[2022-01-05 08:43:50,769] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-01-05 08:43:50,769] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-01-05 08:43:50,769] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-01-05 08:43:50,770] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-01-05 08:43:50,771] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-01-05 08:43:50,771] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWN2LBGXK/merged [2022-01-05 08:43:52,295] multiqc [WARNING] MultiQC Version v1.11 now available! [2022-01-05 08:43:52,296] multiqc [INFO ] This is MultiQC v1.9 [2022-01-05 08:43:52,297] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HWN2LBGXK/merged [2022-01-05 08:43:52,297] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HWN2LBGXK/merged [2022-01-05 08:43:52,297] multiqc [INFO ] Template : default [2022-01-05 08:43:52,297] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-01-05 08:43:52,297] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HWN2LBGXK/merged [2022-01-05 08:43:52,298] 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 [2022-01-05 08:43:52,299] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-13574248/tmpqsxp3wdc [2022-01-05 08:43:52,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA34___fastqc.html [2022-01-05 08:43:52,440] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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[2022-01-05 08:43:53,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA30___fastqc.html [2022-01-05 08:43:53,698] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA22___fastqc.html [2022-01-05 08:43:53,700] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA22___fastqc.html [2022-01-05 08:43:53,743] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA36___fastqc.html [2022-01-05 08:43:53,745] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA36___fastqc.html [2022-01-05 08:43:53,792] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_DJ88___fastqc.html [2022-01-05 08:43:53,794] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_DJ88___fastqc.html [2022-01-05 08:43:53,837] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA22___fastqc.html [2022-01-05 08:43:53,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA22___fastqc.html [2022-01-05 08:43:53,882] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_DJ87___fastqc.html [2022-01-05 08:43:53,884] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_DJ87___fastqc.html [2022-01-05 08:43:53,929] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA21___fastqc.html [2022-01-05 08:43:53,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA21___fastqc.html [2022-01-05 08:43:53,973] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_undetermined_fastqc.html [2022-01-05 08:43:53,975] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_undetermined_fastqc.html [2022-01-05 08:43:54,016] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA37___fastqc.html [2022-01-05 08:43:54,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA37___fastqc.html [2022-01-05 08:43:54,063] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA19___fastqc.html [2022-01-05 08:43:54,065] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA19___fastqc.html [2022-01-05 08:43:54,109] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA37___fastqc.html [2022-01-05 08:43:54,111] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA37___fastqc.html [2022-01-05 08:43:54,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA32___fastqc.html [2022-01-05 08:43:54,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA32___fastqc.html [2022-01-05 08:43:54,207] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA33___fastqc.html [2022-01-05 08:43:54,208] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA33___fastqc.html [2022-01-05 08:43:54,255] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA31___fastqc.html [2022-01-05 08:43:54,257] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA31___fastqc.html [2022-01-05 08:43:54,304] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA20___fastqc.html [2022-01-05 08:43:54,306] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n02_AA20___fastqc.html [2022-01-05 08:43:54,349] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_DJ89___fastqc.html [2022-01-05 08:43:54,351] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_DJ89___fastqc.html [2022-01-05 08:43:54,394] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA33___fastqc.html [2022-01-05 08:43:54,396] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_AA33___fastqc.html [2022-01-05 08:43:54,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HWN2LBGXK_n01_DJ87___fastqc.html [2022-01-05 08:43:54,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HWN2LBGXK_n01_DJ87___fastqc.html [2022-01-05 08:43:54,867] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-05 08:43:54,868] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-01-05 08:43:54,884] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 18 samples (table) [2022-01-05 08:43:54,885] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-01-05 08:43:54,895] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-01-05 08:43:54,900] multiqc [DEBUG ] No samples found: conpair [2022-01-05 08:43:54,906] multiqc [DEBUG ] No samples found: peddy [2022-01-05 08:43:54,916] multiqc [DEBUG ] No samples found: somalier [2022-01-05 08:43:54,927] multiqc [DEBUG ] No samples found: methylQA [2022-01-05 08:43:54,938] multiqc [DEBUG ] No samples found: mosdepth [2022-01-05 08:43:54,943] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-01-05 08:43:54,947] multiqc [DEBUG ] No samples found: qualimap [2022-01-05 08:43:54,952] multiqc [DEBUG ] No samples found: preseq [2022-01-05 08:43:54,958] multiqc [DEBUG ] No samples found: quast [2022-01-05 08:43:54,963] multiqc [DEBUG ] No samples found: qorts [2022-01-05 08:43:54,969] multiqc [DEBUG ] No samples found: rna_seqc [2022-01-05 08:43:54,974] multiqc [DEBUG ] No samples found: rockhopper [2022-01-05 08:43:54,979] multiqc [DEBUG ] No samples found: rsem [2022-01-05 08:43:54,993] multiqc [DEBUG ] No samples found: rseqc [2022-01-05 08:43:54,998] multiqc [DEBUG ] No samples found: busco [2022-01-05 08:43:55,003] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-01-05 08:43:55,009] multiqc [DEBUG ] No samples found: disambiguate [2022-01-05 08:43:55,014] multiqc [DEBUG ] No samples found: supernova [2022-01-05 08:43:55,029] multiqc [DEBUG ] No samples found: deeptools [2022-01-05 08:43:55,036] multiqc [DEBUG ] No samples found: sargasso [2022-01-05 08:43:55,042] multiqc [DEBUG ] No samples found: verifybamid [2022-01-05 08:43:55,048] multiqc [DEBUG ] No samples found: mirtrace [2022-01-05 08:43:55,054] multiqc [DEBUG ] No samples found: happy [2022-01-05 08:43:55,059] multiqc [DEBUG ] No samples found: mirtop [2022-01-05 08:43:55,066] multiqc [DEBUG ] No samples found: homer [2022-01-05 08:43:55,072] multiqc [DEBUG ] No samples found: macs2 [2022-01-05 08:43:55,077] multiqc [DEBUG ] No samples found: theta2 [2022-01-05 08:43:55,082] multiqc [DEBUG ] No samples found: snpeff [2022-01-05 08:43:55,090] multiqc [DEBUG ] No samples found: gatk [2022-01-05 08:43:55,095] multiqc [DEBUG ] No samples found: htseq [2022-01-05 08:43:55,101] multiqc [DEBUG ] No samples found: bcftools [2022-01-05 08:43:55,106] multiqc [DEBUG ] No samples found: featureCounts [2022-01-05 08:43:55,113] multiqc [DEBUG ] No samples found: fgbio [2022-01-05 08:43:55,134] multiqc [DEBUG ] No samples found: dragen [2022-01-05 08:43:55,144] multiqc [DEBUG ] No samples found: dedup [2022-01-05 08:43:55,151] multiqc [DEBUG ] No samples found: damageprofiler [2022-01-05 08:43:55,179] multiqc [DEBUG ] No samples found: biobambam2 [2022-01-05 08:43:55,185] multiqc [DEBUG ] No samples found: mtnucratio [2022-01-05 08:43:55,188] multiqc [DEBUG ] No samples found: picard [2022-01-05 08:43:55,193] multiqc [DEBUG ] No samples found: prokka [2022-01-05 08:43:55,198] multiqc [DEBUG ] No samples found: samblaster [2022-01-05 08:43:55,212] multiqc [DEBUG ] No samples found: samtools [2022-01-05 08:43:55,217] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-01-05 