[2022-06-06 03:11:38,184] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2022-06-06 03:11:38,184] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2022-06-06 03:11:38,184] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-06-06 03:11:38,185] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2022-06-06 03:11:38,185] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2022-06-06 03:11:38,185] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H53Y2DRX2/merged [2022-06-06 03:11:38,745] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-06-06 03:11:38,745] multiqc [INFO ] This is MultiQC v1.9 [2022-06-06 03:11:38,745] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/H53Y2DRX2/merged [2022-06-06 03:11:38,745] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/H53Y2DRX2/merged [2022-06-06 03:11:38,745] multiqc [INFO ] Template : default [2022-06-06 03:11:38,745] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2022-06-06 03:11:38,745] multiqc [INFO ] Searching : /scratch/gencore/logs/html/H53Y2DRX2/merged [2022-06-06 03:11:38,745] 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 [2022-06-06 03:11:38,746] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-20557345/tmpfwwvh9uq [2022-06-06 03:11:38,894] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br19a_fastqc.html [2022-06-06 03:11:38,897] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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H53Y2DRX2_n01_br17a_fastqc.html [2022-06-06 03:11:39,079] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_undetermined_fastqc.html [2022-06-06 03:11:39,081] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_undetermined_fastqc.html [2022-06-06 03:11:39,125] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br27a_fastqc.html [2022-06-06 03:11:39,127] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br27a_fastqc.html [2022-06-06 03:11:39,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br23a_fastqc.html [2022-06-06 03:11:39,173] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br23a_fastqc.html [2022-06-06 03:11:39,216] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br18a_fastqc.html [2022-06-06 03:11:39,218] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br18a_fastqc.html [2022-06-06 03:11:39,261] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br29a_fastqc.html [2022-06-06 03:11:39,263] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br29a_fastqc.html [2022-06-06 03:11:39,306] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br22a_fastqc.html [2022-06-06 03:11:39,308] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br22a_fastqc.html [2022-06-06 03:11:39,351] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br31a_fastqc.html [2022-06-06 03:11:39,353] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br31a_fastqc.html [2022-06-06 03:11:39,397] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br21a_fastqc.html [2022-06-06 03:11:39,399] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br21a_fastqc.html [2022-06-06 03:11:39,442] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br32a_fastqc.html [2022-06-06 03:11:39,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br32a_fastqc.html [2022-06-06 03:11:39,487] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br24a_fastqc.html [2022-06-06 03:11:39,489] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br24a_fastqc.html [2022-06-06 03:11:39,533] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br20a_fastqc.html [2022-06-06 03:11:39,534] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br20a_fastqc.html [2022-06-06 03:11:39,579] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br34a_fastqc.html [2022-06-06 03:11:39,581] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br34a_fastqc.html [2022-06-06 03:11:39,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br35a_fastqc.html [2022-06-06 03:11:39,626] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br35a_fastqc.html [2022-06-06 03:11:39,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br30a_fastqc.html [2022-06-06 