[2022-10-12 12:36:13,669] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-10-12 12:36:13,669] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-10-12 12:36:13,669] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-10-12 12:36:13,670] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-10-12 12:36:13,670] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-10-12 12:36:13,671] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGJHJBGXM/merged [2022-10-12 12:36:14,074] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-10-12 12:36:14,074] multiqc [INFO ] This is MultiQC v1.9 [2022-10-12 12:36:14,074] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HGJHJBGXM/merged [2022-10-12 12:36:14,074] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HGJHJBGXM/merged [2022-10-12 12:36:14,074] multiqc [INFO ] Template : default [2022-10-12 12:36:14,074] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-10-12 12:36:14,074] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HGJHJBGXM/merged [2022-10-12 12:36:14,075] 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 [2022-10-12 12:36:14,075] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-25858856/tmpqwyzap0n [2022-10-12 12:36:14,193] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HGJHJBGXM_n02_CDC1080_1_IL_fastqc.html [2022-10-12 12:36:14,196] multiqc [DEBUG ] File ignored by longranger/invocation because it 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limit: HGJHJBGXM_n01_3690_2_IDT_fastqc.html [2022-10-12 12:36:16,946] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-12 12:36:16,948] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-10-12 12:36:16,956] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-10-12 12:36:16,966] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-10-12 12:36:16,979] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 26 samples (table) [2022-10-12 12:36:16,984] multiqc [DEBUG ] No samples found: conpair [2022-10-12 12:36:16,989] multiqc [DEBUG ] No samples found: peddy [2022-10-12 12:36:16,994] multiqc [DEBUG ] No samples found: somalier [2022-10-12 12:36:16,998] multiqc [DEBUG ] No samples found: methylQA [2022-10-12 12:36:17,006] multiqc [DEBUG ] No samples found: mosdepth [2022-10-12 12:36:17,010] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-10-12 12:36:17,014] multiqc [DEBUG ] No samples found: qualimap [2022-10-12 12:36:17,018] multiqc [DEBUG ] No samples found: preseq [2022-10-12 12:36:17,023] multiqc [DEBUG ] No samples found: quast [2022-10-12 12:36:17,027] multiqc [DEBUG ] No samples found: qorts [2022-10-12 12:36:17,032] multiqc [DEBUG ] No samples found: rna_seqc [2022-10-12 12:36:17,037] multiqc [DEBUG ] No samples found: rockhopper [2022-10-12 12:36:17,041] multiqc [DEBUG ] No samples found: rsem [2022-10-12 12:36:17,052] multiqc [DEBUG ] No samples found: rseqc [2022-10-12 12:36:17,057] multiqc [DEBUG ] No samples found: busco [2022-10-12 12:36:17,061] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-10-12 12:36:17,067] multiqc [DEBUG ] No samples found: disambiguate [2022-10-12 12:36:17,072] multiqc [DEBUG ] No samples found: supernova [2022-10-12 12:36:17,086] multiqc [DEBUG ] No samples found: deeptools [2022-10-12 12:36:17,091] multiqc [DEBUG ] No samples found: sargasso [2022-10-12 12:36:17,095] multiqc [DEBUG ] No samples found: verifybamid [2022-10-12 12:36:17,100] multiqc [DEBUG ] No samples found: mirtrace [2022-10-12 12:36:17,105] multiqc [DEBUG ] No samples found: happy [2022-10-12 12:36:17,111] multiqc [DEBUG ] No samples found: mirtop [2022-10-12 12:36:17,118] multiqc [DEBUG ] No samples found: homer [2022-10-12 12:36:17,123] multiqc [DEBUG ] No samples found: macs2 [2022-10-12 12:36:17,128] multiqc [DEBUG ] No samples found: theta2 [2022-10-12 12:36:17,133] multiqc [DEBUG ] No samples found: snpeff [2022-10-12 12:36:17,140] multiqc [DEBUG ] No samples found: gatk [2022-10-12 12:36:17,145] multiqc [DEBUG ] No samples found: htseq [2022-10-12 12:36:17,152] multiqc [DEBUG ] No samples found: bcftools [2022-10-12 12:36:17,157] multiqc [DEBUG ] No samples found: featureCounts [2022-10-12 12:36:17,165] multiqc [DEBUG ] No samples found: fgbio [2022-10-12 12:36:17,181] multiqc [DEBUG ] No samples found: dragen [2022-10-12 12:36:17,186] multiqc [DEBUG ] No samples found: dedup [2022-10-12 12:36:17,191] multiqc [DEBUG ] No samples found: damageprofiler [2022-10-12 12:36:17,219] multiqc [DEBUG ] No samples found: biobambam2 [2022-10-12 12:36:17,225] multiqc [DEBUG ] No samples found: mtnucratio [2022-10-12 12:36:17,227] multiqc [DEBUG ] No samples