[2022-11-17 15:52:14,037] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-17 15:52:14,037] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-17 15:52:14,037] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-17 15:52:14,038] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-17 15:52:14,038] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-17 15:52:14,038] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKYTKDRX2/2 [2022-11-17 15:52:14,429] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-17 15:52:14,429] multiqc [INFO ] This is MultiQC v1.9 [2022-11-17 15:52:14,429] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKYTKDRX2/2 [2022-11-17 15:52:14,429] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKYTKDRX2/2 [2022-11-17 15:52:14,429] multiqc [INFO ] Template : default [2022-11-17 15:52:14,429] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-17 15:52:14,429] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKYTKDRX2/2 [2022-11-17 15:52:14,429] 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 [2022-11-17 15:52:14,430] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27091901/tmp96zlz2ne [2022-11-17 15:52:14,538] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.01DNAseq_fastqc.html [2022-11-17 15:52:14,541] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.01DNAseq_fastqc.html [2022-11-17 15:52:14,617] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.02DNaseq_fastqc.html [2022-11-17 15:52:14,618] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.02DNaseq_fastqc.html [2022-11-17 15:52:14,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.02DNAseq_fastqc.html [2022-11-17 15:52:14,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.02DNAseq_fastqc.html [2022-11-17 15:52:14,767] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.03DNAseq_fastqc.html [2022-11-17 15:52:14,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.03DNAseq_fastqc.html [2022-11-17 15:52:14,878] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_undetermined_fastqc.html [2022-11-17 15:52:14,880] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_undetermined_fastqc.html [2022-11-17 15:52:14,952] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.04DNAseq_fastqc.html [2022-11-17 15:52:14,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.04DNAseq_fastqc.html [2022-11-17 15:52:15,008] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.04DNAseq_fastqc.html [2022-11-17 15:52:15,010] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.04DNAseq_fastqc.html [2022-11-17 15:52:15,064] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.02DNAseq_fastqc.html [2022-11-17 15:52:15,066] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.02DNAseq_fastqc.html [2022-11-17 15:52:15,266] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.01DNAseq_fastqc.html [2022-11-17 15:52:15,268] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.01DNAseq_fastqc.html [2022-11-17 15:52:15,330] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.01DNAseq_fastqc.html [2022-11-17 15:52:15,332] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.01DNAseq_fastqc.html [2022-11-17 15:52:15,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.04DNAseq_fastqc.html [2022-11-17 15:52:15,387] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.04DNAseq_fastqc.html [2022-11-17 15:52:15,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.03DNAseq_fastqc.html [2022-11-17 15:52:15,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N2.col7.03DNAseq_fastqc.html [2022-11-17 15:52:15,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.03DNAseq_fastqc.html [2022-11-17 15:52:15,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.03DNAseq_fastqc.html [2022-11-17 15:52:15,586] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.01DNAseq_fastqc.html [2022-11-17 15:52:15,588] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.01DNAseq_fastqc.html [2022-11-17 15:52:15,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_undetermined_fastqc.html [2022-11-17 