[2022-08-23 02:02:37,036] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-08-23 02:02:37,036] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-08-23 02:02:37,036] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-08-23 02:02:37,037] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-08-23 02:02:37,037] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-08-23 02:02:37,038] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCMLBGXM/merged [2022-08-23 02:02:37,632] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-08-23 02:02:37,632] multiqc [INFO ] This is MultiQC v1.9 [2022-08-23 02:02:37,632] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCMLBGXM/merged [2022-08-23 02:02:37,632] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGCMLBGXM/merged [2022-08-23 02:02:37,632] multiqc [INFO ] Template : default [2022-08-23 02:02:37,632] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-08-23 02:02:37,632] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGCMLBGXM/merged [2022-08-23 02:02:37,632] 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 [2022-08-23 02:02:37,633] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-23953763/tmpcp9q5c_6 [2022-08-23 02:02:37,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM409_fastqc.html [2022-08-23 02:02:37,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM409_fastqc.html [2022-08-23 02:02:37,785] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-08-23 02:02:37,787] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-08-23 02:02:37,917] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM398_fastqc.html [2022-08-23 02:02:37,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM398_fastqc.html [2022-08-23 02:02:37,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM404_fastqc.html [2022-08-23 02:02:37,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM404_fastqc.html [2022-08-23 02:02:38,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM416_fastqc.html [2022-08-23 02:02:38,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM416_fastqc.html [2022-08-23 02:02:38,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM407_fastqc.html [2022-08-23 02:02:38,043] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM407_fastqc.html [2022-08-23 02:02:38,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM394_fastqc.html [2022-08-23 02:02:38,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM394_fastqc.html [2022-08-23 02:02:38,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM397_fastqc.html [2022-08-23 02:02:38,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM397_fastqc.html [2022-08-23 02:02:38,167] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM400_fastqc.html [2022-08-23 02:02:38,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM400_fastqc.html [2022-08-23 02:02:38,209] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM406_fastqc.html [2022-08-23 02:02:38,211] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM406_fastqc.html [2022-08-23 02:02:38,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM396_fastqc.html [2022-08-23 02:02:38,253] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM396_fastqc.html [2022-08-23 02:02:38,292] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM403_fastqc.html [2022-08-23 02:02:38,294] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM403_fastqc.html [2022-08-23 02:02:38,333] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM402_fastqc.html [2022-08-23 02:02:38,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM402_fastqc.html [2022-08-23 02:02:38,387] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM414_fastqc.html [2022-08-23 02:02:38,389] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM414_fastqc.html [2022-08-23 02:02:38,428] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM412_fastqc.html [2022-08-23 02:02:38,429] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM412_fastqc.html [2022-08-23 02:02:38,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM401_fastqc.html [2022-08-23 02:02:38,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM401_fastqc.html [2022-08-23 02:02:38,511] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM415_fastqc.html [2022-08-23 02:02:38,513] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM415_fastqc.html [2022-08-23 02:02:38,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM411_fastqc.html [2022-08-23 