[2022-09-06 19:12:22,412] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-09-06 19:12:22,412] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-09-06 19:12:22,412] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-09-06 19:12:22,413] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-09-06 19:12:22,413] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-09-06 19:12:22,414] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGGTNBGXM/merged [2022-09-06 19:12:22,897] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-09-06 19:12:22,898] multiqc [INFO ] This is MultiQC v1.9 [2022-09-06 19:12:22,898] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGGTNBGXM/merged [2022-09-06 19:12:22,898] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGGTNBGXM/merged [2022-09-06 19:12:22,898] multiqc [INFO ] Template : default [2022-09-06 19:12:22,898] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-09-06 19:12:22,898] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGGTNBGXM/merged [2022-09-06 19:12:22,898] 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 [2022-09-06 19:12:22,898] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-24556304/tmpb1qcerrv [2022-09-06 19:12:23,020] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO13_2_fastqc.html [2022-09-06 19:12:23,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO13_2_fastqc.html [2022-09-06 19:12:23,067] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-06 19:12:23,069] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-09-06 19:12:23,164] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK131_fastqc.html [2022-09-06 19:12:23,166] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK131_fastqc.html [2022-09-06 19:12:23,210] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK130_fastqc.html [2022-09-06 19:12:23,212] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK130_fastqc.html [2022-09-06 19:12:23,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK127_fastqc.html [2022-09-06 19:12:23,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK127_fastqc.html [2022-09-06 19:12:23,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK125_fastqc.html [2022-09-06 19:12:23,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK125_fastqc.html [2022-09-06 19:12:23,351] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK132_fastqc.html [2022-09-06 19:12:23,353] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK132_fastqc.html [2022-09-06 19:12:23,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_undetermined_fastqc.html [2022-09-06 19:12:23,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_undetermined_fastqc.html [2022-09-06 19:12:23,440] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO28_fastqc.html [2022-09-06 19:12:23,442] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO28_fastqc.html [2022-09-06 19:12:23,483] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO30_fastqc.html [2022-09-06 19:12:23,485] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO30_fastqc.html [2022-09-06 19:12:23,529] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO15_2_fastqc.html [2022-09-06 19:12:23,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO15_2_fastqc.html [2022-09-06 19:12:23,574] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK133_fastqc.html [2022-09-06 19:12:23,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK133_fastqc.html [2022-09-06 19:12:23,619] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO12_2_fastqc.html [2022-09-06 19:12:23,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO12_2_fastqc.html [2022-09-06 19:12:23,662] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK129_fastqc.html [2022-09-06 19:12:23,664] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK129_fastqc.html [2022-09-06 19:12:23,708] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO21_2_fastqc.html [2022-09-06 19:12:23,710] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO21_2_fastqc.html [2022-09-06 19:12:23,750] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO32_fastqc.html [2022-09-06 19:12:23,752] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO32_fastqc.html [2022-09-06 19:12:23,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO29_fastqc.html [2022-09-06 19:12:23,794] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO29_fastqc.html [2022-09-06 