[2022-10-25 04:32:14,287] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-25 04:32:14,287] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-25 04:32:14,287] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-25 04:32:14,288] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-25 04:32:14,288] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-25 04:32:14,288] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H37NLDSX5/merged [2022-10-25 04:32:14,990] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-25 04:32:14,990] multiqc [INFO ] This is MultiQC v1.9 [2022-10-25 04:32:14,990] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H37NLDSX5/merged [2022-10-25 04:32:14,990] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H37NLDSX5/merged [2022-10-25 04:32:14,990] multiqc [INFO ] Template : default [2022-10-25 04:32:14,990] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-25 04:32:14,990] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H37NLDSX5/merged [2022-10-25 04:32:14,991] 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 [2022-10-25 04:32:14,991] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-26242122/tmplrzwrp7y [2022-10-25 04:32:15,106] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2aHRB0248_fastqc.html [2022-10-25 04:32:15,110] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H37NLDSX5_n02_f2aHRB0218_fastqc.html [2022-10-25 04:32:23,430] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2aHRB0342_fastqc.html [2022-10-25 04:32:23,432] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2aHRB0342_fastqc.html [2022-10-25 04:32:23,485] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n02_f2aHRB0316_fastqc.html [2022-10-25 04:32:23,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n02_f2aHRB0316_fastqc.html [2022-10-25 04:32:23,555] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2aHRB0025_fastqc.html [2022-10-25 04:32:23,558] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H37NLDSX5_n01_f2aHRB0025_fastqc.html [2022-10-25 04:32:24,107] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-25 04:32:24,108] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-25 04:32:24,147] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 71 samples (table) [2022-10-25 04:32:24,149] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-25 04:32:24,158] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-25 04:32:24,163] multiqc [DEBUG ] No samples found: conpair [2022-10-25 04:32:24,168] multiqc [DEBUG ] No samples found: peddy [2022-10-25 04:32:24,173] multiqc [DEBUG ] No samples found: somalier [2022-10-25 04:32:24,177] multiqc [DEBUG ] No samples found: methylQA [2022-10-25 04:32:24,185] multiqc [DEBUG ] No samples found: mosdepth [2022-10-25 04:32:24,190] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-25 04:32:24,193] multiqc [DEBUG ] No samples found: qualimap [2022-10-25 04:32:24,197] multiqc [DEBUG ] No samples found: preseq [2022-10-25 04:32:24,201] multiqc [DEBUG ] No samples found: quast [2022-10-25 04:32:24,206] multiqc [DEBUG ] No samples found: qorts [2022-10-25 04:32:24,211] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-25 04:32:24,215] multiqc [DEBUG ] No samples found: rockhopper [2022-10-25 04:32:24,220] multiqc [DEBUG ] No samples found: rsem [2022-10-25 04:32:24,230] multiqc [DEBUG ] No samples found: rseqc [2022-10-25 04:32:24,234] multiqc [DEBUG ] No samples found: busco [2022-10-25 04:32:24,238] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-25 04:32:24,243] multiqc [DEBUG ] No samples found: disambiguate [2022-10-25 04:32:24,247] multiqc [DEBUG ] No samples found: supernova [2022-10-25 04:32:24,258] multiqc [DEBUG ] No samples found: deeptools [2022-10-25 04:32:24,263] multiqc [DEBUG ] No samples found: sargasso [2022-10-25 04:32:24,268] multiqc [DEBUG ] No samples found: verifybamid [2022-10-25 04:32:24,273] multiqc [DEBUG ] No samples found: mirtrace [2022-10-25 04:32:24,277] multiqc [DEBUG ] No samples found: happy [2022-10-25 04:32:24,281] multiqc [DEBUG ] No samples found: mirtop [2022-10-25 04:32:24,287] multiqc [DEBUG ] No samples found: homer [2022-10-25 04:32:24,292] multiqc [DEBUG ] No samples found: macs2 [2022-10-25 04:32:24,296] multiqc [DEBUG ] No samples found: theta2 [2022-10-25 04:32:24,300] multiqc [DEBUG ] No samples found: snpeff [2022-10-25 04:32:24,306] multiqc [DEBUG ] No samples found: gatk [2022-10-25 04:32:24,311] multiqc [DEBUG ] No samples found: htseq [2022-10-25 04:32:24,315] multiqc [DEBUG ] No samples found: bcftools [2022-10-25 04:32:24,320] multiqc [DEBUG ] No samples found: featureCounts [2022-10-25 04:32:24,325] multiqc [DEBUG ] No samples found: fgbio [2022-10-25 04:32:24,337] multiqc [DEBUG ] No samples found: dragen [2022-10-25 04:32:24,341] multiqc [DEBUG ] No samples found: dedup [2022-10-25 04:32:24,345] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-25 04:32:24,365] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-25 04:32:24,369] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-25 04:32:24,371] multiqc [DEBUG ] No samples found: picard [2022-10-25 04:32:24,376] multiqc [DEBUG ] No samples found: prokka [2022-10-25 04:32:24,379] multiqc [DEBUG ] No samples found: samblaster [2022-10-25 04:32:24,387] multiqc [DEBUG ] No samples found: samtools [2022-10-25 04:32:24,391] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-25 04:32:24,396] multiqc [DEBUG ] No samples found: bamtools [2022-10-25 04:32:24,400] multiqc [DEBUG ] No samples found: jellyfish [2022-10-25 04:32:24,406] multiqc [DEBUG ] No samples found: vcftools [2022-10-25 04:32:24,411] multiqc [DEBUG ] No samples found: longranger [2022-10-25 04:32:24,415] multiqc [DEBUG ] No samples found: stacks [2022-10-25 04:32:24,419] multiqc [DEBUG ] No samples found: varscan2 [2022-10-25 04:32:24,434] multiqc [DEBUG ] No samples found: bbmap [2022-10-25 04:32:24,438] multiqc [DEBUG ] No samples found: bismark [2022-10-25 04:32:24,443] multiqc [DEBUG ] No samples found: biscuit [2022-10-25 04:32:24,447] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-25 04:32:24,451] multiqc [DEBUG ] No samples found: hicup [2022-10-25 04:32:24,456] multiqc [DEBUG ] No samples found: hicpro [2022-10-25 04:32:24,460] multiqc [DEBUG ] No samples found: salmon [2022-10-25 04:32:24,464] multiqc [DEBUG ] No samples found: kallisto [2022-10-25 04:32:24,469] multiqc [DEBUG ] No samples found: slamdunk [2022-10-25 04:32:24,474] multiqc [DEBUG ] No samples found: star [2022-10-25 04:32:24,478] multiqc [DEBUG ] No samples found: hisat2 [2022-10-25 04:32:24,482] multiqc [DEBUG ] No samples found: tophat [2022-10-25 04:32:24,487] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-25 04:32:24,491] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-25 04:32:24,495] multiqc [DEBUG ] No samples found: snpsplit [2022-10-25 04:32:24,500] multiqc [DEBUG ] No samples found: kat [2022-10-25 04:32:24,503] multiqc [DEBUG ] No samples found: leehom [2022-10-25 04:32:24,508] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-25 04:32:24,512] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-25 04:32:24,516] multiqc [DEBUG ] No samples found: cutadapt [2022-10-25 04:32:24,520] multiqc [DEBUG ] No samples found: flexbar [2022-10-25 04:32:24,524] multiqc [DEBUG ] No samples found: kaiju [2022-10-25 04:32:24,528] multiqc [DEBUG ] No samples found: kraken [2022-10-25 04:32:24,533] multiqc [DEBUG ] No samples found: malt [2022-10-25 04:32:24,537] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-25 04:32:24,542] multiqc [DEBUG ] No samples found: sickle [2022-10-25 04:32:24,546] multiqc [DEBUG ] No samples found: skewer [2022-10-25 04:32:24,550] multiqc [DEBUG ] No samples found: sortmerna [2022-10-25 04:32:24,555] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-25 04:32:24,559] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-25 04:32:24,564] multiqc [DEBUG ] No samples found: afterqc [2022-10-25 04:32:24,568] multiqc [DEBUG ] No samples found: fastp [2022-10-25 04:32:49,653] multiqc.modules.fastqc.fastqc [INFO ] Found 142 reports [2022-10-25 04:33:10,341] multiqc [DEBUG ] No samples found: pycoqc [2022-10-25 04:33:10,346] multiqc [DEBUG ] No samples found: minionqc [2022-10-25 04:33:10,350] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-25 04:33:10,355] multiqc [DEBUG ] No samples found: clusterflow [2022-10-25 04:33:10,359] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-25 04:33:10,364] multiqc [DEBUG ] No samples found: interop [2022-10-25 04:33:10,368] multiqc [DEBUG ] No samples found: ivar [2022-10-25 04:33:10,372] multiqc [DEBUG ] No samples found: flash [2022-10-25 04:33:10,377] multiqc [DEBUG ] No samples found: seqyclean [2022-10-25 04:33:10,377] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-25 04:33:10,377] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-25 04:33:10,377] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-25 04:33:10,377] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-25 04:33:10,538] multiqc [INFO ] Compressing plot data [2022-10-25 04:33:10,586] multiqc [INFO ] Report : multiqc_report.html [2022-10-25 04:33:10,586] multiqc [INFO ] Data : multiqc_data [2022-10-25 04:33:10,587] multiqc [DEBUG ] Moving data file from '/state/partition1/job-26242122/tmplrzwrp7y/multiqc_data' to '/scratch/gencore/logs/html/H37NLDSX5/merged/multiqc_data' [2022-10-25 04:33:48,469] multiqc [INFO ] MultiQC complete