08:43:55,223] multiqc [DEBUG ] No samples found: bamtools [2022-01-05 08:43:55,228] multiqc [DEBUG ] No samples found: jellyfish [2022-01-05 08:43:55,239] multiqc [DEBUG ] No samples found: vcftools [2022-01-05 08:43:55,245] multiqc [DEBUG ] No samples found: longranger [2022-01-05 08:43:55,250] multiqc [DEBUG ] No samples found: stacks [2022-01-05 08:43:55,255] multiqc [DEBUG ] No samples found: varscan2 [2022-01-05 08:43:55,271] multiqc [DEBUG ] No samples found: bbmap [2022-01-05 08:43:55,278] multiqc [DEBUG ] No samples found: bismark [2022-01-05 08:43:55,283] multiqc [DEBUG ] No samples found: biscuit [2022-01-05 08:43:55,289] multiqc [DEBUG ] No samples found: hicexplorer [2022-01-05 08:43:55,294] multiqc [DEBUG ] No samples found: hicup [2022-01-05 08:43:55,299] multiqc [DEBUG ] No samples found: hicpro [2022-01-05 08:43:55,304] multiqc [DEBUG ] No samples found: salmon [2022-01-05 08:43:55,309] multiqc [DEBUG ] No samples found: kallisto [2022-01-05 08:43:55,314] multiqc [DEBUG ] No samples found: slamdunk [2022-01-05 08:43:55,319] multiqc [DEBUG ] No samples found: star [2022-01-05 08:43:55,324] multiqc [DEBUG ] No samples found: hisat2 [2022-01-05 08:43:55,329] multiqc [DEBUG ] No samples found: tophat [2022-01-05 08:43:55,336] multiqc [DEBUG ] No samples found: bowtie2 [2022-01-05 08:43:55,341] multiqc [DEBUG ] No samples found: bowtie1 [2022-01-05 08:43:55,346] multiqc [DEBUG ] No samples found: snpsplit [2022-01-05 08:43:55,350] multiqc [DEBUG ] No samples found: kat [2022-01-05 08:43:55,356] multiqc [DEBUG ] No samples found: leehom [2022-01-05 08:43:55,366] multiqc [DEBUG ] No samples found: adapterRemoval [2022-01-05 08:43:55,373] multiqc [DEBUG ] No samples found: clipandmerge [2022-01-05 08:43:55,379] multiqc [DEBUG ] No samples found: cutadapt [2022-01-05 08:43:55,383] multiqc [DEBUG ] No samples found: flexbar [2022-01-05 08:43:55,388] multiqc [DEBUG ] No samples found: kaiju [2022-01-05 08:43:55,393] multiqc [DEBUG ] No samples found: kraken [2022-01-05 08:43:55,399] multiqc [DEBUG ] No samples found: malt [2022-01-05 08:43:55,404] multiqc [DEBUG ] No samples found: trimmomatic [2022-01-05 08:43:55,409] multiqc [DEBUG ] No samples found: sickle [2022-01-05 08:43:55,413] multiqc [DEBUG ] No samples found: skewer [2022-01-05 08:43:55,418] multiqc [DEBUG ] No samples found: sortmerna [2022-01-05 08:43:55,422] multiqc [DEBUG ] No samples found: biobloomtools [2022-01-05 08:43:55,427] multiqc [DEBUG ] No samples found: fastq_screen [2022-01-05 08:43:55,432] multiqc [DEBUG ] No samples found: afterqc [2022-01-05 08:43:55,438] multiqc [DEBUG ] No samples found: fastp [2022-01-05 08:43:57,869] multiqc.modules.fastqc.fastqc [INFO ] Found 36 reports [2022-01-05 08:43:58,625] multiqc [DEBUG ] No samples found: pycoqc [2022-01-05 08:43:58,630] multiqc [DEBUG ] No samples found: minionqc [2022-01-05 08:43:58,635] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-01-05 08:43:58,640] multiqc [DEBUG ] No samples found: clusterflow [2022-01-05 08:43:58,645] multiqc [DEBUG ] No samples found: bcl2fastq [2022-01-05 08:43:58,651] multiqc [DEBUG ] No samples found: interop [2022-01-05 08:43:58,655] multiqc [DEBUG ] No samples found: ivar [2022-01-05 08:43:58,660] multiqc [DEBUG ] No samples found: flash [2022-01-05 08:43:58,665] multiqc [DEBUG ] No samples found: seqyclean [2022-01-05 08:43:58,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-01-05 08:43:58,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-01-05 08:43:58,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-01-05 08:43:58,665] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-01-05 08:43:58,707] multiqc [INFO ] Compressing plot data [2022-01-05 08:43:59,366] multiqc [INFO ] Report : multiqc_report.html [2022-01-05 08:43:59,366] multiqc [INFO ] Data : multiqc_data [2022-01-05 08:43:59,366] multiqc [DEBUG ] Moving data file from '/state/partition1/job-13574248/tmpqsxp3wdc/multiqc_data' to '/scratch/gencore/logs/html/HWN2LBGXK/merged/multiqc_data' [2022-01-05 08:43:59,528] multiqc [INFO ] MultiQC complete