[2021-05-27 03:24:46,588] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-05-27 03:24:46,589] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-05-27 03:24:46,589] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-27 03:24:46,590] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-05-27 03:24:46,590] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-05-27 03:24:46,590] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NKYDRXY/merged [2021-05-27 03:24:48,022] multiqc [WARNING] MultiQC Version v1.10.1 now available! [2021-05-27 03:24:48,022] multiqc [INFO ] This is MultiQC v1.9 [2021-05-27 03:24:48,022] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H5NKYDRXY/merged [2021-05-27 03:24:48,022] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H5NKYDRXY/merged [2021-05-27 03:24:48,022] multiqc [INFO ] Template : default [2021-05-27 03:24:48,023] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-05-27 03:24:48,023] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H5NKYDRXY/merged [2021-05-27 03:24:48,023] 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 [2021-05-27 03:24:48,023] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-7171589/tmpxq722u5b [2021-05-27 03:24:48,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei068_fastqc.html [2021-05-27 03:24:48,174] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei068_fastqc.html [2021-05-27 03:24:48,245] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei060_fastqc.html [2021-05-27 03:24:48,247] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei060_fastqc.html [2021-05-27 03:24:48,287] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-27 03:24:48,288] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-05-27 03:24:48,388] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei056_fastqc.html [2021-05-27 03:24:48,390] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei056_fastqc.html [2021-05-27 03:24:48,521] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei064_fastqc.html [2021-05-27 03:24:48,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei064_fastqc.html [2021-05-27 03:24:48,578] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei078_fastqc.html [2021-05-27 03:24:48,580] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei078_fastqc.html [2021-05-27 03:24:48,620] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei065_fastqc.html [2021-05-27 03:24:48,622] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei065_fastqc.html [2021-05-27 03:24:48,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei057_fastqc.html [2021-05-27 03:24:48,683] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei057_fastqc.html [2021-05-27 03:24:48,746] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei058_fastqc.html [2021-05-27 03:24:48,747] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei058_fastqc.html [2021-05-27 03:24:48,813] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei079_fastqc.html [2021-05-27 03:24:48,814] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei079_fastqc.html [2021-05-27 03:24:48,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei066_fastqc.html [2021-05-27 03:24:48,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei066_fastqc.html [2021-05-27 03:24:48,937] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei074_fastqc.html [2021-05-27 03:24:48,938] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei074_fastqc.html [2021-05-27 03:24:49,002] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei075_fastqc.html [2021-05-27 03:24:49,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei075_fastqc.html [2021-05-27 03:24:49,065] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei063_fastqc.html [2021-05-27 03:24:49,067] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei063_fastqc.html [2021-05-27 03:24:49,123] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei071_fastqc.html [2021-05-27 03:24:49,125] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei071_fastqc.html [2021-05-27 03:24:49,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_undetermined_fastqc.html [2021-05-27 03:24:49,173] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_undetermined_fastqc.html [2021-05-27 03:24:49,228] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei059_fastqc.html [2021-05-27 03:24:49,230] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei059_fastqc.html [2021-05-27 03:24:49,285] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei072_fastqc.html [2021-05-27 