[2022-03-16 22:46:46,827] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-03-16 22:46:46,828] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-03-16 22:46:46,828] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-03-16 22:46:46,829] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-03-16 22:46:46,829] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-03-16 22:46:46,829] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H75JHBGXL/merged [2022-03-16 22:46:47,308] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-03-16 22:46:47,309] multiqc [INFO ] This is MultiQC v1.9 [2022-03-16 22:46:47,309] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H75JHBGXL/merged [2022-03-16 22:46:47,309] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H75JHBGXL/merged [2022-03-16 22:46:47,309] multiqc [INFO ] Template : default [2022-03-16 22:46:47,309] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-03-16 22:46:47,309] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H75JHBGXL/merged [2022-03-16 22:46:47,309] 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 [2022-03-16 22:46:47,309] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-16092349/tmpragrzilg [2022-03-16 22:46:47,416] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS34_fastqc.html [2022-03-16 22:46:47,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-03-16 22:46:50,530] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_new5900Mar2_fastqc.html [2022-03-16 22:46:50,532] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_new5900Mar2_fastqc.html [2022-03-16 22:46:50,580] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS14_fastqc.html [2022-03-16 22:46:50,582] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS14_fastqc.html [2022-03-16 22:46:50,630] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS24_fastqc.html [2022-03-16 22:46:50,632] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS24_fastqc.html [2022-03-16 22:46:50,680] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS48_fastqc.html [2022-03-16 22:46:50,682] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS48_fastqc.html [2022-03-16 22:46:50,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS43_fastqc.html [2022-03-16 22:46:50,731] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS43_fastqc.html [2022-03-16 22:46:50,780] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS27_fastqc.html [2022-03-16 22:46:50,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS27_fastqc.html [2022-03-16 22:46:50,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_new5890Mar2_fastqc.html [2022-03-16 22:46:50,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_new5890Mar2_fastqc.html [2022-03-16 22:46:50,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS33_fastqc.html [2022-03-16 22:46:50,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS33_fastqc.html [2022-03-16 22:46:50,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS13_fastqc.html [2022-03-16 22:46:50,931] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS13_fastqc.html [2022-03-16 22:46:50,976] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_new4692Mar2_fastqc.html [2022-03-16 22:46:50,978] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_new4692Mar2_fastqc.html [2022-03-16 22:46:51,025] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS5_fastqc.html [2022-03-16 22:46:51,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H75JHBGXL_n01_newRS5_fastqc.html [2022-03-16 22:46:51,523] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-16 22:46:51,525] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-03-16 