15:52:15,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_undetermined_fastqc.html [2022-11-17 15:52:15,702] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.02DNaseq_fastqc.html [2022-11-17 15:52:15,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n02_N3.02DNaseq_fastqc.html [2022-11-17 15:52:15,759] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.04DNAseq_fastqc.html [2022-11-17 15:52:15,760] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N3.04DNAseq_fastqc.html [2022-11-17 15:52:15,837] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.03DNAseq_fastqc.html [2022-11-17 15:52:15,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l02_n01_N2.col7.03DNAseq_fastqc.html [2022-11-17 15:52:16,176] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 15:52:16,177] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 15:52:16,184] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-17 15:52:16,193] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-17 15:52:16,198] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 9 samples (table) [2022-11-17 15:52:16,201] multiqc [DEBUG ] No samples found: conpair [2022-11-17 15:52:16,205] multiqc [DEBUG ] No samples found: peddy [2022-11-17 15:52:16,208] multiqc [DEBUG ] No samples found: somalier [2022-11-17 15:52:16,211] multiqc [DEBUG ] No samples found: methylQA [2022-11-17 15:52:16,216] multiqc [DEBUG ] No samples found: mosdepth [2022-11-17 15:52:16,219] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-17 15:52:16,222] multiqc [DEBUG ] No samples found: qualimap [2022-11-17 15:52:16,225] multiqc [DEBUG ] No samples found: preseq [2022-11-17 15:52:16,228] multiqc [DEBUG ] No samples found: quast [2022-11-17 15:52:16,231] multiqc [DEBUG ] No samples found: qorts [2022-11-17 15:52:16,234] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-17 15:52:16,237] multiqc [DEBUG ] No samples found: rockhopper [2022-11-17 15:52:16,240] multiqc [DEBUG ] No samples found: rsem [2022-11-17 15:52:16,246] multiqc [DEBUG ] No samples found: rseqc [2022-11-17 15:52:16,249] multiqc [DEBUG ] No samples found: busco [2022-11-17 15:52:16,252] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-17 15:52:16,255] multiqc [DEBUG ] No samples found: disambiguate [2022-11-17 15:52:16,258] multiqc [DEBUG ] No samples found: supernova [2022-11-17 15:52:16,264] multiqc [DEBUG ] No samples found: deeptools [2022-11-17 15:52:16,267] multiqc [DEBUG ] No samples found: sargasso [2022-11-17 15:52:16,270] multiqc [DEBUG ] No samples found: verifybamid [2022-11-17 15:52:16,274] multiqc [DEBUG ] No samples found: mirtrace [2022-11-17 15:52:16,277] multiqc [DEBUG ] No samples found: happy [2022-11-17 15:52:16,280] multiqc [DEBUG ] No samples found: mirtop [2022-11-17 15:52:16,284] multiqc [DEBUG ] No samples found: homer [2022-11-17 15:52:16,287] multiqc [DEBUG ] No samples found: macs2 [2022-11-17 15:52:16,290] multiqc [DEBUG ] No samples found: theta2 [2022-11-17 15:52:16,293] multiqc [DEBUG ] No samples found: snpeff [2022-11-17 15:52:16,297] multiqc [DEBUG ] No samples found: gatk [2022-11-17 15:52:16,300] multiqc [DEBUG ] No samples found: htseq [2022-11-17 15:52:16,303] multiqc [DEBUG ] No samples found: bcftools [2022-11-17 15:52:16,306] multiqc [DEBUG ] No samples found: featureCounts [2022-11-17 15:52:16,310] multiqc [DEBUG ] No samples found: fgbio [2022-11-17 15:52:16,317] multiqc [DEBUG ] No samples found: dragen [2022-11-17 15:52:16,320] multiqc [DEBUG ] No samples found: dedup [2022-11-17 15:52:16,323] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-17 15:52:16,335] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-17 15:52:16,338] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-17 15:52:16,340] multiqc [DEBUG ] No samples found: picard [2022-11-17 15:52:16,343] multiqc [DEBUG ] No samples found: prokka [2022-11-17 15:52:16,346] multiqc [DEBUG ] No samples found: samblaster [2022-11-17 15:52:16,351] multiqc [DEBUG ] No samples found: samtools [2022-11-17 15:52:16,354] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-17 15:52:16,357] multiqc [DEBUG ] No samples found: bamtools [2022-11-17 15:52:16,360] multiqc [DEBUG ] No samples found: jellyfish [2022-11-17 15:52:16,364] multiqc [DEBUG ] No samples found: vcftools [2022-11-17 15:52:16,368] multiqc [DEBUG ] No samples found: longranger [2022-11-17 15:52:16,371] multiqc [DEBUG ] No samples found: stacks [2022-11-17 15:52:16,374] multiqc [DEBUG ] No samples found: varscan2 [2022-11-17 15:52:16,380] multiqc [DEBUG ] No samples found: bbmap [2022-11-17 15:52:16,383] multiqc [DEBUG ] No samples found: bismark [2022-11-17 15:52:16,387] multiqc [DEBUG ] No samples found: biscuit [2022-11-17 15:52:16,390] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-17 15:52:16,394] multiqc [DEBUG ] No samples found: hicup [2022-11-17 15:52:16,397] multiqc [DEBUG ] No samples found: hicpro [2022-11-17 15:52:16,400] multiqc [DEBUG ] No samples found: salmon [2022-11-17 15:52:16,403] multiqc [DEBUG ] No samples found: kallisto [2022-11-17 15:52:16,406] multiqc [DEBUG ] No samples found: slamdunk [2022-11-17 15:52:16,409] multiqc [DEBUG ] No samples found: star [2022-11-17 15:52:16,412] multiqc [DEBUG ] No samples found: hisat2 [2022-11-17 15:52:16,416] multiqc [DEBUG ] No samples found: tophat [2022-11-17 15:52:16,419] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-17 15:52:16,422] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-17 15:52:16,425] multiqc [DEBUG ] No samples found: snpsplit [2022-11-17 15:52:16,428] multiqc [DEBUG ] No samples found: kat [2022-11-17 15:52:16,431] multiqc [DEBUG ] No samples found: leehom [2022-11-17 15:52:16,434] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-17 15:52:16,437] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-17 15:52:16,440] multiqc [DEBUG ] No samples found: cutadapt [2022-11-17 15:52:16,443] multiqc [DEBUG ] No samples found: flexbar [2022-11-17 15:52:16,446] multiqc [DEBUG ] No samples found: kaiju [2022-11-17 15:52:16,449] multiqc [DEBUG ] No samples found: kraken [2022-11-17 15:52:16,452] multiqc [DEBUG ] No samples found: malt [2022-11-17 15:52:16,455] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-17 15:52:16,458] multiqc [DEBUG ] No samples found: sickle [2022-11-17 15:52:16,461] multiqc [DEBUG ] No samples found: skewer [2022-11-17 15:52:16,464] multiqc [DEBUG ] No samples found: sortmerna [2022-11-17 15:52:16,467] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-17 15:52:16,470] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-17 15:52:16,473] multiqc [DEBUG ] No samples found: afterqc [2022-11-17 15:52:16,476] multiqc [DEBUG ] No samples found: fastp [2022-11-17 15:52:17,885] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2022-11-17 15:52:18,061] multiqc [DEBUG ] No samples found: pycoqc [2022-11-17 15:52:18,064] multiqc [DEBUG ] No samples found: minionqc [2022-11-17 15:52:18,067] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-17 15:52:18,070] multiqc [DEBUG ] No samples found: clusterflow [2022-11-17 15:52:18,073] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-17 15:52:18,077] multiqc [DEBUG ] No samples found: interop [2022-11-17 15:52:18,080] multiqc [DEBUG ] No samples found: ivar [2022-11-17 15:52:18,083] multiqc [DEBUG ] No samples found: flash [2022-11-17 15:52:18,086] multiqc [DEBUG ] No samples found: seqyclean [2022-11-17 15:52:18,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-17 15:52:18,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-17 15:52:18,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-17 15:52:18,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2022-11-17 15:52:18,086] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-17 15:52:18,108] multiqc [INFO ] Compressing plot data [2022-11-17 15:52:18,418] multiqc [INFO ] Report : multiqc_report.html [2022-11-17 15:52:18,418] multiqc [INFO ] Data : multiqc_data [2022-11-17 15:52:18,418] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27091901/tmp96zlz2ne/multiqc_data' to '/scratch/gencore/logs/html/HKYTKDRX2/2/multiqc_data' [2022-11-17 15:52:18,518] multiqc [INFO ] MultiQC complete