[2021-10-28 09:02:12,619] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-10-28 09:02:12,619] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-10-28 09:02:12,619] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-10-28 09:02:12,620] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-10-28 09:02:12,620] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-10-28 09:02:12,620] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H57VYAFX3/merged [2021-10-28 09:02:13,992] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-10-28 09:02:13,992] multiqc [INFO ] This is MultiQC v1.9 [2021-10-28 09:02:13,992] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H57VYAFX3/merged [2021-10-28 09:02:13,992] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H57VYAFX3/merged [2021-10-28 09:02:13,992] multiqc [INFO ] Template : default [2021-10-28 09:02:13,992] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-10-28 09:02:13,992] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H57VYAFX3/merged [2021-10-28 09:02:13,993] 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 [2021-10-28 09:02:13,993] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-11272632/tmp2fusjado [2021-10-28 09:02:14,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_undetermined_fastqc.html [2021-10-28 09:02:14,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_undetermined_fastqc.html [2021-10-28 09:02:14,176] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_831_fastqc.html [2021-10-28 09:02:14,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_831_fastqc.html [2021-10-28 09:02:14,253] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_undetermined_fastqc.html [2021-10-28 09:02:14,255] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_undetermined_fastqc.html [2021-10-28 09:02:14,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_830_fastqc.html [2021-10-28 09:02:14,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_830_fastqc.html [2021-10-28 09:02:14,351] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_827_fastqc.html [2021-10-28 09:02:14,353] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_827_fastqc.html [2021-10-28 09:02:14,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_827_fastqc.html [2021-10-28 09:02:14,401] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_827_fastqc.html [2021-10-28 09:02:14,447] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_829_fastqc.html [2021-10-28 09:02:14,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_829_fastqc.html [2021-10-28 09:02:14,495] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_832_fastqc.html [2021-10-28 09:02:14,496] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_832_fastqc.html [2021-10-28 09:02:14,544] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_830_fastqc.html [2021-10-28 09:02:14,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_830_fastqc.html [2021-10-28 09:02:14,592] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_831_fastqc.html [2021-10-28 09:02:14,594] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_831_fastqc.html [2021-10-28 09:02:14,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n02_829_fastqc.html [2021-10-28 09:02:14,641] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n02_829_fastqc.html [2021-10-28 09:02:14,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H57VYAFX3_n01_832_fastqc.html [2021-10-28 09:02:14,689] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H57VYAFX3_n01_832_fastqc.html [2021-10-28 09:02:15,035] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-28 09:02:15,036] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-10-28 09:02:15,043] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-10-28 09:02:15,047] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2021-10-28 09:02:15,056] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-10-28 09:02:15,063] multiqc [DEBUG ] No samples found: conpair [2021-10-28 09:02:15,071] multiqc [DEBUG ] No samples found: peddy [2021-10-28 09:02:15,081] multiqc [DEBUG ] No samples found: somalier [2021-10-28 09:02:15,090] multiqc [DEBUG ] No samples found: methylQA [2021-10-28 09:02:15,102] multiqc [DEBUG ] No samples found: mosdepth [2021-10-28 09:02:15,107] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-10-28 09:02:15,111] multiqc [DEBUG ] No samples found: qualimap [2021-10-28 09:02:15,118] multiqc [DEBUG ] No samples found: preseq [2021-10-28 09:02:15,124] multiqc [DEBUG ] No samples found: quast [2021-10-28 09:02:15,130] multiqc [DEBUG ] No samples found: qorts [2021-10-28 09:02:15,136] multiqc [DEBUG ] No samples found: rna_seqc [2021-10-28 09:02:15,142] multiqc [DEBUG ] No samples found: rockhopper [2021-10-28 09:02:15,150] multiqc [DEBUG ] No samples found: rsem [2021-10-28 09:02:15,162] multiqc [DEBUG ] No samples found: rseqc [2021-10-28 09:02:15,169] multiqc [DEBUG ] No samples found: busco [2021-10-28 09:02:15,175] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-10-28 09:02:15,182] multiqc [DEBUG ] No samples found: disambiguate [2021-10-28 09:02:15,191] multiqc [DEBUG ] No samples found: supernova [2021-10-28 09:02:15,205] multiqc [DEBUG ] No samples found: deeptools [2021-10-28 09:02:15,209] multiqc [DEBUG ] No samples found: sargasso [2021-10-28 09:02:15,217] multiqc [DEBUG ] No samples found: verifybamid [2021-10-28 09:02:15,225] multiqc [DEBUG ] No samples found: mirtrace [2021-10-28 09:02:15,234] multiqc [DEBUG ] No samples found: happy [2021-10-28 09:02:15,239] multiqc [DEBUG ] No samples found: mirtop [2021-10-28 09:02:15,246] multiqc [DEBUG ] No samples found: homer [2021-10-28 09:02:15,252] multiqc [DEBUG ] No samples found: macs2 [2021-10-28 09:02:15,257] multiqc [DEBUG ] No samples found: theta2 [2021-10-28 09:02:15,263] multiqc [DEBUG ] No samples found: snpeff [2021-10-28 09:02:15,271] multiqc [DEBUG ] No samples found: gatk [2021-10-28 09:02:15,276] multiqc [DEBUG ] No samples found: htseq [2021-10-28 09:02:15,281] multiqc [DEBUG ] No samples found: bcftools [2021-10-28 09:02:15,287] multiqc [DEBUG ] No samples found: featureCounts [2021-10-28 09:02:15,293] multiqc [DEBUG ] No samples found: fgbio [2021-10-28 09:02:15,307] multiqc [DEBUG ] No samples found: dragen [2021-10-28 09:02:15,315] multiqc [DEBUG ] No samples found: dedup [2021-10-28 09:02:15,323] multiqc [DEBUG ] No samples found: damageprofiler [2021-10-28 09:02:15,352] multiqc [DEBUG ] No samples found: biobambam2 [2021-10-28 09:02:15,356] multiqc [DEBUG ] No samples found: mtnucratio [2021-10-28 09:02:15,359] multiqc [DEBUG ] No samples found: picard [2021-10-28 09:02:15,363] multiqc [DEBUG ] No samples found: prokka [2021-10-28 09:02:15,370] multiqc [DEBUG ] No samples found: samblaster [2021-10-28 09:02:15,381] multiqc [DEBUG ] No samples found: samtools [2021-10-28 09:02:15,390] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-10-28 09:02:15,396] multiqc [DEBUG ] No samples found: bamtools [2021-10-28 09:02:15,401] multiqc [DEBUG ] No samples found: jellyfish [2021-10-28 09:02:15,409] multiqc [DEBUG ] No samples found: vcftools [2021-10-28 09:02:15,415] multiqc [DEBUG ] No samples found: longranger [2021-10-28 09:02:15,423] multiqc [DEBUG ] No samples found: stacks [2021-10-28 09:02:15,427] multiqc [DEBUG ] No samples found: varscan2 [2021-10-28 09:02:15,442] multiqc [DEBUG ] No samples found: bbmap [2021-10-28 09:02:15,447] multiqc [DEBUG ] No samples found: bismark [2021-10-28 09:02:15,453] multiqc [DEBUG ] No samples found: biscuit [2021-10-28 09:02:15,459] multiqc [DEBUG ] No samples found: hicexplorer [2021-10-28 09:02:15,465] multiqc [DEBUG ] No samples found: hicup [2021-10-28 09:02:15,473] multiqc [DEBUG ] No samples found: hicpro [2021-10-28 09:02:15,476] multiqc [DEBUG ] No samples found: salmon [2021-10-28 09:02:15,481] multiqc [DEBUG ] No samples found: kallisto [2021-10-28 09:02:15,487] multiqc [DEBUG ] No samples found: slamdunk [2021-10-28 09:02:15,495] multiqc [DEBUG ] No samples found: star [2021-10-28 09:02:15,501] multiqc [DEBUG ] No samples found: hisat2 [2021-10-28 09:02:15,505] multiqc [DEBUG ] No samples found: tophat [2021-10-28 09:02:15,511] multiqc [DEBUG ] No samples found: bowtie2 [2021-10-28 09:02:15,517] multiqc [DEBUG ] No samples found: bowtie1 [2021-10-28 09:02:15,522] multiqc [DEBUG ] No samples found: snpsplit [2021-10-28 09:02:15,529] multiqc [DEBUG ] No samples found: kat [2021-10-28 09:02:15,535] multiqc [DEBUG ] No samples found: leehom [2021-10-28 09:02:15,540] multiqc [DEBUG ] No samples found: adapterRemoval [2021-10-28 09:02:15,546] multiqc [DEBUG ] No samples found: clipandmerge [2021-10-28 09:02:15,551] multiqc [DEBUG ] No samples found: cutadapt [2021-10-28 09:02:15,555] multiqc [DEBUG ] No samples found: flexbar [2021-10-28 09:02:15,561] multiqc [DEBUG ] No samples found: kaiju [2021-10-28 09:02:15,569] multiqc [DEBUG ] No samples found: kraken [2021-10-28 09:02:15,573] multiqc [DEBUG ] No samples found: malt [2021-10-28 09:02:15,580] multiqc [DEBUG ] No samples found: trimmomatic [2021-10-28 09:02:15,585] multiqc [DEBUG ] No samples found: sickle [2021-10-28 09:02:15,590] multiqc [DEBUG ] No samples found: skewer [2021-10-28 09:02:15,595] multiqc [DEBUG ] No samples found: sortmerna [2021-10-28 09:02:15,600] multiqc [DEBUG ] No samples found: biobloomtools [2021-10-28 09:02:15,606] multiqc [DEBUG ] No samples found: fastq_screen [2021-10-28 09:02:15,612] multiqc [DEBUG ] No samples found: afterqc [2021-10-28 09:02:15,617] multiqc [DEBUG ] No samples found: fastp [2021-10-28 09:02:16,091] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2021-10-28 09:02:16,363] multiqc [DEBUG ] No samples found: pycoqc [2021-10-28 09:02:16,368] multiqc [DEBUG ] No samples found: minionqc [2021-10-28 09:02:16,372] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-10-28 09:02:16,376] multiqc [DEBUG ] No samples found: clusterflow [2021-10-28 09:02:16,382] multiqc [DEBUG ] No samples found: bcl2fastq [2021-10-28 09:02:16,388] multiqc [DEBUG ] No samples found: interop [2021-10-28 09:02:16,395] multiqc [DEBUG ] No samples found: ivar [2021-10-28 09:02:16,401] multiqc [DEBUG ] No samples found: flash [2021-10-28 09:02:16,406] multiqc [DEBUG ] No samples found: seqyclean [2021-10-28 09:02:16,406] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-10-28 09:02:16,406] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-10-28 09:02:16,406] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-10-28 09:02:16,406] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-10-28 09:02:16,421] multiqc [INFO ] Compressing plot data [2021-10-28 09:02:16,680] multiqc [INFO ] Report : multiqc_report.html [2021-10-28 09:02:16,680] multiqc [INFO ] Data : multiqc_data [2021-10-28 09:02:16,680] multiqc [DEBUG ] Moving data file from '/state/partition1/job-11272632/tmp2fusjado/multiqc_data' to '/scratch/gencore/logs/html/H57VYAFX3/merged/multiqc_data' [2021-10-28 09:02:16,812] multiqc [INFO ] MultiQC complete