[2021-07-14 13:21:31,393] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-07-14 13:21:31,393] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-07-14 13:21:31,393] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-07-14 13:21:31,394] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-07-14 13:21:31,394] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-07-14 13:21:31,395] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HH723DRXY/merged [2021-07-14 13:21:32,945] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-07-14 13:21:32,945] multiqc [INFO ] This is MultiQC v1.9 [2021-07-14 13:21:32,945] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HH723DRXY/merged [2021-07-14 13:21:32,945] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HH723DRXY/merged [2021-07-14 13:21:32,945] multiqc [INFO ] Template : default [2021-07-14 13:21:32,945] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-07-14 13:21:32,945] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HH723DRXY/merged [2021-07-14 13:21:32,946] 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 [2021-07-14 13:21:32,946] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-8645070/tmpmwp6sjav [2021-07-14 13:21:33,048] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:33,051] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-07-14 13:21:36,737] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ88_fastqc.html [2021-07-14 13:21:36,739] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ88_fastqc.html [2021-07-14 13:21:36,798] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_undetermined_fastqc.html [2021-07-14 13:21:36,799] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_undetermined_fastqc.html [2021-07-14 13:21:36,838] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_JK16_hic_fastqc.html [2021-07-14 13:21:36,840] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_JK16_hic_fastqc.html [2021-07-14 13:21:36,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_JK15_hic_fastqc.html [2021-07-14 13:21:36,880] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_JK15_hic_fastqc.html [2021-07-14 13:21:36,919] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_JK16_hic_fastqc.html [2021-07-14 13:21:36,921] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_JK16_hic_fastqc.html [2021-07-14 13:21:36,976] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ88_fastqc.html [2021-07-14 13:21:36,978] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ88_fastqc.html [2021-07-14 13:21:37,029] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_undetermined_fastqc.html [2021-07-14 13:21:37,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_undetermined_fastqc.html [2021-07-14 13:21:37,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ89_fastqc.html [2021-07-14 13:21:37,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ89_fastqc.html [2021-07-14 13:21:37,110] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ87_fastqc.html [2021-07-14 13:21:37,112] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ87_fastqc.html [2021-07-14 13:21:37,165] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ89_fastqc.html [2021-07-14 13:21:37,166] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n02_DJ89_fastqc.html [2021-07-14 13:21:37,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_JK15_hic_fastqc.html [2021-07-14 13:21:37,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_JK15_hic_fastqc.html [2021-07-14 13:21:37,245] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ87_fastqc.html [2021-07-14 13:21:37,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HH723DRXY_n01_DJ87_fastqc.html [2021-07-14 