found: picard [2022-10-12 12:36:17,233] multiqc [DEBUG ] No samples found: prokka [2022-10-12 12:36:17,238] multiqc [DEBUG ] No samples found: samblaster [2022-10-12 12:36:17,247] multiqc [DEBUG ] No samples found: samtools [2022-10-12 12:36:17,251] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-10-12 12:36:17,257] multiqc [DEBUG ] No samples found: bamtools [2022-10-12 12:36:17,262] multiqc [DEBUG ] No samples found: jellyfish [2022-10-12 12:36:17,273] multiqc [DEBUG ] No samples found: vcftools [2022-10-12 12:36:17,279] multiqc [DEBUG ] No samples found: longranger [2022-10-12 12:36:17,284] multiqc [DEBUG ] No samples found: stacks [2022-10-12 12:36:17,291] multiqc [DEBUG ] No samples found: varscan2 [2022-10-12 12:36:17,313] multiqc [DEBUG ] No samples found: bbmap [2022-10-12 12:36:17,318] multiqc [DEBUG ] No samples found: bismark [2022-10-12 12:36:17,323] multiqc [DEBUG ] No samples found: biscuit [2022-10-12 12:36:17,329] multiqc [DEBUG ] No samples found: hicexplorer [2022-10-12 12:36:17,335] multiqc [DEBUG ] No samples found: hicup [2022-10-12 12:36:17,340] multiqc [DEBUG ] No samples found: hicpro [2022-10-12 12:36:17,345] multiqc [DEBUG ] No samples found: salmon [2022-10-12 12:36:17,350] multiqc [DEBUG ] No samples found: kallisto [2022-10-12 12:36:17,355] multiqc [DEBUG ] No samples found: slamdunk [2022-10-12 12:36:17,360] multiqc [DEBUG ] No samples found: star [2022-10-12 12:36:17,365] multiqc [DEBUG ] No samples found: hisat2 [2022-10-12 12:36:17,371] multiqc [DEBUG ] No samples found: tophat [2022-10-12 12:36:17,377] multiqc [DEBUG ] No samples found: bowtie2 [2022-10-12 12:36:17,382] multiqc [DEBUG ] No samples found: bowtie1 [2022-10-12 12:36:17,387] multiqc [DEBUG ] No samples found: snpsplit [2022-10-12 12:36:17,393] multiqc [DEBUG ] No samples found: kat [2022-10-12 12:36:17,400] multiqc [DEBUG ] No samples found: leehom [2022-10-12 12:36:17,405] multiqc [DEBUG ] No samples found: adapterRemoval [2022-10-12 12:36:17,410] multiqc [DEBUG ] No samples found: clipandmerge [2022-10-12 12:36:17,415] multiqc [DEBUG ] No samples found: cutadapt [2022-10-12 12:36:17,420] multiqc [DEBUG ] No samples found: flexbar [2022-10-12 12:36:17,425] multiqc [DEBUG ] No samples found: kaiju [2022-10-12 12:36:17,430] multiqc [DEBUG ] No samples found: kraken [2022-10-12 12:36:17,435] multiqc [DEBUG ] No samples found: malt [2022-10-12 12:36:17,439] multiqc [DEBUG ] No samples found: trimmomatic [2022-10-12 12:36:17,444] multiqc [DEBUG ] No samples found: sickle [2022-10-12 12:36:17,450] multiqc [DEBUG ] No samples found: skewer [2022-10-12 12:36:17,455] multiqc [DEBUG ] No samples found: sortmerna [2022-10-12 12:36:17,460] multiqc [DEBUG ] No samples found: biobloomtools [2022-10-12 12:36:17,465] multiqc [DEBUG ] No samples found: fastq_screen [2022-10-12 12:36:17,470] multiqc [DEBUG ] No samples found: afterqc [2022-10-12 12:36:17,475] multiqc [DEBUG ] No samples found: fastp [2022-10-12 12:36:22,417] multiqc.modules.fastqc.fastqc [INFO ] Found 52 reports [2022-10-12 12:36:22,419] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HGJHJBGXM_n01_CDC888_2_IL' [2022-10-12 12:36:22,419] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HGJHJBGXM_n02_CDC888_2_IL' [2022-10-12 12:36:23,057] multiqc [DEBUG ] No samples found: pycoqc [2022-10-12 12:36:23,062] multiqc [DEBUG ] No samples found: minionqc [2022-10-12 12:36:23,068] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-10-12 12:36:23,073] multiqc [DEBUG ] No samples found: clusterflow [2022-10-12 12:36:23,078] multiqc [DEBUG ] No samples found: bcl2fastq [2022-10-12 12:36:23,083] multiqc [DEBUG ] No samples found: interop [2022-10-12 12:36:23,088] multiqc [DEBUG ] No samples found: ivar [2022-10-12 12:36:23,094] multiqc [DEBUG ] No samples found: flash [2022-10-12 12:36:23,099] multiqc [DEBUG ] No samples found: seqyclean [2022-10-12 12:36:23,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-10-12 12:36:23,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-10-12 12:36:23,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-10-12 12:36:23,099] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-10-12 12:36:23,164] multiqc [INFO ] Compressing plot data [2022-10-12 12:36:24,055] multiqc [INFO ] Report : multiqc_report.html [2022-10-12 12:36:24,056] multiqc [INFO ] Data : multiqc_data [2022-10-12 12:36:24,056] multiqc [DEBUG ] Moving data file from '/state/partition1/job-25858856/tmpqwyzap0n/multiqc_data' to '/scratch/gencore/logs/html/HGJHJBGXM/merged/multiqc_data' [2022-10-12 12:36:24,198] multiqc [INFO ] MultiQC complete