[2021-11-21 13:22:12,560] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-11-21 13:22:12,560] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-11-21 13:22:12,560] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-11-21 13:22:12,561] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-11-21 13:22:12,561] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-11-21 13:22:12,561] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTTCNDSX2/2 [2021-11-21 13:22:13,871] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-11-21 13:22:13,871] multiqc [INFO ] This is MultiQC v1.9 [2021-11-21 13:22:13,871] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HTTCNDSX2/2 [2021-11-21 13:22:13,871] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HTTCNDSX2/2 [2021-11-21 13:22:13,871] multiqc [INFO ] Template : default [2021-11-21 13:22:13,871] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-11-21 13:22:13,871] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HTTCNDSX2/2 [2021-11-21 13:22:13,872] 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 [2021-11-21 13:22:13,872] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-12141206/tmp4kvhausy [2021-11-21 13:22:13,977] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1b_fastqc.html [2021-11-21 13:22:13,979] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern 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undetermined_barcodes.txt [2021-11-21 13:22:14,184] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 13:22:14,184] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 13:22:14,184] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 13:22:14,184] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 13:22:14,184] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-11-21 13:22:14,926] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2c_fastqc.html [2021-11-21 13:22:14,928] multiqc 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multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1d_fastqc.html [2021-11-21 13:22:15,829] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_HTO2_fastqc.html [2021-11-21 13:22:15,831] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_HTO2_fastqc.html [2021-11-21 13:22:15,891] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1c_fastqc.html [2021-11-21 13:22:15,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1c_fastqc.html [2021-11-21 13:22:15,969] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2b_fastqc.html [2021-11-21 13:22:15,971] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2b_fastqc.html [2021-11-21 13:22:16,034] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_undetermined_fastqc.html [2021-11-21 13:22:16,036] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_undetermined_fastqc.html [2021-11-21 13:22:16,092] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1b_fastqc.html [2021-11-21 13:22:16,093] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1b_fastqc.html [2021-11-21 13:22:16,148] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1b_fastqc.html [2021-11-21 13:22:16,150] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1b_fastqc.html [2021-11-21 13:22:16,204] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1d_fastqc.html [2021-11-21 13:22:16,206] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1d_fastqc.html [2021-11-21 13:22:16,258] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_HTO1_fastqc.html [2021-11-21 13:22:16,260] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_HTO1_fastqc.html [2021-11-21 13:22:16,319] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO2d_fastqc.html [2021-11-21 13:22:16,321] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO2d_fastqc.html [2021-11-21 13:22:16,400] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1c_fastqc.html [2021-11-21 13:22:16,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA1c_fastqc.html [2021-11-21 13:22:16,472] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO2a_fastqc.html [2021-11-21 13:22:16,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO2a_fastqc.html [2021-11-21 13:22:16,545] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO1b_fastqc.html [2021-11-21 13:22:16,546] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO1b_fastqc.html [2021-11-21 13:22:16,600] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1d_fastqc.html [2021-11-21 13:22:16,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1d_fastqc.html [2021-11-21 13:22:16,643] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2a_fastqc.html [2021-11-21 