[2021-05-01 03:28:16,247] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-01 03:28:16,248] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-01 03:28:16,248] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-01 03:28:16,249] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-01 03:28:16,249] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-01 03:28:16,249] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK3VMBGXH/merged [2021-05-01 03:28:18,492] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-01 03:28:18,492] multiqc [INFO ] This is MultiQC v1.9 [2021-05-01 03:28:18,492] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HK3VMBGXH/merged [2021-05-01 03:28:18,493] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HK3VMBGXH/merged [2021-05-01 03:28:18,493] multiqc [INFO ] Template : default [2021-05-01 03:28:18,493] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-01 03:28:18,493] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HK3VMBGXH/merged [2021-05-01 03:28:18,493] 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 [2021-05-01 03:28:18,493] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-6227456/tmpg05emt7u [2021-05-01 03:28:18,617] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S8_R1_A05_FD_fastqc.html [2021-05-01 03:28:18,620] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S10_R1_F11_FD_fastqc.html [2021-05-01 03:28:52,392] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S7_R1_D07_FD_fastqc.html [2021-05-01 03:28:52,393] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S7_R1_D07_FD_fastqc.html [2021-05-01 03:28:52,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_F01_FD_fastqc.html [2021-05-01 03:28:52,439] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_F01_FD_fastqc.html [2021-05-01 03:28:52,500] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S8_R1_E09_FD_fastqc.html [2021-05-01 03:28:52,502] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S8_R1_E09_FD_fastqc.html [2021-05-01 03:28:52,563] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S10_R1_H01_FD_fastqc.html [2021-05-01 03:28:52,565] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S10_R1_H01_FD_fastqc.html [2021-05-01 03:28:52,630] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_E06_FD_fastqc.html [2021-05-01 03:28:52,632] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_E06_FD_fastqc.html [2021-05-01 03:28:52,685] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S7_R1_D09_FD_fastqc.html [2021-05-01 03:28:52,687] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S7_R1_D09_FD_fastqc.html [2021-05-01 03:28:52,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S8_R1_G05_FD_fastqc.html [2021-05-01 03:28:52,747] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S8_R1_G05_FD_fastqc.html [2021-05-01 03:28:52,800] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S10_R1_C10_FD_fastqc.html [2021-05-01 03:28:52,801] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S10_R1_C10_FD_fastqc.html [2021-05-01 03:28:52,851] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S7_R1_A07_FD_fastqc.html [2021-05-01 03:28:52,852] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n01_S7_R1_A07_FD_fastqc.html [2021-05-01 03:28:52,935] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_B06_FD_fastqc.html [2021-05-01 03:28:52,936] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HK3VMBGXH_n02_S8_R1_B06_FD_fastqc.html [2021-05-01 03:28:53,350] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-01 03:28:53,352] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-01 03:28:53,489] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 289 samples (table) [2021-05-01 03:28:53,491] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-01 03:28:53,500] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-01 03:28:53,505] multiqc [DEBUG ] No samples found: conpair [2021-05-01 03:28:53,510] multiqc [DEBUG ] No samples found: peddy [2021-05-01 03:28:53,514] multiqc [DEBUG ] No samples found: somalier [2021-05-01 03:28:53,519] multiqc [DEBUG ] No samples found: methylQA [2021-05-01 03:28:53,526] multiqc [DEBUG ] No samples found: mosdepth [2021-05-01 03:28:53,530] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-01 03:28:53,534] multiqc [DEBUG ] No samples found: qualimap [2021-05-01 03:28:53,538] multiqc [DEBUG ] No samples found: preseq [2021-05-01 03:28:53,543] multiqc [DEBUG ] No samples found: quast [2021-05-01 03:28:53,547] multiqc [DEBUG ] No samples found: qorts [2021-05-01 03:28:53,552] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-01 03:28:53,556] multiqc [DEBUG ] No samples found: rockhopper [2021-05-01 03:28:53,561] multiqc [DEBUG ] No samples found: rsem [2021-05-01 03:28:53,571] multiqc [DEBUG ] No samples found: rseqc [2021-05-01 03:28:53,576] multiqc [DEBUG ] No samples found: busco [2021-05-01 03:28:53,580] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-01 03:28:53,584] multiqc [DEBUG ] No samples found: disambiguate [2021-05-01 03:28:53,589] multiqc [DEBUG ] No samples found: supernova [2021-05-01 03:28:53,602] multiqc [DEBUG ] No samples found: deeptools [2021-05-01 03:28:53,607] multiqc [DEBUG ] No samples found: sargasso [2021-05-01 03:28:53,611] multiqc [DEBUG ] No samples found: verifybamid [2021-05-01 03:28:53,616] multiqc [DEBUG ] No samples found: mirtrace [2021-05-01 03:28:53,621] multiqc [DEBUG ] No samples found: happy [2021-05-01 03:28:53,625] multiqc [DEBUG ] No samples found: