[2021-01-15 05:00:37,844] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-01-15 05:00:37,845] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-01-15 05:00:37,845] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-15 05:00:37,845] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-01-15 05:00:37,845] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-01-15 05:00:37,846] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCTDRXX/2 [2021-01-15 05:00:39,147] multiqc [DEBUG ] Latest MultiQC version is v1.9 [2021-01-15 05:00:39,147] multiqc [INFO ] This is MultiQC v1.9 [2021-01-15 05:00:39,147] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTHCTDRXX/2 [2021-01-15 05:00:39,147] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTHCTDRXX/2 [2021-01-15 05:00:39,147] multiqc [INFO ] Template : default [2021-01-15 05:00:39,148] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-01-15 05:00:39,148] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTHCTDRXX/2 [2021-01-15 05:00:39,148] 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 [2021-01-15 05:00:39,148] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-1143371/tmpuc1rmz_q [2021-01-15 05:00:39,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-minusN-01_fastqc.html [2021-01-15 05:00:39,241] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-minusN-01_fastqc.html [2021-01-15 05:00:39,289] multiqc [DEBUG ] File ignored by 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[2021-01-15 05:00:40,191] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_undetermined_fastqc.html [2021-01-15 05:00:40,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-minusN-03_fastqc.html [2021-01-15 05:00:40,231] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-minusN-03_fastqc.html [2021-01-15 05:00:40,276] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-01_fastqc.html [2021-01-15 05:00:40,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-01_fastqc.html [2021-01-15 05:00:40,322] multiqc [DEBUG ] File 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HTHCTDRXX_l02_n01_ZmTARGET.20190625-3125-minusN-03_fastqc.html [2021-01-15 05:00:40,941] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3687-minusN-03_fastqc.html [2021-01-15 05:00:40,943] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3687-minusN-03_fastqc.html [2021-01-15 05:00:40,988] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-1141-plusN-01_fastqc.html [2021-01-15 05:00:40,990] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-1141-plusN-01_fastqc.html [2021-01-15 05:00:41,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-02_fastqc.html [2021-01-15 05:00:41,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-02_fastqc.html [2021-01-15 05:00:41,082] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3125-plusN-02_fastqc.html [2021-01-15 05:00:41,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3125-plusN-02_fastqc.html [2021-01-15 05:00:41,129] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3125-plusN-03_fastqc.html [2021-01-15 05:00:41,130] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3125-plusN-03_fastqc.html [2021-01-15 05:00:41,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-04_fastqc.html [2021-01-15 05:00:41,181] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-p1107NLSGFP-minusN-04_fastqc.html [2021-01-15 05:00:41,228] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-4432-minusN-02_fastqc.html [2021-01-15 05:00:41,230] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-4432-minusN-02_fastqc.html [2021-01-15 05:00:41,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-plusN-02_fastqc.html [2021-01-15 05:00:41,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-plusN-02_fastqc.html [2021-01-15 05:00:41,322] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-4432-plusN-02_fastqc.html [2021-01-15 05:00:41,324] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-4432-plusN-02_fastqc.html [2021-01-15 05:00:41,370] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-plusN-01_fastqc.html [2021-01-15 05:00:41,372] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3038-plusN-01_fastqc.html [2021-01-15 05:00:41,418] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3460-minusN-01_fastqc.html [2021-01-15 05:00:41,419] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTHCTDRXX_l02_n01_ZmTARGET.20190625-3460-minusN-01_fastqc.html [2021-01-15 05:00:41,697] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-15 05:00:41,697] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-01-15 05:00:41,704] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-01-15 05:00:41,714] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-01-15 05:00:41,734] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 45 samples (table) [2021-01-15 05:00:41,738] multiqc [DEBUG ] No samples found: conpair [2021-01-15 05:00:41,740] multiqc [DEBUG ] No samples found: peddy [2021-01-15 05:00:41,743] multiqc [DEBUG ] No samples found: somalier [2021-01-15 05:00:41,746] multiqc [DEBUG ] No samples found: methylQA [2021-01-15 05:00:41,749] multiqc [DEBUG ] No samples found: mosdepth [2021-01-15 05:00:41,752] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-15 05:00:41,755] multiqc [DEBUG ] No samples found: qualimap [2021-01-15 05:00:41,757] multiqc [DEBUG ] No samples found: preseq [2021-01-15 05:00:41,760] multiqc [DEBUG ] No samples found: quast [2021-01-15 05:00:41,763] multiqc [DEBUG ] No samples found: qorts [2021-01-15 05:00:41,766] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-15 05:00:41,768] multiqc [DEBUG ] No samples found: rockhopper [2021-01-15 05:00:41,771] multiqc [DEBUG ] No samples found: rsem [2021-01-15 05:00:41,775] multiqc [DEBUG ] No samples found: rseqc [2021-01-15 05:00:41,778] multiqc [DEBUG ] No samples found: busco [2021-01-15 05:00:41,781] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-15 05:00:41,783] multiqc [DEBUG ] No samples found: disambiguate [2021-01-15 05:00:41,786] multiqc [DEBUG ] No samples found: supernova [2021-01-15 05:00:41,791] multiqc [DEBUG ] No samples found: deeptools [2021-01-15 05:00:41,794] multiqc [DEBUG ] No samples found: sargasso [2021-01-15 05:00:41,796] multiqc [DEBUG ] No samples found: verifybamid [2021-01-15 05:00:41,799] multiqc [DEBUG ] No samples found: mirtrace [2021-01-15 05:00:41,802] multiqc [DEBUG ] No samples found: happy [2021-01-15 05:00:41,804] multiqc [DEBUG ] No samples found: mirtop [2021-01-15 05:00:41,807] multiqc [DEBUG ] No samples found: homer [2021-01-15 05:00:41,810] multiqc [DEBUG ] No samples found: macs2 [2021-01-15 05:00:41,813] multiqc [DEBUG ] No samples found: theta2 [2021-01-15 05:00:41,815] multiqc [DEBUG ] No samples found: snpeff [2021-01-15 05:00:41,819] multiqc [DEBUG ] No samples found: gatk [2021-01-15 05:00:41,821] multiqc [DEBUG ] No samples found: htseq [2021-01-15 05:00:41,824] multiqc [DEBUG ] No samples found: bcftools [2021-01-15 05:00:41,827] multiqc [DEBUG ] No samples found: featureCounts [2021-01-15 05:00:41,830] multiqc [DEBUG ] No samples found: fgbio [2021-01-15 05:00:41,835] multiqc [DEBUG ] No samples found: dragen [2021-01-15 05:00:41,837] multiqc [DEBUG ] No samples found: dedup [2021-01-15 05:00:41,840] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-15 05:00:41,847] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-15 05:00:41,850] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-15 05:00:41,852] multiqc [DEBUG ] No samples found: picard [2021-01-15 05:00:41,855] multiqc [DEBUG ] No samples found: prokka [2021-01-15 05:00:41,857] multiqc [DEBUG ] No samples found: samblaster [2021-01-15 05:00:41,861] multiqc [DEBUG ] No samples found: samtools [2021-01-15 05:00:41,863] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-15 05:00:41,866] multiqc [DEBUG ] No samples found: bamtools [2021-01-15 05:00:41,869] multiqc [DEBUG ] No samples found: jellyfish [2021-01-15 