03:11:39,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br30a_fastqc.html [2022-06-06 03:11:39,715] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br33a_fastqc.html [2022-06-06 03:11:39,717] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br33a_fastqc.html [2022-06-06 03:11:39,760] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br26a_fastqc.html [2022-06-06 03:11:39,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br26a_fastqc.html [2022-06-06 03:11:39,805] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br36a_fastqc.html [2022-06-06 03:11:39,807] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H53Y2DRX2_n01_br36a_fastqc.html [2022-06-06 03:11:40,565] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-06 03:11:40,567] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2022-06-06 03:11:40,578] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2022-06-06 03:11:40,589] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 21 samples (table) [2022-06-06 03:11:40,599] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2022-06-06 03:11:40,607] multiqc [DEBUG ] No samples found: conpair [2022-06-06 03:11:40,614] multiqc [DEBUG ] No samples found: peddy [2022-06-06 03:11:40,620] multiqc [DEBUG ] No samples found: somalier [2022-06-06 03:11:40,627] multiqc [DEBUG ] No samples found: methylQA [2022-06-06 03:11:40,645] multiqc [DEBUG ] No samples found: mosdepth [2022-06-06 03:11:40,651] multiqc [DEBUG ] No samples found: phantompeakqualtools [2022-06-06 03:11:40,654] multiqc [DEBUG ] No samples found: qualimap [2022-06-06 03:11:40,663] multiqc [DEBUG ] No samples found: preseq [2022-06-06 03:11:40,669] multiqc [DEBUG ] No samples found: quast [2022-06-06 03:11:40,677] multiqc [DEBUG ] No samples found: qorts [2022-06-06 03:11:40,685] multiqc [DEBUG ] No samples found: rna_seqc [2022-06-06 03:11:40,694] multiqc [DEBUG ] No samples found: rockhopper [2022-06-06 03:11:40,699] multiqc [DEBUG ] No samples found: rsem [2022-06-06 03:11:40,720] multiqc [DEBUG ] No samples found: rseqc [2022-06-06 03:11:40,726] multiqc [DEBUG ] No samples found: busco [2022-06-06 03:11:40,735] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-06-06 03:11:40,741] multiqc [DEBUG ] No samples found: disambiguate [2022-06-06 03:11:40,749] multiqc [DEBUG ] No samples found: supernova [2022-06-06 03:11:40,776] multiqc [DEBUG ] No samples found: deeptools [2022-06-06 03:11:40,784] multiqc [DEBUG ] No samples found: sargasso [2022-06-06 03:11:40,795] multiqc [DEBUG ] No samples found: verifybamid [2022-06-06 03:11:40,804] multiqc [DEBUG ] No samples found: mirtrace [2022-06-06 03:11:40,811] multiqc [DEBUG ] No samples found: happy [2022-06-06 03:11:40,817] multiqc [DEBUG ] No samples found: mirtop [2022-06-06 03:11:40,829] multiqc [DEBUG ] No samples found: homer [2022-06-06 03:11:40,835] multiqc [DEBUG ] No samples found: macs2 [2022-06-06 03:11:40,842] multiqc [DEBUG ] No samples found: theta2 [2022-06-06 03:11:40,853] multiqc [DEBUG ] No samples found: snpeff [2022-06-06 03:11:40,867] multiqc [DEBUG ] No samples found: gatk [2022-06-06 03:11:40,873] multiqc [DEBUG ] No samples found: htseq [2022-06-06 03:11:40,885] multiqc [DEBUG ] No samples found: bcftools [2022-06-06 03:11:40,893] multiqc [DEBUG ] No samples found: featureCounts [2022-06-06 03:11:40,903] multiqc [DEBUG ] No samples found: fgbio [2022-06-06 03:11:40,932] multiqc [DEBUG ] No samples found: dragen [2022-06-06 03:11:40,938] multiqc [DEBUG ] No samples found: dedup [2022-06-06 03:11:40,944] multiqc [DEBUG ] No samples found: damageprofiler [2022-06-06 03:11:40,989] multiqc [DEBUG ] No samples found: biobambam2 [2022-06-06 03:11:40,995] multiqc [DEBUG ] No samples found: mtnucratio [2022-06-06 03:11:40,997] multiqc [DEBUG ] No samples found: picard [2022-06-06 03:11:41,003] multiqc [DEBUG ] No samples found: prokka [2022-06-06 03:11:41,012] multiqc [DEBUG ] No samples found: samblaster [2022-06-06 03:11:41,030] multiqc [DEBUG ] No samples found: samtools [2022-06-06 03:11:41,038] multiqc [DEBUG ] No samples found: sexdeterrmine [2022-06-06 