02:02:38,555] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM411_fastqc.html [2022-08-23 02:02:38,595] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM408_fastqc.html [2022-08-23 02:02:38,597] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM408_fastqc.html [2022-08-23 02:02:38,635] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM395_fastqc.html [2022-08-23 02:02:38,637] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM395_fastqc.html [2022-08-23 02:02:38,676] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM399_fastqc.html [2022-08-23 02:02:38,678] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM399_fastqc.html [2022-08-23 02:02:38,718] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM413_fastqc.html [2022-08-23 02:02:38,719] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM413_fastqc.html [2022-08-23 02:02:38,759] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM410_fastqc.html [2022-08-23 02:02:38,761] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM410_fastqc.html [2022-08-23 02:02:38,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_undetermined_fastqc.html [2022-08-23 02:02:38,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_undetermined_fastqc.html [2022-08-23 02:02:38,840] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM405_fastqc.html [2022-08-23 02:02:38,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCMLBGXM_n01_AKM405_fastqc.html [2022-08-23 02:02:39,382] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-23 02:02:39,384] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-23 02:02:39,403] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 24 samples (table) [2022-08-23 02:02:39,413] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-08-23 02:02:39,415] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-08-23 02:02:39,420] multiqc [DEBUG ] No samples found: conpair [2022-08-23 02:02:39,425] multiqc [DEBUG ] No samples found: peddy [2022-08-23 02:02:39,431] multiqc [DEBUG ] No samples found: somalier [2022-08-23 02:02:39,435] multiqc [DEBUG ] No samples found: methylQA [2022-08-23 02:02:39,443] multiqc [DEBUG ] No samples found: mosdepth [2022-08-23 02:02:39,448] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-08-23 02:02:39,451] multiqc [DEBUG ] No samples found: qualimap [2022-08-23 02:02:39,456] multiqc [DEBUG ] No samples found: preseq [2022-08-23 02:02:39,460] multiqc [DEBUG ] No samples found: quast [2022-08-23 02:02:39,465] multiqc [DEBUG ] No samples found: qorts [2022-08-23 02:02:39,470] multiqc [DEBUG ] No samples found: rna_seqc [2022-08-23 02:02:39,475] multiqc [DEBUG ] No samples found: rockhopper [2022-08-23 02:02:39,480] multiqc [DEBUG ] No samples found: rsem [2022-08-23 02:02:39,490] multiqc [DEBUG ] No samples found: rseqc [2022-08-23 02:02:39,495] multiqc [DEBUG ] No samples found: busco [2022-08-23 02:02:39,500] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-08-23 02:02:39,504] multiqc [DEBUG ] No samples found: disambiguate [2022-08-23 02:02:39,509] multiqc [DEBUG ] No samples found: supernova [2022-08-23 02:02:39,523] multiqc [DEBUG ] No samples found: deeptools [2022-08-23 02:02:39,528] multiqc [DEBUG ] No samples found: sargasso [2022-08-23 02:02:39,532] multiqc [DEBUG ] No samples found: verifybamid [2022-08-23 02:02:39,537] multiqc [DEBUG ] No samples found: mirtrace [2022-08-23 02:02:39,541] multiqc [DEBUG ] No samples found: happy [2022-08-23 02:02:39,546] multiqc [DEBUG ] No samples found: mirtop [2022-08-23 02:02:39,552] multiqc [DEBUG ] No samples found: homer [2022-08-23 02:02:39,557] multiqc [DEBUG ] No samples found: macs2 [2022-08-23 02:02:39,561] multiqc [DEBUG ] No samples found: theta2 [2022-08-23 02:02:39,566] multiqc [DEBUG ] No samples found: snpeff [2022-08-23 02:02:39,572] multiqc [DEBUG ] No samples found: gatk [2022-08-23 02:02:39,576] multiqc [DEBUG ] No samples found: htseq [2022-08-23 02:02:39,582] multiqc [DEBUG ] No samples found: bcftools [2022-08-23 02:02:39,586] multiqc [DEBUG ] No samples found: featureCounts [2022-08-23 02:02:39,592] multiqc [DEBUG ] No samples found: fgbio [2022-08-23 02:02:39,605] multiqc [DEBUG ] No samples found: dragen [2022-08-23 02:02:39,610] multiqc [DEBUG ] No samples found: dedup [2022-08-23 02:02:39,615] multiqc [DEBUG ] No samples found: damageprofiler [2022-08-23 02:02:39,639] multiqc [DEBUG ] No samples found: biobambam2 [2022-08-23 02:02:39,644] multiqc [DEBUG ] No samples found: mtnucratio [2022-08-23 02:02:39,646] multiqc [DEBUG ] No samples found: picard [2022-08-23 02:02:39,651] multiqc [DEBUG ] No samples found: prokka [2022-08-23 02:02:39,656] multiqc [DEBUG ] No samples found: samblaster [2022-08-23 02:02:39,665] multiqc [DEBUG ] No samples found: samtools [2022-08-23 02:02:39,670] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-08-23 02:02:39,676] multiqc [DEBUG ] No samples found: bamtools [2022-08-23 02:02:39,680] multiqc [DEBUG ] No samples found: jellyfish [2022-08-23 02:02:39,688] multiqc [DEBUG ] No samples found: vcftools [2022-08-23 02:02:39,693] multiqc [DEBUG ] No samples found: longranger [2022-08-23 02:02:39,699] multiqc [DEBUG ] No samples found: stacks [2022-08-23 02:02:39,704] multiqc [DEBUG ] No samples found: varscan2 [2022-08-23 02:02:39,717] multiqc [DEBUG ] No samples found: bbmap [2022-08-23 02:02:39,722] multiqc [DEBUG ] No samples found: bismark [2022-08-23 02:02:39,727] multiqc [DEBUG ] No samples found: biscuit [2022-08-23 02:02:39,732] multiqc [DEBUG ] No samples found: hicexplorer [2022-08-23 02:02:39,736] multiqc [DEBUG ] No samples found: hicup [2022-08-23 02:02:39,741] multiqc [DEBUG ] No samples found: hicpro [2022-08-23 02:02:39,745] multiqc [DEBUG ] No samples found: salmon [2022-08-23 02:02:39,749] multiqc [DEBUG ] No samples found: kallisto [2022-08-23 02:02:39,754] multiqc [DEBUG ] No samples found: slamdunk [2022-08-23 02:02:39,759] multiqc [DEBUG ] No samples found: star [2022-08-23 02:02:39,763] multiqc [DEBUG ] No samples found: hisat2 [2022-08-23 02:02:39,768] multiqc [DEBUG ] No samples found: tophat [2022-08-23 02:02:39,773] multiqc [DEBUG ] No samples found: bowtie2 [2022-08-23 02:02:39,777] multiqc [DEBUG ] No samples found: bowtie1 [2022-08-23 02:02:39,781] multiqc [DEBUG ] No samples found: snpsplit [2022-08-23 02:02:39,786] multiqc [DEBUG ] No samples found: kat [2022-08-23 02:02:39,790] multiqc [DEBUG ] No samples found: leehom [2022-08-23 02:02:39,795] multiqc [DEBUG ] No samples found: adapterRemoval [2022-08-23 02:02:39,799] multiqc [DEBUG ] No samples found: clipandmerge [2022-08-23 02:02:39,804] multiqc [DEBUG ] No samples found: cutadapt [2022-08-23 02:02:39,808] multiqc [DEBUG ] No samples found: flexbar [2022-08-23 02:02:39,813] multiqc [DEBUG ] No samples found: kaiju [2022-08-23 02:02:39,818] multiqc [DEBUG ] No samples found: kraken [2022-08-23 02:02:39,822] multiqc [DEBUG ] No samples found: malt [2022-08-23 02:02:39,827] multiqc [DEBUG ] No samples found: trimmomatic [2022-08-23 02:02:39,831] multiqc [DEBUG ] No samples found: sickle [2022-08-23 02:02:39,836] multiqc [DEBUG ] No samples found: skewer [2022-08-23 02:02:39,841] multiqc [DEBUG ] No samples found: sortmerna [2022-08-23 02:02:39,845] multiqc [DEBUG ] No samples found: biobloomtools [2022-08-23 02:02:39,849] multiqc [DEBUG ] No samples found: fastq_screen [2022-08-23 02:02:39,854] multiqc [DEBUG ] No samples found: afterqc [2022-08-23 02:02:39,859] multiqc [DEBUG ] No samples found: fastp [2022-08-23 02:02:41,510] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2022-08-23 02:02:42,051] multiqc [DEBUG ] No samples found: pycoqc [2022-08-23 02:02:42,056] multiqc [DEBUG ] No samples found: minionqc [2022-08-23 02:02:42,061] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-08-23 02:02:42,066] multiqc [DEBUG ] No samples found: clusterflow [2022-08-23 02:02:42,071] multiqc [DEBUG ] No samples found: bcl2fastq [2022-08-23 02:02:42,075] multiqc [DEBUG ] No samples found: interop [2022-08-23 02:02:42,080] multiqc [DEBUG ] No samples found: ivar [2022-08-23 02:02:42,085] multiqc [DEBUG ] No samples found: flash [2022-08-23 02:02:42,089] multiqc [DEBUG ] No samples found: seqyclean [2022-08-23 02:02:42,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-08-23 02:02:42,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-08-23 02:02:42,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-08-23 02:02:42,089] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-08-23 02:02:42,119] multiqc [INFO ] Compressing plot data [2022-08-23 02:02:42,563] multiqc [INFO ] Report : multiqc_report.html [2022-08-23 02:02:42,563] multiqc [INFO ] Data : multiqc_data [2022-08-23 02:02:42,563] multiqc [DEBUG ] Moving data file from '/state/partition1/job-23953763/tmpcp9q5c_6/multiqc_data' to '/scratch/gencore/logs/html/HGCMLBGXM/merged/multiqc_data' [2022-08-23 02:02:42,690] multiqc [INFO ] MultiQC complete