[2022-05-20 16:25:49,668] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-20 16:25:49,668] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-20 16:25:49,668] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-20 16:25:49,669] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-20 16:25:49,669] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-20 16:25:49,669] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5L2HDRX2/merged [2022-05-20 16:25:50,223] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-20 16:25:50,224] multiqc [INFO ] This is MultiQC v1.9 [2022-05-20 16:25:50,224] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5L2HDRX2/merged [2022-05-20 16:25:50,224] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5L2HDRX2/merged [2022-05-20 16:25:50,224] multiqc [INFO ] Template : default [2022-05-20 16:25:50,224] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-20 16:25:50,224] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5L2HDRX2/merged [2022-05-20 16:25:50,224] 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 [2022-05-20 16:25:50,224] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19876834/tmpp96f4p06 [2022-05-20 16:25:50,346] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_DJ66_2_fastqc.html [2022-05-20 16:25:50,349] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_DJ66_2_fastqc.html [2022-05-20 16:25:50,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,391] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:50,470] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-05-20 16:25:53,901] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK124_fastqc.html [2022-05-20 16:25:53,903] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK124_fastqc.html [2022-05-20 16:25:53,942] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK124_fastqc.html [2022-05-20 16:25:53,944] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK124_fastqc.html [2022-05-20 16:25:53,982] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_DJ65_2_fastqc.html [2022-05-20 16:25:53,984] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_DJ65_2_fastqc.html [2022-05-20 16:25:54,023] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK123_fastqc.html [2022-05-20 16:25:54,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK123_fastqc.html [2022-05-20 16:25:54,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_undetermined_fastqc.html [2022-05-20 16:25:54,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_undetermined_fastqc.html [2022-05-20 16:25:54,105] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_DJ66_2_fastqc.html [2022-05-20 16:25:54,107] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_DJ66_2_fastqc.html [2022-05-20 16:25:54,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_DJ65_2_fastqc.html [2022-05-20 16:25:54,147] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_DJ65_2_fastqc.html [2022-05-20 16:25:54,186] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK122_fastqc.html [2022-05-20 16:25:54,188] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK122_fastqc.html [2022-05-20 16:25:54,227] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK122_fastqc.html [2022-05-20 16:25:54,229] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_JK122_fastqc.html [2022-05-20 16:25:54,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK123_fastqc.html [2022-05-20 16:25:54,268] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n02_JK123_fastqc.html [2022-05-20 16:25:54,307] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5L2HDRX2_n01_undetermined_fastqc.html [2022-05-20 16:25:54,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5L2HDRX2_n01_undetermined_fastqc.html [2022-05-20 16:25:54,670] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-20 16:25:54,671] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-20 16:25:54,679] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-20 16:25:54,683] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2022-05-20 16:25:54,692] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-05-20 16:25:54,697] multiqc [DEBUG ] No samples found: conpair [2022-05-20 16:25:54,701] multiqc [DEBUG ] No samples found: peddy [2022-05-20 16:25:54,706] multiqc [DEBUG ] No samples found: somalier [2022-05-20 16:25:54,710] multiqc [DEBUG ] No samples found: methylQA [2022-05-20 16:25:54,721] multiqc [DEBUG ] No samples found: mosdepth [2022-05-20 16:25:54,725] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-20 16:25:54,729] multiqc [DEBUG ] No samples found: qualimap [2022-05-20 16:25:54,734] multiqc [DEBUG ] No samples found: preseq [2022-05-20 16:25:54,738] multiqc [DEBUG ] No samples found: quast [2022-05-20 16:25:54,743] multiqc [DEBUG ] No samples found: qorts [2022-05-20 16:25:54,747] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-20 16:25:54,752] multiqc [DEBUG ] No samples found: rockhopper [2022-05-20 16:25:54,758] multiqc [DEBUG ] No samples found: rsem [2022-05-20 16:25:54,770] multiqc [DEBUG ] No samples found: rseqc [2022-05-20 16:25:54,774] multiqc [DEBUG ] No samples found: busco [2022-05-20 16:25:54,786] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-20 16:25:54,790] multiqc [DEBUG ] No samples found: disambiguate [2022-05-20 16:25:54,796] multiqc [DEBUG ] No samples found: supernova [2022-05-20 16:25:54,810] multiqc [DEBUG ] No samples found: deeptools [2022-05-20 16:25:54,814] multiqc [DEBUG ] No samples found: sargasso [2022-05-20 16:25:54,819] multiqc [DEBUG ] No samples found: verifybamid [2022-05-20 16:25:54,824] multiqc [DEBUG ] No samples found: mirtrace [2022-05-20 16:25:54,828] multiqc [DEBUG ] No samples found: happy [2022-05-20 16:25:54,833] multiqc [DEBUG ] No samples found: mirtop [2022-05-20 16:25:54,840] multiqc [DEBUG ] No samples found: homer [2022-05-20 16:25:54,845] multiqc [DEBUG ] No samples found: macs2 [2022-05-20 16:25:54,849] multiqc [DEBUG ] No samples found: theta2 [2022-05-20 16:25:54,853] multiqc [DEBUG ] No samples found: snpeff [2022-05-20 16:25:54,859] multiqc [DEBUG ] No samples found: gatk [2022-05-20 16:25:54,864] multiqc [DEBUG ] No samples found: htseq [2022-05-20 16:25:54,869] multiqc [DEBUG ] No samples found: bcftools [2022-05-20 16:25:54,873] multiqc [DEBUG ] No samples found: featureCounts [2022-05-20 16:25:54,879] multiqc [DEBUG ] No samples found: fgbio [2022-05-20 16:25:54,893] multiqc [DEBUG ] No samples found: dragen [2022-05-20 16:25:54,898] multiqc [DEBUG ] No samples found: dedup [2022-05-20 16:25:54,903] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-20 16:25:54,928] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-20 16:25:54,932] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-20 16:25:54,935] multiqc [DEBUG ] No samples found: picard [2022-05-20 16:25:54,939] multiqc [DEBUG ] No samples found: prokka [2022-05-20 16:25:54,943] multiqc [DEBUG ] No samples found: samblaster [2022-05-20 16:25:54,953] multiqc [DEBUG ] No samples found: samtools [2022-05-20 16:25:54,957] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-20 16:25:54,963] multiqc [DEBUG ] No samples found: bamtools [2022-05-20 16:25:54,968] multiqc [DEBUG ] No samples found: jellyfish [2022-05-20 16:25:54,975] multiqc [DEBUG ] No samples found: vcftools [2022-05-20 16:25:54,979] multiqc [DEBUG ] No samples found: longranger [2022-05-20 16:25:54,984] multiqc [DEBUG ] No samples found: stacks [2022-05-20 16:25:54,990] multiqc [DEBUG ] No samples found: varscan2 [2022-05-20 16:25:55,004] multiqc [DEBUG ] No samples found: bbmap [2022-05-20 16:25:55,008] multiqc [DEBUG ] No samples found: bismark [2022-05-20 16:25:55,013] multiqc [DEBUG ] No samples found: biscuit [2022-05-20 16:25:55,018] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-20 16:25:55,022] multiqc [DEBUG ] No samples found: hicup [2022-05-20 16:25:55,033] multiqc [DEBUG ] No samples found: hicpro [2022-05-20 16:25:55,037] multiqc [DEBUG ] No samples found: salmon [2022-05-20 16:25:55,041] multiqc [DEBUG ] No samples found: kallisto [2022-05-20 16:25:55,046] multiqc [DEBUG ] No samples found: slamdunk [2022-05-20 16:25:55,050] multiqc [DEBUG ] No samples found: star [2022-05-20 16:25:55,055] multiqc [DEBUG ] No samples found: hisat2 [2022-05-20 16:25:55,061] multiqc [DEBUG ] No samples found: tophat [2022-05-20 16:25:55,066] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-20 16:25:55,070] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-20 16:25:55,076] multiqc [DEBUG ] No samples found: snpsplit [2022-05-20 16:25:55,082] multiqc [DEBUG ] No samples found: kat [2022-05-20 16:25:55,086] multiqc [DEBUG ] No samples found: leehom [2022-05-20 16:25:55,091] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-20 16:25:55,095] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-20 16:25:55,099] multiqc [DEBUG ] No samples found: cutadapt [2022-05-20 16:25:55,103] multiqc [DEBUG ] No samples found: flexbar [2022-05-20 16:25:55,109] multiqc [DEBUG ] No samples found: kaiju [2022-05-20 16:25:55,113] multiqc [DEBUG ] No samples found: kraken [2022-05-20 16:25:55,118] multiqc [DEBUG ] No samples found: malt [2022-05-20 16:25:55,122] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-20 16:25:55,127] multiqc [DEBUG ] No samples found: sickle [2022-05-20 16:25:55,132] multiqc [DEBUG ] No samples found: skewer [2022-05-20 16:25:55,136] multiqc [DEBUG ] No samples found: sortmerna [2022-05-20 16:25:55,140] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-20 16:25:55,146] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-20 16:25:55,150] multiqc [DEBUG ] No samples found: afterqc [2022-05-20 16:25:55,155] multiqc [DEBUG ] No samples found: fastp [2022-05-20 16:25:55,554] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2022-05-20 16:25:55,762] multiqc [DEBUG ] No samples found: pycoqc [2022-05-20 16:25:55,768] multiqc [DEBUG ] No samples found: minionqc [2022-05-20 16:25:55,773] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-20 16:25:55,777] multiqc [DEBUG ] No samples found: clusterflow [2022-05-20 16:25:55,781] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-20 16:25:55,786] multiqc [DEBUG ] No samples found: interop [2022-05-20 16:25:55,792] multiqc [DEBUG ] No samples found: ivar [2022-05-20 16:25:55,796] multiqc [DEBUG ] No samples found: flash [2022-05-20 16:25:55,801] multiqc [DEBUG ] No samples found: seqyclean [2022-05-20 16:25:55,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-05-20 16:25:55,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-20 16:25:55,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-05-20 16:25:55,801] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-20 16:25:55,816] multiqc [INFO ] Compressing plot data [2022-05-20 16:25:56,017] multiqc [INFO ] Report : multiqc_report.html [2022-05-20 16:25:56,018] multiqc [INFO ] Data : multiqc_data [2022-05-20 16:25:56,018] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19876834/tmpp96f4p06/multiqc_data' to '/scratch/gencore/logs/html/H5L2HDRX2/merged/multiqc_data' [2022-05-20 16:25:56,146] multiqc [INFO ] MultiQC complete