13:22:16,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2a_fastqc.html [2021-11-21 13:22:16,687] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2c_fastqc.html [2021-11-21 13:22:16,688] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2c_fastqc.html [2021-11-21 13:22:16,748] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_HTO1_fastqc.html [2021-11-21 13:22:16,749] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_HTO1_fastqc.html [2021-11-21 13:22:16,808] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2d_fastqc.html [2021-11-21 13:22:16,809] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2d_fastqc.html [2021-11-21 13:22:16,873] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2a_fastqc.html [2021-11-21 13:22:16,874] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_cDNA2a_fastqc.html [2021-11-21 13:22:16,930] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1a_fastqc.html [2021-11-21 13:22:16,932] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA1a_fastqc.html [2021-11-21 13:22:16,990] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO2b_fastqc.html [2021-11-21 13:22:16,992] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n01_EP_GDO2b_fastqc.html [2021-11-21 13:22:17,059] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1a_fastqc.html [2021-11-21 13:22:17,061] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_GDO1a_fastqc.html [2021-11-21 13:22:17,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2b_fastqc.html [2021-11-21 13:22:17,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTTCNDSX2_l02_n02_EP_cDNA2b_fastqc.html [2021-11-21 13:22:17,405] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-21 13:22:17,406] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-11-21 13:22:17,420] multiqc.modules.custom_content.custom_content [INFO ] demux_report-2: Found 19 samples (table) [2021-11-21 13:22:17,429] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-11-21 13:22:17,431] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-11-21 13:22:17,434] multiqc [DEBUG ] No samples found: conpair [2021-11-21 13:22:17,436] multiqc [DEBUG ] No samples found: peddy [2021-11-21 13:22:17,439] multiqc [DEBUG ] No samples found: somalier [2021-11-21 13:22:17,442] multiqc [DEBUG ] No samples found: methylQA [2021-11-21 13:22:17,445] multiqc [DEBUG ] No samples found: mosdepth [2021-11-21 13:22:17,448] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-11-21 13:22:17,450] multiqc [DEBUG ] No samples found: qualimap [2021-11-21 13:22:17,453] multiqc [DEBUG ] No samples found: preseq [2021-11-21 13:22:17,456] multiqc [DEBUG ] No samples found: quast [2021-11-21 13:22:17,459] multiqc [DEBUG ] No samples found: qorts [2021-11-21 13:22:17,461] multiqc [DEBUG ] No samples found: rna_seqc [2021-11-21 13:22:17,464] multiqc [DEBUG ] No samples found: rockhopper [2021-11-21 13:22:17,467] multiqc [DEBUG ] No samples found: rsem [2021-11-21 13:22:17,471] multiqc [DEBUG ] No samples found: rseqc [2021-11-21 13:22:17,474] multiqc [DEBUG ] No samples found: busco [2021-11-21 13:22:17,476] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-11-21 13:22:17,479] multiqc [DEBUG ] No samples found: disambiguate [2021-11-21 13:22:17,482] multiqc [DEBUG ] No samples found: supernova [2021-11-21 13:22:17,486] multiqc [DEBUG ] No samples found: deeptools [2021-11-21 13:22:17,489] multiqc [DEBUG ] No samples found: sargasso [2021-11-21 13:22:17,492] multiqc [DEBUG ] No samples found: verifybamid [2021-11-21 13:22:17,494] multiqc [DEBUG ] No samples found: mirtrace [2021-11-21 13:22:17,497] multiqc [DEBUG ] No samples found: happy [2021-11-21 13:22:17,500] multiqc [DEBUG ] No samples found: mirtop [2021-11-21 13:22:17,503] multiqc [DEBUG ] No samples found: homer [2021-11-21 13:22:17,506] multiqc [DEBUG ] No samples found: macs2 [2021-11-21 13:22:17,508] multiqc [DEBUG ] No samples found: theta2 [2021-11-21 13:22:17,511] multiqc [DEBUG ] No samples found: snpeff [2021-11-21 13:22:17,514] multiqc [DEBUG ] No samples found: gatk [2021-11-21 13:22:17,517] multiqc [DEBUG ] No samples found: htseq [2021-11-21 13:22:17,520] multiqc [DEBUG ] No samples found: bcftools [2021-11-21 13:22:17,522] multiqc [DEBUG ] No samples found: featureCounts [2021-11-21 13:22:17,525] multiqc [DEBUG ] No samples found: fgbio [2021-11-21 13:22:17,530] multiqc [DEBUG ] No samples found: dragen [2021-11-21 13:22:17,533] multiqc [DEBUG ] No samples found: dedup [2021-11-21 13:22:17,536] multiqc [DEBUG ] No samples found: damageprofiler [2021-11-21 13:22:17,543] multiqc [DEBUG ] No samples found: biobambam2 [2021-11-21 