[2021-09-30 21:16:48,519] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-30 21:16:48,520] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-30 21:16:48,520] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-30 21:16:48,521] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-30 21:16:48,521] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-30 21:16:48,521] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGW75DRXY/1 [2021-09-30 21:16:49,904] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-30 21:16:49,904] multiqc [INFO ] This is MultiQC v1.9 [2021-09-30 21:16:49,904] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGW75DRXY/1 [2021-09-30 21:16:49,904] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGW75DRXY/1 [2021-09-30 21:16:49,904] multiqc [INFO ] Template : default [2021-09-30 21:16:49,904] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-30 21:16:49,904] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGW75DRXY/1 [2021-09-30 21:16:49,905] 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 [2021-09-30 21:16:49,905] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10445661/tmpy9fk8s9z [2021-09-30 21:16:50,055] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_undetermined_fastqc.html [2021-09-30 21:16:50,058] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_undetermined_fastqc.html [2021-09-30 21:16:50,118] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0001_fastqc.html [2021-09-30 21:16:50,120] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0001_fastqc.html [2021-09-30 21:16:50,161] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-30 21:16:50,163] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-30 21:16:50,225] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0001_fastqc.html [2021-09-30 21:16:50,227] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0001_fastqc.html [2021-09-30 21:16:50,316] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0002_fastqc.html [2021-09-30 21:16:50,318] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0002_fastqc.html [2021-09-30 21:16:50,391] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0003._fastqc.html [2021-09-30 21:16:50,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_N1_0003._fastqc.html [2021-09-30 21:16:50,449] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0001_fastqc.html [2021-09-30 21:16:50,451] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0001_fastqc.html [2021-09-30 21:16:50,507] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_undetermined_fastqc.html [2021-09-30 21:16:50,509] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_undetermined_fastqc.html [2021-09-30 21:16:50,552] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0001_fastqc.html [2021-09-30 21:16:50,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0001_fastqc.html [2021-09-30 21:16:50,599] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0004_fastqc.html [2021-09-30 21:16:50,601] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0004_fastqc.html [2021-09-30 21:16:50,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0002_fastqc.html [2021-09-30 21:16:50,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0002_fastqc.html [2021-09-30 21:16:50,695] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0003_fastqc.html [2021-09-30 21:16:50,697] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0003_fastqc.html [2021-09-30 21:16:50,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0004_fastqc.html [2021-09-30 21:16:50,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0004_fastqc.html [2021-09-30 21:16:50,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0002_fastqc.html [2021-09-30 21:16:50,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_WT_0002_fastqc.html [2021-09-30 21:16:50,863] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0002_fastqc.html [2021-09-30 21:16:50,865] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0002_fastqc.html [2021-09-30 21:16:50,911] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0003_fastqc.html [2021-09-30 21:16:50,913] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n01_WT_0003_fastqc.html [2021-09-30 21:16:50,992] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0003._fastqc.html [2021-09-30 21:16:50,994] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGW75DRXY_l01_n02_N1_0003._fastqc.html [2021-09-30 21:16:51,395] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-30 21:16:51,396] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-30 21:16:51,407] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-30 21:16:51,417] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-30 21:16:51,422] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 8 samples (table) [2021-09-30 21:16:51,427] multiqc [DEBUG ] No samples found: conpair [2021-09-30 21:16:51,433] multiqc [DEBUG ] No samples found: peddy [2021-09-30 21:16:51,441] multiqc [DEBUG ] No samples found: somalier [2021-09-30 21:16:51,446] multiqc [DEBUG ] No samples found: methylQA [2021-09-30 21:16:51,457] multiqc [DEBUG ] No samples found: mosdepth [2021-09-30 21:16:51,463] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-30 21:16:51,467] multiqc [DEBUG ] No samples found: qualimap [2021-09-30 21:16:51,473] multiqc [DEBUG ] No samples found: preseq [2021-09-30 21:16:51,477] multiqc [DEBUG ] No samples found: quast [2021-09-30 21:16:51,482] multiqc [DEBUG ] No samples found: qorts [2021-09-30 21:16:51,487] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-30 21:16:51,493] multiqc [DEBUG ] No samples found: rockhopper [2021-09-30 21:16:51,498] multiqc [DEBUG ] No samples found: rsem [2021-09-30 21:16:51,518] multiqc [DEBUG ] No samples found: rseqc [2021-09-30 21:16:51,522] multiqc [DEBUG ] No samples found: busco [2021-09-30 21:16:51,526] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-30 21:16:51,532] multiqc [DEBUG ] No samples found: