[2021-11-09 19:17:21,558] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-09 19:17:21,558] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-09 19:17:21,558] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-09 19:17:21,559] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-09 19:17:21,559] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-09 19:17:21,559] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H57H7AFX3/merged [2021-11-09 19:17:22,979] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-09 19:17:22,979] multiqc [INFO ] This is MultiQC v1.9 [2021-11-09 19:17:22,979] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H57H7AFX3/merged [2021-11-09 19:17:22,980] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H57H7AFX3/merged [2021-11-09 19:17:22,980] multiqc [INFO ] Template : default [2021-11-09 19:17:22,980] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-09 19:17:22,980] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H57H7AFX3/merged [2021-11-09 19:17:22,980] 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 [2021-11-09 19:17:22,980] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11759457/tmp5adt2xd2 [2021-11-09 19:17:23,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4579_fastqc.html [2021-11-09 19:17:23,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4579_fastqc.html [2021-11-09 19:17:23,134] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4658_fastqc.html [2021-11-09 19:17:23,136] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4658_fastqc.html [2021-11-09 19:17:23,176] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-09 19:17:23,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-09 19:17:23,264] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in_red1_fastqc.html [2021-11-09 19:17:23,266] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in_red1_fastqc.html [2021-11-09 19:17:23,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_10965chp_red1_fastqc.html [2021-11-09 19:17:23,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_10965chp_red1_fastqc.html [2021-11-09 19:17:23,350] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4658_fastqc.html [2021-11-09 19:17:23,352] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4658_fastqc.html [2021-11-09 19:17:23,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in_red1_fastqc.html [2021-11-09 19:17:23,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in_red1_fastqc.html [2021-11-09 19:17:23,438] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4657_fastqc.html [2021-11-09 19:17:23,440] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp-4657_fastqc.html [2021-11-09 19:17:23,482] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_10965in_red1_fastqc.html [2021-11-09 19:17:23,484] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_10965in_red1_fastqc.html [2021-11-09 19:17:23,528] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4579_fastqc.html [2021-11-09 19:17:23,529] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4579_fastqc.html [2021-11-09 19:17:23,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4579_fastqc.html [2021-11-09 19:17:23,572] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4579_fastqc.html [2021-11-09 19:17:23,613] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4658_fastqc.html [2021-11-09 19:17:23,615] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4658_fastqc.html [2021-11-09 19:17:23,657] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4579_fastqc.html [2021-11-09 19:17:23,659] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4579_fastqc.html [2021-11-09 19:17:23,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_10517in_red1_fastqc.html [2021-11-09 19:17:23,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_10517in_red1_fastqc.html [2021-11-09 19:17:23,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4657_fastqc.html [2021-11-09 19:17:23,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251in-4657_fastqc.html [2021-11-09 19:17:23,786] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4657_fastqc.html [2021-11-09 19:17:23,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4657_fastqc.html [2021-11-09 19:17:23,829] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_undetermined_fastqc.html [2021-11-09 19:17:23,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_undetermined_fastqc.html [2021-11-09 19:17:23,872] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4657_fastqc.html [2021-11-09 19:17:23,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251in-4657_fastqc.html [2021-11-09 