[2021-11-18 21:23:10,299] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-18 21:23:10,300] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-18 21:23:10,300] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-18 21:23:10,301] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-18 21:23:10,301] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-18 21:23:10,301] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLGLLBGXK/merged [2021-11-18 21:23:11,720] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-18 21:23:11,720] multiqc [INFO ] This is MultiQC v1.9 [2021-11-18 21:23:11,720] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLGLLBGXK/merged [2021-11-18 21:23:11,720] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLGLLBGXK/merged [2021-11-18 21:23:11,720] multiqc [INFO ] Template : default [2021-11-18 21:23:11,720] 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 21:23:11,720] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLGLLBGXK/merged [2021-11-18 21:23:11,720] 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 21:23:11,721] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12141114/tmpez6goiao [2021-11-18 21:23:11,826] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_910_fastqc.html [2021-11-18 21:23:11,829] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_910_fastqc.html [2021-11-18 21:23:11,888] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_898_fastqc.html [2021-11-18 21:23:11,890] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_898_fastqc.html [2021-11-18 21:23:11,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 21:23:11,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-18 21:23:12,527] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_907_fastqc.html [2021-11-18 21:23:12,529] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_907_fastqc.html [2021-11-18 21:23:12,572] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_900_fastqc.html [2021-11-18 21:23:12,574] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_900_fastqc.html [2021-11-18 21:23:12,636] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_906_fastqc.html [2021-11-18 21:23:12,638] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_906_fastqc.html [2021-11-18 21:23:12,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_909_fastqc.html [2021-11-18 21:23:12,682] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_909_fastqc.html [2021-11-18 21:23:12,738] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_903_fastqc.html [2021-11-18 21:23:12,739] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_903_fastqc.html [2021-11-18 21:23:12,800] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_902_fastqc.html [2021-11-18 21:23:12,802] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_902_fastqc.html [2021-11-18 21:23:12,868] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_903_fastqc.html [2021-11-18 21:23:12,870] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_903_fastqc.html [2021-11-18 21:23:12,957] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_902_fastqc.html [2021-11-18 21:23:12,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_902_fastqc.html [2021-11-18 21:23:13,002] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_908_fastqc.html [2021-11-18 21:23:13,004] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_908_fastqc.html [2021-11-18 21:23:13,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_908_fastqc.html [2021-11-18 21:23:13,047] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_908_fastqc.html [2021-11-18 21:23:13,088] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_910_fastqc.html [2021-11-18 21:23:13,090] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_910_fastqc.html [2021-11-18 21:23:13,148] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_898_fastqc.html [2021-11-18 21:23:13,150] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_898_fastqc.html [2021-11-18 21:23:13,205] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_undetermined_fastqc.html [2021-11-18 21:23:13,207] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_undetermined_fastqc.html [2021-11-18 21:23:13,247] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_900_fastqc.html [2021-11-18 21:23:13,249] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_900_fastqc.html [2021-11-18 21:23:13,294] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_907_fastqc.html [2021-11-18 21:23:13,295] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_907_fastqc.html [2021-11-18 