19:12:23,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK126_fastqc.html [2022-09-06 19:12:23,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK126_fastqc.html [2022-09-06 19:12:23,880] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK134_fastqc.html [2022-09-06 19:12:23,882] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK134_fastqc.html [2022-09-06 19:12:23,927] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK136_fastqc.html [2022-09-06 19:12:23,929] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK136_fastqc.html [2022-09-06 19:12:23,972] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK135_fastqc.html [2022-09-06 19:12:23,974] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK135_fastqc.html [2022-09-06 19:12:24,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO31_fastqc.html [2022-09-06 19:12:24,020] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO31_fastqc.html [2022-09-06 19:12:24,067] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO14_2_fastqc.html [2022-09-06 19:12:24,069] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_DO14_2_fastqc.html [2022-09-06 19:12:24,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK128_fastqc.html [2022-09-06 19:12:24,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGGTNBGXM_n01_JK128_fastqc.html [2022-09-06 19:12:24,479] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-06 19:12:24,481] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-09-06 19:12:24,499] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2022-09-06 19:12:24,500] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-09-06 19:12:24,510] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-09-06 19:12:24,515] multiqc [DEBUG ] No samples found: conpair [2022-09-06 19:12:24,520] multiqc [DEBUG ] No samples found: peddy [2022-09-06 19:12:24,529] multiqc [DEBUG ] No samples found: somalier [2022-09-06 19:12:24,534] multiqc [DEBUG ] No samples found: methylQA [2022-09-06 19:12:24,543] multiqc [DEBUG ] No samples found: mosdepth [2022-09-06 19:12:24,548] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-09-06 19:12:24,553] multiqc [DEBUG ] No samples found: qualimap [2022-09-06 19:12:24,558] multiqc [DEBUG ] No samples found: preseq [2022-09-06 19:12:24,563] multiqc [DEBUG ] No samples found: quast [2022-09-06 19:12:24,569] multiqc [DEBUG ] No samples found: qorts [2022-09-06 19:12:24,574] multiqc [DEBUG ] No samples found: rna_seqc [2022-09-06 19:12:24,579] multiqc [DEBUG ] No samples found: rockhopper [2022-09-06 19:12:24,584] multiqc [DEBUG ] No samples found: rsem [2022-09-06 19:12:24,598] multiqc [DEBUG ] No samples found: rseqc [2022-09-06 19:12:24,602] multiqc [DEBUG ] No samples found: busco [2022-09-06 19:12:24,607] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-09-06 19:12:24,612] multiqc [DEBUG ] No samples found: disambiguate [2022-09-06 19:12:24,617] multiqc [DEBUG ] No samples found: supernova [2022-09-06 19:12:24,634] multiqc [DEBUG ] No samples found: deeptools [2022-09-06 19:12:24,638] multiqc [DEBUG ] No samples found: sargasso [2022-09-06 19:12:24,643] multiqc [DEBUG ] No samples found: verifybamid [2022-09-06 19:12:24,648] multiqc [DEBUG ] No samples found: mirtrace [2022-09-06 19:12:24,652] multiqc [DEBUG ] No samples found: happy [2022-09-06 19:12:24,657] multiqc [DEBUG ] No samples found: mirtop [2022-09-06 19:12:24,664] multiqc [DEBUG ] No samples found: homer [2022-09-06 19:12:24,668] multiqc [DEBUG ] No samples found: macs2 [2022-09-06 19:12:24,672] multiqc [DEBUG ] No samples found: theta2 [2022-09-06 19:12:24,677] multiqc [DEBUG ] No samples found: snpeff [2022-09-06 19:12:24,684] multiqc [DEBUG ] No samples found: gatk [2022-09-06 19:12:24,688] multiqc [DEBUG ] No samples found: htseq [2022-09-06 19:12:24,693] multiqc [DEBUG ] No samples found: bcftools [2022-09-06 19:12:24,698] multiqc [DEBUG ] No samples found: featureCounts [2022-09-06 19:12:24,704] multiqc [DEBUG ] No samples found: fgbio [2022-09-06 19:12:24,721] multiqc [DEBUG ] No samples found: dragen [2022-09-06 19:12:24,726] multiqc [DEBUG ] No samples found: dedup [2022-09-06 19:12:24,731] multiqc [DEBUG ] No samples found: damageprofiler [2022-09-06 19:12:24,758] multiqc [DEBUG ] No samples found: biobambam2 [2022-09-06 19:12:24,762] multiqc [DEBUG ] No samples found: mtnucratio [2022-09-06 19:12:24,765] multiqc [DEBUG ] No samples found: