[2022-11-17 15:39:25,740] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-17 15:39:25,741] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-17 15:39:25,741] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-17 15:39:25,741] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-17 15:39:25,742] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-17 15:39:25,742] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKYTKDRX2/1 [2022-11-17 15:39:26,147] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-17 15:39:26,147] multiqc [INFO ] This is MultiQC v1.9 [2022-11-17 15:39:26,147] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKYTKDRX2/1 [2022-11-17 15:39:26,147] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKYTKDRX2/1 [2022-11-17 15:39:26,147] multiqc [INFO ] Template : default [2022-11-17 15:39:26,148] 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 15:39:26,148] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKYTKDRX2/1 [2022-11-17 15:39:26,148] 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 15:39:26,148] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27091901/tmpzk6xyaeh [2022-11-17 15:39:26,257] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.01DNAseq_fastqc.html [2022-11-17 15:39:26,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.01DNAseq_fastqc.html [2022-11-17 15:39:26,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_01DNASeq_fastqc.html [2022-11-17 15:39:26,305] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_01DNASeq_fastqc.html [2022-11-17 15:39:26,344] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.04DNAseq_fastqc.html [2022-11-17 15:39:26,346] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.04DNAseq_fastqc.html [2022-11-17 15:39:26,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_03DNASeq_fastqc.html [2022-11-17 15:39:26,387] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_03DNASeq_fastqc.html [2022-11-17 15:39:26,426] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_03DNASeq_fastqc.html [2022-11-17 15:39:26,428] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_03DNASeq_fastqc.html [2022-11-17 15:39:26,483] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_undetermined_fastqc.html [2022-11-17 15:39:26,485] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_undetermined_fastqc.html [2022-11-17 15:39:26,524] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.03DNAseq_fastqc.html [2022-11-17 15:39:26,526] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.03DNAseq_fastqc.html [2022-11-17 15:39:26,565] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_undetermined_fastqc.html [2022-11-17 15:39:26,567] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_undetermined_fastqc.html [2022-11-17 15:39:26,606] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT.02DNASeq_fastqc.html [2022-11-17 15:39:26,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT.02DNASeq_fastqc.html [2022-11-17 15:39:26,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT.02DNASeq_fastqc.html [2022-11-17 15:39:26,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT.02DNASeq_fastqc.html [2022-11-17 15:39:26,689] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_04DNASeq_fastqc.html [2022-11-17 15:39:26,691] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_WT_04DNASeq_fastqc.html [2022-11-17 15:39:26,730] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_04DNASeq_fastqc.html [2022-11-17 15:39:26,732] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_04DNASeq_fastqc.html [2022-11-17 15:39:26,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.02DNAseq_fastqc.html [2022-11-17 15:39:26,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.02DNAseq_fastqc.html [2022-11-17 15:39:26,812] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.04DNAseq_fastqc.html [2022-11-17 15:39:26,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.04DNAseq_fastqc.html [2022-11-17 15:39:26,867] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_01DNASeq_fastqc.html [2022-11-17 