05:00:41,872] multiqc [DEBUG ] No samples found: vcftools [2021-01-15 05:00:41,875] multiqc [DEBUG ] No samples found: longranger [2021-01-15 05:00:41,878] multiqc [DEBUG ] No samples found: stacks [2021-01-15 05:00:41,880] multiqc [DEBUG ] No samples found: varscan2 [2021-01-15 05:00:41,885] multiqc [DEBUG ] No samples found: bbmap [2021-01-15 05:00:41,888] multiqc [DEBUG ] No samples found: bismark [2021-01-15 05:00:41,891] multiqc [DEBUG ] No samples found: biscuit [2021-01-15 05:00:41,894] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-15 05:00:41,896] multiqc [DEBUG ] No samples found: hicup [2021-01-15 05:00:41,899] multiqc [DEBUG ] No samples found: hicpro [2021-01-15 05:00:41,902] multiqc [DEBUG ] No samples found: salmon [2021-01-15 05:00:41,904] multiqc [DEBUG ] No samples found: kallisto [2021-01-15 05:00:41,907] multiqc [DEBUG ] No samples found: slamdunk [2021-01-15 05:00:41,910] multiqc [DEBUG ] No samples found: star [2021-01-15 05:00:41,912] multiqc [DEBUG ] No samples found: hisat2 [2021-01-15 05:00:41,915] multiqc [DEBUG ] No samples found: tophat [2021-01-15 05:00:41,918] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-15 05:00:41,920] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-15 05:00:41,923] multiqc [DEBUG ] No samples found: snpsplit [2021-01-15 05:00:41,926] multiqc [DEBUG ] No samples found: kat [2021-01-15 05:00:41,928] multiqc [DEBUG ] No samples found: leehom [2021-01-15 05:00:41,931] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-15 05:00:41,934] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-15 05:00:41,936] multiqc [DEBUG ] No samples found: cutadapt [2021-01-15 05:00:41,939] multiqc [DEBUG ] No samples found: flexbar [2021-01-15 05:00:41,942] multiqc [DEBUG ] No samples found: kaiju [2021-01-15 05:00:41,944] multiqc [DEBUG ] No samples found: kraken [2021-01-15 05:00:41,947] multiqc [DEBUG ] No samples found: malt [2021-01-15 05:00:41,950] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-15 05:00:41,952] multiqc [DEBUG ] No samples found: sickle [2021-01-15 05:00:41,955] multiqc [DEBUG ] No samples found: skewer [2021-01-15 05:00:41,958] multiqc [DEBUG ] No samples found: sortmerna [2021-01-15 05:00:41,960] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-15 05:00:41,963] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-15 05:00:41,965] multiqc [DEBUG ] No samples found: afterqc [2021-01-15 05:00:41,968] multiqc [DEBUG ] No samples found: fastp [2021-01-15 05:00:43,139] multiqc.modules.fastqc.fastqc [INFO ] Found 45 reports [2021-01-15 05:00:44,030] multiqc [DEBUG ] No samples found: pycoqc [2021-01-15 05:00:44,034] multiqc [DEBUG ] No samples found: minionqc [2021-01-15 05:00:44,036] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-01-15 05:00:44,039] multiqc [DEBUG ] No samples found: clusterflow [2021-01-15 05:00:44,042] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-15 05:00:44,045] multiqc [DEBUG ] No samples found: interop [2021-01-15 05:00:44,047] multiqc [DEBUG ] No samples found: ivar [2021-01-15 05:00:44,050] multiqc [DEBUG ] No samples found: flash [2021-01-15 05:00:44,053] multiqc [DEBUG ] No samples found: seqyclean [2021-01-15 05:00:44,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-01-15 05:00:44,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-01-15 05:00:44,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-01-15 05:00:44,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2021-01-15 05:00:44,053] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-01-15 05:00:44,105] multiqc [INFO ] Compressing plot data [2021-01-15 05:00:44,895] multiqc [INFO ] Report : multiqc_report.html [2021-01-15 05:00:44,895] multiqc [INFO ] Data : multiqc_data [2021-01-15 05:00:44,895] multiqc [DEBUG ] Moving data file from '/state/partition1/job-1143371/tmpuc1rmz_q/multiqc_data' to '/scratch/gencore/logs/html/HTHCTDRXX/2/multiqc_data' [2021-01-15 05:00:48,602] multiqc [INFO ] MultiQC complete