[2021-11-18 23:15:00,938] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-18 23:15:00,938] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-18 23:15:00,938] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-18 23:15:00,939] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-18 23:15:00,939] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-18 23:15:00,939] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT2GDRXY/1 [2021-11-18 23:15:02,483] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-18 23:15:02,483] multiqc [INFO ] This is MultiQC v1.9 [2021-11-18 23:15:02,483] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLT2GDRXY/1 [2021-11-18 23:15:02,483] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLT2GDRXY/1 [2021-11-18 23:15:02,483] multiqc [INFO ] Template : default [2021-11-18 23:15:02,483] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-18 23:15:02,483] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLT2GDRXY/1 [2021-11-18 23:15:02,483] 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 [2021-11-18 23:15:02,484] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12141232/tmpm7098wqa [2021-11-18 23:15:02,593] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.4_fastqc.html [2021-11-18 23:15:02,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.4_fastqc.html [2021-11-18 23:15:02,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 23:15:02,638] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 23:15:02,684] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.1_fastqc.html [2021-11-18 23:15:02,686] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.1_fastqc.html [2021-11-18 23:15:02,726] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.4_fastqc.html [2021-11-18 23:15:02,727] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.4_fastqc.html [2021-11-18 23:15:02,769] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.4_fastqc.html [2021-11-18 23:15:02,771] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.4_fastqc.html [2021-11-18 23:15:02,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.2_fastqc.html [2021-11-18 23:15:02,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.2_fastqc.html [2021-11-18 23:15:02,855] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.3_fastqc.html [2021-11-18 23:15:02,856] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.3_fastqc.html [2021-11-18 23:15:02,898] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.3_fastqc.html [2021-11-18 23:15:02,900] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.3_fastqc.html [2021-11-18 23:15:02,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.4_fastqc.html [2021-11-18 23:15:02,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.4_fastqc.html [2021-11-18 23:15:02,984] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.1_fastqc.html [2021-11-18 23:15:02,986] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.1_fastqc.html [2021-11-18 23:15:03,028] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.1_fastqc.html [2021-11-18 23:15:03,030] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.1_fastqc.html [2021-11-18 23:15:03,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.2_fastqc.html [2021-11-18 23:15:03,072] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.2_fastqc.html [2021-11-18 23:15:03,112] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_undetermined_fastqc.html [2021-11-18 23:15:03,114] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_undetermined_fastqc.html [2021-11-18 23:15:03,151] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.3_fastqc.html [2021-11-18 23:15:03,153] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col7.3_fastqc.html [2021-11-18 23:15:03,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_undetermined_fastqc.html [2021-11-18 23:15:03,195] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_undetermined_fastqc.html [2021-11-18 23:15:03,232] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.3_fastqc.html [2021-11-18 23:15:03,234] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.3_fastqc.html [2021-11-18 23:15:03,274] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.2_fastqc.html [2021-11-18 23:15:03,276] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n01_N2.col2.2_fastqc.html [2021-11-18 23:15:03,317] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.1_fastqc.html [2021-11-18 23:15:03,319] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col2.1_fastqc.html [2021-11-18 23:15:03,359] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.2_fastqc.html [2021-11-18 23:15:03,360] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLT2GDRXY_l01_n02_N2.col7.2_fastqc.html [2021-11-18 23:15:03,676] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 23:15:03,680] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 23:15:03,694] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 9 samples (table) [2021-11-18 23:15:03,695] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-18 23:15:03,705] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-18 23:15:03,713] multiqc [DEBUG ] No samples found: conpair [2021-11-18 23:15:03,722] multiqc [DEBUG ] No samples found: peddy [2021-11-18 23:15:03,731] multiqc [DEBUG ] No samples found: somalier [2021-11-18 23:15:03,738] multiqc [DEBUG ] No samples found: methylQA [2021-11-18 23:15:03,752] multiqc [DEBUG ] No samples found: mosdepth [2021-11-18 23:15:03,761] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-18 23:15:03,767] multiqc [DEBUG ] No samples found: qualimap [2021-11-18 23:15:03,775] multiqc [DEBUG ] No samples found: preseq [2021-11-18 23:15:03,784] multiqc [DEBUG ] No samples found: quast [2021-11-18 23:15:03,793] multiqc [DEBUG ] No samples found: qorts [2021-11-18 23:15:03,803] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-18 23:15:03,813] multiqc [DEBUG ] No samples found: rockhopper [2021-11-18 23:15:03,824] multiqc [DEBUG ] No samples found: rsem [2021-11-18 23:15:03,853] multiqc [DEBUG ] No samples found: rseqc [2021-11-18 23:15:03,861] multiqc [DEBUG ] No samples found: busco [2021-11-18 23:15:03,872] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-18 23:15:03,879] multiqc [DEBUG ] No samples found: disambiguate [2021-11-18 23:15:03,886] multiqc [DEBUG ] No samples found: supernova [2021-11-18 23:15:03,924] multiqc [DEBUG ] No samples found: deeptools [2021-11-18 23:15:03,936] multiqc [DEBUG ] No samples found: sargasso [2021-11-18 23:15:03,945] multiqc [DEBUG ] No samples found: verifybamid [2021-11-18 23:15:03,954] multiqc [DEBUG ] No samples found: mirtrace [2021-11-18 23:15:03,961] multiqc [DEBUG ] No samples found: happy [2021-11-18 23:15:03,971] multiqc [DEBUG ] No samples found: mirtop [2021-11-18 23:15:03,983] multiqc [DEBUG ] No samples found: homer [2021-11-18 23:15:03,991] multiqc [DEBUG ] No samples found: macs2 [2021-11-18 23:15:03,997] multiqc [DEBUG ] No samples found: theta2 [2021-11-18 23:15:04,006] multiqc [DEBUG ] No samples found: snpeff [2021-11-18 23:15:04,017] multiqc [DEBUG ] No samples found: gatk [2021-11-18 23:15:04,026] multiqc [DEBUG ] No samples found: htseq [2021-11-18 23:15:04,039] multiqc [DEBUG ] No samples found: bcftools [2021-11-18 23:15:04,045] multiqc [DEBUG ] No samples found: featureCounts [2021-11-18 23:15:04,059] multiqc [DEBUG ] No samples found: fgbio [2021-11-18 23:15:04,093] multiqc [DEBUG ] No samples found: dragen [2021-11-18 23:15:04,101] multiqc [DEBUG ] No samples found: dedup [2021-11-18 23:15:04,108] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-18 23:15:04,160] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-18 23:15:04,169] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-18 23:15:04,171] multiqc [DEBUG ] No samples found: picard [2021-11-18 23:15:04,182] multiqc [DEBUG ] No samples found: prokka [2021-11-18 23:15:04,191] multiqc [DEBUG ] No samples found: samblaster [2021-11-18 23:15:04,208] multiqc [DEBUG ] No samples found: samtools [2021-11-18 23:15:04,217] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-18 23:15:04,229] multiqc [DEBUG ] No samples found: bamtools [2021-11-18 23:15:04,237] multiqc [DEBUG ] No samples found: jellyfish [2021-11-18 23:15:04,256] multiqc [DEBUG ] No samples found: vcftools [2021-11-18 23:15:04,264] multiqc [DEBUG ] No samples found: longranger [2021-11-18 23:15:04,272] multiqc [DEBUG ] No samples found: stacks [2021-11-18 23:15:04,282] multiqc [DEBUG ] No samples found: varscan2 [2021-11-18 23:15:04,320] multiqc [DEBUG ] No samples found: bbmap [2021-11-18 23:15:04,329] multiqc [DEBUG ] No samples found: bismark [2021-11-18 23:15:04,335] multiqc [DEBUG ] No samples found: biscuit [2021-11-18 23:15:04,344] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-18 23:15:04,352] multiqc [DEBUG ] No samples found: hicup [2021-11-18 23:15:04,358] multiqc [DEBUG ] No samples found: hicpro [2021-11-18 23:15:04,364] multiqc [DEBUG ] No samples found: salmon [2021-11-18 23:15:04,373] multiqc [DEBUG ] No samples found: kallisto [2021-11-18 23:15:04,384] multiqc [DEBUG ] No samples found: slamdunk [2021-11-18 23:15:04,393] multiqc [DEBUG ] No samples found: star [2021-11-18 23:15:04,401] multiqc [DEBUG ] No samples found: hisat2 [2021-11-18 23:15:04,411] multiqc [DEBUG ] No samples found: tophat [2021-11-18 23:15:04,422] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-18 23:15:04,431] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-18 23:15:04,440] multiqc [DEBUG ] No samples found: snpsplit [2021-11-18 23:15:04,446] multiqc [DEBUG ] No samples found: kat [2021-11-18 23:15:04,452] multiqc [DEBUG ] No samples found: leehom [2021-11-18 23:15:04,464] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-18 23:15:04,473] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-18 23:15:04,481] multiqc [DEBUG ] No samples found: cutadapt [2021-11-18 23:15:04,490] multiqc [DEBUG ] No samples found: flexbar [2021-11-18 23:15:04,499] multiqc [DEBUG ] No samples found: kaiju [2021-11-18 23:15:04,507] multiqc [DEBUG ] No samples found: kraken [2021-11-18 23:15:04,512] multiqc [DEBUG ] No samples found: malt [2021-11-18 23:15:04,518] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-18 23:15:04,524] multiqc [DEBUG ] No samples found: sickle [2021-11-18 23:15:04,530] multiqc [DEBUG ] No samples found: skewer [2021-11-18 23:15:04,535] multiqc [DEBUG ] No samples found: sortmerna [2021-11-18 23:15:04,541] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-18 23:15:04,545] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-18 23:15:04,553] multiqc [DEBUG ] No samples found: afterqc [2021-11-18 23:15:04,561] multiqc [DEBUG ] No samples found: fastp [2021-11-18 23:15:04,982] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-11-18 23:15:05,162] multiqc [DEBUG ] No samples found: pycoqc [2021-11-18 23:15:05,172] multiqc [DEBUG ] No samples found: minionqc [2021-11-18 23:15:05,181] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-18 23:15:05,189] multiqc [DEBUG ] No samples found: clusterflow [2021-11-18 23:15:05,196] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-18 23:15:05,204] multiqc [DEBUG ] No samples found: interop [2021-11-18 23:15:05,212] multiqc [DEBUG ] No samples found: ivar [2021-11-18 23:15:05,219] multiqc [DEBUG ] No samples found: flash [2021-11-18 23:15:05,226] multiqc [DEBUG ] No samples found: seqyclean [2021-11-18 23:15:05,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-11-18 23:15:05,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-11-18 23:15:05,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-11-18 23:15:05,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-18 23:15:05,226] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-18 23:15:05,248] multiqc [INFO ] Compressing plot data [2021-11-18 23:15:05,539] multiqc [INFO ] Report : multiqc_report.html [2021-11-18 23:15:05,539] multiqc [INFO ] Data : multiqc_data [2021-11-18 23:15:05,539] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12141232/tmpm7098wqa/multiqc_data' to '/scratch/gencore/logs/html/HLT2GDRXY/1/multiqc_data' [2021-11-18 23:15:05,698] multiqc [INFO ] MultiQC complete