[2022-07-30 04:08:45,584] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-07-30 04:08:45,585] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-07-30 04:08:45,585] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-07-30 04:08:45,586] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-07-30 04:08:45,586] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-07-30 04:08:45,586] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCLNBGXM/merged [2022-07-30 04:08:46,141] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-07-30 04:08:46,141] multiqc [INFO ] This is MultiQC v1.9 [2022-07-30 04:08:46,141] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGCLNBGXM/merged [2022-07-30 04:08:46,141] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGCLNBGXM/merged [2022-07-30 04:08:46,141] multiqc [INFO ] Template : default [2022-07-30 04:08:46,141] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-07-30 04:08:46,141] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGCLNBGXM/merged [2022-07-30 04:08:46,142] 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 [2022-07-30 04:08:46,142] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-23014777/tmprv6tfqy9 [2022-07-30 04:08:46,262] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n02_undetermined_fastqc.html [2022-07-30 04:08:46,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n02_undetermined_fastqc.html [2022-07-30 04:08:46,308] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,310] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,310] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,310] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,310] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,310] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:46,378] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2022-07-30 04:08:49,460] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n01_undetermined_fastqc.html [2022-07-30 04:08:49,462] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n01_undetermined_fastqc.html [2022-07-30 04:08:49,506] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n01_Ruf-1_fastqc.html [2022-07-30 04:08:49,508] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n01_Ruf-1_fastqc.html [2022-07-30 04:08:49,551] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n01_Ruf-2_fastqc.html [2022-07-30 04:08:49,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n01_Ruf-2_fastqc.html [2022-07-30 04:08:49,594] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n02_Ruf-1_fastqc.html [2022-07-30 04:08:49,596] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n02_Ruf-1_fastqc.html [2022-07-30 04:08:49,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGCLNBGXM_n02_Ruf-2_fastqc.html [2022-07-30 04:08:49,639] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HGCLNBGXM_n02_Ruf-2_fastqc.html [2022-07-30 04:08:50,025] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-30 04:08:50,027] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-07-30 04:08:50,036] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2022-07-30 04:08:50,046] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-07-30 04:08:50,047] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-07-30 04:08:50,053] multiqc [DEBUG ] No samples found: conpair [2022-07-30 04:08:50,058] multiqc [DEBUG ] No samples found: peddy [2022-07-30 04:08:50,064] multiqc [DEBUG ] No samples found: somalier [2022-07-30 04:08:50,069] multiqc [DEBUG ] No samples found: methylQA [2022-07-30 04:08:50,079] multiqc [DEBUG ] No samples found: mosdepth [2022-07-30 04:08:50,084] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-07-30 04:08:50,088] multiqc [DEBUG ] No samples found: qualimap [2022-07-30 04:08:50,093] multiqc [DEBUG ] No samples found: preseq [2022-07-30 04:08:50,098] multiqc [DEBUG ] No samples found: quast [2022-07-30 04:08:50,104] multiqc [DEBUG ] No samples found: qorts [2022-07-30 04:08:50,109] multiqc [DEBUG ] No samples found: rna_seqc [2022-07-30 04:08:50,114] multiqc [DEBUG ] No samples found: rockhopper [2022-07-30 04:08:50,120] multiqc [DEBUG ] No samples found: rsem [2022-07-30 04:08:50,131] multiqc [DEBUG ] No samples found: rseqc [2022-07-30 04:08:50,136] multiqc [DEBUG ] No samples found: busco [2022-07-30 04:08:50,142] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-07-30 04:08:50,146] multiqc [DEBUG ] No samples found: disambiguate [2022-07-30 04:08:50,152] multiqc [DEBUG ] No samples found: supernova [2022-07-30 04:08:50,165] multiqc [DEBUG ] No samples found: deeptools [2022-07-30 04:08:50,171] multiqc [DEBUG ] No samples found: sargasso [2022-07-30 04:08:50,176] multiqc [DEBUG ] No samples found: verifybamid [2022-07-30 04:08:50,181] multiqc [DEBUG ] No samples found: mirtrace [2022-07-30 04:08:50,187] multiqc [DEBUG ] No samples found: happy [2022-07-30 04:08:50,192] multiqc [DEBUG ] No samples found: mirtop [2022-07-30 04:08:50,199] multiqc [DEBUG ] No samples found: homer [2022-07-30 04:08:50,205] multiqc [DEBUG ] No samples found: macs2 [2022-07-30 04:08:50,210] multiqc [DEBUG ] No samples found: theta2 [2022-07-30 04:08:50,215] multiqc [DEBUG ] No samples