[2021-04-24 05:33:05,285] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-04-24 05:33:05,285] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-04-24 05:33:05,286] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-04-24 05:33:05,286] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-04-24 05:33:05,286] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-04-24 05:33:05,287] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYH2AFX2/merged [2021-04-24 05:33:08,101] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-04-24 05:33:08,101] multiqc [INFO ] This is MultiQC v1.9 [2021-04-24 05:33:08,101] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNYH2AFX2/merged [2021-04-24 05:33:08,101] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNYH2AFX2/merged [2021-04-24 05:33:08,101] multiqc [INFO ] Template : default [2021-04-24 05:33:08,101] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-04-24 05:33:08,101] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNYH2AFX2/merged [2021-04-24 05:33:08,101] 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 [2021-04-24 05:33:08,101] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-5941274/tmpce9sqtgk [2021-04-24 05:33:08,202] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_hFT_fastqc.html [2021-04-24 05:33:08,204] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search 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[2021-04-24 05:33:16,263] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_AP1h_sSEP4_C_fastqc.html [2021-04-24 05:33:16,265] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n02_AP1h_sSEP4_C_fastqc.html [2021-04-24 05:33:16,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_SEP33h_fastqc.html [2021-04-24 05:33:16,304] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n02_SEP33h_fastqc.html [2021-04-24 05:33:16,342] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_undetermined_fastqc.html [2021-04-24 05:33:16,344] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_undetermined_fastqc.html [2021-04-24 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HNYH2AFX2_n01_hGRF7_sFT_sFDE_C_fastqc.html [2021-04-24 05:33:17,832] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hGRF7_sFT_sFDE_C_fastqc.html [2021-04-24 05:33:17,870] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_AP1h_FULs_C_fastqc.html [2021-04-24 05:33:17,872] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n02_AP1h_FULs_C_fastqc.html [2021-04-24 05:33:17,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_AP1h_sAGL24_C_fastqc.html [2021-04-24 05:33:17,912] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_AP1h_sAGL24_C_fastqc.html [2021-04-24 05:33:17,998] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hFD_fastqc.html [2021-04-24 05:33:18,000] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hFD_fastqc.html [2021-04-24 05:33:18,037] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_hAGL24_fastqc.html [2021-04-24 05:33:18,039] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n02_hAGL24_fastqc.html [2021-04-24 05:33:18,078] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hGRF7_sFDE_C_fastqc.html [2021-04-24 05:33:18,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hGRF7_sFDE_C_fastqc.html [2021-04-24 05:33:18,118] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_AP1h_sSVP_C_fastqc.html [2021-04-24 05:33:18,119] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_AP1h_sSVP_C_fastqc.html [2021-04-24 05:33:18,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hBZIP63_sBZIP53_C_fastqc.html [2021-04-24 05:33:18,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n01_hBZIP63_sBZIP53_C_fastqc.html [2021-04-24 05:33:18,198] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNYH2AFX2_n02_hFDE_sSPL5_M_fastqc.html [2021-04-24 05:33:18,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNYH2AFX2_n02_hFDE_sSPL5_M_fastqc.html [2021-04-24 05:33:18,683] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-24 05:33:18,684] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-04-24 05:33:18,693] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-04-24 05:33:18,717] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 51 samples (table) [2021-04-24 05:33:18,726] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-04-24 05:33:18,731] multiqc [DEBUG ] No samples found: conpair [2021-04-24 05:33:18,736] multiqc [DEBUG ] No samples found: peddy [2021-04-24 05:33:18,741] multiqc [DEBUG ] No samples found: somalier [2021-04-24 05:33:18,746] multiqc [DEBUG ] No samples found: methylQA [2021-04-24 05:33:18,754] multiqc [DEBUG ] No samples found: mosdepth [2021-04-24 05:33:18,758] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-04-24 05:33:18,762] multiqc [DEBUG ] No samples found: qualimap [2021-04-24 05:33:18,767] multiqc [DEBUG ] No samples found: preseq [2021-04-24 05:33:18,771] multiqc [DEBUG ] No samples found: quast [2021-04-24 05:33:18,776] multiqc [DEBUG ] No samples found: qorts [2021-04-24 05:33:18,781] multiqc [DEBUG ] No samples found: rna_seqc [2021-04-24 05:33:18,786] multiqc [DEBUG ] No samples found: rockhopper [2021-04-24 05:33:18,790] multiqc [DEBUG ] No samples found: rsem [2021-04-24 05:33:18,801] multiqc [DEBUG ] No samples found: rseqc [2021-04-24 05:33:18,806] multiqc [DEBUG ] No samples found: busco [2021-04-24 05:33:18,810] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-04-24 05:33:18,815] multiqc [DEBUG ] No samples found: disambiguate [2021-04-24 05:33:18,820] multiqc [DEBUG ] No samples found: supernova [2021-04-24 05:33:18,832] multiqc [DEBUG ] No samples found: deeptools [2021-04-24 05:33:18,837] multiqc [DEBUG ] No samples found: sargasso [2021-04-24 05:33:18,842] multiqc [DEBUG ] No samples found: verifybamid [2021-04-24 05:33:18,847] multiqc [DEBUG ] No samples found: mirtrace [2021-04-24 05:33:18,851] multiqc [DEBUG ] No samples found: happy [2021-04-24 05:33:18,856] multiqc [DEBUG ] No samples found: mirtop [2021-04-24 05:33:18,862] multiqc [DEBUG ] No samples found: homer [2021-04-24 05:33:18,867] multiqc [DEBUG ] No samples found: macs2 [2021-04-24 05:33:18,871] multiqc [DEBUG ] No samples found: theta2 [2021-04-24 05:33:18,876] multiqc [DEBUG ] No samples found: snpeff [2021-04-24 05:33:18,883] multiqc [DEBUG ] No samples found: gatk [2021-04-24 05:33:18,888] multiqc [DEBUG ] No samples found: htseq [2021-04-24 05:33:18,893] multiqc [DEBUG ] No samples found: bcftools [2021-04-24 05:33:18,898] multiqc [DEBUG ] No samples found: featureCounts [2021-04-24 05:33:18,904] multiqc [DEBUG ] No samples found: fgbio [2021-04-24 05:33:18,917] multiqc [DEBUG ] No samples found: dragen [2021-04-24 05:33:18,922] multiqc [DEBUG ] No samples found: dedup [2021-04-24 05:33:18,927] multiqc [DEBUG ] No samples found: damageprofiler [2021-04-24 05:33:18,953] multiqc [DEBUG ] No samples found: biobambam2 [2021-04-24 05:33:18,958] multiqc [DEBUG ] No samples found: mtnucratio [2021-04-24 05:33:18,960] multiqc [DEBUG ] No samples found: picard [2021-04-24 05:33:18,965] multiqc [DEBUG ] No samples found: prokka [2021-04-24 05:33:18,969] multiqc [DEBUG ] No samples found: samblaster [2021-04-24 05:33:18,978] multiqc [DEBUG ] No samples found: samtools [2021-04-24 05:33:18,983] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-04-24 05:33:18,988] multiqc [DEBUG ] No samples found: bamtools [2021-04-24 05:33:18,992] multiqc [DEBUG ] No samples found: jellyfish [2021-04-24 05:33:18,999] multiqc [DEBUG ] No samples found: vcftools [2021-04-24 05:33:19,004] multiqc [DEBUG ] No samples found: longranger [2021-04-24 