[2022-02-23 19:04:30,625] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-02-23 19:04:30,625] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-02-23 19:04:30,625] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-02-23 19:04:30,626] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-02-23 19:04:30,626] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-02-23 19:04:30,626] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHMMVAFX3/merged [2022-02-23 19:04:31,361] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-02-23 19:04:31,362] multiqc [INFO ] This is MultiQC v1.9 [2022-02-23 19:04:31,362] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHMMVAFX3/merged [2022-02-23 19:04:31,362] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHMMVAFX3/merged [2022-02-23 19:04:31,362] multiqc [INFO ] Template : default [2022-02-23 19:04:31,362] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-02-23 19:04:31,362] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHMMVAFX3/merged [2022-02-23 19:04:31,362] 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 [2022-02-23 19:04:31,362] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-15208599/tmplbtwlmrh [2022-02-23 19:04:31,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr495_fastqc.html [2022-02-23 19:04:31,481] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr495_fastqc.html [2022-02-23 19:04:31,525] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr494_fastqc.html [2022-02-23 19:04:31,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr494_fastqc.html [2022-02-23 19:04:31,568] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:31,570] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-02-23 19:04:32,212] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr489_fastqc.html [2022-02-23 19:04:32,214] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr489_fastqc.html [2022-02-23 19:04:32,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr492_fastqc.html [2022-02-23 19:04:32,264] multiqc [DEBUG ] File ignored 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exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr491_fastqc.html [2022-02-23 19:04:32,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_undetermined_fastqc.html [2022-02-23 19:04:32,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_undetermined_fastqc.html [2022-02-23 19:04:32,493] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr496_fastqc.html [2022-02-23 19:04:32,495] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr496_fastqc.html [2022-02-23 19:04:32,540] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr492_fastqc.html [2022-02-23 19:04:32,542] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr492_fastqc.html [2022-02-23 19:04:32,586] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr493_fastqc.html [2022-02-23 19:04:32,588] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr493_fastqc.html [2022-02-23 19:04:32,633] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_undetermined_fastqc.html [2022-02-23 19:04:32,635] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_undetermined_fastqc.html [2022-02-23 19:04:32,677] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr495_fastqc.html [2022-02-23 19:04:32,679] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr495_fastqc.html [2022-02-23 19:04:32,723] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr489_fastqc.html [2022-02-23 19:04:32,725] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr489_fastqc.html [2022-02-23 19:04:32,771] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr498_fastqc.html [2022-02-23 19:04:32,773] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr498_fastqc.html [2022-02-23 19:04:32,817] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr496_fastqc.html [2022-02-23 19:04:32,819] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr496_fastqc.html [2022-02-23 19:04:32,864] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr498_fastqc.html [2022-02-23 19:04:32,866] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr498_fastqc.html [2022-02-23 19:04:32,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr490_fastqc.html [2022-02-23 19:04:32,912] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr490_fastqc.html [2022-02-23 19:04:32,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr497_fastqc.html [2022-02-23 19:04:32,960] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr497_fastqc.html [2022-02-23 19:04:33,007] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr491_fastqc.html [2022-02-23 19:04:33,008] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n02_dpr491_fastqc.html [2022-02-23 19:04:33,053] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr490_fastqc.html [2022-02-23 19:04:33,055] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr490_fastqc.html [2022-02-23 19:04:33,100] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr494_fastqc.html [2022-02-23 19:04:33,102] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHMMVAFX3_n01_dpr494_fastqc.html [2022-02-23 19:04:33,474] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-23 19:04:33,475] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-02-23 19:04:33,484] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-02-23 19:04:33,490] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 11 samples (table) [2022-02-23 19:04:33,500] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-02-23 19:04:33,505] multiqc [DEBUG ] No samples found: conpair [2022-02-23 19:04:33,511] multiqc [DEBUG ] No samples found: peddy [2022-02-23 19:04:33,516] multiqc [DEBUG ] No samples found: somalier [2022-02-23 19:04:33,522] multiqc [DEBUG ] No samples found: methylQA [2022-02-23 19:04:33,531] multiqc [DEBUG ] No samples found: mosdepth [2022-02-23 19:04:33,536] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-02-23 19:04:33,539] multiqc [DEBUG ] No samples found: qualimap [2022-02-23 19:04:33,545] multiqc [DEBUG ] No samples found: preseq [2022-02-23 19:04:33,550] multiqc [DEBUG ] No samples found: quast [2022-02-23 19:04:33,555] multiqc [DEBUG ] No samples found: qorts [2022-02-23 19:04:33,561] multiqc [DEBUG ] No samples found: rna_seqc [2022-02-23 19:04:33,566] multiqc [DEBUG ] No samples found: rockhopper [2022-02-23 19:04:33,571] multiqc [DEBUG ] No samples found: rsem [2022-02-23 19:04:33,583] multiqc [DEBUG ] No samples found: rseqc [2022-02-23 19:04:33,588] multiqc [DEBUG ] No samples found: busco [2022-02-23 19:04:33,593] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-02-23 19:04:33,598] multiqc [DEBUG ] No samples found: disambiguate [2022-02-23 19:04:33,604] multiqc [DEBUG ] No samples found: supernova [2022-02-23 19:04:33,620] multiqc [DEBUG ] No samples found: deeptools [2022-02-23 19:04:33,625] multiqc [DEBUG ] No samples found: sargasso [2022-02-23 19:04:33,631] multiqc [DEBUG ] No samples found: verifybamid [2022-02-23 19:04:33,637] multiqc [DEBUG ] No samples found: mirtrace [2022-02-23 19:04:33,642] multiqc [DEBUG ] No samples found: happy [2022-02-23 19:04:33,647] multiqc [DEBUG ] No samples found: mirtop [2022-02-23 19:04:33,654] multiqc [DEBUG ] No samples found: homer [2022-02-23 19:04:33,660] multiqc [DEBUG ] No samples found: macs2 [2022-02-23 19:04:33,664] multiqc [DEBUG ] No samples found: theta2 [2022-02-23 19:04:33,670] multiqc [DEBUG ] No samples found: snpeff [2022-02-23 19:04:33,677] multiqc [DEBUG ] No samples found: gatk [2022-02-23 19:04:33,683] multiqc [DEBUG ] No samples found: htseq [2022-02-23 19:04:33,689] multiqc [DEBUG ] No samples found: bcftools [2022-02-23 19:04:33,695] multiqc [DEBUG ] No samples found: featureCounts [2022-02-23 19:04:33,702] multiqc [DEBUG ] No samples found: fgbio [2022-02-23 19:04:33,717] multiqc [DEBUG ] No samples found: dragen [2022-02-23 19:04:33,723] multiqc [DEBUG ] No samples found: dedup [2022-02-23 19:04:33,729] multiqc [DEBUG ] No samples found: damageprofiler [2022-02-23 19:04:33,753] multiqc [DEBUG ] No samples found: biobambam2 [2022-02-23 19:04:33,759] multiqc [DEBUG ] No samples found: mtnucratio [2022-02-23 19:04:33,761] multiqc [DEBUG ] No samples found: picard [2022-02-23 19:04:33,767] multiqc [DEBUG ] No samples found: prokka [2022-02-23 19:04:33,771] multiqc [DEBUG ] No samples found: samblaster [2022-02-23 19:04:33,781] multiqc [DEBUG ] No