13:21:37,550] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-14 13:21:37,551] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-07-14 13:21:37,560] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2021-07-14 13:21:37,570] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-07-14 13:21:37,571] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-07-14 13:21:37,576] multiqc [DEBUG ] No samples found: conpair [2021-07-14 13:21:37,581] multiqc [DEBUG ] No samples found: peddy [2021-07-14 13:21:37,586] multiqc [DEBUG ] No samples found: somalier [2021-07-14 13:21:37,591] multiqc [DEBUG ] No samples found: methylQA [2021-07-14 13:21:37,600] multiqc [DEBUG ] No samples found: mosdepth [2021-07-14 13:21:37,605] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-07-14 13:21:37,608] multiqc [DEBUG ] No samples found: qualimap [2021-07-14 13:21:37,613] multiqc [DEBUG ] No samples found: preseq [2021-07-14 13:21:37,618] multiqc [DEBUG ] No samples found: quast [2021-07-14 13:21:37,623] multiqc [DEBUG ] No samples found: qorts [2021-07-14 13:21:37,628] multiqc [DEBUG ] No samples found: rna_seqc [2021-07-14 13:21:37,633] multiqc [DEBUG ] No samples found: rockhopper [2021-07-14 13:21:37,637] multiqc [DEBUG ] No samples found: rsem [2021-07-14 13:21:37,647] multiqc [DEBUG ] No samples found: rseqc [2021-07-14 13:21:37,652] multiqc [DEBUG ] No samples found: busco [2021-07-14 13:21:37,657] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-07-14 13:21:37,662] multiqc [DEBUG ] No samples found: disambiguate [2021-07-14 13:21:37,667] multiqc [DEBUG ] No samples found: supernova [2021-07-14 13:21:37,680] multiqc [DEBUG ] No samples found: deeptools [2021-07-14 13:21:37,685] multiqc [DEBUG ] No samples found: sargasso [2021-07-14 13:21:37,690] multiqc [DEBUG ] No samples found: verifybamid [2021-07-14 13:21:37,695] multiqc [DEBUG ] No samples found: mirtrace [2021-07-14 13:21:37,700] multiqc [DEBUG ] No samples found: happy [2021-07-14 13:21:37,705] multiqc [DEBUG ] No samples found: mirtop [2021-07-14 13:21:37,711] multiqc [DEBUG ] No samples found: homer [2021-07-14 13:21:37,716] multiqc [DEBUG ] No samples found: macs2 [2021-07-14 13:21:37,721] multiqc [DEBUG ] No samples found: theta2 [2021-07-14 13:21:37,726] multiqc [DEBUG ] No samples found: snpeff [2021-07-14 13:21:37,733] multiqc [DEBUG ] No samples found: gatk [2021-07-14 13:21:37,738] multiqc [DEBUG ] No samples found: htseq [2021-07-14 13:21:37,743] multiqc [DEBUG ] No samples found: bcftools [2021-07-14 13:21:37,748] multiqc [DEBUG ] No samples found: featureCounts [2021-07-14 13:21:37,754] multiqc [DEBUG ] No samples found: fgbio [2021-07-14 13:21:37,768] multiqc [DEBUG ] No samples found: dragen [2021-07-14 13:21:37,773] multiqc [DEBUG ] No samples found: dedup [2021-07-14 13:21:37,777] multiqc [DEBUG ] No samples found: damageprofiler [2021-07-14 13:21:37,798] multiqc [DEBUG ] No samples found: biobambam2 [2021-07-14 13:21:37,803] multiqc [DEBUG ] No samples found: mtnucratio [2021-07-14 13:21:37,805] multiqc [DEBUG ] No samples found: picard [2021-07-14 13:21:37,810] multiqc [DEBUG ] No samples found: prokka [2021-07-14 13:21:37,815] multiqc [DEBUG ] No samples found: samblaster [2021-07-14 13:21:37,822] multiqc [DEBUG ] No samples found: samtools [2021-07-14 13:21:37,828] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-07-14 13:21:37,832] multiqc [DEBUG ] No samples found: bamtools [2021-07-14 13:21:37,837] multiqc [DEBUG ] No samples found: jellyfish [2021-07-14 13:21:37,845] multiqc [DEBUG ] No samples found: vcftools [2021-07-14 13:21:37,850] multiqc [DEBUG ] No samples found: longranger [2021-07-14 13:21:37,856] multiqc [DEBUG ] No samples found: stacks [2021-07-14 13:21:37,861] multiqc [DEBUG ] No samples found: varscan2 [2021-07-14 13:21:37,875] multiqc [DEBUG ] No samples found: bbmap [2021-07-14 13:21:37,879] multiqc [DEBUG ] No samples found: bismark [2021-07-14 13:21:37,884] multiqc [DEBUG ] No samples found: biscuit [2021-07-14 13:21:37,890] multiqc [DEBUG ] No samples found: hicexplorer [2021-07-14 13:21:37,895] multiqc [DEBUG ] No samples found: hicup [2021-07-14 13:21:37,900] multiqc [DEBUG ] No samples found: hicpro [2021-07-14 13:21:37,904] multiqc [DEBUG ] No samples found: salmon [2021-07-14 13:21:37,909] multiqc [DEBUG ] No samples found: kallisto [2021-07-14 13:21:37,915] multiqc [DEBUG ] No samples found: slamdunk [2021-07-14 13:21:37,919] multiqc [DEBUG ] No samples found: star [2021-07-14 13:21:37,924] multiqc [DEBUG ] No samples found: hisat2 [2021-07-14 13:21:37,928] multiqc [DEBUG ] No samples found: tophat [2021-07-14 13:21:37,935] multiqc [DEBUG ] No samples found: bowtie2 [2021-07-14 13:21:37,940] multiqc [DEBUG ] No samples found: bowtie1 [2021-07-14 13:21:37,945] multiqc [DEBUG ] No samples found: snpsplit [2021-07-14 13:21:37,950] multiqc [DEBUG ] No samples found: kat [2021-07-14 13:21:37,954] multiqc [DEBUG ] No samples found: leehom [2021-07-14 13:21:37,959] multiqc [DEBUG ] No samples found: adapterRemoval [2021-07-14 13:21:37,963] multiqc [DEBUG ] No samples found: clipandmerge [2021-07-14 13:21:37,967] multiqc [DEBUG ] No samples found: cutadapt [2021-07-14 13:21:37,972] multiqc [DEBUG ] No samples found: flexbar [2021-07-14 13:21:37,976] multiqc [DEBUG ] No samples found: kaiju [2021-07-14 13:21:37,981] multiqc [DEBUG ] No samples found: kraken [2021-07-14 13:21:37,986] multiqc [DEBUG ] No samples found: malt [2021-07-14 13:21:37,991] multiqc [DEBUG ] No samples found: trimmomatic [2021-07-14 13:21:37,996] multiqc [DEBUG ] No samples found: sickle [2021-07-14 13:21:38,000] multiqc [DEBUG ] No samples found: skewer [2021-07-14 13:21:38,004] multiqc [DEBUG ] No samples found: sortmerna [2021-07-14 13:21:38,009] multiqc [DEBUG ] No samples found: biobloomtools [2021-07-14 13:21:38,014] multiqc [DEBUG ] No samples found: fastq_screen [2021-07-14 13:21:38,018] multiqc [DEBUG ] No samples found: afterqc [2021-07-14 13:21:38,024] multiqc [DEBUG ] No samples found: fastp [2021-07-14 13:21:38,530] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2021-07-14 13:21:38,729] multiqc [DEBUG ] No samples found: pycoqc [2021-07-14 13:21:38,733] multiqc [DEBUG ] No samples found: minionqc [2021-07-14 13:21:38,738] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-07-14 13:21:38,743] multiqc [DEBUG ] No samples found: clusterflow [2021-07-14 13:21:38,748] multiqc [DEBUG ] No samples found: bcl2fastq [2021-07-14 13:21:38,753] multiqc [DEBUG ] No samples found: interop [2021-07-14 13:21:38,758] multiqc [DEBUG ] No samples found: ivar [2021-07-14 13:21:38,762] multiqc [DEBUG ] No samples found: flash [2021-07-14 13:21:38,769] multiqc [DEBUG ] No samples found: seqyclean [2021-07-14 13:21:38,769] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-07-14 13:21:38,769] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-07-14 13:21:38,769] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-07-14 13:21:38,769] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-07-14 13:21:38,784] multiqc [INFO ] Compressing plot data [2021-07-14 13:21:38,985] multiqc [INFO ] Report : multiqc_report.html [2021-07-14 13:21:38,985] multiqc [INFO ] Data : multiqc_data [2021-07-14 13:21:38,985] multiqc [DEBUG ] Moving data file from '/state/partition1/job-8645070/tmpmwp6sjav/multiqc_data' to '/scratch/gencore/logs/html/HH723DRXY/merged/multiqc_data' [2021-07-14 13:21:39,382] multiqc [INFO ] MultiQC complete