disambiguate [2021-09-30 21:16:51,537] multiqc [DEBUG ] No samples found: supernova [2021-09-30 21:16:51,559] multiqc [DEBUG ] No samples found: deeptools [2021-09-30 21:16:51,563] multiqc [DEBUG ] No samples found: sargasso [2021-09-30 21:16:51,571] multiqc [DEBUG ] No samples found: verifybamid [2021-09-30 21:16:51,575] multiqc [DEBUG ] No samples found: mirtrace [2021-09-30 21:16:51,582] multiqc [DEBUG ] No samples found: happy [2021-09-30 21:16:51,588] multiqc [DEBUG ] No samples found: mirtop [2021-09-30 21:16:51,597] multiqc [DEBUG ] No samples found: homer [2021-09-30 21:16:51,601] multiqc [DEBUG ] No samples found: macs2 [2021-09-30 21:16:51,606] multiqc [DEBUG ] No samples found: theta2 [2021-09-30 21:16:51,610] multiqc [DEBUG ] No samples found: snpeff [2021-09-30 21:16:51,620] multiqc [DEBUG ] No samples found: gatk [2021-09-30 21:16:51,626] multiqc [DEBUG ] No samples found: htseq [2021-09-30 21:16:51,630] multiqc [DEBUG ] No samples found: bcftools [2021-09-30 21:16:51,635] multiqc [DEBUG ] No samples found: featureCounts [2021-09-30 21:16:51,646] multiqc [DEBUG ] No samples found: fgbio [2021-09-30 21:16:51,668] multiqc [DEBUG ] No samples found: dragen [2021-09-30 21:16:51,673] multiqc [DEBUG ] No samples found: dedup [2021-09-30 21:16:51,679] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-30 21:16:51,710] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-30 21:16:51,715] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-30 21:16:51,718] multiqc [DEBUG ] No samples found: picard [2021-09-30 21:16:51,722] multiqc [DEBUG ] No samples found: prokka [2021-09-30 21:16:51,727] multiqc [DEBUG ] No samples found: samblaster [2021-09-30 21:16:51,739] multiqc [DEBUG ] No samples found: samtools [2021-09-30 21:16:51,744] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-30 21:16:51,748] multiqc [DEBUG ] No samples found: bamtools [2021-09-30 21:16:51,754] multiqc [DEBUG ] No samples found: jellyfish [2021-09-30 21:16:51,762] multiqc [DEBUG ] No samples found: vcftools [2021-09-30 21:16:51,770] multiqc [DEBUG ] No samples found: longranger [2021-09-30 21:16:51,778] multiqc [DEBUG ] No samples found: stacks [2021-09-30 21:16:51,785] multiqc [DEBUG ] No samples found: varscan2 [2021-09-30 21:16:51,806] multiqc [DEBUG ] No samples found: bbmap [2021-09-30 21:16:51,812] multiqc [DEBUG ] No samples found: bismark [2021-09-30 21:16:51,818] multiqc [DEBUG ] No samples found: biscuit [2021-09-30 21:16:51,825] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-30 21:16:51,830] multiqc [DEBUG ] No samples found: hicup [2021-09-30 21:16:51,836] multiqc [DEBUG ] No samples found: hicpro [2021-09-30 21:16:51,845] multiqc [DEBUG ] No samples found: salmon [2021-09-30 21:16:51,850] multiqc [DEBUG ] No samples found: kallisto [2021-09-30 21:16:51,857] multiqc [DEBUG ] No samples found: slamdunk [2021-09-30 21:16:51,862] multiqc [DEBUG ] No samples found: star [2021-09-30 21:16:51,866] multiqc [DEBUG ] No samples found: hisat2 [2021-09-30 21:16:51,873] multiqc [DEBUG ] No samples found: tophat [2021-09-30 21:16:51,879] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-30 21:16:51,885] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-30 21:16:51,889] multiqc [DEBUG ] No samples found: snpsplit [2021-09-30 21:16:51,893] multiqc [DEBUG ] No samples found: kat [2021-09-30 21:16:51,897] multiqc [DEBUG ] No samples found: leehom [2021-09-30 21:16:51,904] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-30 21:16:51,910] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-30 21:16:51,916] multiqc [DEBUG ] No samples found: cutadapt [2021-09-30 21:16:51,922] multiqc [DEBUG ] No samples found: flexbar [2021-09-30 21:16:51,929] multiqc [DEBUG ] No samples found: kaiju [2021-09-30 21:16:51,935] multiqc [DEBUG ] No samples found: kraken [2021-09-30 21:16:51,939] multiqc [DEBUG ] No samples found: malt [2021-09-30 21:16:51,944] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-30 21:16:51,949] multiqc [DEBUG ] No samples found: sickle [2021-09-30 21:16:51,954] multiqc [DEBUG ] No samples found: skewer [2021-09-30 21:16:51,960] multiqc [DEBUG ] No samples found: sortmerna [2021-09-30 21:16:51,965] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-30 21:16:51,971] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-30 21:16:51,978] multiqc [DEBUG ] No samples found: afterqc [2021-09-30 21:16:51,984] multiqc [DEBUG ] No samples found: fastp [2021-09-30 21:16:52,711] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2021-09-30 21:16:52,850] multiqc [DEBUG ] No samples found: pycoqc [2021-09-30 21:16:52,854] multiqc [DEBUG ] No samples found: minionqc [2021-09-30 21:16:52,858] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-30 21:16:52,864] multiqc [DEBUG ] No samples found: clusterflow [2021-09-30 21:16:52,871] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-30 21:16:52,875] multiqc [DEBUG ] No samples found: interop [2021-09-30 21:16:52,882] multiqc [DEBUG ] No samples found: ivar [2021-09-30 21:16:52,888] multiqc [DEBUG ] No samples found: flash [2021-09-30 21:16:52,895] multiqc [DEBUG ] No samples found: seqyclean [2021-09-30 21:16:52,895] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-09-30 21:16:52,895] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-09-30 21:16:52,895] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-30 21:16:52,895] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-09-30 21:16:52,895] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-30 21:16:52,914] multiqc [INFO ] Compressing plot data [2021-09-30 21:16:53,192] multiqc [INFO ] Report : multiqc_report.html [2021-09-30 21:16:53,192] multiqc [INFO ] Data : multiqc_data [2021-09-30 21:16:53,192] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10445661/tmpy9fk8s9z/multiqc_data' to '/scratch/gencore/logs/html/HGW75DRXY/1/multiqc_data' [2021-09-30 21:16:53,356] multiqc [INFO ] MultiQC complete