:42,357] multiqc [DEBUG ] No samples found: slamdunk [2022-06-03 07:44:42,364] multiqc [DEBUG ] No samples found: star [2022-06-03 07:44:42,370] multiqc [DEBUG ] No samples found: hisat2 [2022-06-03 07:44:42,375] multiqc [DEBUG ] No samples found: tophat [2022-06-03 07:44:42,380] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-03 07:44:42,387] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-03 07:44:42,393] multiqc [DEBUG ] No samples found: snpsplit [2022-06-03 07:44:42,398] multiqc [DEBUG ] No samples found: kat [2022-06-03 07:44:42,403] multiqc [DEBUG ] No samples found: leehom [2022-06-03 07:44:42,408] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-03 07:44:42,414] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-03 07:44:42,419] multiqc [DEBUG ] No samples found: cutadapt [2022-06-03 07:44:42,424] multiqc [DEBUG ] No samples found: flexbar [2022-06-03 07:44:42,430] multiqc [DEBUG ] No samples found: kaiju [2022-06-03 07:44:42,436] multiqc [DEBUG ] No samples found: kraken [2022-06-03 07:44:42,442] multiqc [DEBUG ] No samples found: malt [2022-06-03 07:44:42,448] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-03 07:44:42,455] multiqc [DEBUG ] No samples found: sickle [2022-06-03 07:44:42,461] multiqc [DEBUG ] No samples found: skewer [2022-06-03 07:44:42,466] multiqc [DEBUG ] No samples found: sortmerna [2022-06-03 07:44:42,473] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-03 07:44:42,481] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-03 07:44:42,487] multiqc [DEBUG ] No samples found: afterqc [2022-06-03 07:44:42,493] multiqc [DEBUG ] No samples found: fastp [2022-06-03 07:44:43,165] multiqc.modules.fastqc.fastqc [INFO ] Found 28 reports [2022-06-03 07:44:43,743] multiqc [DEBUG ] No samples found: pycoqc [2022-06-03 07:44:43,748] multiqc [DEBUG ] No samples found: minionqc [2022-06-03 07:44:43,753] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-03 07:44:43,758] multiqc [DEBUG ] No samples found: clusterflow [2022-06-03 07:44:43,768] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-03 07:44:43,775] multiqc [DEBUG ] No samples found: interop [2022-06-03 07:44:43,782] multiqc [DEBUG ] No samples found: ivar [2022-06-03 07:44:43,788] multiqc [DEBUG ] No samples found: flash [2022-06-03 07:44:43,793] multiqc [DEBUG ] No samples found: seqyclean [2022-06-03 07:44:43,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-03 07:44:43,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-03 07:44:43,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-03 07:44:43,793] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-03 07:44:43,826] multiqc [INFO ] Compressing plot data [2022-06-03 07:44:44,332] multiqc [INFO ] Report : multiqc_report.html [2022-06-03 07:44:44,332] multiqc [INFO ] Data : multiqc_data [2022-06-03 07:44:44,332] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20486911/tmpy4yid8i2/multiqc_data' to '/scratch/gencore/logs/html/HLMCVAFX3/merged/multiqc_data' [2022-06-03 07:44:44,465] multiqc [INFO ] MultiQC complete