[2022-08-22 20:28:56,867] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-08-22 20:28:56,868] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-08-22 20:28:56,868] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-08-22 20:28:56,869] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-08-22 20:28:56,869] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-08-22 20:28:56,869] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KG266/1 [2022-08-22 20:28:57,464] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-08-22 20:28:57,465] multiqc [INFO ] This is MultiQC v1.9 [2022-08-22 20:28:57,465] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/000000000-KG266/1 [2022-08-22 20:28:57,465] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/000000000-KG266/1 [2022-08-22 20:28:57,465] multiqc [INFO ] Template : default [2022-08-22 20:28:57,465] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-08-22 20:28:57,465] multiqc [INFO ] Searching : /scratch/gencore/logs/html/000000000-KG266/1 [2022-08-22 20:28:57,465] 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 [2022-08-22 20:28:57,465] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-23947689/tmp8wjoas3a [2022-08-22 20:28:57,571] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C8I4c_T1_rc_fastqc.html [2022-08-22 20:28:57,574] multiqc [DEBUG ] File ignored by longranger/invocation 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000000000-KG266_l01_n01_Tr4_C3I3a_T1_rc_fastqc.html [2022-08-22 20:29:18,788] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C6I3b_T1_rc_fastqc.html [2022-08-22 20:29:18,790] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C6I3b_T1_rc_fastqc.html [2022-08-22 20:29:18,831] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C14I2b_T1_rc_fastqc.html [2022-08-22 20:29:18,833] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C14I2b_T1_rc_fastqc.html [2022-08-22 20:29:18,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C12I1a_T1_rc_fastqc.html [2022-08-22 20:29:18,877] multiqc [DEBUG ] File ignored 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000000000-KG266_l01_n01_Tr4_C12I3c_T1_rc_fastqc.html [2022-08-22 20:29:19,005] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C12I3c_T1_rc_fastqc.html [2022-08-22 20:29:19,046] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C15I1b_T1_rc_fastqc.html [2022-08-22 20:29:19,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C15I1b_T1_rc_fastqc.html [2022-08-22 20:29:19,089] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_NCI3c_T1_rc_fastqc.html [2022-08-22 20:29:19,091] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_NCI3c_T1_rc_fastqc.html [2022-08-22 20:29:19,132] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C8I1a_T1_rc_fastqc.html [2022-08-22 20:29:19,134] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C8I1a_T1_rc_fastqc.html [2022-08-22 20:29:19,174] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C10I3a_T1_rc_fastqc.html [2022-08-22 20:29:19,176] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C10I3a_T1_rc_fastqc.html [2022-08-22 20:29:19,218] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C7I3b_T1_rc_fastqc.html [2022-08-22 20:29:19,219] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C7I3b_T1_rc_fastqc.html [2022-08-22 20:29:19,261] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C2I1c_T1_rc_fastqc.html [2022-08-22 20:29:19,263] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C2I1c_T1_rc_fastqc.html [2022-08-22 20:29:19,303] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C8I1b_T1_rc_fastqc.html [2022-08-22 20:29:19,305] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C8I1b_T1_rc_fastqc.html [2022-08-22 20:29:19,347] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C12I3a_T1_rc_fastqc.html [2022-08-22 20:29:19,349] multiqc [DEBUG ] File ignored 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000000000-KG266_l01_n01_Tr4_C4I2b_T1_rc_fastqc.html [2022-08-22 20:29:19,478] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C4I2b_T1_rc_fastqc.html [2022-08-22 20:29:19,519] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C4I2c_T1_rc_fastqc.html [2022-08-22 20:29:19,521] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C4I2c_T1_rc_fastqc.html [2022-08-22 20:29:19,562] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C15I4b_T1_rc_fastqc.html [2022-08-22 20:29:19,564] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C15I4b_T1_rc_fastqc.html [2022-08-22 20:29:19,605] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C6I3c_T1_rc_fastqc.html [2022-08-22 20:29:19,607] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C6I3c_T1_rc_fastqc.html [2022-08-22 20:29:19,648] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C12I4a_T1_rc_fastqc.html [2022-08-22 20:29:19,650] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C12I4a_T1_rc_fastqc.html [2022-08-22 20:29:19,691] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C14I4a_T1_rc_fastqc.html [2022-08-22 20:29:19,693] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C14I4a_T1_rc_fastqc.html [2022-08-22 20:29:19,734] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C1I3a_T1_rc_fastqc.html [2022-08-22 20:29:19,735] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n01_Tr4_C1I3a_T1_rc_fastqc.html [2022-08-22 20:29:19,776] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C12I4c_T1_rc_fastqc.html [2022-08-22 20:29:19,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C12I4c_T1_rc_fastqc.html [2022-08-22 20:29:19,818] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C14I4a_T1_rc_fastqc.html [2022-08-22 20:29:19,820] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-KG266_l01_n02_Tr4_C14I4a_T1_rc_fastqc.html [2022-08-22 20:29:20,153] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-22 20:29:20,154] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-08-22 20:29:20,248] multiqc.modules.custom_content.custom_content [INFO ] demux_report-1: Found 194 samples (table) [2022-08-22 20:29:20,249] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-08-22 20:29:20,258] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-08-22 20:29:20,263] multiqc [DEBUG ] No samples found: conpair [2022-08-22 20:29:20,267] multiqc [DEBUG ] No samples found: peddy [2022-08-22 20:29:20,272] multiqc [DEBUG ] No samples found: somalier [2022-08-22 20:29:20,277] multiqc [DEBUG ] No samples found: methylQA [2022-08-22 20:29:20,284] multiqc [DEBUG ] No samples found: mosdepth [2022-08-22 20:29:20,288] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-08-22 20:29:20,291] multiqc [DEBUG ] No samples found: qualimap [2022-08-22 20:29:20,296] multiqc [DEBUG ] No samples found: preseq [2022-08-22 20:29:20,300] multiqc [DEBUG ] No samples found: quast [2022-08-22 20:29:20,304] multiqc [DEBUG ] No samples found: qorts [2022-08-22 20:29:20,309] multiqc [DEBUG ] No samples found: rna_seqc [2022-08-22 20:29:20,313] multiqc [DEBUG ] No samples found: rockhopper [2022-08-22 20:29:20,318] multiqc [DEBUG ] No samples found: rsem [2022-08-22 20:29:20,328] multiqc [DEBUG ] No samples found: rseqc [2022-08-22 20:29:20,332] multiqc [DEBUG ] No samples found: busco [2022-08-22 20:29:20,336] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-08-22 20:29:20,340] multiqc [DEBUG ] No samples found: disambiguate [2022-08-22 20:29:20,345] multiqc [DEBUG ] No samples found: supernova [2022-08-22 20:29:20,356] multiqc [DEBUG ] No samples found: deeptools [2022-08-22 20:29:20,361] multiqc [DEBUG ] No samples found: sargasso [2022-08-22 20:29:20,365] multiqc [DEBUG ] No samples found: verifybamid [2022-08-22 20:29:20,370] multiqc [DEBUG ] No samples found: mirtrace [2022-08-22 20:29:20,374] multiqc [DEBUG ] No samples found: happy [2022-08-22 20:29:20,378] multiqc [DEBUG ] No samples found: mirtop [2022-08-22 20:29:20,384] multiqc [DEBUG ] No samples found: homer [2022-08-22 20:29:20,389] multiqc [DEBUG ] No samples found: macs2 [2022-08-22 20:29:20,393] multiqc [DEBUG ] No samples found: theta2 [2022-08-22 20:29:20,397] multiqc [DEBUG ] No samples found: snpeff [2022-08-22 20:29:20,403] multiqc [DEBUG ] No samples found: gatk [2022-08-22 20:29:20,408] multiqc [DEBUG ] No samples found: htseq [2022-08-22 20:29:20,413] multiqc [DEBUG ] No samples found: bcftools [2022-08-22 20:29:20,417] multiqc [DEBUG ] No samples found: featureCounts [2022-08-22 20:29:20,422] multiqc [DEBUG ] No samples found: fgbio [2022-08-22 20:29:20,434] multiqc [DEBUG ] No samples found: dragen [2022-08-22 20:29:20,438] multiqc [DEBUG ] No samples found: dedup [2022-08-22 20:29:20,442] multiqc [DEBUG ] No samples found: damageprofiler [2022-08-22 20:29:20,463] multiqc [DEBUG ] No samples found: biobambam2 [2022-08-22 20:29:20,467] multiqc [DEBUG ] No samples found: mtnucratio [2022-08-22 20:29:20,470] multiqc [DEBUG ] No samples found: picard [2022-08-22 20:29:20,474] multiqc [DEBUG ] No