mirtop [2021-05-01 03:28:53,631] multiqc [DEBUG ] No samples found: homer [2021-05-01 03:28:53,636] multiqc [DEBUG ] No samples found: macs2 [2021-05-01 03:28:53,640] multiqc [DEBUG ] No samples found: theta2 [2021-05-01 03:28:53,644] multiqc [DEBUG ] No samples found: snpeff [2021-05-01 03:28:53,650] multiqc [DEBUG ] No samples found: gatk [2021-05-01 03:28:53,655] multiqc [DEBUG ] No samples found: htseq [2021-05-01 03:28:53,660] multiqc [DEBUG ] No samples found: bcftools [2021-05-01 03:28:53,665] multiqc [DEBUG ] No samples found: featureCounts [2021-05-01 03:28:53,671] multiqc [DEBUG ] No samples found: fgbio [2021-05-01 03:28:53,684] multiqc [DEBUG ] No samples found: dragen [2021-05-01 03:28:53,689] multiqc [DEBUG ] No samples found: dedup [2021-05-01 03:28:53,694] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-01 03:28:53,716] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-01 03:28:53,720] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-01 03:28:53,722] multiqc [DEBUG ] No samples found: picard [2021-05-01 03:28:53,727] multiqc [DEBUG ] No samples found: prokka [2021-05-01 03:28:53,731] multiqc [DEBUG ] No samples found: samblaster [2021-05-01 03:28:53,742] multiqc [DEBUG ] No samples found: samtools [2021-05-01 03:28:53,746] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-01 03:28:53,751] multiqc [DEBUG ] No samples found: bamtools [2021-05-01 03:28:53,755] multiqc [DEBUG ] No samples found: jellyfish [2021-05-01 03:28:53,763] multiqc [DEBUG ] No samples found: vcftools [2021-05-01 03:28:53,768] multiqc [DEBUG ] No samples found: longranger [2021-05-01 03:28:53,773] multiqc [DEBUG ] No samples found: stacks [2021-05-01 03:28:53,777] multiqc [DEBUG ] No samples found: varscan2 [2021-05-01 03:28:53,790] multiqc [DEBUG ] No samples found: bbmap [2021-05-01 03:28:53,795] multiqc [DEBUG ] No samples found: bismark [2021-05-01 03:28:53,800] multiqc [DEBUG ] No samples found: biscuit [2021-05-01 03:28:53,805] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-01 03:28:53,809] multiqc [DEBUG ] No samples found: hicup [2021-05-01 03:28:53,814] multiqc [DEBUG ] No samples found: hicpro [2021-05-01 03:28:53,818] multiqc [DEBUG ] No samples found: salmon [2021-05-01 03:28:53,822] multiqc [DEBUG ] No samples found: kallisto [2021-05-01 03:28:53,827] multiqc [DEBUG ] No samples found: slamdunk [2021-05-01 03:28:53,832] multiqc [DEBUG ] No samples found: star [2021-05-01 03:28:53,836] multiqc [DEBUG ] No samples found: hisat2 [2021-05-01 03:28:53,841] multiqc [DEBUG ] No samples found: tophat [2021-05-01 03:28:53,845] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-01 03:28:53,850] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-01 03:28:53,854] multiqc [DEBUG ] No samples found: snpsplit [2021-05-01 03:28:53,858] multiqc [DEBUG ] No samples found: kat [2021-05-01 03:28:53,862] multiqc [DEBUG ] No samples found: leehom [2021-05-01 03:28:53,866] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-01 03:28:53,870] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-01 03:28:53,875] multiqc [DEBUG ] No samples found: cutadapt [2021-05-01 03:28:53,879] multiqc [DEBUG ] No samples found: flexbar [2021-05-01 03:28:53,883] multiqc [DEBUG ] No samples found: kaiju [2021-05-01 03:28:53,888] multiqc [DEBUG ] No samples found: kraken [2021-05-01 03:28:53,892] multiqc [DEBUG ] No samples found: malt [2021-05-01 03:28:53,896] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-01 03:28:53,900] multiqc [DEBUG ] No samples found: sickle [2021-05-01 03:28:53,905] multiqc [DEBUG ] No samples found: skewer [2021-05-01 03:28:53,909] multiqc [DEBUG ] No samples found: sortmerna [2021-05-01 03:28:53,913] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-01 03:28:53,918] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-01 03:28:53,922] multiqc [DEBUG ] No samples found: afterqc [2021-05-01 03:28:53,927] multiqc [DEBUG ] No samples found: fastp [2021-05-01 03:29:49,106] multiqc.modules.fastqc.fastqc [INFO ] Found 578 reports [2021-05-01 03:30:31,525] multiqc [DEBUG ] No samples found: pycoqc [2021-05-01 03:30:31,530] multiqc [DEBUG ] No samples found: minionqc [2021-05-01 03:30:31,534] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-01 03:30:31,539] multiqc [DEBUG ] No samples found: clusterflow [2021-05-01 03:30:31,543] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-01 03:30:31,548] multiqc [DEBUG ] No samples found: interop [2021-05-01 03:30:31,552] multiqc [DEBUG ] No samples found: ivar [2021-05-01 03:30:31,557] multiqc [DEBUG ] No samples found: flash [2021-05-01 03:30:31,561] multiqc [DEBUG ] No samples found: seqyclean [2021-05-01 03:30:31,562] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-05-01 03:30:31,562] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-05-01 03:30:31,562] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-01 03:30:31,562] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-01 03:30:31,565] multiqc.plots.table [DEBUG ] Plotting beeswarm instead of table, 578 samples [2021-05-01 03:30:31,568] multiqc [INFO ] Compressing plot data [2021-05-01 03:30:31,873] multiqc [INFO ] Report : multiqc_report.html [2021-05-01 03:30:31,873] multiqc [INFO ] Data : multiqc_data [2021-05-01 03:30:31,873] multiqc [DEBUG ] Moving data file from '/state/partition1/job-6227456/tmpg05emt7u/multiqc_data' to '/scratch/gencore/logs/html/HK3VMBGXH/merged/multiqc_data' [2021-05-01 03:30:32,043] multiqc [INFO ] MultiQC complete