13:22:17,546] multiqc [DEBUG ] No samples found: mtnucratio [2021-11-21 13:22:17,548] multiqc [DEBUG ] No samples found: picard [2021-11-21 13:22:17,550] multiqc [DEBUG ] No samples found: prokka [2021-11-21 13:22:17,553] multiqc [DEBUG ] No samples found: samblaster [2021-11-21 13:22:17,557] multiqc [DEBUG ] No samples found: samtools [2021-11-21 13:22:17,559] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-11-21 13:22:17,562] multiqc [DEBUG ] No samples found: bamtools [2021-11-21 13:22:17,565] multiqc [DEBUG ] No samples found: jellyfish [2021-11-21 13:22:17,568] multiqc [DEBUG ] No samples found: vcftools [2021-11-21 13:22:17,571] multiqc [DEBUG ] No samples found: longranger [2021-11-21 13:22:17,574] multiqc [DEBUG ] No samples found: stacks [2021-11-21 13:22:17,576] multiqc [DEBUG ] No samples found: varscan2 [2021-11-21 13:22:17,581] multiqc [DEBUG ] No samples found: bbmap [2021-11-21 13:22:17,584] multiqc [DEBUG ] No samples found: bismark [2021-11-21 13:22:17,587] multiqc [DEBUG ] No samples found: biscuit [2021-11-21 13:22:17,590] multiqc [DEBUG ] No samples found: hicexplorer [2021-11-21 13:22:17,592] multiqc [DEBUG ] No samples found: hicup [2021-11-21 13:22:17,595] multiqc [DEBUG ] No samples found: hicpro [2021-11-21 13:22:17,598] multiqc [DEBUG ] No samples found: salmon [2021-11-21 13:22:17,600] multiqc [DEBUG ] No samples found: kallisto [2021-11-21 13:22:17,603] multiqc [DEBUG ] No samples found: slamdunk [2021-11-21 13:22:17,606] multiqc [DEBUG ] No samples found: star [2021-11-21 13:22:17,608] multiqc [DEBUG ] No samples found: hisat2 [2021-11-21 13:22:17,611] multiqc [DEBUG ] No samples found: tophat [2021-11-21 13:22:17,614] multiqc [DEBUG ] No samples found: bowtie2 [2021-11-21 13:22:17,616] multiqc [DEBUG ] No samples found: bowtie1 [2021-11-21 13:22:17,619] multiqc [DEBUG ] No samples found: snpsplit [2021-11-21 13:22:17,622] multiqc [DEBUG ] No samples found: kat [2021-11-21 13:22:17,624] multiqc [DEBUG ] No samples found: leehom [2021-11-21 13:22:17,627] multiqc [DEBUG ] No samples found: adapterRemoval [2021-11-21 13:22:17,630] multiqc [DEBUG ] No samples found: clipandmerge [2021-11-21 13:22:17,632] multiqc [DEBUG ] No samples found: cutadapt [2021-11-21 13:22:17,635] multiqc [DEBUG ] No samples found: flexbar [2021-11-21 13:22:17,637] multiqc [DEBUG ] No samples found: kaiju [2021-11-21 13:22:17,640] multiqc [DEBUG ] No samples found: kraken [2021-11-21 13:22:17,643] multiqc [DEBUG ] No samples found: malt [2021-11-21 13:22:17,645] multiqc [DEBUG ] No samples found: trimmomatic [2021-11-21 13:22:17,648] multiqc [DEBUG ] No samples found: sickle [2021-11-21 13:22:17,651] multiqc [DEBUG ] No samples found: skewer [2021-11-21 13:22:17,653] multiqc [DEBUG ] No samples found: sortmerna [2021-11-21 13:22:17,656] multiqc [DEBUG ] No samples found: biobloomtools [2021-11-21 13:22:17,658] multiqc [DEBUG ] No samples found: fastq_screen [2021-11-21 13:22:17,661] multiqc [DEBUG ] No samples found: afterqc [2021-11-21 13:22:17,664] multiqc [DEBUG ] No samples found: fastp [2021-11-21 13:22:26,060] multiqc.modules.fastqc.fastqc [INFO ] Found 38 reports [2021-11-21 13:22:26,535] multiqc [DEBUG ] No samples found: pycoqc [2021-11-21 13:22:26,538] multiqc [DEBUG ] No samples found: minionqc [2021-11-21 13:22:26,541] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-11-21 13:22:26,543] multiqc [DEBUG ] No samples found: clusterflow [2021-11-21 13:22:26,546] multiqc [DEBUG ] No samples found: bcl2fastq [2021-11-21 13:22:26,549] multiqc [DEBUG ] No samples found: interop [2021-11-21 13:22:26,551] multiqc [DEBUG ] No samples found: ivar [2021-11-21 13:22:26,554] multiqc [DEBUG ] No samples found: flash [2021-11-21 13:22:26,557] multiqc [DEBUG ] No samples found: seqyclean [2021-11-21 13:22:26,557] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2021-11-21 13:22:26,557] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 2 Demultiplexing Report'. [2021-11-21 13:22:26,557] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-11-21 13:22:26,557] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2021-11-21 13:22:26,557] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-11-21 13:22:26,601] multiqc [INFO ] Compressing plot data [2021-11-21 13:22:27,284] multiqc [INFO ] Report : multiqc_report.html [2021-11-21 13:22:27,284] multiqc [INFO ] Data : multiqc_data [2021-11-21 13:22:27,284] multiqc [DEBUG ] Moving data file from '/state/partition1/job-12141206/tmp4kvhausy/multiqc_data' to '/scratch/gencore/logs/html/HTTCNDSX2/2/multiqc_data' [2021-11-21 13:22:27,376] multiqc [INFO ] MultiQC complete