[2021-08-17 04:56:01,208] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-08-17 04:56:01,208] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-08-17 04:56:01,208] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-17 04:56:01,209] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-08-17 04:56:01,209] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-08-17 04:56:01,209] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGFHNDRXY/merged [2021-08-17 04:56:02,571] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-08-17 04:56:02,571] multiqc [INFO ] This is MultiQC v1.9 [2021-08-17 04:56:02,571] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGFHNDRXY/merged [2021-08-17 04:56:02,571] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGFHNDRXY/merged [2021-08-17 04:56:02,571] multiqc [INFO ] Template : default [2021-08-17 04:56:02,571] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-08-17 04:56:02,571] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGFHNDRXY/merged [2021-08-17 04:56:02,572] 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 [2021-08-17 04:56:02,572] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-9422390/tmp25hxpl0q [2021-08-17 04:56:02,683] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-17 04:56:02,685] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-08-17 04:56:03,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glutamate_fastqc.html [2021-08-17 04:56:03,060] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glutamate_fastqc.html [2021-08-17 04:56:03,099] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col2_fastqc.html [2021-08-17 04:56:03,100] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col2_fastqc.html [2021-08-17 04:56:03,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col3_fastqc.html [2021-08-17 04:56:03,142] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col3_fastqc.html [2021-08-17 04:56:03,196] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant2_fastqc.html [2021-08-17 04:56:03,198] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant2_fastqc.html [2021-08-17 04:56:03,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col1_fastqc.html [2021-08-17 04:56:03,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_col1_fastqc.html [2021-08-17 04:56:03,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant3_fastqc.html [2021-08-17 04:56:03,281] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant3_fastqc.html [2021-08-17 04:56:03,354] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_undetermined_fastqc.html [2021-08-17 04:56:03,356] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_undetermined_fastqc.html [2021-08-17 04:56:03,395] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant1_fastqc.html [2021-08-17 04:56:03,397] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGFHNDRXY_n01_glr4mutant1_fastqc.html [2021-08-17 04:56:03,887] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-17 04:56:03,888] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-08-17 04:56:03,898] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2021-08-17 04:56:03,908] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-08-17 04:56:03,909] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-08-17 04:56:03,915] multiqc [DEBUG ] No samples found: conpair [2021-08-17 04:56:03,920] multiqc [DEBUG ] No samples found: peddy [2021-08-17 04:56:03,925] multiqc [DEBUG ] No samples found: somalier [2021-08-17 04:56:03,930] multiqc [DEBUG ] No samples found: methylQA [2021-08-17 04:56:03,941] multiqc [DEBUG ] No samples found: mosdepth [2021-08-17 04:56:03,945] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-17 04:56:03,948] multiqc [DEBUG ] No samples found: qualimap [2021-08-17 04:56:03,954] multiqc [DEBUG ] No samples found: preseq [2021-08-17 04:56:03,960] multiqc [DEBUG ] No samples found: quast [2021-08-17 04:56:03,964] multiqc [DEBUG ] No samples found: qorts [2021-08-17 04:56:03,969] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-17 04:56:03,973] multiqc [DEBUG ] No samples found: rockhopper [2021-08-17 04:56:03,979] multiqc [DEBUG ] No samples found: rsem [2021-08-17 04:56:03,992] multiqc [DEBUG ] No samples found: rseqc [2021-08-17 04:56:03,996] multiqc [DEBUG ] No samples found: busco [2021-08-17 04:56:04,001] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-17 04:56:04,007] multiqc [DEBUG ] No samples found: disambiguate [2021-08-17 04:56:04,012] multiqc [DEBUG ] No samples found: supernova [2021-08-17 04:56:04,030] multiqc [DEBUG ] No samples found: deeptools [2021-08-17 04:56:04,035] multiqc [DEBUG ] No samples found: sargasso [2021-08-17 04:56:04,041] multiqc [DEBUG ] No samples found: verifybamid [2021-08-17 04:56:04,046] multiqc [DEBUG ] No samples found: mirtrace [2021-08-17 04:56:04,051] multiqc [DEBUG ] No samples found: happy [2021-08-17 04:56:04,057] multiqc [DEBUG ] No samples found: mirtop [2021-08-17 04:56:04,064] multiqc [DEBUG ] No samples found: homer [2021-08-17 04:56:04,070] multiqc [DEBUG ] No samples found: macs2 [2021-08-17 04:56:04,074] multiqc [DEBUG ] No samples found: theta2 [2021-08-17 04:56:04,080] multiqc [DEBUG ] No samples found: snpeff [2021-08-17 04:56:04,090] multiqc [DEBUG ] No samples found: gatk [2021-08-17 04:56:04,095] multiqc [DEBUG ] No samples found: htseq [2021-08-17 04:56:04,101] multiqc [DEBUG ] No samples found: bcftools [2021-08-17 04:56:04,106] multiqc [DEBUG ] No samples found: featureCounts [2021-08-17 04:56:04,113] multiqc [DEBUG ] No samples found: fgbio [2021-08-17 04:56:04,127] multiqc [DEBUG ] No samples found: dragen [2021-08-17 04:56:04,132] multiqc [DEBUG ] No samples found: dedup [2021-08-17 04:56:04,138] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-17 04:56:04,167] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-17 04:56:04,171] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-17 04:56:04,173] multiqc [DEBUG ] No samples found: picard [2021-08-17 04:56:04,179] multiqc [DEBUG ] No samples found: prokka [2021-08-17 04:56:04,184] multiqc [DEBUG ] No samples found: samblaster [2021-08-17 04:56:04,192] multiqc [DEBUG ] No samples found: samtools [2021-08-17 04:56:04,196] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-17 04:56:04,202] multiqc [DEBUG ] No samples found: bamtools [2021-08-17 04:56:04,206] multiqc [DEBUG ] No samples found: jellyfish [2021-08-17 04:56:04,214] multiqc [DEBUG ] No samples found: vcftools [2021-08-17 04:56:04,220] multiqc [DEBUG ] No samples found: longranger [2021-08-17 04:56:04,226] multiqc [DEBUG ] No samples found: stacks [2021-08-17 04:56:04,230] multiqc [DEBUG ] No samples found: varscan2 [2021-08-17 04:56:04,251] multiqc [DEBUG ] No samples found: bbmap [2021-08-17 04:56:04,256] multiqc [DEBUG ] No samples found: bismark [2021-08-17 04:56:04,262] multiqc [DEBUG ] No samples found: biscuit [2021-08-17 04:56:04,267] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-17 04:56:04,272] multiqc [DEBUG ] No samples found: hicup [2021-08-17 04:56:04,277] multiqc [DEBUG ] No samples found: hicpro [2021-08-17 04:56:04,282] multiqc [DEBUG ] No samples found: salmon [2021-08-17 04:56:04,289] multiqc [DEBUG ] No samples found: kallisto [2021-08-17 04:56:04,297] multiqc [DEBUG ] No samples found: slamdunk [2021-08-17 04:56:04,302] multiqc [DEBUG ] No samples found: star [2021-08-17 04:56:04,308] multiqc [DEBUG ] No samples found: hisat2 [2021-08-17 04:56:04,313] multiqc [DEBUG ] No samples found: tophat [2021-08-17 04:56:04,319] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-17 04:56:04,324] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-17 04:56:04,330] multiqc [DEBUG ] No samples found: snpsplit [2021-08-17 04:56:04,334] multiqc [DEBUG ] No samples found: kat [2021-08-17 04:56:04,338] multiqc [DEBUG ] No samples found: leehom [2021-08-17 04:56:04,343] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-17 04:56:04,348] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-17 04:56:04,352] multiqc [DEBUG ] No samples found: cutadapt [2021-08-17 04:56:04,356] multiqc [DEBUG ] No samples found: flexbar [2021-08-17 04:56:04,361] multiqc [DEBUG ] No samples found: kaiju [2021-08-17 04:56:04,367] multiqc [DEBUG ] No samples found: kraken [2021-08-17 04:56:04,373] multiqc [DEBUG ] No samples found: malt [2021-08-17 04:56:04,380] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-17 04:56:04,386] multiqc [DEBUG ] No samples found: sickle [2021-08-17 04:56:04,392] multiqc [DEBUG ] No samples found: skewer [2021-08-17 04:56:04,397] multiqc [DEBUG ] No samples found: sortmerna [2021-08-17 04:56:04,401] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-17 04:56:04,405] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-17 04:56:04,410] multiqc [DEBUG ] No samples found: afterqc [2021-08-17 04:56:04,416] multiqc [DEBUG ] No samples found: fastp [2021-08-17 04:56:04,750] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2021-08-17 04:56:04,877] multiqc [DEBUG ] No samples found: pycoqc [2021-08-17 04:56:04,882] multiqc [DEBUG ] No samples found: minionqc [2021-08-17 04:56:04,889] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-08-17 04:56:04,895] multiqc [DEBUG ] No samples found: clusterflow [2021-08-17 04:56:04,902] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-17 04:56:04,911] multiqc [DEBUG ] No samples found: interop [2021-08-17 04:56:04,916] multiqc [DEBUG ] No samples found: ivar [2021-08-17 04:56:04,925] multiqc [DEBUG ] No samples found: flash [2021-08-17 04:56:04,930] multiqc [DEBUG ] No samples found: seqyclean [2021-08-17 04:56:04,931] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-08-17 04:56:04,931] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-08-17 04:56:04,931] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-08-17 04:56:04,931] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-08-17 04:56:04,941] multiqc [INFO ] Compressing plot data [2021-08-17 04:56:05,102] multiqc [INFO ] Report : multiqc_report.html [2021-08-17 04:56:05,102] multiqc [INFO ] Data : multiqc_data [2021-08-17 04:56:05,102] multiqc [DEBUG ] Moving data file from '/state/partition1/job-9422390/tmp25hxpl0q/multiqc_data' to '/scratch/gencore/logs/html/HGFHNDRXY/merged/multiqc_data' [2021-08-17 04:56:05,262] multiqc [INFO ] MultiQC complete