22:46:51,569] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 72 samples (table) [2022-03-16 22:46:51,579] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-03-16 22:46:51,580] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-03-16 22:46:51,585] multiqc [DEBUG ] No samples found: conpair [2022-03-16 22:46:51,590] multiqc [DEBUG ] No samples found: peddy [2022-03-16 22:46:51,595] multiqc [DEBUG ] No samples found: somalier [2022-03-16 22:46:51,600] multiqc [DEBUG ] No samples found: methylQA [2022-03-16 22:46:51,608] multiqc [DEBUG ] No samples found: mosdepth [2022-03-16 22:46:51,613] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-03-16 22:46:51,616] multiqc [DEBUG ] No samples found: qualimap [2022-03-16 22:46:51,621] multiqc [DEBUG ] No samples found: preseq [2022-03-16 22:46:51,626] multiqc [DEBUG ] No samples found: quast [2022-03-16 22:46:51,631] multiqc [DEBUG ] No samples found: qorts [2022-03-16 22:46:51,637] multiqc [DEBUG ] No samples found: rna_seqc [2022-03-16 22:46:51,642] multiqc [DEBUG ] No samples found: rockhopper [2022-03-16 22:46:51,647] multiqc [DEBUG ] No samples found: rsem [2022-03-16 22:46:51,661] multiqc [DEBUG ] No samples found: rseqc [2022-03-16 22:46:51,665] multiqc [DEBUG ] No samples found: busco [2022-03-16 22:46:51,670] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-03-16 22:46:51,675] multiqc [DEBUG ] No samples found: disambiguate [2022-03-16 22:46:51,680] multiqc [DEBUG ] No samples found: supernova [2022-03-16 22:46:51,694] multiqc [DEBUG ] No samples found: deeptools [2022-03-16 22:46:51,699] multiqc [DEBUG ] No samples found: sargasso [2022-03-16 22:46:51,704] multiqc [DEBUG ] No samples found: verifybamid [2022-03-16 22:46:51,709] multiqc [DEBUG ] No samples found: mirtrace [2022-03-16 22:46:51,714] multiqc [DEBUG ] No samples found: happy [2022-03-16 22:46:51,719] multiqc [DEBUG ] No samples found: mirtop [2022-03-16 22:46:51,725] multiqc [DEBUG ] No samples found: homer [2022-03-16 22:46:51,730] multiqc [DEBUG ] No samples found: macs2 [2022-03-16 22:46:51,735] multiqc [DEBUG ] No samples found: theta2 [2022-03-16 22:46:51,740] multiqc [DEBUG ] No samples found: snpeff [2022-03-16 22:46:51,747] multiqc [DEBUG ] No samples found: gatk [2022-03-16 22:46:51,751] multiqc [DEBUG ] No samples found: htseq [2022-03-16 22:46:51,757] multiqc [DEBUG ] No samples found: bcftools [2022-03-16 22:46:51,762] multiqc [DEBUG ] No samples found: featureCounts [2022-03-16 22:46:51,768] multiqc [DEBUG ] No samples found: fgbio [2022-03-16 22:46:51,782] multiqc [DEBUG ] No samples found: dragen [2022-03-16 22:46:51,787] multiqc [DEBUG ] No samples found: dedup [2022-03-16 22:46:51,792] multiqc [DEBUG ] No samples found: damageprofiler [2022-03-16 22:46:51,815] multiqc [DEBUG ] No samples found: biobambam2 [2022-03-16 22:46:51,819] multiqc [DEBUG ] No samples found: mtnucratio [2022-03-16 22:46:51,822] multiqc [DEBUG ] No samples found: picard [2022-03-16 22:46:51,826] multiqc [DEBUG ] No samples found: prokka [2022-03-16 22:46:51,831] multiqc [DEBUG ] No samples found: samblaster [2022-03-16 22:46:51,841] multiqc [DEBUG ] No samples found: samtools [2022-03-16 22:46:51,846] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-03-16 22:46:51,851] multiqc [DEBUG ] No samples found: bamtools [2022-03-16 22:46:51,855] multiqc [DEBUG ] No samples found: jellyfish [2022-03-16 22:46:51,864] multiqc [DEBUG ] No samples found: vcftools [2022-03-16 22:46:51,870] multiqc [DEBUG ] No samples found: longranger [2022-03-16 22:46:51,875] multiqc [DEBUG ] No samples found: stacks [2022-03-16 22:46:51,880] multiqc [DEBUG ] No samples found: varscan2 [2022-03-16 