15:39:26,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_WT_01DNASeq_fastqc.html [2022-11-17 15:39:26,908] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.02DNAseq_fastqc.html [2022-11-17 15:39:26,910] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n02_N2.col2.02DNAseq_fastqc.html [2022-11-17 15:39:26,950] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.03DNAseq_fastqc.html [2022-11-17 15:39:26,951] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.03DNAseq_fastqc.html [2022-11-17 15:39:26,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.01DNAseq_fastqc.html [2022-11-17 15:39:26,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKYTKDRX2_l01_n01_N2.col2.01DNAseq_fastqc.html [2022-11-17 15:39:27,335] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 15:39:27,336] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-17 15:39:27,344] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-17 15:39:27,348] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 9 samples (table) [2022-11-17 15:39:27,358] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-17 15:39:27,364] multiqc [DEBUG ] No samples found: conpair [2022-11-17 15:39:27,370] multiqc [DEBUG ] No samples found: peddy [2022-11-17 15:39:27,375] multiqc [DEBUG ] No samples found: somalier [2022-11-17 15:39:27,380] multiqc [DEBUG ] No samples found: methylQA [2022-11-17 15:39:27,391] multiqc [DEBUG ] No samples found: mosdepth [2022-11-17 15:39:27,396] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-17 15:39:27,399] multiqc [DEBUG ] No samples found: qualimap [2022-11-17 15:39:27,405] multiqc [DEBUG ] No samples found: preseq [2022-11-17 15:39:27,410] multiqc [DEBUG ] No samples found: quast [2022-11-17 15:39:27,416] multiqc [DEBUG ] No samples found: qorts [2022-11-17 15:39:27,422] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-17 15:39:27,427] multiqc [DEBUG ] No samples found: rockhopper [2022-11-17 15:39:27,434] multiqc [DEBUG ] No samples found: rsem [2022-11-17 15:39:27,450] multiqc [DEBUG ] No samples found: rseqc [2022-11-17 15:39:27,455] multiqc [DEBUG ] No samples found: busco [2022-11-17 15:39:27,460] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-17 15:39:27,465] multiqc [DEBUG ] No samples found: disambiguate [2022-11-17 15:39:27,471] multiqc [DEBUG ] No samples found: supernova [2022-11-17 15:39:27,483] multiqc [DEBUG ] No samples found: deeptools [2022-11-17 15:39:27,488] multiqc [DEBUG ] No samples found: sargasso [2022-11-17 15:39:27,492] multiqc [DEBUG ] No samples found: verifybamid [2022-11-17 15:39:27,497] multiqc [DEBUG ] No samples found: mirtrace [2022-11-17 15:39:27,503] multiqc [DEBUG ] No samples found: happy [2022-11-17 15:39:27,509] multiqc [DEBUG ] No samples found: mirtop [2022-11-17 15:39:27,516] multiqc [DEBUG ] No samples found: homer [2022-11-17 15:39:27,520] multiqc [DEBUG ] No samples found: macs2 [2022-11-17 15:39:27,528] multiqc [DEBUG ] No samples found: theta2 [2022-11-17 15:39:27,534] multiqc [DEBUG ] No samples found: snpeff [2022-11-17 15:39:27,543] multiqc [DEBUG ] No samples found: gatk [2022-11-17 15:39:27,551] multiqc [DEBUG ] No samples found: htseq [2022-11-17 15:39:27,560] multiqc [DEBUG ] No samples found: bcftools [2022-11-17 15:39:27,568] multiqc [DEBUG ] No samples found: featureCounts [2022-11-17 15:39:27,578] multiqc [DEBUG ] No samples found: fgbio [2022-11-17 15:39:27,593] multiqc [DEBUG ] No samples found: dragen [2022-11-17 15:39:27,600] multiqc [DEBUG ] No samples found: dedup [2022-11-17 15:39:27,607] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-17 15:39:27,638] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-17 15:39:27,646] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-17 15:39:27,648] multiqc [DEBUG ] No samples found: picard [2022-11-17 15:39:27,654] multiqc [DEBUG ] No samples found: prokka [2022-11-17 15:39:27,658] multiqc [DEBUG ] No samples found: samblaster [2022-11-17 15:39:27,668] multiqc [DEBUG ] No samples found: samtools [2022-11-17 15:39:27,674] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-17 15:39:27,679] multiqc [DEBUG ] No samples found: bamtools [2022-11-17 15:39:27,683] multiqc [DEBUG ] No samples found: jellyfish [2022-11-17 15:39:27,689] multiqc [DEBUG ] No samples found: vcftools [2022-11-17 15:39:27,694] multiqc [DEBUG ] No samples found: longranger [2022-11-17 15:39:27,701] multiqc [DEBUG ] No samples found: stacks [2022-11-17 15:39:27,711] multiqc [DEBUG ] No samples found: varscan2 [2022-11-17 15:39:27,729] multiqc [DEBUG ] No samples found: bbmap [2022-11-17 15:39:27,737] multiqc [DEBUG ] No samples found: bismark [2022-11-17 15:39:27,744] multiqc [DEBUG ] No samples found: biscuit [2022-11-17 15:39:27,752] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-17 15:39:27,760] multiqc [DEBUG ] No samples found: hicup [2022-11-17 15:39:27,768] multiqc [DEBUG ] No samples found: hicpro [2022-11-17 15:39:27,774] multiqc [DEBUG ] No samples found: salmon [2022-11-17 15:39:27,781] multiqc [DEBUG ] No samples found: kallisto [2022-11-17 15:39:27,787] multiqc [DEBUG ] No samples found: slamdunk [2022-11-17 15:39:27,791] multiqc [DEBUG ] No samples found: star [2022-11-17 15:39:27,798] multiqc [DEBUG ] No samples found: hisat2 [2022-11-17 15:39:27,807] multiqc [DEBUG ] No samples found: tophat [2022-11-17 15:39:27,816] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-17 15:39:27,824] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-17 15:39:27,829] multiqc [DEBUG ] No samples found: snpsplit [2022-11-17 15:39:27,833] multiqc [DEBUG ] No samples found: kat [2022-11-17 15:39:27,837] multiqc [DEBUG ] No samples found: leehom [2022-11-17 15:39:27,844] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-17 15:39:27,851] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-17 15:39:27,857] multiqc [DEBUG ] No samples found: cutadapt [2022-11-17 15:39:27,865] multiqc [DEBUG ] No samples found: flexbar [2022-11-17 15:39:27,872] multiqc [DEBUG ] No samples found: kaiju [2022-11-17 15:39:27,878] multiqc [DEBUG ] No samples found: kraken [2022-11-17 15:39:27,887] multiqc [DEBUG ] No samples found: malt [2022-11-17 15:39:27,893] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-17 15:39:27,899] multiqc [DEBUG ] No samples found: sickle [2022-11-17 15:39:27,903] multiqc [DEBUG ] No samples found: skewer [2022-11-17 15:39:27,907] multiqc [DEBUG ] No samples found: sortmerna [2022-11-17 15:39:27,914] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-17 15:39:27,921] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-17 15:39:27,928] multiqc [DEBUG ] No samples found: afterqc [2022-11-17 15:39:27,935] multiqc [DEBUG ] No samples found: fastp [2022-11-17 15:39:28,419] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2022-11-17 15:39:28,598] multiqc [DEBUG ] No samples found: pycoqc [2022-11-17 15:39:28,602] multiqc [DEBUG ] No samples found: minionqc [2022-11-17 15:39:28,606] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-17 15:39:28,611] multiqc [DEBUG ] No samples found: clusterflow [2022-11-17 15:39:28,616] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-17 15:39:28,620] multiqc [DEBUG ] No samples found: interop [2022-11-17 15:39:28,625] multiqc [DEBUG ] No samples found: ivar [2022-11-17 15:39:28,630] multiqc [DEBUG ] No samples found: flash [2022-11-17 15:39:28,635] multiqc [DEBUG ] No samples found: seqyclean [2022-11-17 15:39:28,635] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-17 15:39:28,635] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-17 15:39:28,635] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-11-17 15:39:28,635] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-17 15:39:28,636] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-17 15:39:28,657] multiqc [INFO ] Compressing plot data [2022-11-17 15:39:28,965] multiqc [INFO ] Report : multiqc_report.html [2022-11-17 15:39:28,965] multiqc [INFO ] Data : multiqc_data [2022-11-17 15:39:28,965] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27091901/tmpzk6xyaeh/multiqc_data' to '/scratch/gencore/logs/html/HKYTKDRX2/1/multiqc_data' [2022-11-17 15:39:29,084] multiqc [INFO ] MultiQC complete