[2022-05-18 06:04:16,451] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-05-18 06:04:16,451] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-05-18 06:04:16,451] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-05-18 06:04:16,452] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-05-18 06:04:16,452] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-05-18 06:04:16,452] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNVGAFX3/merged [2022-05-18 06:04:17,084] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-05-18 06:04:17,085] multiqc [INFO ] This is MultiQC v1.9 [2022-05-18 06:04:17,085] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HLNVGAFX3/merged [2022-05-18 06:04:17,085] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HLNVGAFX3/merged [2022-05-18 06:04:17,085] multiqc [INFO ] Template : default [2022-05-18 06:04:17,085] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-05-18 06:04:17,085] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HLNVGAFX3/merged [2022-05-18 06:04:17,085] 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 [2022-05-18 06:04:17,085] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-19704709/tmpdfjwkn1q [2022-05-18 06:04:17,201] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGAFX3_4_fastqc.html [2022-05-18 06:04:17,204] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGAFX3_4_fastqc.html [2022-05-18 06:04:17,248] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGAFX3_2_fastqc.html [2022-05-18 06:04:17,250] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGAFX3_2_fastqc.html [2022-05-18 06:04:17,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGAFX3_1_fastqc.html [2022-05-18 06:04:17,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGAFX3_1_fastqc.html [2022-05-18 06:04:17,343] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLNVGAFX3_3_fastqc.html [2022-05-18 06:04:17,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLNVGAFX3_3_fastqc.html [2022-05-18 06:04:17,927] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-18 06:04:17,928] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-05-18 06:04:17,933] multiqc.modules.custom_content.custom_content [WARNING] Not able to parse custom data in undetermined_barcodes_mqc.txt [2022-05-18 06:04:17,935] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-05-18 06:04:17,940] multiqc [DEBUG ] No samples found: conpair [2022-05-18 06:04:17,945] multiqc [DEBUG ] No samples found: peddy [2022-05-18 06:04:17,950] multiqc [DEBUG ] No samples found: somalier [2022-05-18 06:04:17,955] multiqc [DEBUG ] No samples found: methylQA [2022-05-18 06:04:17,967] multiqc [DEBUG ] No samples found: mosdepth [2022-05-18 06:04:17,972] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-05-18 06:04:17,976] multiqc [DEBUG ] No samples found: qualimap [2022-05-18 06:04:17,981] multiqc [DEBUG ] No samples found: preseq [2022-05-18 06:04:17,986] multiqc [DEBUG ] No samples found: quast [2022-05-18 06:04:17,991] multiqc [DEBUG ] No samples found: qorts [2022-05-18 06:04:17,996] multiqc [DEBUG ] No samples found: rna_seqc [2022-05-18 06:04:18,001] multiqc [DEBUG ] No samples found: rockhopper [2022-05-18 06:04:18,007] multiqc [DEBUG ] No samples found: rsem [2022-05-18 06:04:18,020] multiqc [DEBUG ] No samples found: rseqc [2022-05-18 06:04:18,025] multiqc [DEBUG ] No samples found: busco [2022-05-18 06:04:18,031] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-05-18 06:04:18,035] multiqc [DEBUG ] No samples found: disambiguate [2022-05-18 06:04:18,041] multiqc [DEBUG ] No samples found: supernova [2022-05-18 06:04:18,056] multiqc [DEBUG ] No samples found: deeptools [2022-05-18 06:04:18,061] multiqc [DEBUG ] No samples found: sargasso [2022-05-18 06:04:18,066] multiqc [DEBUG ] No samples found: verifybamid [2022-05-18 06:04:18,072] multiqc [DEBUG ] No samples found: mirtrace [2022-05-18 06:04:18,077] multiqc [DEBUG ] No samples found: happy [2022-05-18 06:04:18,082] multiqc [DEBUG ] No samples found: mirtop [2022-05-18 06:04:18,089] multiqc [DEBUG ] No samples found: homer [2022-05-18 06:04:18,095] multiqc [DEBUG ] No samples found: macs2 [2022-05-18 06:04:18,099] multiqc [DEBUG ] No samples found: theta2 [2022-05-18 06:04:18,104] multiqc [DEBUG ] No samples found: snpeff [2022-05-18 06:04:18,111] multiqc [DEBUG ] No samples found: gatk [2022-05-18 06:04:18,116] multiqc [DEBUG ] No samples found: htseq [2022-05-18 06:04:18,122] multiqc [DEBUG ] No samples found: bcftools [2022-05-18 06:04:18,127] multiqc [DEBUG ] No samples found: featureCounts [2022-05-18 06:04:18,134] multiqc [DEBUG ] No samples found: fgbio [2022-05-18 06:04:18,148] multiqc [DEBUG ] No