21:23:13,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_undetermined_fastqc.html [2021-11-18 21:23:13,359] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_undetermined_fastqc.html [2021-11-18 21:23:13,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_912_fastqc.html [2021-11-18 21:23:13,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_912_fastqc.html [2021-11-18 21:23:13,445] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_912_fastqc.html [2021-11-18 21:23:13,447] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_912_fastqc.html [2021-11-18 21:23:13,490] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_909_fastqc.html [2021-11-18 21:23:13,492] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_909_fastqc.html [2021-11-18 21:23:13,553] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_911_fastqc.html [2021-11-18 21:23:13,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_911_fastqc.html [2021-11-18 21:23:13,651] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_911_fastqc.html [2021-11-18 21:23:13,652] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_911_fastqc.html [2021-11-18 21:23:13,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_906_fastqc.html [2021-11-18 21:23:13,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_906_fastqc.html [2021-11-18 21:23:13,753] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n02_913_fastqc.html [2021-11-18 21:23:13,755] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n02_913_fastqc.html [2021-11-18 21:23:13,797] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLGLLBGXK_n01_913_fastqc.html [2021-11-18 21:23:13,799] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLGLLBGXK_n01_913_fastqc.html [2021-11-18 21:23:14,146] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 21:23:14,147] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-18 21:23:14,160] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 13 samples (table) [2021-11-18 21:23:14,169] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-18 21:23:14,171] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-18 21:23:14,175] multiqc [DEBUG ] No samples found: conpair [2021-11-18 21:23:14,180] multiqc [DEBUG ] No samples found: peddy [2021-11-18 21:23:14,187] multiqc [DEBUG ] No samples found: somalier [2021-11-18 21:23:14,192] multiqc [DEBUG ] No samples found: methylQA [2021-11-18 21:23:14,199] multiqc [DEBUG ] No samples found: mosdepth [2021-11-18 21:23:14,203] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-18 21:23:14,206] multiqc [DEBUG ] No samples found: qualimap [2021-11-18 21:23:14,211] multiqc [DEBUG ] No samples found: preseq [2021-11-18 21:23:14,215] multiqc [DEBUG ] No samples found: quast [2021-11-18 21:23:14,219] multiqc [DEBUG ] No samples found: qorts [2021-11-18 21:23:14,224] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-18 21:23:14,228] multiqc [DEBUG ] No samples found: rockhopper [2021-11-18 21:23:14,232] multiqc [DEBUG ] No samples found: rsem [2021-11-18 21:23:14,243] multiqc [DEBUG ] No samples found: rseqc [2021-11-18 21:23:14,247] multiqc [DEBUG ] No samples found: busco [2021-11-18 21:23:14,251] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-18 21:23:14,255] multiqc [DEBUG ] No samples found: disambiguate [2021-11-18 21:23:14,260] multiqc [DEBUG ] No samples found: supernova [2021-11-18 21:23:14,273] multiqc [DEBUG ] No samples found: deeptools [2021-11-18 21:23:14,277] multiqc [DEBUG ] No samples found: sargasso [2021-11-18 21:23:14,281] multiqc [DEBUG ] No samples found: verifybamid [2021-11-18 21:23:14,285] multiqc [DEBUG ] No samples found: mirtrace [2021-11-18 21:23:14,290] multiqc [DEBUG ] No samples found: happy [2021-11-18 21:23:14,294] multiqc [DEBUG ] No samples found: mirtop [2021-11-18 21:23:14,300] multiqc [DEBUG ] No samples found: homer [2021-11-18 21:23:14,304] multiqc [DEBUG ] No samples found: macs2 [2021-11-18 21:23:14,307] multiqc [DEBUG ] No samples found: theta2 [2021-11-18 21:23:14,312] multiqc [DEBUG ] No samples found: snpeff [2021-11-18 21:23:14,318] multiqc [DEBUG ] No samples found: gatk [2021-11-18 21:23:14,323] multiqc [DEBUG ] No samples found: htseq [2021-11-18 21:23:14,327] multiqc [DEBUG ] No samples found: bcftools [2021-11-18 21:23:14,332] multiqc [DEBUG ] No samples found: featureCounts [2021-11-18 21:23:14,337] multiqc [DEBUG ] No samples found: fgbio [2021-11-18 21:23:14,351] multiqc [DEBUG ] No samples found: dragen [2021-11-18 21:23:14,355] multiqc [DEBUG ] No samples found: dedup [2021-11-18 