[2021-10-26 14:01:45,522] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-26 14:01:45,523] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-26 14:01:45,523] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-26 14:01:45,524] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-26 14:01:45,524] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-26 14:01:45,524] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK7CCDRXY/merged [2021-10-26 14:01:46,906] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-26 14:01:46,907] multiqc [INFO ] This is MultiQC v1.9 [2021-10-26 14:01:46,907] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK7CCDRXY/merged [2021-10-26 14:01:46,907] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HK7CCDRXY/merged [2021-10-26 14:01:46,907] multiqc [INFO ] Template : default [2021-10-26 14:01:46,907] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-26 14:01:46,907] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HK7CCDRXY/merged [2021-10-26 14:01:46,907] 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 [2021-10-26 14:01:46,907] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11201633/tmphn2onwc0 [2021-10-26 14:01:47,031] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_48H_fastqc.html [2021-10-26 14:01:47,034] multiqc [DEBUG ] File ignored by longranger/invocation because it 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_N-LIM_8H_fastqc.html [2021-10-26 14:01:48,287] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_N-LIM_48H_fastqc.html [2021-10-26 14:01:48,289] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_N-LIM_48H_fastqc.html [2021-10-26 14:01:48,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_N-LIM_24H_fastqc.html [2021-10-26 14:01:48,351] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_N-LIM_24H_fastqc.html [2021-10-26 14:01:48,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_5H_fastqc.html [2021-10-26 14:01:48,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_5H_fastqc.html [2021-10-26 14:01:48,433] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_5H_fastqc.html [2021-10-26 14:01:48,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_5H_fastqc.html [2021-10-26 14:01:48,474] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_5H_fastqc.html [2021-10-26 14:01:48,476] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_5H_fastqc.html [2021-10-26 14:01:48,517] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_5H_fastqc.html [2021-10-26 14:01:48,519] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_5H_fastqc.html [2021-10-26 14:01:48,576] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_11H_fastqc.html [2021-10-26 14:01:48,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_11H_fastqc.html [2021-10-26 14:01:48,619] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_undetermined_fastqc.html [2021-10-26 14:01:48,621] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_undetermined_fastqc.html [2021-10-26 14:01:48,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_C-LIM_11H_fastqc.html [2021-10-26 14:01:48,662] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_C-LIM_11H_fastqc.html [2021-10-26 14:01:48,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_undetermined_fastqc.html [2021-10-26 14:01:48,702] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_undetermined_fastqc.html [2021-10-26 14:01:48,742] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_8H_fastqc.html [2021-10-26 14:01:48,743] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_8H_fastqc.html [2021-10-26 14:01:48,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_48H_fastqc.html [2021-10-26 14:01:48,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_48H_fastqc.html [2021-10-26 14:01:48,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_8H_fastqc.html [2021-10-26 14:01:48,847] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_8H_fastqc.html [2021-10-26 14:01:48,889] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_2H_fastqc.html [2021-10-26 14:01:48,891] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_2H_fastqc.html [2021-10-26 14:01:48,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_C-LIM_24H_fastqc.html [2021-10-26 14:01:48,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_C-LIM_24H_fastqc.html [2021-10-26 14:01:48,991] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_11H_fastqc.html [2021-10-26 