19:17:23,914] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_10517chp_red1_fastqc.html [2021-11-09 19:17:23,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_10517chp_red1_fastqc.html [2021-11-09 19:17:23,957] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp_red1_fastqc.html [2021-11-09 19:17:23,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp_red1_fastqc.html [2021-11-09 19:17:24,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4658_fastqc.html [2021-11-09 19:17:24,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_9251chp-4658_fastqc.html [2021-11-09 19:17:24,044] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_10965chp_red1_fastqc.html [2021-11-09 19:17:24,046] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_10965chp_red1_fastqc.html [2021-11-09 19:17:24,087] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_10517in_red1_fastqc.html [2021-11-09 19:17:24,089] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_10517in_red1_fastqc.html [2021-11-09 19:17:24,129] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_10965in_red1_fastqc.html [2021-11-09 19:17:24,131] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_10965in_red1_fastqc.html [2021-11-09 19:17:24,172] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_undetermined_fastqc.html [2021-11-09 19:17:24,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_undetermined_fastqc.html [2021-11-09 19:17:24,215] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp_red1_fastqc.html [2021-11-09 19:17:24,217] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n01_9251chp_red1_fastqc.html [2021-11-09 19:17:24,259] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57H7AFX3_n02_10517chp_red1_fastqc.html [2021-11-09 19:17:24,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57H7AFX3_n02_10517chp_red1_fastqc.html [2021-11-09 19:17:24,607] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-09 19:17:24,608] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-09 19:17:24,621] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2021-11-09 19:17:24,623] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-09 19:17:24,633] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-09 19:17:24,637] multiqc [DEBUG ] No samples found: conpair [2021-11-09 19:17:24,642] multiqc [DEBUG ] No samples found: peddy [2021-11-09 19:17:24,646] multiqc [DEBUG ] No samples found: somalier [2021-11-09 19:17:24,651] multiqc [DEBUG ] No samples found: methylQA [2021-11-09 19:17:24,658] multiqc [DEBUG ] No samples found: mosdepth [2021-11-09 19:17:24,662] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-09 19:17:24,666] multiqc [DEBUG ] No samples found: qualimap [2021-11-09 19:17:24,670] multiqc [DEBUG ] No samples found: preseq [2021-11-09 19:17:24,675] multiqc [DEBUG ] No samples found: quast [2021-11-09 19:17:24,679] multiqc [DEBUG ] No samples found: qorts [2021-11-09 19:17:24,684] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-09 19:17:24,689] multiqc [DEBUG ] No samples found: rockhopper [2021-11-09 19:17:24,693] multiqc [DEBUG ] No samples found: rsem [2021-11-09 19:17:24,703] multiqc [DEBUG ] No samples found: rseqc [2021-11-09 19:17:24,707] multiqc [DEBUG ] No samples found: busco [2021-11-09 19:17:24,711] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-09 19:17:24,715] multiqc [DEBUG ] No samples found: disambiguate [2021-11-09 19:17:24,720] multiqc [DEBUG ] No samples found: supernova [2021-11-09 19:17:24,733] multiqc [DEBUG ] No samples found: deeptools [2021-11-09 19:17:24,737] multiqc [DEBUG ] No samples found: sargasso [2021-11-09 19:17:24,742] multiqc [DEBUG ] No samples found: verifybamid [2021-11-09 19:17:24,747] multiqc [DEBUG ] No samples found: mirtrace [2021-11-09 19:17:24,752] multiqc [DEBUG ] No samples found: happy [2021-11-09 19:17:24,756] multiqc [DEBUG ] No samples found: mirtop [2021-11-09 19:17:24,762] multiqc [DEBUG ] No samples found: homer [2021-11-09 19:17:24,766] multiqc [DEBUG ] No samples found: macs2 [2021-11-09 19:17:24,770] multiqc [DEBUG ] No samples found: theta2 [2021-11-09 19:17:24,775] multiqc [DEBUG ] No samples found: snpeff [2021-11-09 19:17:24,781] multiqc [DEBUG ] No samples found: gatk [2021-11-09 19:17:24,785] multiqc [DEBUG ] No samples found: htseq [2021-11-09 19:17:24,790] multiqc [DEBUG ] No samples found: bcftools [2021-11-09 19:17:24,794] multiqc [DEBUG ] No samples found: featureCounts [2021-11-09 19:17:24,800] multiqc [DEBUG ] No samples found: fgbio [2021-11-09 19:17:24,813] multiqc [DEBUG ] No samples found: dragen [2021-11-09 19:17:24,817] multiqc [DEBUG ] No