found: snpeff [2022-07-30 04:08:50,222] multiqc [DEBUG ] No samples found: gatk [2022-07-30 04:08:50,227] multiqc [DEBUG ] No samples found: htseq [2022-07-30 04:08:50,233] multiqc [DEBUG ] No samples found: bcftools [2022-07-30 04:08:50,238] multiqc [DEBUG ] No samples found: featureCounts [2022-07-30 04:08:50,245] multiqc [DEBUG ] No samples found: fgbio [2022-07-30 04:08:50,259] multiqc [DEBUG ] No samples found: dragen [2022-07-30 04:08:50,264] multiqc [DEBUG ] No samples found: dedup [2022-07-30 04:08:50,269] multiqc [DEBUG ] No samples found: damageprofiler [2022-07-30 04:08:50,294] multiqc [DEBUG ] No samples found: biobambam2 [2022-07-30 04:08:50,299] multiqc [DEBUG ] No samples found: mtnucratio [2022-07-30 04:08:50,302] multiqc [DEBUG ] No samples found: picard [2022-07-30 04:08:50,307] multiqc [DEBUG ] No samples found: prokka [2022-07-30 04:08:50,311] multiqc [DEBUG ] No samples found: samblaster [2022-07-30 04:08:50,320] multiqc [DEBUG ] No samples found: samtools [2022-07-30 04:08:50,326] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-07-30 04:08:50,331] multiqc [DEBUG ] No samples found: bamtools [2022-07-30 04:08:50,336] multiqc [DEBUG ] No samples found: jellyfish [2022-07-30 04:08:50,344] multiqc [DEBUG ] No samples found: vcftools [2022-07-30 04:08:50,349] multiqc [DEBUG ] No samples found: longranger [2022-07-30 04:08:50,354] multiqc [DEBUG ] No samples found: stacks [2022-07-30 04:08:50,360] multiqc [DEBUG ] No samples found: varscan2 [2022-07-30 04:08:50,373] multiqc [DEBUG ] No samples found: bbmap [2022-07-30 04:08:50,379] multiqc [DEBUG ] No samples found: bismark [2022-07-30 04:08:50,384] multiqc [DEBUG ] No samples found: biscuit [2022-07-30 04:08:50,390] multiqc [DEBUG ] No samples found: hicexplorer [2022-07-30 04:08:50,395] multiqc [DEBUG ] No samples found: hicup [2022-07-30 04:08:50,400] multiqc [DEBUG ] No samples found: hicpro [2022-07-30 04:08:50,405] multiqc [DEBUG ] No samples found: salmon [2022-07-30 04:08:50,410] multiqc [DEBUG ] No samples found: kallisto [2022-07-30 04:08:50,415] multiqc [DEBUG ] No samples found: slamdunk [2022-07-30 04:08:50,420] multiqc [DEBUG ] No samples found: star [2022-07-30 04:08:50,425] multiqc [DEBUG ] No samples found: hisat2 [2022-07-30 04:08:50,430] multiqc [DEBUG ] No samples found: tophat [2022-07-30 04:08:50,435] multiqc [DEBUG ] No samples found: bowtie2 [2022-07-30 04:08:50,440] multiqc [DEBUG ] No samples found: bowtie1 [2022-07-30 04:08:50,446] multiqc [DEBUG ] No samples found: snpsplit [2022-07-30 04:08:50,450] multiqc [DEBUG ] No samples found: kat [2022-07-30 04:08:50,455] multiqc [DEBUG ] No samples found: leehom [2022-07-30 04:08:50,460] multiqc [DEBUG ] No samples found: adapterRemoval [2022-07-30 04:08:50,464] multiqc [DEBUG ] No samples found: clipandmerge [2022-07-30 04:08:50,469] multiqc [DEBUG ] No samples found: cutadapt [2022-07-30 04:08:50,473] multiqc [DEBUG ] No samples found: flexbar [2022-07-30 04:08:50,479] multiqc [DEBUG ] No samples found: kaiju [2022-07-30 04:08:50,484] multiqc [DEBUG ] No samples found: kraken [2022-07-30 04:08:50,489] multiqc [DEBUG ] No samples found: malt [2022-07-30 04:08:50,494] multiqc [DEBUG ] No samples found: trimmomatic [2022-07-30 04:08:50,498] multiqc [DEBUG ] No samples found: sickle [2022-07-30 04:08:50,504] multiqc [DEBUG ] No samples found: skewer [2022-07-30 04:08:50,508] multiqc [DEBUG ] No samples found: sortmerna [2022-07-30 04:08:50,513] multiqc [DEBUG ] No samples found: biobloomtools [2022-07-30 04:08:50,518] multiqc [DEBUG ] No samples found: fastq_screen [2022-07-30 04:08:50,523] multiqc [DEBUG ] No samples found: afterqc [2022-07-30 04:08:50,528] multiqc [DEBUG ] No samples found: fastp [2022-07-30 04:08:50,904] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2022-07-30 04:08:50,979] multiqc [DEBUG ] No samples found: pycoqc [2022-07-30 04:08:50,984] multiqc [DEBUG ] No samples found: minionqc [2022-07-30 04:08:50,990] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-07-30 04:08:50,995] multiqc [DEBUG ] No samples found: clusterflow [2022-07-30 04:08:51,000] multiqc [DEBUG ] No samples found: bcl2fastq [2022-07-30 04:08:51,006] multiqc [DEBUG ] No samples found: interop [2022-07-30 04:08:51,012] multiqc [DEBUG ] No samples found: ivar [2022-07-30 04:08:51,017] multiqc [DEBUG ] No samples found: flash [2022-07-30 04:08:51,023] multiqc [DEBUG ] No samples found: seqyclean [2022-07-30 04:08:51,023] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-07-30 04:08:51,023] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-07-30 04:08:51,023] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-07-30 04:08:51,023] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-07-30 04:08:51,032] multiqc [INFO ] Compressing plot data [2022-07-30 04:08:51,147] multiqc [INFO ] Report : multiqc_report.html [2022-07-30 04:08:51,147] multiqc [INFO ] Data : multiqc_data [2022-07-30 04:08:51,147] multiqc [DEBUG ] Moving data file from '/state/partition1/job-23014777/tmprv6tfqy9/multiqc_data' to '/scratch/gencore/logs/html/HGCLNBGXM/merged/multiqc_data' [2022-07-30 04:08:51,701] multiqc [INFO ] MultiQC complete