[2021-08-31 01:09:25,868] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-31 01:09:25,868] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-31 01:09:25,868] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-31 01:09:25,869] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-31 01:09:25,869] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-31 01:09:25,869] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLWFFBGXJ/merged [2021-08-31 01:09:27,284] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-31 01:09:27,285] multiqc [INFO ] This is MultiQC v1.9 [2021-08-31 01:09:27,285] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLWFFBGXJ/merged [2021-08-31 01:09:27,285] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLWFFBGXJ/merged [2021-08-31 01:09:27,285] multiqc [INFO ] Template : default [2021-08-31 01:09:27,285] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-31 01:09:27,285] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLWFFBGXJ/merged [2021-08-31 01:09:27,285] 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 [2021-08-31 01:09:27,285] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9639721/tmpogsbvflt [2021-08-31 01:09:27,390] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK34_fastqc.html [2021-08-31 01:09:27,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK34_fastqc.html [2021-08-31 01:09:27,434] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-31 01:09:27,435] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-31 01:09:27,564] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK32_fastqc.html [2021-08-31 01:09:27,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK32_fastqc.html [2021-08-31 01:09:27,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK36_fastqc.html [2021-08-31 01:09:27,605] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK36_fastqc.html [2021-08-31 01:09:27,644] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK33_fastqc.html [2021-08-31 01:09:27,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK33_fastqc.html [2021-08-31 01:09:27,704] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_undetermined_fastqc.html [2021-08-31 01:09:27,706] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_undetermined_fastqc.html [2021-08-31 01:09:27,745] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK38_fastqc.html [2021-08-31 01:09:27,746] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK38_fastqc.html [2021-08-31 01:09:27,806] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK37_fastqc.html [2021-08-31 01:09:27,808] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK37_fastqc.html [2021-08-31 01:09:27,846] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK39_fastqc.html [2021-08-31 01:09:27,848] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK39_fastqc.html [2021-08-31 01:09:27,886] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK30_fastqc.html [2021-08-31 01:09:27,888] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK30_fastqc.html [2021-08-31 01:09:27,927] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK29_fastqc.html [2021-08-31 01:09:27,929] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK29_fastqc.html [2021-08-31 01:09:27,967] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK28_fastqc.html [2021-08-31 01:09:27,969] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK28_fastqc.html [2021-08-31 01:09:28,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK40_fastqc.html [2021-08-31 01:09:28,008] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK40_fastqc.html [2021-08-31 01:09:28,047] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK35_fastqc.html [2021-08-31 01:09:28,049] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK35_fastqc.html [2021-08-31 01:09:28,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK31_fastqc.html [2021-08-31 01:09:28,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLWFFBGXJ_n01_JK31_fastqc.html [2021-08-31 01:09:28,554] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-31 01:09:28,557] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-31 01:09:28,569] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 14 samples (table) [2021-08-31 01:09:28,571] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-31 01:09:28,580] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-31 01:09:28,587] multiqc [DEBUG ] No samples found: conpair [2021-08-31 01:09:28,592] multiqc [DEBUG ] No samples found: peddy [2021-08-31 01:09:28,596] multiqc [DEBUG ] No samples found: somalier [2021-08-31 01:09:28,601] multiqc [DEBUG ] No samples found: methylQA [2021-08-31 01:09:28,608] multiqc [DEBUG ] No samples found: mosdepth [2021-08-31 01:09:28,613] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-31 01:09:28,617] multiqc [DEBUG ] No samples found: qualimap [2021-08-31 01:09:28,623] multiqc [DEBUG ] No samples found: preseq [2021-08-31 01:09:28,630] multiqc [DEBUG ] No samples found: quast [2021-08-31 01:09:28,637] multiqc [DEBUG ] No samples found: qorts [2021-08-31 01:09:28,645] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-31 01:09:28,651] multiqc [DEBUG ] No samples found: rockhopper [2021-08-31 01:09:28,657] multiqc [DEBUG ] No samples found: rsem [2021-08-31 01:09:28,672] multiqc [DEBUG ] No samples found: rseqc [2021-08-31 01:09:28,683] multiqc [DEBUG ] No samples found: busco [2021-08-31 01:09:28,691] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-31 01:09:28,695] multiqc [DEBUG ] No samples found: disambiguate [2021-08-31 01:09:28,702] multiqc [DEBUG ] No samples found: supernova [2021-08-31 01:09:28,720] multiqc [DEBUG ] No samples found: deeptools [2021-08-31 