[2021-09-10 09:54:51,889] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-10 09:54:51,889] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-10 09:54:51,889] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-10 09:54:51,890] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-10 09:54:51,890] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-10 09:54:51,890] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G64RH/1 [2021-09-10 09:54:53,257] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-10 09:54:53,257] multiqc [INFO ] This is MultiQC v1.9 [2021-09-10 09:54:53,257] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-G64RH/1 [2021-09-10 09:54:53,257] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-G64RH/1 [2021-09-10 09:54:53,257] multiqc [INFO ] Template : default [2021-09-10 09:54:53,257] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-10 09:54:53,257] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-G64RH/1 [2021-09-10 09:54:53,258] 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 [2021-09-10 09:54:53,258] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9890394/tmp8cyqgnwf [2021-09-10 09:54:53,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:53,366] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-10 09:54:54,211] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-4_fastqc.html [2021-09-10 09:54:54,213] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-4_fastqc.html [2021-09-10 09:54:54,274] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-5_fastqc.html [2021-09-10 09:54:54,276] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-5_fastqc.html [2021-09-10 09:54:54,330] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-2_fastqc.html [2021-09-10 09:54:54,332] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-2_fastqc.html [2021-09-10 09:54:54,392] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-1_fastqc.html [2021-09-10 09:54:54,394] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-1_fastqc.html [2021-09-10 09:54:54,448] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-1_fastqc.html [2021-09-10 09:54:54,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-1_fastqc.html [2021-09-10 09:54:54,512] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-7_fastqc.html [2021-09-10 09:54:54,514] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-7_fastqc.html [2021-09-10 09:54:54,576] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-8_fastqc.html [2021-09-10 09:54:54,578] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-8_fastqc.html [2021-09-10 09:54:54,641] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-6_fastqc.html [2021-09-10 09:54:54,643] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-6_fastqc.html [2021-09-10 09:54:54,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-4_fastqc.html [2021-09-10 09:54:54,708] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-4_fastqc.html [2021-09-10 09:54:54,762] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-3_fastqc.html [2021-09-10 09:54:54,764] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-3_fastqc.html [2021-09-10 09:54:54,825] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_undetermined_fastqc.html [2021-09-10 09:54:54,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_undetermined_fastqc.html [2021-09-10 09:54:54,868] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-6_fastqc.html [2021-09-10 09:54:54,869] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-6_fastqc.html [2021-09-10 09:54:54,922] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-5_fastqc.html [2021-09-10 09:54:54,924] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_WGS19-5_fastqc.html [2021-09-10 09:54:54,983] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-3_fastqc.html [2021-09-10 09:54:54,985] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-3_fastqc.html [2021-09-10 09:54:55,039] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-7_fastqc.html [2021-09-10 09:54:55,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-7_fastqc.html [2021-09-10 09:54:55,102] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-8_fastqc.html [2021-09-10 09:54:55,103] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-8_fastqc.html [2021-09-10 09:54:55,156] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_undetermined_fastqc.html [2021-09-10 09:54:55,158] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n02_undetermined_fastqc.html [2021-09-10 09:54:55,199] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-2_fastqc.html [2021-09-10 09:54:55,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-G64RH_l01_n01_WGS19-2_fastqc.html [2021-09-10 09:54:55,673] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-10 09:54:55,674] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-10 09:54:55,681] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-10 09:54:55,691] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-10 09:54:55,696] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 9 samples (table) [2021-09-10 09:54:55,700] multiqc [DEBUG ] No samples found: conpair [2021-09-10 09:54:55,705] multiqc [DEBUG ] No samples found: peddy [2021-09-10 09:54:55,710] multiqc [DEBUG ] No samples found: somalier [2021-09-10 09:54:55,715] multiqc [DEBUG ] No samples found: methylQA [2021-09-10 09:54:55,723] multiqc [DEBUG ] No samples found: mosdepth [2021-09-10 09:54:55,728] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-10 09:54:55,731] multiqc [DEBUG ] No samples found: qualimap [2021-09-10 09:54:55,736] multiqc [DEBUG ] No samples found: preseq [2021-09-10 09:54:55,741] multiqc [DEBUG ] No samples found: quast [2021-09-10 09:54:55,746] multiqc [DEBUG ] No samples found: qorts [2021-09-10 09:54:55,751] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-10 09:54:55,756] multiqc [DEBUG ] No samples found: rockhopper [2021-09-10 09:54:55,761] multiqc [DEBUG ] No samples found: rsem [2021-09-10 09:54:55,772] multiqc [DEBUG ] No samples found: rseqc [2021-09-10 09:54:55,776] multiqc [DEBUG ] No samples found: busco [2021-09-10 09:54:55,781] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-10 09:54:55,785] multiqc [DEBUG ] No samples found: disambiguate [2021-09-10 09:54:55,790] multiqc [DEBUG ] No samples found: supernova [2021-09-10 09:54:55,803] multiqc [DEBUG ] No samples found: deeptools [2021-09-10 09:54:55,808] multiqc [DEBUG ] No samples found: sargasso [2021-09-10 09:54:55,813] multiqc [DEBUG ] No samples found: verifybamid [2021-09-10 09:54:55,818] multiqc [DEBUG ] No samples found: mirtrace [2021-09-10 09:54:55,823] multiqc [DEBUG ] No samples found: happy [2021-09-10 09:54:55,828] multiqc [DEBUG ] No samples found: mirtop [2021-09-10 09:54:55,834] multiqc [DEBUG ] No samples found: homer [2021-09-10 09:54:55,839] multiqc [DEBUG ] No samples found: macs2 [2021-09-10 09:54:55,844] multiqc [DEBUG ] No samples found: theta2 [2021-09-10 09:54:55,849] multiqc [DEBUG ] No samples found: snpeff [2021-09-10 09:54:55,856] multiqc [DEBUG ] No samples found: gatk [2021-09-10 09:54:55,860] multiqc [DEBUG ] No samples found: htseq [2021-09-10 09:54:55,866] multiqc [DEBUG ] No samples found: bcftools [2021-09-10 09:54:55,871] multiqc [DEBUG ] No samples found: featureCounts [2021-09-10 09:54:55,878] multiqc [DEBUG ] No samples found: fgbio [2021-09-10 09:54:55,892] multiqc [DEBUG ] No samples found: dragen [2021-09-10 09:54:55,896] multiqc [DEBUG ] No samples found: dedup [2021-09-10 09:54:55,901] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-10 09:54:55,925] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-10 09:54:55,929] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-10 09:54:55,931] multiqc [DEBUG ] No samples found: picard [2021-09-10 09:54:55,935] multiqc [DEBUG ] No samples found: prokka [2021-09-10 09:54:55,940] multiqc [DEBUG ] No samples found: samblaster [2021-09-10 09:54:55,948] multiqc [DEBUG ] No samples found: samtools [2021-09-10 09:54:55,953] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-10 09:54:55,958] multiqc [DEBUG ] No samples found: bamtools [2021-09-10 09:54:55,963] multiqc [DEBUG ] No samples found: jellyfish [2021-09-10 09:54:55,970] multiqc [DEBUG ] No samples found: vcftools [2021-09-10 09:54:55,975] multiqc [DEBUG ] No samples found: longranger [2021-09-10 09:54:55,980] multiqc [DEBUG ] No samples found: stacks [2021-09-10 09:54:55,984] multiqc [DEBUG ] No samples found: varscan2 [2021-09-10 09:54:56,003] multiqc [DEBUG ] No samples found: bbmap [2021-09-10 09:54:56,008] multiqc [DEBUG ] No samples found: bismark [2021-09-10 09:54:56,013] multiqc [DEBUG ] No samples found: biscuit [2021-09-10 09:54:56,018] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-10 09:54:56,023] multiqc [DEBUG ] No samples found: hicup [2021-09-10 09:54:56,028] multiqc [DEBUG ] No samples found: hicpro [2021-09-10 09:54:56,032] multiqc [DEBUG ] No samples found: salmon [2021-09-10 09:54:56,036] multiqc [DEBUG ] No samples found: kallisto [2021-09-10 09:54:56,041] multiqc [DEBUG ] No samples found: slamdunk [2021-09-10 09:54:56,046] multiqc [DEBUG ] No samples found: star [2021-09-10 09:54:56,051] multiqc [DEBUG ] No samples found: hisat2 [2021-09-10 09:54:56,055] multiqc [DEBUG ] No samples found: tophat [2021-09-10 09:54:56,060] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-10 09:54:56,064] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-10 09:54:56,069] multiqc [DEBUG ] No samples found: snpsplit [2021-09-10 09:54:56,074] multiqc [DEBUG ] No samples found: kat [2021-09-10 09:54:56,078] multiqc [DEBUG ] No samples found: leehom [2021-09-10 09:54:56,083] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-10 09:54:56,087] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-10 09:54:56,092] multiqc [DEBUG ] No samples found: cutadapt [2021-09-10 09:54:56,096] multiqc [DEBUG ] No samples found: flexbar [2021-09-10 09:54:56,102] multiqc [DEBUG ] No samples found: kaiju [2021-09-10 09:54:56,107] multiqc [DEBUG ] No samples found: kraken [2021-09-10 09:54:56,112] multiqc [DEBUG ] No samples found: malt [2021-09-10 09:54:56,116] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-10 09:54:56,121] multiqc [DEBUG ] No samples found: sickle [2021-09-10 09:54:56,125] multiqc [DEBUG ] No samples found: skewer [2021-09-10 09:54:56,130] multiqc [DEBUG ] No samples found: sortmerna [2021-09-10 09:54:56,134] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-10 09:54:56,138] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-10 09:54:56,143] multiqc [DEBUG ] No samples found: afterqc [2021-09-10 09:54:56,148] multiqc [DEBUG ] No samples found: fastp [2021-09-10 09:54:56,214] multiqc.modules.fastqc.fastqc [INFO ] Found 18 reports [2021-09-10 09:54:56,427] multiqc [DEBUG ] No samples found: pycoqc [2021-09-10 09:54:56,432] multiqc [DEBUG ] No samples found: minionqc [2021-09-10 09:54:56,436] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-10 09:54:56,441] multiqc [DEBUG ] No samples found: clusterflow [2021-09-10 09:54:56,447] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-10 09:54:56,452] multiqc [DEBUG ] No samples found: interop [2021-09-10 09:54:56,457] multiqc [DEBUG ] No samples found: ivar [2021-09-10 09:54:56,461] multiqc [DEBUG ] No samples found: flash [2021-09-10 09:54:56,465] multiqc [DEBUG ] No samples found: seqyclean [2021-09-10 09:54:56,466] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-09-10 09:54:56,466] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-09-10 09:54:56,466] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-10 09:54:56,466] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2021-09-10 09:54:56,466] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-10 09:54:56,487] multiqc [INFO ] Compressing plot data [2021-09-10 09:54:56,758] multiqc [INFO ] Report : multiqc_report.html [2021-09-10 09:54:56,758] multiqc [INFO ] Data : multiqc_data [2021-09-10 09:54:56,758] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9890394/tmp8cyqgnwf/multiqc_data' to '/scratch/gencore/logs/html/000000000-G64RH/1/multiqc_data' [2021-09-10 09:54:56,892] multiqc [INFO ] MultiQC complete