samples found: samtools [2022-02-23 19:04:33,786] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-02-23 19:04:33,792] multiqc [DEBUG ] No samples found: bamtools [2022-02-23 19:04:33,797] multiqc [DEBUG ] No samples found: jellyfish [2022-02-23 19:04:33,805] multiqc [DEBUG ] No samples found: vcftools [2022-02-23 19:04:33,810] multiqc [DEBUG ] No samples found: longranger [2022-02-23 19:04:33,815] multiqc [DEBUG ] No samples found: stacks [2022-02-23 19:04:33,821] multiqc [DEBUG ] No samples found: varscan2 [2022-02-23 19:04:33,839] multiqc [DEBUG ] No samples found: bbmap [2022-02-23 19:04:33,844] multiqc [DEBUG ] No samples found: bismark [2022-02-23 19:04:33,850] multiqc [DEBUG ] No samples found: biscuit [2022-02-23 19:04:33,855] multiqc [DEBUG ] No samples found: hicexplorer [2022-02-23 19:04:33,861] multiqc [DEBUG ] No samples found: hicup [2022-02-23 19:04:33,866] multiqc [DEBUG ] No samples found: hicpro [2022-02-23 19:04:33,871] multiqc [DEBUG ] No samples found: salmon [2022-02-23 19:04:33,876] multiqc [DEBUG ] No samples found: kallisto [2022-02-23 19:04:33,881] multiqc [DEBUG ] No samples found: slamdunk [2022-02-23 19:04:33,886] multiqc [DEBUG ] No samples found: star [2022-02-23 19:04:33,891] multiqc [DEBUG ] No samples found: hisat2 [2022-02-23 19:04:33,896] multiqc [DEBUG ] No samples found: tophat [2022-02-23 19:04:33,902] multiqc [DEBUG ] No samples found: bowtie2 [2022-02-23 19:04:33,907] multiqc [DEBUG ] No samples found: bowtie1 [2022-02-23 19:04:33,913] multiqc [DEBUG ] No samples found: snpsplit [2022-02-23 19:04:33,917] multiqc [DEBUG ] No samples found: kat [2022-02-23 19:04:33,922] multiqc [DEBUG ] No samples found: leehom [2022-02-23 19:04:33,928] multiqc [DEBUG ] No samples found: adapterRemoval [2022-02-23 19:04:33,932] multiqc [DEBUG ] No samples found: clipandmerge [2022-02-23 19:04:33,938] multiqc [DEBUG ] No samples found: cutadapt [2022-02-23 19:04:33,942] multiqc [DEBUG ] No samples found: flexbar [2022-02-23 19:04:33,948] multiqc [DEBUG ] No samples found: kaiju [2022-02-23 19:04:33,953] multiqc [DEBUG ] No samples found: kraken [2022-02-23 19:04:33,958] multiqc [DEBUG ] No samples found: malt [2022-02-23 19:04:33,964] multiqc [DEBUG ] No samples found: trimmomatic [2022-02-23 19:04:33,969] multiqc [DEBUG ] No samples found: sickle [2022-02-23 19:04:33,974] multiqc [DEBUG ] No samples found: skewer [2022-02-23 19:04:33,979] multiqc [DEBUG ] No samples found: sortmerna [2022-02-23 19:04:33,984] multiqc [DEBUG ] No samples found: biobloomtools [2022-02-23 19:04:33,989] multiqc [DEBUG ] No samples found: fastq_screen [2022-02-23 19:04:33,994] multiqc [DEBUG ] No samples found: afterqc [2022-02-23 19:04:34,000] multiqc [DEBUG ] No samples found: fastp [2022-02-23 19:04:34,533] multiqc.modules.fastqc.fastqc [INFO ] Found 22 reports [2022-02-23 19:04:35,025] multiqc [DEBUG ] No samples found: pycoqc [2022-02-23 19:04:35,030] multiqc [DEBUG ] No samples found: minionqc [2022-02-23 19:04:35,037] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-02-23 19:04:35,043] multiqc [DEBUG ] No samples found: clusterflow [2022-02-23 19:04:35,048] multiqc [DEBUG ] No samples found: bcl2fastq [2022-02-23 19:04:35,053] multiqc [DEBUG ] No samples found: interop [2022-02-23 19:04:35,058] multiqc [DEBUG ] No samples found: ivar [2022-02-23 19:04:35,063] multiqc [DEBUG ] No samples found: flash [2022-02-23 19:04:35,068] multiqc [DEBUG ] No samples found: seqyclean [2022-02-23 19:04:35,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-02-23 19:04:35,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-02-23 19:04:35,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-02-23 19:04:35,068] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-02-23 19:04:35,095] multiqc [INFO ] Compressing plot data [2022-02-23 19:04:35,490] multiqc [INFO ] Report : multiqc_report.html [2022-02-23 19:04:35,490] multiqc [INFO ] Data : multiqc_data [2022-02-23 19:04:35,490] multiqc [DEBUG ] Moving data file from '/state/partition1/job-15208599/tmplbtwlmrh/multiqc_data' to '/scratch/gencore/logs/html/HHMMVAFX3/merged/multiqc_data' [2022-02-23 19:04:35,633] multiqc [INFO ] MultiQC complete