[2022-06-02 00:59:48,441] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-02 00:59:48,441] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-02 00:59:48,441] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-02 00:59:48,442] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-02 00:59:48,442] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-02 00:59:48,442] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTCK2BGXL/merged [2022-06-02 00:59:49,004] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-02 00:59:49,004] multiqc [INFO ] This is MultiQC v1.9 [2022-06-02 00:59:49,004] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTCK2BGXL/merged [2022-06-02 00:59:49,004] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTCK2BGXL/merged [2022-06-02 00:59:49,004] multiqc [INFO ] Template : default [2022-06-02 00:59:49,004] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-02 00:59:49,004] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTCK2BGXL/merged [2022-06-02 00:59:49,005] 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 [2022-06-02 00:59:49,005] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20404573/tmph08cqflc [2022-06-02 00:59:49,113] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA05_fastqc.html [2022-06-02 00:59:49,116] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA05_fastqc.html [2022-06-02 00:59:49,159] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA03_fastqc.html [2022-06-02 00:59:49,161] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA03_fastqc.html [2022-06-02 00:59:49,202] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA01_fastqc.html [2022-06-02 00:59:49,203] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA01_fastqc.html [2022-06-02 00:59:49,243] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-02 00:59:49,244] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-06-02 00:59:49,356] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM370_fastqc.html [2022-06-02 00:59:49,358] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM370_fastqc.html [2022-06-02 00:59:49,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM363_fastqc.html [2022-06-02 00:59:49,398] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM363_fastqc.html [2022-06-02 00:59:49,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA11_fastqc.html [2022-06-02 00:59:49,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA11_fastqc.html [2022-06-02 00:59:49,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA07_fastqc.html [2022-06-02 00:59:49,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA07_fastqc.html [2022-06-02 00:59:49,523] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_undetermined_fastqc.html [2022-06-02 00:59:49,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_undetermined_fastqc.html [2022-06-02 00:59:49,564] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA12_fastqc.html [2022-06-02 00:59:49,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA12_fastqc.html [2022-06-02 00:59:49,606] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA13_fastqc.html [2022-06-02 00:59:49,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA13_fastqc.html [2022-06-02 00:59:49,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA02_fastqc.html [2022-06-02 00:59:49,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA02_fastqc.html [2022-06-02 00:59:49,690] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM367_fastqc.html [2022-06-02 00:59:49,692] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM367_fastqc.html [2022-06-02 00:59:49,730] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA10_fastqc.html [2022-06-02 00:59:49,732] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA10_fastqc.html [2022-06-02 00:59:49,774] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA08_fastqc.html [2022-06-02 00:59:49,775] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA08_fastqc.html [2022-06-02 00:59:49,816] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM362_fastqc.html [2022-06-02 00:59:49,817] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM362_fastqc.html [2022-06-02 00:59:49,857] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA06_fastqc.html [2022-06-02 00:59:49,858] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA06_fastqc.html [2022-06-02 