14:01:48,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_11H_fastqc.html [2021-10-26 14:01:49,048] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_11H_fastqc.html [2021-10-26 14:01:49,050] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_11H_fastqc.html [2021-10-26 14:01:49,090] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_48H_fastqc.html [2021-10-26 14:01:49,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_YPD_48H_fastqc.html [2021-10-26 14:01:49,134] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_72H_fastqc.html [2021-10-26 14:01:49,136] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_C-LIM_72H_fastqc.html [2021-10-26 14:01:49,177] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_2H_fastqc.html [2021-10-26 14:01:49,179] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_2H_fastqc.html [2021-10-26 14:01:49,230] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_8H_fastqc.html [2021-10-26 14:01:49,232] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n01_CAWT1_YPD_8H_fastqc.html [2021-10-26 14:01:49,271] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_2H_fastqc.html [2021-10-26 14:01:49,273] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_2H_fastqc.html [2021-10-26 14:01:49,336] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_11H_fastqc.html [2021-10-26 14:01:49,338] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK7CCDRXY_n02_CAWT1_N-LIM_11H_fastqc.html [2021-10-26 14:01:49,716] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-26 14:01:49,719] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-26 14:01:49,737] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 22 samples (table) [2021-10-26 14:01:49,739] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-26 14:01:49,749] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-26 14:01:49,756] multiqc [DEBUG ] No samples found: conpair [2021-10-26 14:01:49,763] multiqc [DEBUG ] No samples found: peddy [2021-10-26 14:01:49,769] multiqc [DEBUG ] No samples found: somalier [2021-10-26 14:01:49,775] multiqc [DEBUG ] No samples found: methylQA [2021-10-26 14:01:49,789] multiqc [DEBUG ] No samples found: mosdepth [2021-10-26 14:01:49,797] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-26 14:01:49,802] multiqc [DEBUG ] No samples found: qualimap [2021-10-26 14:01:49,808] multiqc [DEBUG ] No samples found: preseq [2021-10-26 14:01:49,815] multiqc [DEBUG ] No samples found: quast [2021-10-26 14:01:49,822] multiqc [DEBUG ] No samples found: qorts [2021-10-26 14:01:49,829] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-26 14:01:49,838] multiqc [DEBUG ] No samples found: rockhopper [2021-10-26 14:01:49,845] multiqc [DEBUG ] No samples found: rsem [2021-10-26 14:01:49,865] multiqc [DEBUG ] No samples found: rseqc [2021-10-26 14:01:49,871] multiqc [DEBUG ] No samples found: busco [2021-10-26 14:01:49,877] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-26 14:01:49,882] multiqc [DEBUG ] No samples found: disambiguate [2021-10-26 14:01:49,889] multiqc [DEBUG ] No samples found: supernova [2021-10-26 14:01:49,918] multiqc [DEBUG ] No samples found: deeptools [2021-10-26 14:01:49,926] multiqc [DEBUG ] No samples found: sargasso [2021-10-26 14:01:49,932] multiqc [DEBUG ] No samples found: verifybamid [2021-10-26 14:01:49,937] multiqc [DEBUG ] No samples found: mirtrace [2021-10-26 14:01:49,942] multiqc [DEBUG ] No samples found: happy [2021-10-26 14:01:49,949] multiqc [DEBUG ] No samples found: mirtop [2021-10-26 14:01:49,959] multiqc [DEBUG ] No samples found: homer [2021-10-26 14:01:49,966] multiqc [DEBUG ] No samples found: macs2 [2021-10-26 14:01:49,974] multiqc [DEBUG ] No samples found: theta2 [2021-10-26 14:01:49,982] multiqc [DEBUG ] No samples found: snpeff [2021-10-26 14:01:49,993] multiqc [DEBUG ] No samples found: gatk [2021-10-26 14:01:50,000] multiqc [DEBUG ] No samples found: htseq [2021-10-26 14:01:50,009] multiqc [DEBUG ] No samples found: bcftools [2021-10-26 14:01:50,020] multiqc [DEBUG ] No samples found: featureCounts [2021-10-26 14:01:50,033] multiqc [DEBUG ] No samples found: fgbio [2021-10-26 14:01:50,061] multiqc [DEBUG ] No samples found: dragen [2021-10-26 14:01:50,066] multiqc [DEBUG ] No samples found: dedup [2021-10-26 14:01:50,071] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-26 14:01:50,115] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-26 