01:09:28,727] multiqc [DEBUG ] No samples found: sargasso [2021-08-31 01:09:28,733] multiqc [DEBUG ] No samples found: verifybamid [2021-08-31 01:09:28,740] multiqc [DEBUG ] No samples found: mirtrace [2021-08-31 01:09:28,746] multiqc [DEBUG ] No samples found: happy [2021-08-31 01:09:28,752] multiqc [DEBUG ] No samples found: mirtop [2021-08-31 01:09:28,764] multiqc [DEBUG ] No samples found: homer [2021-08-31 01:09:28,772] multiqc [DEBUG ] No samples found: macs2 [2021-08-31 01:09:28,777] multiqc [DEBUG ] No samples found: theta2 [2021-08-31 01:09:28,784] multiqc [DEBUG ] No samples found: snpeff [2021-08-31 01:09:28,790] multiqc [DEBUG ] No samples found: gatk [2021-08-31 01:09:28,795] multiqc [DEBUG ] No samples found: htseq [2021-08-31 01:09:28,804] multiqc [DEBUG ] No samples found: bcftools [2021-08-31 01:09:28,811] multiqc [DEBUG ] No samples found: featureCounts [2021-08-31 01:09:28,819] multiqc [DEBUG ] No samples found: fgbio [2021-08-31 01:09:28,839] multiqc [DEBUG ] No samples found: dragen [2021-08-31 01:09:28,846] multiqc [DEBUG ] No samples found: dedup [2021-08-31 01:09:28,852] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-31 01:09:28,894] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-31 01:09:28,900] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-31 01:09:28,903] multiqc [DEBUG ] No samples found: picard [2021-08-31 01:09:28,910] multiqc [DEBUG ] No samples found: prokka [2021-08-31 01:09:28,915] multiqc [DEBUG ] No samples found: samblaster [2021-08-31 01:09:28,931] multiqc [DEBUG ] No samples found: samtools [2021-08-31 01:09:28,938] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-31 01:09:28,946] multiqc [DEBUG ] No samples found: bamtools [2021-08-31 01:09:28,952] multiqc [DEBUG ] No samples found: jellyfish [2021-08-31 01:09:28,969] multiqc [DEBUG ] No samples found: vcftools [2021-08-31 01:09:28,976] multiqc [DEBUG ] No samples found: longranger [2021-08-31 01:09:28,980] multiqc [DEBUG ] No samples found: stacks [2021-08-31 01:09:28,987] multiqc [DEBUG ] No samples found: varscan2 [2021-08-31 01:09:29,012] multiqc [DEBUG ] No samples found: bbmap [2021-08-31 01:09:29,019] multiqc [DEBUG ] No samples found: bismark [2021-08-31 01:09:29,025] multiqc [DEBUG ] No samples found: biscuit [2021-08-31 01:09:29,031] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-31 01:09:29,038] multiqc [DEBUG ] No samples found: hicup [2021-08-31 01:09:29,042] multiqc [DEBUG ] No samples found: hicpro [2021-08-31 01:09:29,046] multiqc [DEBUG ] No samples found: salmon [2021-08-31 01:09:29,053] multiqc [DEBUG ] No samples found: kallisto [2021-08-31 01:09:29,057] multiqc [DEBUG ] No samples found: slamdunk [2021-08-31 01:09:29,064] multiqc [DEBUG ] No samples found: star [2021-08-31 01:09:29,070] multiqc [DEBUG ] No samples found: hisat2 [2021-08-31 01:09:29,076] multiqc [DEBUG ] No samples found: tophat [2021-08-31 01:09:29,080] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-31 01:09:29,084] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-31 01:09:29,090] multiqc [DEBUG ] No samples found: snpsplit [2021-08-31 01:09:29,098] multiqc [DEBUG ] No samples found: kat [2021-08-31 01:09:29,109] multiqc [DEBUG ] No samples found: leehom [2021-08-31 01:09:29,115] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-31 01:09:29,119] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-31 01:09:29,124] multiqc [DEBUG ] No samples found: cutadapt [2021-08-31 01:09:29,128] multiqc [DEBUG ] No samples found: flexbar [2021-08-31 01:09:29,134] multiqc [DEBUG ] No samples found: kaiju [2021-08-31 01:09:29,140] multiqc [DEBUG ] No samples found: kraken [2021-08-31 01:09:29,147] multiqc [DEBUG ] No samples found: malt [2021-08-31 01:09:29,153] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-31 01:09:29,160] multiqc [DEBUG ] No samples found: sickle [2021-08-31 01:09:29,166] multiqc [DEBUG ] No samples found: skewer [2021-08-31 01:09:29,171] multiqc [DEBUG ] No samples found: sortmerna [2021-08-31 01:09:29,176] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-31 01:09:29,182] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-31 01:09:29,187] multiqc [DEBUG ] No samples found: afterqc [2021-08-31 01:09:29,192] multiqc [DEBUG ] No samples found: fastp [2021-08-31 01:09:30,247] multiqc.modules.fastqc.fastqc [INFO ] Found 14 reports [2021-08-31 01:09:30,570] multiqc [DEBUG ] No samples found: pycoqc [2021-08-31 01:09:30,577] multiqc [DEBUG ] No samples found: minionqc [2021-08-31 01:09:30,583] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-31 01:09:30,589] multiqc [DEBUG ] No samples found: clusterflow [2021-08-31 01:09:30,595] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-31 01:09:30,599] multiqc [DEBUG ] No samples found: interop [2021-08-31 01:09:30,604] multiqc [DEBUG ] No samples found: ivar [2021-08-31 01:09:30,609] multiqc [DEBUG ] No samples found: flash [2021-08-31 01:09:30,613] multiqc [DEBUG ] No samples found: seqyclean [2021-08-31 01:09:30,613] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-31 01:09:30,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-31 01:09:30,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-31 01:09:30,614] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-31 01:09:30,631] multiqc [INFO ] Compressing plot data [2021-08-31 01:09:30,887] multiqc [INFO ] Report : multiqc_report.html [2021-08-31 01:09:30,888] multiqc [INFO ] Data : multiqc_data [2021-08-31 01:09:30,888] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9639721/tmpogsbvflt/multiqc_data' to '/scratch/gencore/logs/html/HLWFFBGXJ/merged/multiqc_data' [2021-08-31 01:09:31,010] multiqc [INFO ] MultiQC complete