[2022-11-28 16:44:04,255] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-11-28 16:44:04,255] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-11-28 16:44:04,255] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-11-28 16:44:04,256] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-11-28 16:44:04,256] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-11-28 16:44:04,256] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGC3DRX2/1 [2022-11-28 16:44:04,741] multiqc [WARNING] MultiQC Version v1.13 now available! [2022-11-28 16:44:04,741] multiqc [INFO ] This is MultiQC v1.9 [2022-11-28 16:44:04,741] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNGC3DRX2/1 [2022-11-28 16:44:04,741] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNGC3DRX2/1 [2022-11-28 16:44:04,741] multiqc [INFO ] Template : default [2022-11-28 16:44:04,741] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-11-28 16:44:04,741] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNGC3DRX2/1 [2022-11-28 16:44:04,742] 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 [2022-11-28 16:44:04,742] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-27440387/tmpa0kak2my [2022-11-28 16:44:04,852] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_G4_b_fastqc.html [2022-11-28 16:44:04,854] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_C6_b_fastqc.html [2022-11-28 16:44:06,108] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_C6_b_fastqc.html [2022-11-28 16:44:06,108] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_C6_b_fastqc.html [2022-11-28 16:44:06,108] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_C6_b_fastqc.html [2022-11-28 16:44:06,108] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_C6_b_fastqc.html [2022-11-28 16:44:06,173] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,175] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_E4_b_fastqc.html [2022-11-28 16:44:06,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_undetermined_fastqc.html [2022-11-28 16:44:06,242] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_undetermined_fastqc.html [2022-11-28 16:44:06,301] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_D3_b_fastqc.html [2022-11-28 16:44:06,303] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_D3_b_fastqc.html [2022-11-28 16:44:06,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_undetermined_fastqc.html [2022-11-28 16:44:06,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_undetermined_fastqc.html [2022-11-28 16:44:06,433] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A4_b_fastqc.html [2022-11-28 16:44:06,434] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A4_b_fastqc.html [2022-11-28 16:44:06,504] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,506] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n02_T12_A6_b_fastqc.html [2022-11-28 16:44:06,570] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_E6_b_fastqc.html [2022-11-28 16:44:06,572] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNGC3DRX2_l01_n01_T12_E6_b_fastqc.html [2022-11-28 16:44:07,111] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 16:44:07,112] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-11-28 16:44:07,125] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 13 samples (table) [2022-11-28 16:44:07,127] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-11-28 16:44:07,136] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-11-28 16:44:07,142] multiqc [DEBUG ] No samples found: conpair [2022-11-28 16:44:07,147] multiqc [DEBUG ] No samples found: peddy [2022-11-28 16:44:07,152] multiqc [DEBUG ] No samples found: somalier [2022-11-28 16:44:07,158] multiqc [DEBUG ] No samples found: methylQA [2022-11-28 16:44:07,166] multiqc [DEBUG ] No samples found: mosdepth [2022-11-28 16:44:07,170] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-11-28 16:44:07,174] multiqc [DEBUG ] No samples found: qualimap [2022-11-28 16:44:07,179] multiqc [DEBUG ] No samples found: preseq [2022-11-28 16:44:07,183] multiqc [DEBUG ] No samples found: quast [2022-11-28 16:44:07,188] multiqc [DEBUG ] No samples found: qorts [2022-11-28 16:44:07,194] multiqc [DEBUG ] No samples found: rna_seqc [2022-11-28 16:44:07,199] multiqc [DEBUG ] No samples found: rockhopper [2022-11-28 16:44:07,204] multiqc [DEBUG ] No samples found: rsem [2022-11-28 16:44:07,220] multiqc [DEBUG ] No samples found: rseqc [2022-11-28 16:44:07,224] multiqc [DEBUG ] No samples found: busco [2022-11-28 16:44:07,230] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-11-28 16:44:07,234] multiqc [DEBUG ] No samples found: disambiguate [2022-11-28 16:44:07,240] multiqc [DEBUG ] No samples found: supernova [2022-11-28 16:44:07,253] multiqc [DEBUG ] No samples found: deeptools [2022-11-28 16:44:07,258] multiqc [DEBUG ] No samples found: sargasso [2022-11-28 16:44:07,263] multiqc [DEBUG ] No samples found: verifybamid [2022-11-28 16:44:07,268] multiqc [DEBUG ] No samples found: mirtrace [2022-11-28 16:44:07,274] multiqc [DEBUG ] No samples found: happy [2022-11-28 16:44:07,279] multiqc [DEBUG ] No samples found: mirtop [2022-11-28 16:44:07,284] multiqc [DEBUG ] No samples found: homer [2022-11-28 16:44:07,289] multiqc [DEBUG ] No samples found: macs2 [2022-11-28 16:44:07,294] multiqc [DEBUG ] No samples found: theta2 [2022-11-28 16:44:07,300] multiqc [DEBUG ] No samples found: snpeff [2022-11-28 16:44:07,307] multiqc [DEBUG ] No samples found: gatk [2022-11-28 16:44:07,311] multiqc [DEBUG ] No samples found: htseq [2022-11-28 16:44:07,318] multiqc [DEBUG ] No samples found: bcftools [2022-11-28 16:44:07,322] multiqc [DEBUG ] No samples found: featureCounts [2022-11-28 16:44:07,330] multiqc [DEBUG ] No samples found: fgbio [2022-11-28 16:44:07,344] multiqc [DEBUG ] No samples found: dragen [2022-11-28 16:44:07,350] multiqc [DEBUG ] No samples found: dedup [2022-11-28 16:44:07,355] multiqc [DEBUG ] No samples found: damageprofiler [2022-11-28 16:44:07,381] multiqc [DEBUG ] No samples found: biobambam2 [2022-11-28 16:44:07,386] multiqc [DEBUG ] No samples found: mtnucratio [2022-11-28 16:44:07,388] multiqc [DEBUG ] No samples found: picard [2022-11-28 16:44:07,395] multiqc [DEBUG ] No samples found: prokka [2022-11-28 16:44:07,402] multiqc [DEBUG ] No samples found: samblaster [2022-11-28 16:44:07,413] multiqc [DEBUG ] No samples found: samtools [2022-11-28 16:44:07,419] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-11-28 16:44:07,424] multiqc [DEBUG ] No samples found: bamtools [2022-11-28 16:44:07,429] multiqc [DEBUG ] No samples found: jellyfish [2022-11-28 16:44:07,438] multiqc [DEBUG ] No samples found: vcftools [2022-11-28 16:44:07,443] multiqc [DEBUG ] No samples found: longranger [2022-11-28 16:44:07,447] multiqc [DEBUG ] No samples found: stacks [2022-11-28 16:44:07,452] multiqc [DEBUG ] No samples found: varscan2 [2022-11-28 16:44:07,465] multiqc [DEBUG ] No samples found: bbmap [2022-11-28 16:44:07,469] multiqc [DEBUG ] No samples found: bismark [2022-11-28 16:44:07,474] multiqc [DEBUG ] No samples found: biscuit [2022-11-28 16:44:07,478] multiqc [DEBUG ] No samples found: hicexplorer [2022-11-28 16:44:07,483] multiqc [DEBUG ] No samples found: hicup [2022-11-28 16:44:07,487] multiqc [DEBUG ] No samples found: hicpro [2022-11-28 16:44:07,491] multiqc [DEBUG ] No samples found: salmon [2022-11-28 16:44:07,496] multiqc [DEBUG ] No samples found: kallisto [2022-11-28 16:44:07,500] multiqc [DEBUG ] No samples found: slamdunk [2022-11-28 16:44:07,505] multiqc [DEBUG ] No samples found: star [2022-11-28 16:44:07,509] multiqc [DEBUG ] No samples found: hisat2 [2022-11-28 16:44:07,515] multiqc [DEBUG ] No samples found: tophat [2022-11-28 16:44:07,519] multiqc [DEBUG ] No samples found: bowtie2 [2022-11-28 16:44:07,525] multiqc [DEBUG ] No samples found: bowtie1 [2022-11-28 16:44:07,533] multiqc [DEBUG ] No samples found: snpsplit [2022-11-28 16:44:07,538] multiqc [DEBUG ] No samples found: kat [2022-11-28 16:44:07,543] multiqc [DEBUG ] No samples found: leehom [2022-11-28 16:44:07,549] multiqc [DEBUG ] No samples found: adapterRemoval [2022-11-28 16:44:07,555] multiqc [DEBUG ] No samples found: clipandmerge [2022-11-28 16:44:07,561] multiqc [DEBUG ] No samples found: cutadapt [2022-11-28 16:44:07,570] multiqc [DEBUG ] No samples found: flexbar [2022-11-28 16:44:07,579] multiqc [DEBUG ] No samples found: kaiju [2022-11-28 16:44:07,587] multiqc [DEBUG ] No samples found: kraken [2022-11-28 16:44:07,595] multiqc [DEBUG ] No samples found: malt [2022-11-28 16:44:07,600] multiqc [DEBUG ] No samples found: trimmomatic [2022-11-28 16:44:07,606] multiqc [DEBUG ] No samples found: sickle [2022-11-28 16:44:07,612] multiqc [DEBUG ] No samples found: skewer [2022-11-28 16:44:07,617] multiqc [DEBUG ] No samples found: sortmerna [2022-11-28 16:44:07,621] multiqc [DEBUG ] No samples found: biobloomtools [2022-11-28 16:44:07,626] multiqc [DEBUG ] No samples found: fastq_screen [2022-11-28 16:44:07,633] multiqc [DEBUG ] No samples found: afterqc [2022-11-28 16:44:07,637] multiqc [DEBUG ] No samples found: fastp [2022-11-28 16:44:08,481] multiqc.modules.fastqc.fastqc [INFO ] Found 26 reports [2022-11-28 16:44:08,849] multiqc [DEBUG ] No samples found: pycoqc [2022-11-28 16:44:08,857] multiqc [DEBUG ] No samples found: minionqc [2022-11-28 16:44:08,864] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-11-28 16:44:08,869] multiqc [DEBUG ] No samples found: clusterflow [2022-11-28 16:44:08,874] multiqc [DEBUG ] No samples found: bcl2fastq [2022-11-28 16:44:08,882] multiqc [DEBUG ] No samples found: interop [2022-11-28 16:44:08,891] multiqc [DEBUG ] No samples found: ivar [2022-11-28 16:44:08,899] multiqc [DEBUG ] No samples found: flash [2022-11-28 16:44:08,905] multiqc [DEBUG ] No samples found: seqyclean [2022-11-28 16:44:08,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-11-28 16:44:08,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-11-28 16:44:08,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-11-28 16:44:08,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-11-28 16:44:08,905] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-11-28 16:44:08,936] multiqc [INFO ] Compressing plot data [2022-11-28 16:44:09,337] multiqc [INFO ] Report : multiqc_report.html [2022-11-28 16:44:09,337] multiqc [INFO ] Data : multiqc_data [2022-11-28 16:44:09,337] multiqc [DEBUG ] Moving data file from '/state/partition1/job-27440387/tmpa0kak2my/multiqc_data' to '/scratch/gencore/logs/html/HNGC3DRX2/1/multiqc_data' [2022-11-28 16:44:35,750] multiqc [INFO ] MultiQC complete