21:23:14,360] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-18 21:23:14,381] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-18 21:23:14,386] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-18 21:23:14,388] multiqc [DEBUG ] No samples found: picard [2021-11-18 21:23:14,393] multiqc [DEBUG ] No samples found: prokka [2021-11-18 21:23:14,396] multiqc [DEBUG ] No samples found: samblaster [2021-11-18 21:23:14,406] multiqc [DEBUG ] No samples found: samtools [2021-11-18 21:23:14,410] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-18 21:23:14,415] multiqc [DEBUG ] No samples found: bamtools [2021-11-18 21:23:14,419] multiqc [DEBUG ] No samples found: jellyfish [2021-11-18 21:23:14,427] multiqc [DEBUG ] No samples found: vcftools [2021-11-18 21:23:14,431] multiqc [DEBUG ] No samples found: longranger [2021-11-18 21:23:14,435] multiqc [DEBUG ] No samples found: stacks [2021-11-18 21:23:14,440] multiqc [DEBUG ] No samples found: varscan2 [2021-11-18 21:23:14,453] multiqc [DEBUG ] No samples found: bbmap [2021-11-18 21:23:14,457] multiqc [DEBUG ] No samples found: bismark [2021-11-18 21:23:14,462] multiqc [DEBUG ] No samples found: biscuit [2021-11-18 21:23:14,466] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-18 21:23:14,471] multiqc [DEBUG ] No samples found: hicup [2021-11-18 21:23:14,475] multiqc [DEBUG ] No samples found: hicpro [2021-11-18 21:23:14,479] multiqc [DEBUG ] No samples found: salmon [2021-11-18 21:23:14,483] multiqc [DEBUG ] No samples found: kallisto [2021-11-18 21:23:14,487] multiqc [DEBUG ] No samples found: slamdunk [2021-11-18 21:23:14,491] multiqc [DEBUG ] No samples found: star [2021-11-18 21:23:14,495] multiqc [DEBUG ] No samples found: hisat2 [2021-11-18 21:23:14,500] multiqc [DEBUG ] No samples found: tophat [2021-11-18 21:23:14,504] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-18 21:23:14,508] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-18 21:23:14,512] multiqc [DEBUG ] No samples found: snpsplit [2021-11-18 21:23:14,515] multiqc [DEBUG ] No samples found: kat [2021-11-18 21:23:14,519] multiqc [DEBUG ] No samples found: leehom [2021-11-18 21:23:14,523] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-18 21:23:14,527] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-18 21:23:14,531] multiqc [DEBUG ] No samples found: cutadapt [2021-11-18 21:23:14,535] multiqc [DEBUG ] No samples found: flexbar [2021-11-18 21:23:14,540] multiqc [DEBUG ] No samples found: kaiju [2021-11-18 21:23:14,544] multiqc [DEBUG ] No samples found: kraken [2021-11-18 21:23:14,548] multiqc [DEBUG ] No samples found: malt [2021-11-18 21:23:14,552] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-18 21:23:14,556] multiqc [DEBUG ] No samples found: sickle [2021-11-18 21:23:14,560] multiqc [DEBUG ] No samples found: skewer [2021-11-18 21:23:14,564] multiqc [DEBUG ] No samples found: sortmerna [2021-11-18 21:23:14,567] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-18 21:23:14,572] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-18 21:23:14,575] multiqc [DEBUG ] No samples found: afterqc [2021-11-18 21:23:14,580] multiqc [DEBUG ] No samples found: fastp [2021-11-18 21:23:16,697] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2021-11-18 21:23:16,940] multiqc [DEBUG ] No samples found: pycoqc [2021-11-18 21:23:16,945] multiqc [DEBUG ] No samples found: minionqc [2021-11-18 21:23:16,949] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-18 21:23:16,953] multiqc [DEBUG ] No samples found: clusterflow [2021-11-18 21:23:16,958] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-18 21:23:16,962] multiqc [DEBUG ] No samples found: interop [2021-11-18 21:23:16,967] multiqc [DEBUG ] No samples found: ivar [2021-11-18 21:23:16,971] multiqc [DEBUG ] No samples found: flash [2021-11-18 21:23:16,975] multiqc [DEBUG ] No samples found: seqyclean [2021-11-18 21:23:16,975] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-18 21:23:16,975] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-11-18 21:23:16,975] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-11-18 21:23:16,975] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-18 21:23:17,006] multiqc [INFO ] Compressing plot data [2021-11-18 21:23:17,445] multiqc [INFO ] Report : multiqc_report.html [2021-11-18 21:23:17,446] multiqc [INFO ] Data : multiqc_data [2021-11-18 21:23:17,446] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12141114/tmpez6goiao/multiqc_data' to '/scratch/gencore/logs/html/HLGLLBGXK/merged/multiqc_data' [2021-11-18 21:23:17,578] multiqc [INFO ] MultiQC complete