03:24:49,287] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei072_fastqc.html [2021-05-27 03:24:49,329] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei077_fastqc.html [2021-05-27 03:24:49,330] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei077_fastqc.html [2021-05-27 03:24:49,389] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei070_fastqc.html [2021-05-27 03:24:49,391] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei070_fastqc.html [2021-05-27 03:24:49,432] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei061_fastqc.html [2021-05-27 03:24:49,434] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei061_fastqc.html [2021-05-27 03:24:49,489] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei062_fastqc.html [2021-05-27 03:24:49,491] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei062_fastqc.html [2021-05-27 03:24:49,552] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei073_fastqc.html [2021-05-27 03:24:49,554] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei073_fastqc.html [2021-05-27 03:24:49,601] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei076_fastqc.html [2021-05-27 03:24:49,603] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei076_fastqc.html [2021-05-27 03:24:49,674] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei067_fastqc.html [2021-05-27 03:24:49,675] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei067_fastqc.html [2021-05-27 03:24:49,726] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei069_fastqc.html [2021-05-27 03:24:49,728] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5NKYDRXY_n01_dei069_fastqc.html [2021-05-27 03:24:50,139] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-27 03:24:50,140] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-05-27 03:24:50,148] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-05-27 03:24:50,161] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2021-05-27 03:24:50,170] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-05-27 03:24:50,175] multiqc [DEBUG ] No samples found: conpair [2021-05-27 03:24:50,184] multiqc [DEBUG ] No samples found: peddy [2021-05-27 03:24:50,189] multiqc [DEBUG ] No samples found: somalier [2021-05-27 03:24:50,195] multiqc [DEBUG ] No samples found: methylQA [2021-05-27 03:24:50,212] multiqc [DEBUG ] No samples found: mosdepth [2021-05-27 03:24:50,216] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-27 03:24:50,221] multiqc [DEBUG ] No samples found: qualimap [2021-05-27 03:24:50,227] multiqc [DEBUG ] No samples found: preseq [2021-05-27 03:24:50,234] multiqc [DEBUG ] No samples found: quast [2021-05-27 03:24:50,241] multiqc [DEBUG ] No samples found: qorts [2021-05-27 03:24:50,246] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-27 03:24:50,252] multiqc [DEBUG ] No samples found: rockhopper [2021-05-27 03:24:50,262] multiqc [DEBUG ] No samples found: rsem [2021-05-27 03:24:50,281] multiqc [DEBUG ] No samples found: rseqc [2021-05-27 03:24:50,286] multiqc [DEBUG ] No samples found: busco [2021-05-27 03:24:50,293] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-27 03:24:50,299] multiqc [DEBUG ] No samples found: disambiguate [2021-05-27 03:24:50,304] multiqc [DEBUG ] No samples found: supernova [2021-05-27 03:24:50,323] multiqc [DEBUG ] No samples found: deeptools [2021-05-27 03:24:50,329] multiqc [DEBUG ] No samples found: sargasso [2021-05-27 03:24:50,334] multiqc [DEBUG ] No samples found: verifybamid [2021-05-27 03:24:50,342] multiqc [DEBUG ] No samples found: mirtrace [2021-05-27 03:24:50,347] multiqc [DEBUG ] No samples found: happy [2021-05-27 03:24:50,354] multiqc [DEBUG ] No samples found: mirtop [2021-05-27 03:24:50,360] multiqc [DEBUG ] No samples found: homer [2021-05-27 03:24:50,365] multiqc [DEBUG ] No samples found: macs2 [2021-05-27 03:24:50,370] multiqc [DEBUG ] No samples found: theta2 [2021-05-27 03:24:50,376] multiqc [DEBUG ] No samples found: snpeff [2021-05-27 03:24:50,387] multiqc [DEBUG ] No samples found: gatk [2021-05-27 03:24:50,396] multiqc [DEBUG ] No samples found: htseq [2021-05-27 03:24:50,403] multiqc [DEBUG ] No samples found: bcftools [2021-05-27 03:24:50,408] multiqc [DEBUG ] No samples found: featureCounts [2021-05-27 03:24:50,419] multiqc [DEBUG ] No samples found: fgbio [2021-05-27 03:24:50,445] multiqc [DEBUG ] No samples found: dragen [2021-05-27 03:24:50,451] multiqc [DEBUG ] No samples found: dedup [2021-05-27 03:24:50,461] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-27 