00:59:49,899] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM369_fastqc.html [2022-06-02 00:59:49,901] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM369_fastqc.html [2022-06-02 00:59:49,939] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA09_fastqc.html [2022-06-02 00:59:49,941] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA09_fastqc.html [2022-06-02 00:59:49,981] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM366_fastqc.html [2022-06-02 00:59:49,983] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM366_fastqc.html [2022-06-02 00:59:50,022] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM364_fastqc.html [2022-06-02 00:59:50,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM364_fastqc.html [2022-06-02 00:59:50,063] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM365_fastqc.html [2022-06-02 00:59:50,064] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM365_fastqc.html [2022-06-02 00:59:50,104] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM368_fastqc.html [2022-06-02 00:59:50,106] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_AKM368_fastqc.html [2022-06-02 00:59:50,145] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA04_fastqc.html [2022-06-02 00:59:50,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTCK2BGXL_n01_RA04_fastqc.html [2022-06-02 00:59:50,701] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-02 00:59:50,702] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-02 00:59:50,710] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-02 00:59:50,721] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 23 samples (table) [2022-06-02 00:59:50,731] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-02 00:59:50,738] multiqc [DEBUG ] No samples found: conpair [2022-06-02 00:59:50,744] multiqc [DEBUG ] No samples found: peddy [2022-06-02 00:59:50,750] multiqc [DEBUG ] No samples found: somalier [2022-06-02 00:59:50,755] multiqc [DEBUG ] No samples found: methylQA [2022-06-02 00:59:50,766] multiqc [DEBUG ] No samples found: mosdepth [2022-06-02 00:59:50,771] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-02 00:59:50,774] multiqc [DEBUG ] No samples found: qualimap [2022-06-02 00:59:50,780] multiqc [DEBUG ] No samples found: preseq [2022-06-02 00:59:50,785] multiqc [DEBUG ] No samples found: quast [2022-06-02 00:59:50,791] multiqc [DEBUG ] No samples found: qorts [2022-06-02 00:59:50,796] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-02 00:59:50,801] multiqc [DEBUG ] No samples found: rockhopper [2022-06-02 00:59:50,807] multiqc [DEBUG ] No samples found: rsem [2022-06-02 00:59:50,825] multiqc [DEBUG ] No samples found: rseqc [2022-06-02 00:59:50,832] multiqc [DEBUG ] No samples found: busco [2022-06-02 00:59:50,839] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-02 00:59:50,845] multiqc [DEBUG ] No samples found: disambiguate [2022-06-02 00:59:50,853] multiqc [DEBUG ] No samples found: supernova [2022-06-02 00:59:50,875] multiqc [DEBUG ] No samples found: deeptools [2022-06-02 00:59:50,882] multiqc [DEBUG ] No samples found: sargasso [2022-06-02 00:59:50,888] multiqc [DEBUG ] No samples found: verifybamid [2022-06-02 00:59:50,893] multiqc [DEBUG ] No samples found: mirtrace [2022-06-02 00:59:50,899] multiqc [DEBUG ] No samples found: happy [2022-06-02 00:59:50,905] multiqc [DEBUG ] No samples found: mirtop [2022-06-02 00:59:50,915] multiqc [DEBUG ] No samples found: homer [2022-06-02 00:59:50,921] multiqc [DEBUG ] No samples found: macs2 [2022-06-02 00:59:50,929] multiqc [DEBUG ] No samples found: theta2 [2022-06-02 00:59:50,937] multiqc [DEBUG ] No samples found: snpeff [2022-06-02 00:59:50,947] multiqc [DEBUG ] No samples found: gatk [2022-06-02 00:59:50,952] multiqc [DEBUG ] No samples found: htseq [2022-06-02 00:59:50,960] multiqc [DEBUG ] No samples found: bcftools [2022-06-02 00:59:50,966] multiqc [DEBUG ] No samples found: featureCounts [2022-06-02 00:59:50,974] multiqc [DEBUG ] No samples found: fgbio [2022-06-02 00:59:50,992] multiqc [DEBUG ] No samples found: dragen [2022-06-02 00:59:50,997] multiqc [DEBUG ] No samples found: dedup [2022-06-02 00:59:51,004] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-02 00:59:51,031] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-02 00:59:51,037] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-02 00:59:51,039] multiqc [DEBUG ] No samples found: picard [2022-06-02 00:59:51,046] multiqc [DEBUG ] No samples found: prokka [2022-06-02 00:59:51,052] multiqc [DEBUG ] No samples found: samblaster [2022-06-02 00:59:51,065] multiqc [DEBUG ] No samples found: samtools [2022-06-02 00:59:51,071] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-02 00:59:51,077] multiqc [DEBUG ] No samples found: bamtools [2022-06-02 00:59:51,085] multiqc [DEBUG ] No samples found: jellyfish [2022-06-02 00:59:51,098] multiqc [DEBUG ] No samples found: vcftools [2022-06-02 00:59:51,105] multiqc [DEBUG ] No samples found: longranger [2022-06-02 00:59:51,111] multiqc [DEBUG ] No samples found: stacks [2022-06-02 00:59:51,119] multiqc [DEBUG ] No samples found: varscan2 [2022-06-02 00:59:51,139] multiqc [DEBUG ] No samples found: bbmap [2022-06-02 00:59:51,146] multiqc [DEBUG ] No samples found: bismark [2022-06-02 00:59:51,153] multiqc [DEBUG ] No samples found: biscuit [2022-06-02 00:59:51,159] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-02 00:59:51,167] multiqc [DEBUG ] No samples found: hicup [2022-06-02 00:59:51,173] multiqc [DEBUG ] No samples found: hicpro [2022-06-02 00:59:51,179] multiqc [DEBUG ] No samples found: salmon [2022-06-02 00:59:51,184] multiqc [DEBUG ] No samples found: kallisto [2022-06-02 00:59:51,190] multiqc [DEBUG ] No samples found: slamdunk [2022-06-02 00:59:51,195] multiqc [DEBUG ] No samples found: star [2022-06-02 00:59:51,200] multiqc [DEBUG ] No samples found: hisat2 [2022-06-02 00:59:51,205] multiqc [DEBUG ] No samples found: tophat [2022-06-02 00:59:51,211] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-02 00:59:51,216] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-02 00:59:51,221] multiqc [DEBUG ] No samples found: snpsplit [2022-06-02 00:59:51,226] multiqc [DEBUG ] No samples found: kat [2022-06-02 00:59:51,231] multiqc [DEBUG ] No samples found: leehom [2022-06-02 00:59:51,236] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-02 00:59:51,241] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-02 00:59:51,246] multiqc [DEBUG ] No samples found: cutadapt [2022-06-02 00:59:51,252] multiqc [DEBUG ] No samples found: flexbar [2022-06-02 00:59:51,258] multiqc [DEBUG ] No samples found: kaiju [2022-06-02 00:59:51,263] multiqc [DEBUG ] No samples found: kraken [2022-06-02 00:59:51,269] multiqc [DEBUG ] No samples found: malt [2022-06-02 00:59:51,275] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-02 00:59:51,281] multiqc [DEBUG ] No samples found: sickle [2022-06-02 00:59:51,286] multiqc [DEBUG ] No samples found: skewer [2022-06-02 00:59:51,291] multiqc [DEBUG ] No samples found: sortmerna [2022-06-02 00:59:51,297] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-02 00:59:51,305] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-02 00:59:51,312] multiqc [DEBUG ] No samples found: afterqc [2022-06-02 00:59:51,318] multiqc [DEBUG ] No samples found: fastp [2022-06-02 00:59:52,877] multiqc.modules.fastqc.fastqc [INFO ] Found 23 reports [2022-06-02 00:59:53,370] multiqc [DEBUG ] No samples found: pycoqc [2022-06-02 00:59:53,376] multiqc [DEBUG ] No samples found: minionqc [2022-06-02 00:59:53,383] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-02 00:59:53,389] multiqc [DEBUG ] No samples found: clusterflow [2022-06-02 00:59:53,395] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-02 00:59:53,402] multiqc [DEBUG ] No samples found: interop [2022-06-02 00:59:53,407] multiqc [DEBUG ] No samples found: ivar [2022-06-02 00:59:53,412] multiqc [DEBUG ] No samples found: flash [2022-06-02 00:59:53,417] multiqc [DEBUG ] No samples found: seqyclean [2022-06-02 00:59:53,417] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-02 00:59:53,417] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-02 00:59:53,417] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-02 00:59:53,417] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-02 00:59:53,444] multiqc [INFO ] Compressing plot data [2022-06-02 00:59:53,859] multiqc [INFO ] Report : multiqc_report.html [2022-06-02 00:59:53,859] multiqc [INFO ] Data : multiqc_data [2022-06-02 00:59:53,859] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20404573/tmph08cqflc/multiqc_data' to '/scratch/gencore/logs/html/HTCK2BGXL/merged/multiqc_data' [2022-06-02 00:59:58,126] multiqc [INFO ] MultiQC complete