22:46:51,894] multiqc [DEBUG ] No samples found: bbmap [2022-03-16 22:46:51,899] multiqc [DEBUG ] No samples found: bismark [2022-03-16 22:46:51,905] multiqc [DEBUG ] No samples found: biscuit [2022-03-16 22:46:51,910] multiqc [DEBUG ] No samples found: hicexplorer [2022-03-16 22:46:51,914] multiqc [DEBUG ] No samples found: hicup [2022-03-16 22:46:51,919] multiqc [DEBUG ] No samples found: hicpro [2022-03-16 22:46:51,924] multiqc [DEBUG ] No samples found: salmon [2022-03-16 22:46:51,929] multiqc [DEBUG ] No samples found: kallisto [2022-03-16 22:46:51,934] multiqc [DEBUG ] No samples found: slamdunk [2022-03-16 22:46:51,939] multiqc [DEBUG ] No samples found: star [2022-03-16 22:46:51,944] multiqc [DEBUG ] No samples found: hisat2 [2022-03-16 22:46:51,949] multiqc [DEBUG ] No samples found: tophat [2022-03-16 22:46:51,953] multiqc [DEBUG ] No samples found: bowtie2 [2022-03-16 22:46:51,958] multiqc [DEBUG ] No samples found: bowtie1 [2022-03-16 22:46:51,963] multiqc [DEBUG ] No samples found: snpsplit [2022-03-16 22:46:51,968] multiqc [DEBUG ] No samples found: kat [2022-03-16 22:46:51,972] multiqc [DEBUG ] No samples found: leehom [2022-03-16 22:46:51,976] multiqc [DEBUG ] No samples found: adapterRemoval [2022-03-16 22:46:51,981] multiqc [DEBUG ] No samples found: clipandmerge [2022-03-16 22:46:51,985] multiqc [DEBUG ] No samples found: cutadapt [2022-03-16 22:46:51,990] multiqc [DEBUG ] No samples found: flexbar [2022-03-16 22:46:51,994] multiqc [DEBUG ] No samples found: kaiju [2022-03-16 22:46:51,999] multiqc [DEBUG ] No samples found: kraken [2022-03-16 22:46:52,004] multiqc [DEBUG ] No samples found: malt [2022-03-16 22:46:52,009] multiqc [DEBUG ] No samples found: trimmomatic [2022-03-16 22:46:52,013] multiqc [DEBUG ] No samples found: sickle [2022-03-16 22:46:52,018] multiqc [DEBUG ] No samples found: skewer [2022-03-16 22:46:52,022] multiqc [DEBUG ] No samples found: sortmerna [2022-03-16 22:46:52,026] multiqc [DEBUG ] No samples found: biobloomtools [2022-03-16 22:46:52,032] multiqc [DEBUG ] No samples found: fastq_screen [2022-03-16 22:46:52,036] multiqc [DEBUG ] No samples found: afterqc [2022-03-16 22:46:52,041] multiqc [DEBUG ] No samples found: fastp [2022-03-16 22:46:57,155] multiqc.modules.fastqc.fastqc [INFO ] Found 72 reports [2022-03-16 22:46:58,614] multiqc [DEBUG ] No samples found: pycoqc [2022-03-16 22:46:58,619] multiqc [DEBUG ] No samples found: minionqc [2022-03-16 22:46:58,624] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-03-16 22:46:58,629] multiqc [DEBUG ] No samples found: clusterflow [2022-03-16 22:46:58,634] multiqc [DEBUG ] No samples found: bcl2fastq [2022-03-16 22:46:58,640] multiqc [DEBUG ] No samples found: interop [2022-03-16 22:46:58,645] multiqc [DEBUG ] No samples found: ivar [2022-03-16 22:46:58,649] multiqc [DEBUG ] No samples found: flash [2022-03-16 22:46:58,654] multiqc [DEBUG ] No samples found: seqyclean [2022-03-16 22:46:58,655] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-03-16 22:46:58,655] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-03-16 22:46:58,655] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-03-16 22:46:58,655] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-03-16 22:46:58,743] multiqc [INFO ] Compressing plot data [2022-03-16 22:47:00,028] multiqc [INFO ] Report : multiqc_report.html [2022-03-16 22:47:00,028] multiqc [INFO ] Data : multiqc_data [2022-03-16 22:47:00,028] multiqc [DEBUG ] Moving data file from '/state/partition1/job-16092349/tmpragrzilg/multiqc_data' to '/scratch/gencore/logs/html/H75JHBGXL/merged/multiqc_data' [2022-03-16 22:47:00,173] multiqc [INFO ] MultiQC complete