03:24:50,487] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-27 03:24:50,495] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-27 03:24:50,497] multiqc [DEBUG ] No samples found: picard [2021-05-27 03:24:50,502] multiqc [DEBUG ] No samples found: prokka [2021-05-27 03:24:50,507] multiqc [DEBUG ] No samples found: samblaster [2021-05-27 03:24:50,518] multiqc [DEBUG ] No samples found: samtools [2021-05-27 03:24:50,527] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-27 03:24:50,534] multiqc [DEBUG ] No samples found: bamtools [2021-05-27 03:24:50,538] multiqc [DEBUG ] No samples found: jellyfish [2021-05-27 03:24:50,552] multiqc [DEBUG ] No samples found: vcftools [2021-05-27 03:24:50,557] multiqc [DEBUG ] No samples found: longranger [2021-05-27 03:24:50,562] multiqc [DEBUG ] No samples found: stacks [2021-05-27 03:24:50,568] multiqc [DEBUG ] No samples found: varscan2 [2021-05-27 03:24:50,592] multiqc [DEBUG ] No samples found: bbmap [2021-05-27 03:24:50,598] multiqc [DEBUG ] No samples found: bismark [2021-05-27 03:24:50,604] multiqc [DEBUG ] No samples found: biscuit [2021-05-27 03:24:50,609] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-27 03:24:50,614] multiqc [DEBUG ] No samples found: hicup [2021-05-27 03:24:50,621] multiqc [DEBUG ] No samples found: hicpro [2021-05-27 03:24:50,626] multiqc [DEBUG ] No samples found: salmon [2021-05-27 03:24:50,631] multiqc [DEBUG ] No samples found: kallisto [2021-05-27 03:24:50,638] multiqc [DEBUG ] No samples found: slamdunk [2021-05-27 03:24:50,642] multiqc [DEBUG ] No samples found: star [2021-05-27 03:24:50,648] multiqc [DEBUG ] No samples found: hisat2 [2021-05-27 03:24:50,654] multiqc [DEBUG ] No samples found: tophat [2021-05-27 03:24:50,660] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-27 03:24:50,665] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-27 03:24:50,672] multiqc [DEBUG ] No samples found: snpsplit [2021-05-27 03:24:50,677] multiqc [DEBUG ] No samples found: kat [2021-05-27 03:24:50,681] multiqc [DEBUG ] No samples found: leehom [2021-05-27 03:24:50,691] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-27 03:24:50,701] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-27 03:24:50,706] multiqc [DEBUG ] No samples found: cutadapt [2021-05-27 03:24:50,712] multiqc [DEBUG ] No samples found: flexbar [2021-05-27 03:24:50,717] multiqc [DEBUG ] No samples found: kaiju [2021-05-27 03:24:50,724] multiqc [DEBUG ] No samples found: kraken [2021-05-27 03:24:50,730] multiqc [DEBUG ] No samples found: malt [2021-05-27 03:24:50,737] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-27 03:24:50,742] multiqc [DEBUG ] No samples found: sickle [2021-05-27 03:24:50,747] multiqc [DEBUG ] No samples found: skewer [2021-05-27 03:24:50,755] multiqc [DEBUG ] No samples found: sortmerna [2021-05-27 03:24:50,760] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-27 03:24:50,767] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-27 03:24:50,771] multiqc [DEBUG ] No samples found: afterqc [2021-05-27 03:24:50,776] multiqc [DEBUG ] No samples found: fastp [2021-05-27 03:24:52,322] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2021-05-27 03:24:52,694] multiqc [DEBUG ] No samples found: pycoqc [2021-05-27 03:24:52,704] multiqc [DEBUG ] No samples found: minionqc [2021-05-27 03:24:52,710] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-05-27 03:24:52,717] multiqc [DEBUG ] No samples found: clusterflow [2021-05-27 03:24:52,722] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-27 03:24:52,727] multiqc [DEBUG ] No samples found: interop [2021-05-27 03:24:52,737] multiqc [DEBUG ] No samples found: ivar [2021-05-27 03:24:52,745] multiqc [DEBUG ] No samples found: flash [2021-05-27 03:24:52,749] multiqc [DEBUG ] No samples found: seqyclean [2021-05-27 03:24:52,749] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-05-27 03:24:52,749] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-05-27 03:24:52,749] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-05-27 03:24:52,749] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-05-27 03:24:52,780] multiqc [INFO ] Compressing plot data [2021-05-27 03:24:53,264] multiqc [INFO ] Report : multiqc_report.html [2021-05-27 03:24:53,264] multiqc [INFO ] Data : multiqc_data [2021-05-27 03:24:53,264] multiqc [DEBUG ] Moving data file from '/state/partition1/job-7171589/tmpxq722u5b/multiqc_data' to '/scratch/gencore/logs/html/H5NKYDRXY/merged/multiqc_data' [2021-05-27 03:24:53,413] multiqc [INFO ] MultiQC complete