samples found: dragen [2022-05-18 06:04:18,154] multiqc [DEBUG ] No samples found: dedup [2022-05-18 06:04:18,159] multiqc [DEBUG ] No samples found: damageprofiler [2022-05-18 06:04:18,185] multiqc [DEBUG ] No samples found: biobambam2 [2022-05-18 06:04:18,191] multiqc [DEBUG ] No samples found: mtnucratio [2022-05-18 06:04:18,193] multiqc [DEBUG ] No samples found: picard [2022-05-18 06:04:18,198] multiqc [DEBUG ] No samples found: prokka [2022-05-18 06:04:18,202] multiqc [DEBUG ] No samples found: samblaster [2022-05-18 06:04:18,212] multiqc [DEBUG ] No samples found: samtools [2022-05-18 06:04:18,217] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-05-18 06:04:18,223] multiqc [DEBUG ] No samples found: bamtools [2022-05-18 06:04:18,228] multiqc [DEBUG ] No samples found: jellyfish [2022-05-18 06:04:18,236] multiqc [DEBUG ] No samples found: vcftools [2022-05-18 06:04:18,242] multiqc [DEBUG ] No samples found: longranger [2022-05-18 06:04:18,248] multiqc [DEBUG ] No samples found: stacks [2022-05-18 06:04:18,253] multiqc [DEBUG ] No samples found: varscan2 [2022-05-18 06:04:18,268] multiqc [DEBUG ] No samples found: bbmap [2022-05-18 06:04:18,273] multiqc [DEBUG ] No samples found: bismark [2022-05-18 06:04:18,278] multiqc [DEBUG ] No samples found: biscuit [2022-05-18 06:04:18,284] multiqc [DEBUG ] No samples found: hicexplorer [2022-05-18 06:04:18,289] multiqc [DEBUG ] No samples found: hicup [2022-05-18 06:04:18,294] multiqc [DEBUG ] No samples found: hicpro [2022-05-18 06:04:18,298] multiqc [DEBUG ] No samples found: salmon [2022-05-18 06:04:18,304] multiqc [DEBUG ] No samples found: kallisto [2022-05-18 06:04:18,309] multiqc [DEBUG ] No samples found: slamdunk [2022-05-18 06:04:18,314] multiqc [DEBUG ] No samples found: star [2022-05-18 06:04:18,319] multiqc [DEBUG ] No samples found: hisat2 [2022-05-18 06:04:18,325] multiqc [DEBUG ] No samples found: tophat [2022-05-18 06:04:18,330] multiqc [DEBUG ] No samples found: bowtie2 [2022-05-18 06:04:18,335] multiqc [DEBUG ] No samples found: bowtie1 [2022-05-18 06:04:18,340] multiqc [DEBUG ] No samples found: snpsplit [2022-05-18 06:04:18,345] multiqc [DEBUG ] No samples found: kat [2022-05-18 06:04:18,349] multiqc [DEBUG ] No samples found: leehom [2022-05-18 06:04:18,354] multiqc [DEBUG ] No samples found: adapterRemoval [2022-05-18 06:04:18,359] multiqc [DEBUG ] No samples found: clipandmerge [2022-05-18 06:04:18,364] multiqc [DEBUG ] No samples found: cutadapt [2022-05-18 06:04:18,368] multiqc [DEBUG ] No samples found: flexbar [2022-05-18 06:04:18,374] multiqc [DEBUG ] No samples found: kaiju [2022-05-18 06:04:18,379] multiqc [DEBUG ] No samples found: kraken [2022-05-18 06:04:18,384] multiqc [DEBUG ] No samples found: malt [2022-05-18 06:04:18,388] multiqc [DEBUG ] No samples found: trimmomatic [2022-05-18 06:04:18,393] multiqc [DEBUG ] No samples found: sickle [2022-05-18 06:04:18,399] multiqc [DEBUG ] No samples found: skewer [2022-05-18 06:04:18,403] multiqc [DEBUG ] No samples found: sortmerna [2022-05-18 06:04:18,407] multiqc [DEBUG ] No samples found: biobloomtools [2022-05-18 06:04:18,413] multiqc [DEBUG ] No samples found: fastq_screen [2022-05-18 06:04:18,418] multiqc [DEBUG ] No samples found: afterqc [2022-05-18 06:04:18,423] multiqc [DEBUG ] No samples found: fastp [2022-05-18 06:04:18,483] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2022-05-18 06:04:18,534] multiqc [DEBUG ] No samples found: pycoqc [2022-05-18 06:04:18,541] multiqc [DEBUG ] No samples found: minionqc [2022-05-18 06:04:18,546] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-05-18 06:04:18,551] multiqc [DEBUG ] No samples found: clusterflow [2022-05-18 06:04:18,556] multiqc [DEBUG ] No samples found: bcl2fastq [2022-05-18 06:04:18,561] multiqc [DEBUG ] No samples found: interop [2022-05-18 06:04:18,566] multiqc [DEBUG ] No samples found: ivar [2022-05-18 06:04:18,571] multiqc [DEBUG ] No samples found: flash [2022-05-18 06:04:18,577] multiqc [DEBUG ] No samples found: seqyclean [2022-05-18 06:04:18,577] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-05-18 06:04:18,577] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-05-18 06:04:18,577] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-05-18 06:04:18,583] multiqc [INFO ] Compressing plot data [2022-05-18 06:04:18,648] multiqc [INFO ] Report : multiqc_report.html [2022-05-18 06:04:18,649] multiqc [INFO ] Data : multiqc_data [2022-05-18 06:04:18,649] multiqc [DEBUG ] Moving data file from '/state/partition1/job-19704709/tmpdfjwkn1q/multiqc_data' to '/scratch/gencore/logs/html/HLNVGAFX3/merged/multiqc_data' [2022-05-18 06:04:18,785] multiqc [INFO ] MultiQC complete