picard [2022-09-06 19:12:24,769] multiqc [DEBUG ] No samples found: prokka [2022-09-06 19:12:24,773] multiqc [DEBUG ] No samples found: samblaster [2022-09-06 19:12:24,786] multiqc [DEBUG ] No samples found: samtools [2022-09-06 19:12:24,791] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-09-06 19:12:24,796] multiqc [DEBUG ] No samples found: bamtools [2022-09-06 19:12:24,800] multiqc [DEBUG ] No samples found: jellyfish [2022-09-06 19:12:24,810] multiqc [DEBUG ] No samples found: vcftools [2022-09-06 19:12:24,815] multiqc [DEBUG ] No samples found: longranger [2022-09-06 19:12:24,820] multiqc [DEBUG ] No samples found: stacks [2022-09-06 19:12:24,825] multiqc [DEBUG ] No samples found: varscan2 [2022-09-06 19:12:24,840] multiqc [DEBUG ] No samples found: bbmap [2022-09-06 19:12:24,845] multiqc [DEBUG ] No samples found: bismark [2022-09-06 19:12:24,850] multiqc [DEBUG ] No samples found: biscuit [2022-09-06 19:12:24,856] multiqc [DEBUG ] No samples found: hicexplorer [2022-09-06 19:12:24,860] multiqc [DEBUG ] No samples found: hicup [2022-09-06 19:12:24,865] multiqc [DEBUG ] No samples found: hicpro [2022-09-06 19:12:24,869] multiqc [DEBUG ] No samples found: salmon [2022-09-06 19:12:24,874] multiqc [DEBUG ] No samples found: kallisto [2022-09-06 19:12:24,879] multiqc [DEBUG ] No samples found: slamdunk [2022-09-06 19:12:24,883] multiqc [DEBUG ] No samples found: star [2022-09-06 19:12:24,888] multiqc [DEBUG ] No samples found: hisat2 [2022-09-06 19:12:24,893] multiqc [DEBUG ] No samples found: tophat [2022-09-06 19:12:24,897] multiqc [DEBUG ] No samples found: bowtie2 [2022-09-06 19:12:24,901] multiqc [DEBUG ] No samples found: bowtie1 [2022-09-06 19:12:24,906] multiqc [DEBUG ] No samples found: snpsplit [2022-09-06 19:12:24,910] multiqc [DEBUG ] No samples found: kat [2022-09-06 19:12:24,914] multiqc [DEBUG ] No samples found: leehom [2022-09-06 19:12:24,919] multiqc [DEBUG ] No samples found: adapterRemoval [2022-09-06 19:12:24,923] multiqc [DEBUG ] No samples found: clipandmerge [2022-09-06 19:12:24,928] multiqc [DEBUG ] No samples found: cutadapt [2022-09-06 19:12:24,932] multiqc [DEBUG ] No samples found: flexbar [2022-09-06 19:12:24,937] multiqc [DEBUG ] No samples found: kaiju [2022-09-06 19:12:24,941] multiqc [DEBUG ] No samples found: kraken [2022-09-06 19:12:24,946] multiqc [DEBUG ] No samples found: malt [2022-09-06 19:12:24,950] multiqc [DEBUG ] No samples found: trimmomatic [2022-09-06 19:12:24,955] multiqc [DEBUG ] No samples found: sickle [2022-09-06 19:12:24,959] multiqc [DEBUG ] No samples found: skewer [2022-09-06 19:12:24,963] multiqc [DEBUG ] No samples found: sortmerna [2022-09-06 19:12:24,967] multiqc [DEBUG ] No samples found: biobloomtools [2022-09-06 19:12:24,972] multiqc [DEBUG ] No samples found: fastq_screen [2022-09-06 19:12:24,977] multiqc [DEBUG ] No samples found: afterqc [2022-09-06 19:12:24,982] multiqc [DEBUG ] No samples found: fastp [2022-09-06 19:12:26,573] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2022-09-06 19:12:27,099] multiqc [DEBUG ] No samples found: pycoqc [2022-09-06 19:12:27,104] multiqc [DEBUG ] No samples found: minionqc [2022-09-06 19:12:27,110] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-09-06 19:12:27,114] multiqc [DEBUG ] No samples found: clusterflow [2022-09-06 19:12:27,119] multiqc [DEBUG ] No samples found: bcl2fastq [2022-09-06 19:12:27,124] multiqc [DEBUG ] No samples found: interop [2022-09-06 19:12:27,129] multiqc [DEBUG ] No samples found: ivar [2022-09-06 19:12:27,134] multiqc [DEBUG ] No samples found: flash [2022-09-06 19:12:27,138] multiqc [DEBUG ] No samples found: seqyclean [2022-09-06 19:12:27,138] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-09-06 19:12:27,138] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-09-06 19:12:27,138] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-09-06 19:12:27,138] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-09-06 19:12:27,165] multiqc [INFO ] Compressing plot data [2022-09-06 19:12:27,584] multiqc [INFO ] Report : multiqc_report.html [2022-09-06 19:12:27,585] multiqc [INFO ] Data : multiqc_data [2022-09-06 19:12:27,585] multiqc [DEBUG ] Moving data file from '/state/partition1/job-24556304/tmpb1qcerrv/multiqc_data' to '/scratch/gencore/logs/html/HGGTNBGXM/merged/multiqc_data' [2022-09-06 19:12:28,645] multiqc [INFO ] MultiQC complete