samples found: prokka [2022-08-22 20:29:20,478] multiqc [DEBUG ] No samples found: samblaster [2022-08-22 20:29:20,486] multiqc [DEBUG ] No samples found: samtools [2022-08-22 20:29:20,490] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-08-22 20:29:20,495] multiqc [DEBUG ] No samples found: bamtools [2022-08-22 20:29:20,499] multiqc [DEBUG ] No samples found: jellyfish [2022-08-22 20:29:20,506] multiqc [DEBUG ] No samples found: vcftools [2022-08-22 20:29:20,510] multiqc [DEBUG ] No samples found: longranger [2022-08-22 20:29:20,515] multiqc [DEBUG ] No samples found: stacks [2022-08-22 20:29:20,519] multiqc [DEBUG ] No samples found: varscan2 [2022-08-22 20:29:20,532] multiqc [DEBUG ] No samples found: bbmap [2022-08-22 20:29:20,536] multiqc [DEBUG ] No samples found: bismark [2022-08-22 20:29:20,541] multiqc [DEBUG ] No samples found: biscuit [2022-08-22 20:29:20,545] multiqc [DEBUG ] No samples found: hicexplorer [2022-08-22 20:29:20,549] multiqc [DEBUG ] No samples found: hicup [2022-08-22 20:29:20,554] multiqc [DEBUG ] No samples found: hicpro [2022-08-22 20:29:20,558] multiqc [DEBUG ] No samples found: salmon [2022-08-22 20:29:20,562] multiqc [DEBUG ] No samples found: kallisto [2022-08-22 20:29:20,566] multiqc [DEBUG ] No samples found: slamdunk [2022-08-22 20:29:20,570] multiqc [DEBUG ] No samples found: star [2022-08-22 20:29:20,575] multiqc [DEBUG ] No samples found: hisat2 [2022-08-22 20:29:20,579] multiqc [DEBUG ] No samples found: tophat [2022-08-22 20:29:20,583] multiqc [DEBUG ] No samples found: bowtie2 [2022-08-22 20:29:20,588] multiqc [DEBUG ] No samples found: bowtie1 [2022-08-22 20:29:20,592] multiqc [DEBUG ] No samples found: snpsplit [2022-08-22 20:29:20,596] multiqc [DEBUG ] No samples found: kat [2022-08-22 20:29:20,600] multiqc [DEBUG ] No samples found: leehom [2022-08-22 20:29:20,604] multiqc [DEBUG ] No samples found: adapterRemoval [2022-08-22 20:29:20,608] multiqc [DEBUG ] No samples found: clipandmerge [2022-08-22 20:29:20,613] multiqc [DEBUG ] No samples found: cutadapt [2022-08-22 20:29:20,617] multiqc [DEBUG ] No samples found: flexbar [2022-08-22 20:29:20,621] multiqc [DEBUG ] No samples found: kaiju [2022-08-22 20:29:20,625] multiqc [DEBUG ] No samples found: kraken [2022-08-22 20:29:20,630] multiqc [DEBUG ] No samples found: malt [2022-08-22 20:29:20,634] multiqc [DEBUG ] No samples found: trimmomatic [2022-08-22 20:29:20,638] multiqc [DEBUG ] No samples found: sickle [2022-08-22 20:29:20,643] multiqc [DEBUG ] No samples found: skewer [2022-08-22 20:29:20,647] multiqc [DEBUG ] No samples found: sortmerna [2022-08-22 20:29:20,651] multiqc [DEBUG ] No samples found: biobloomtools [2022-08-22 20:29:20,655] multiqc [DEBUG ] No samples found: fastq_screen [2022-08-22 20:29:20,660] multiqc [DEBUG ] No samples found: afterqc [2022-08-22 20:29:20,664] multiqc [DEBUG ] No samples found: fastp [2022-08-22 20:29:23,794] multiqc.modules.fastqc.fastqc [INFO ] Found 388 reports [2022-08-22 20:30:03,967] multiqc [DEBUG ] No samples found: pycoqc [2022-08-22 20:30:03,972] multiqc [DEBUG ] No samples found: minionqc [2022-08-22 20:30:03,976] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-08-22 20:30:03,980] multiqc [DEBUG ] No samples found: clusterflow [2022-08-22 20:30:03,985] multiqc [DEBUG ] No samples found: bcl2fastq [2022-08-22 20:30:03,989] multiqc [DEBUG ] No samples found: interop [2022-08-22 20:30:03,993] multiqc [DEBUG ] No samples found: ivar [2022-08-22 20:30:03,998] multiqc [DEBUG ] No samples found: flash [2022-08-22 20:30:04,002] multiqc [DEBUG ] No samples found: seqyclean [2022-08-22 20:30:04,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2022-08-22 20:30:04,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane 1 Demultiplexing Report'. [2022-08-22 20:30:04,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Lane Statistics'. [2022-08-22 20:30:04,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-08-22 20:30:04,002] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-08-22 20:30:04,435] multiqc [INFO ] Compressing plot data [2022-08-22 20:30:04,567] multiqc [INFO ] Report : multiqc_report.html [2022-08-22 20:30:04,567] multiqc [INFO ] Data : multiqc_data [2022-08-22 20:30:04,567] multiqc [DEBUG ] Moving data file from '/state/partition1/job-23947689/tmp8wjoas3a/multiqc_data' to '/scratch/gencore/logs/html/000000000-KG266/1/multiqc_data' [2022-08-22 20:30:31,131] multiqc [INFO ] MultiQC complete