samples found: dedup [2021-11-09 19:17:24,822] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-09 19:17:24,841] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-09 19:17:24,845] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-09 19:17:24,847] multiqc [DEBUG ] No samples found: picard [2021-11-09 19:17:24,851] multiqc [DEBUG ] No samples found: prokka [2021-11-09 19:17:24,855] multiqc [DEBUG ] No samples found: samblaster [2021-11-09 19:17:24,862] multiqc [DEBUG ] No samples found: samtools [2021-11-09 19:17:24,867] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-09 19:17:24,871] multiqc [DEBUG ] No samples found: bamtools [2021-11-09 19:17:24,875] multiqc [DEBUG ] No samples found: jellyfish [2021-11-09 19:17:24,883] multiqc [DEBUG ] No samples found: vcftools [2021-11-09 19:17:24,888] multiqc [DEBUG ] No samples found: longranger [2021-11-09 19:17:24,892] multiqc [DEBUG ] No samples found: stacks [2021-11-09 19:17:24,896] multiqc [DEBUG ] No samples found: varscan2 [2021-11-09 19:17:24,908] multiqc [DEBUG ] No samples found: bbmap [2021-11-09 19:17:24,913] multiqc [DEBUG ] No samples found: bismark [2021-11-09 19:17:24,917] multiqc [DEBUG ] No samples found: biscuit [2021-11-09 19:17:24,922] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-09 19:17:24,926] multiqc [DEBUG ] No samples found: hicup [2021-11-09 19:17:24,930] multiqc [DEBUG ] No samples found: hicpro [2021-11-09 19:17:24,934] multiqc [DEBUG ] No samples found: salmon [2021-11-09 19:17:24,938] multiqc [DEBUG ] No samples found: kallisto [2021-11-09 19:17:24,943] multiqc [DEBUG ] No samples found: slamdunk [2021-11-09 19:17:24,947] multiqc [DEBUG ] No samples found: star [2021-11-09 19:17:24,951] multiqc [DEBUG ] No samples found: hisat2 [2021-11-09 19:17:24,956] multiqc [DEBUG ] No samples found: tophat [2021-11-09 19:17:24,960] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-09 19:17:24,964] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-09 19:17:24,968] multiqc [DEBUG ] No samples found: snpsplit [2021-11-09 19:17:24,972] multiqc [DEBUG ] No samples found: kat [2021-11-09 19:17:24,975] multiqc [DEBUG ] No samples found: leehom [2021-11-09 19:17:24,980] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-09 19:17:24,983] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-09 19:17:24,987] multiqc [DEBUG ] No samples found: cutadapt [2021-11-09 19:17:24,991] multiqc [DEBUG ] No samples found: flexbar [2021-11-09 19:17:24,995] multiqc [DEBUG ] No samples found: kaiju [2021-11-09 19:17:25,000] multiqc [DEBUG ] No samples found: kraken [2021-11-09 19:17:25,004] multiqc [DEBUG ] No samples found: malt [2021-11-09 19:17:25,008] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-09 19:17:25,012] multiqc [DEBUG ] No samples found: sickle [2021-11-09 19:17:25,016] multiqc [DEBUG ] No samples found: skewer [2021-11-09 19:17:25,020] multiqc [DEBUG ] No samples found: sortmerna [2021-11-09 19:17:25,023] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-09 19:17:25,028] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-09 19:17:25,032] multiqc [DEBUG ] No samples found: afterqc [2021-11-09 19:17:25,036] multiqc [DEBUG ] No samples found: fastp [2021-11-09 19:17:25,653] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2021-11-09 19:17:25,892] multiqc [DEBUG ] No samples found: pycoqc [2021-11-09 19:17:25,897] multiqc [DEBUG ] No samples found: minionqc [2021-11-09 19:17:25,902] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-09 19:17:25,906] multiqc [DEBUG ] No samples found: clusterflow [2021-11-09 19:17:25,911] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-09 19:17:25,915] multiqc [DEBUG ] No samples found: interop [2021-11-09 19:17:25,920] multiqc [DEBUG ] No samples found: ivar [2021-11-09 19:17:25,924] multiqc [DEBUG ] No samples found: flash [2021-11-09 19:17:25,929] multiqc [DEBUG ] No samples found: seqyclean [2021-11-09 19:17:25,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-09 19:17:25,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-09 19:17:25,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-09 19:17:25,929] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-09 19:17:25,962] multiqc [INFO ] Compressing plot data [2021-11-09 19:17:26,400] multiqc [INFO ] Report : multiqc_report.html [2021-11-09 19:17:26,400] multiqc [INFO ] Data : multiqc_data [2021-11-09 19:17:26,400] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11759457/tmp5adt2xd2/multiqc_data' to '/scratch/gencore/logs/html/H57H7AFX3/merged/multiqc_data' [2021-11-09 19:17:26,523] multiqc [INFO ] MultiQC complete