05:33:19,009] multiqc [DEBUG ] No samples found: stacks [2021-04-24 05:33:19,014] multiqc [DEBUG ] No samples found: varscan2 [2021-04-24 05:33:19,027] multiqc [DEBUG ] No samples found: bbmap [2021-04-24 05:33:19,032] multiqc [DEBUG ] No samples found: bismark [2021-04-24 05:33:19,038] multiqc [DEBUG ] No samples found: biscuit [2021-04-24 05:33:19,043] multiqc [DEBUG ] No samples found: hicexplorer [2021-04-24 05:33:19,047] multiqc [DEBUG ] No samples found: hicup [2021-04-24 05:33:19,052] multiqc [DEBUG ] No samples found: hicpro [2021-04-24 05:33:19,057] multiqc [DEBUG ] No samples found: salmon [2021-04-24 05:33:19,061] multiqc [DEBUG ] No samples found: kallisto [2021-04-24 05:33:19,066] multiqc [DEBUG ] No samples found: slamdunk [2021-04-24 05:33:19,071] multiqc [DEBUG ] No samples found: star [2021-04-24 05:33:19,076] multiqc [DEBUG ] No samples found: hisat2 [2021-04-24 05:33:19,080] multiqc [DEBUG ] No samples found: tophat [2021-04-24 05:33:19,085] multiqc [DEBUG ] No samples found: bowtie2 [2021-04-24 05:33:19,090] multiqc [DEBUG ] No samples found: bowtie1 [2021-04-24 05:33:19,095] multiqc [DEBUG ] No samples found: snpsplit [2021-04-24 05:33:19,099] multiqc [DEBUG ] No samples found: kat [2021-04-24 05:33:19,103] multiqc [DEBUG ] No samples found: leehom [2021-04-24 05:33:19,108] multiqc [DEBUG ] No samples found: adapterRemoval [2021-04-24 05:33:19,113] multiqc [DEBUG ] No samples found: clipandmerge [2021-04-24 05:33:19,117] multiqc [DEBUG ] No samples found: cutadapt [2021-04-24 05:33:19,121] multiqc [DEBUG ] No samples found: flexbar [2021-04-24 05:33:19,126] multiqc [DEBUG ] No samples found: kaiju [2021-04-24 05:33:19,131] multiqc [DEBUG ] No samples found: kraken [2021-04-24 05:33:19,135] multiqc [DEBUG ] No samples found: malt [2021-04-24 05:33:19,140] multiqc [DEBUG ] No samples found: trimmomatic [2021-04-24 05:33:19,144] multiqc [DEBUG ] No samples found: sickle [2021-04-24 05:33:19,149] multiqc [DEBUG ] No samples found: skewer [2021-04-24 05:33:19,153] multiqc [DEBUG ] No samples found: sortmerna [2021-04-24 05:33:19,157] multiqc [DEBUG ] No samples found: biobloomtools [2021-04-24 05:33:19,162] multiqc [DEBUG ] No samples found: fastq_screen [2021-04-24 05:33:19,167] multiqc [DEBUG ] No samples found: afterqc [2021-04-24 05:33:19,171] multiqc [DEBUG ] No samples found: fastp [2021-04-24 05:33:22,379] multiqc.modules.fastqc.fastqc [INFO ] Found 102 reports [2021-04-24 05:33:39,414] multiqc [DEBUG ] No samples found: pycoqc [2021-04-24 05:33:39,419] multiqc [DEBUG ] No samples found: minionqc [2021-04-24 05:33:39,424] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-04-24 05:33:39,429] multiqc [DEBUG ] No samples found: clusterflow [2021-04-24 05:33:39,435] multiqc [DEBUG ] No samples found: bcl2fastq [2021-04-24 05:33:39,440] multiqc [DEBUG ] No samples found: interop [2021-04-24 05:33:39,445] multiqc [DEBUG ] No samples found: ivar [2021-04-24 05:33:39,450] multiqc [DEBUG ] No samples found: flash [2021-04-24 05:33:39,454] multiqc [DEBUG ] No samples found: seqyclean [2021-04-24 05:33:39,454] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-04-24 05:33:39,454] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-04-24 05:33:39,454] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-04-24 05:33:39,454] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-04-24 05:33:39,572] multiqc [INFO ] Compressing plot data [2021-04-24 05:33:39,855] multiqc [INFO ] Report : multiqc_report.html [2021-04-24 05:33:39,855] multiqc [INFO ] Data : multiqc_data [2021-04-24 05:33:39,855] multiqc [DEBUG ] Moving data file from '/state/partition1/job-5941274/tmpce9sqtgk/multiqc_data' to '/scratch/gencore/logs/html/HNYH2AFX2/merged/multiqc_data' [2021-04-24 05:33:39,992] multiqc [INFO ] MultiQC complete