14:01:50,121] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-26 14:01:50,124] multiqc [DEBUG ] No samples found: picard [2021-10-26 14:01:50,131] multiqc [DEBUG ] No samples found: prokka [2021-10-26 14:01:50,138] multiqc [DEBUG ] No samples found: samblaster [2021-10-26 14:01:50,153] multiqc [DEBUG ] No samples found: samtools [2021-10-26 14:01:50,160] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-26 14:01:50,167] multiqc [DEBUG ] No samples found: bamtools [2021-10-26 14:01:50,174] multiqc [DEBUG ] No samples found: jellyfish [2021-10-26 14:01:50,189] multiqc [DEBUG ] No samples found: vcftools [2021-10-26 14:01:50,196] multiqc [DEBUG ] No samples found: longranger [2021-10-26 14:01:50,201] multiqc [DEBUG ] No samples found: stacks [2021-10-26 14:01:50,207] multiqc [DEBUG ] No samples found: varscan2 [2021-10-26 14:01:50,240] multiqc [DEBUG ] No samples found: bbmap [2021-10-26 14:01:50,247] multiqc [DEBUG ] No samples found: bismark [2021-10-26 14:01:50,255] multiqc [DEBUG ] No samples found: biscuit [2021-10-26 14:01:50,263] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-26 14:01:50,271] multiqc [DEBUG ] No samples found: hicup [2021-10-26 14:01:50,277] multiqc [DEBUG ] No samples found: hicpro [2021-10-26 14:01:50,281] multiqc [DEBUG ] No samples found: salmon [2021-10-26 14:01:50,288] multiqc [DEBUG ] No samples found: kallisto [2021-10-26 14:01:50,296] multiqc [DEBUG ] No samples found: slamdunk [2021-10-26 14:01:50,303] multiqc [DEBUG ] No samples found: star [2021-10-26 14:01:50,309] multiqc [DEBUG ] No samples found: hisat2 [2021-10-26 14:01:50,316] multiqc [DEBUG ] No samples found: tophat [2021-10-26 14:01:50,324] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-26 14:01:50,334] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-26 14:01:50,342] multiqc [DEBUG ] No samples found: snpsplit [2021-10-26 14:01:50,347] multiqc [DEBUG ] No samples found: kat [2021-10-26 14:01:50,352] multiqc [DEBUG ] No samples found: leehom [2021-10-26 14:01:50,362] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-26 14:01:50,370] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-26 14:01:50,376] multiqc [DEBUG ] No samples found: cutadapt [2021-10-26 14:01:50,383] multiqc [DEBUG ] No samples found: flexbar [2021-10-26 14:01:50,392] multiqc [DEBUG ] No samples found: kaiju [2021-10-26 14:01:50,398] multiqc [DEBUG ] No samples found: kraken [2021-10-26 14:01:50,403] multiqc [DEBUG ] No samples found: malt [2021-10-26 14:01:50,409] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-26 14:01:50,416] multiqc [DEBUG ] No samples found: sickle [2021-10-26 14:01:50,423] multiqc [DEBUG ] No samples found: skewer [2021-10-26 14:01:50,429] multiqc [DEBUG ] No samples found: sortmerna [2021-10-26 14:01:50,437] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-26 14:01:50,444] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-26 14:01:50,452] multiqc [DEBUG ] No samples found: afterqc [2021-10-26 14:01:50,459] multiqc [DEBUG ] No samples found: fastp [2021-10-26 14:01:53,128] multiqc.modules.fastqc.fastqc [INFO ] Found 44 reports [2021-10-26 14:01:53,741] multiqc [DEBUG ] No samples found: pycoqc [2021-10-26 14:01:53,749] multiqc [DEBUG ] No samples found: minionqc [2021-10-26 14:01:53,756] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-26 14:01:53,763] multiqc [DEBUG ] No samples found: clusterflow [2021-10-26 14:01:53,769] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-26 14:01:53,775] multiqc [DEBUG ] No samples found: interop [2021-10-26 14:01:53,781] multiqc [DEBUG ] No samples found: ivar [2021-10-26 14:01:53,789] multiqc [DEBUG ] No samples found: flash [2021-10-26 14:01:53,799] multiqc [DEBUG ] No samples found: seqyclean [2021-10-26 14:01:53,799] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-26 14:01:53,799] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-26 14:01:53,799] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-26 14:01:53,799] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-26 14:01:53,851] multiqc [INFO ] Compressing plot data [2021-10-26 14:01:54,703] multiqc [INFO ] Report : multiqc_report.html [2021-10-26 14:01:54,703] multiqc [INFO ] Data : multiqc_data [2021-10-26 14:01:54,703] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11201633/tmphn2onwc0/multiqc_data' to '/scratch/gencore/logs/html/HK7CCDRXY/merged/multiqc_data' [2021-10-26 14:01:56,733] multiqc [INFO ] MultiQC complete