03:11:41,047] multiqc [DEBUG ] No samples found: bamtools [2022-06-06 03:11:41,058] multiqc [DEBUG ] No samples found: jellyfish [2022-06-06 03:11:41,071] multiqc [DEBUG ] No samples found: vcftools [2022-06-06 03:11:41,077] multiqc [DEBUG ] No samples found: longranger [2022-06-06 03:11:41,087] multiqc [DEBUG ] No samples found: stacks [2022-06-06 03:11:41,096] multiqc [DEBUG ] No samples found: varscan2 [2022-06-06 03:11:41,124] multiqc [DEBUG ] No samples found: bbmap [2022-06-06 03:11:41,139] multiqc [DEBUG ] No samples found: bismark [2022-06-06 03:11:41,148] multiqc [DEBUG ] No samples found: biscuit [2022-06-06 03:11:41,157] multiqc [DEBUG ] No samples found: hicexplorer [2022-06-06 03:11:41,165] multiqc [DEBUG ] No samples found: hicup [2022-06-06 03:11:41,173] multiqc [DEBUG ] No samples found: hicpro [2022-06-06 03:11:41,183] multiqc [DEBUG ] No samples found: salmon [2022-06-06 03:11:41,192] multiqc [DEBUG ] No samples found: kallisto [2022-06-06 03:11:41,201] multiqc [DEBUG ] No samples found: slamdunk [2022-06-06 03:11:41,210] multiqc [DEBUG ] No samples found: star [2022-06-06 03:11:41,220] multiqc [DEBUG ] No samples found: hisat2 [2022-06-06 03:11:41,228] multiqc [DEBUG ] No samples found: tophat [2022-06-06 03:11:41,235] multiqc [DEBUG ] No samples found: bowtie2 [2022-06-06 03:11:41,246] multiqc [DEBUG ] No samples found: bowtie1 [2022-06-06 03:11:41,255] multiqc [DEBUG ] No samples found: snpsplit [2022-06-06 03:11:41,261] multiqc [DEBUG ] No samples found: kat [2022-06-06 03:11:41,270] multiqc [DEBUG ] No samples found: leehom [2022-06-06 03:11:41,280] multiqc [DEBUG ] No samples found: adapterRemoval [2022-06-06 03:11:41,290] multiqc [DEBUG ] No samples found: clipandmerge [2022-06-06 03:11:41,297] multiqc [DEBUG ] No samples found: cutadapt [2022-06-06 03:11:41,306] multiqc [DEBUG ] No samples found: flexbar [2022-06-06 03:11:41,313] multiqc [DEBUG ] No samples found: kaiju [2022-06-06 03:11:41,325] multiqc [DEBUG ] No samples found: kraken [2022-06-06 03:11:41,332] multiqc [DEBUG ] No samples found: malt [2022-06-06 03:11:41,344] multiqc [DEBUG ] No samples found: trimmomatic [2022-06-06 03:11:41,354] multiqc [DEBUG ] No samples found: sickle [2022-06-06 03:11:41,361] multiqc [DEBUG ] No samples found: skewer [2022-06-06 03:11:41,371] multiqc [DEBUG ] No samples found: sortmerna [2022-06-06 03:11:41,379] multiqc [DEBUG ] No samples found: biobloomtools [2022-06-06 03:11:41,386] multiqc [DEBUG ] No samples found: fastq_screen [2022-06-06 03:11:41,393] multiqc [DEBUG ] No samples found: afterqc [2022-06-06 03:11:41,401] multiqc [DEBUG ] No samples found: fastp [2022-06-06 03:11:42,098] multiqc.modules.fastqc.fastqc [INFO ] Found 21 reports [2022-06-06 03:11:42,432] multiqc [DEBUG ] No samples found: pycoqc [2022-06-06 03:11:42,445] multiqc [DEBUG ] No samples found: minionqc [2022-06-06 03:11:42,451] multiqc [DEBUG ] No samples found: multivcfanalyzer [2022-06-06 03:11:42,461] multiqc [DEBUG ] No samples found: clusterflow [2022-06-06 03:11:42,469] multiqc [DEBUG ] No samples found: bcl2fastq [2022-06-06 03:11:42,477] multiqc [DEBUG ] No samples found: interop [2022-06-06 03:11:42,485] multiqc [DEBUG ] No samples found: ivar [2022-06-06 03:11:42,492] multiqc [DEBUG ] No samples found: flash [2022-06-06 03:11:42,500] multiqc [DEBUG ] No samples found: seqyclean [2022-06-06 03:11:42,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2022-06-06 03:11:42,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2022-06-06 03:11:42,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2022-06-06 03:11:42,500] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2022-06-06 03:11:42,525] multiqc [INFO ] Compressing plot data [2022-06-06 03:11:42,907] multiqc [INFO ] Report : multiqc_report.html [2022-06-06 03:11:42,907] multiqc [INFO ] Data : multiqc_data [2022-06-06 03:11:42,907] multiqc [DEBUG ] Moving data file from '/state/partition1/job-20557345/tmpfwwvh9uq/multiqc_data' to '/scratch/gencore/logs/html/H53Y2DRX2/merged/multiqc_data' [2022-06-06 03:11:43,068] multiqc [INFO ] MultiQC complete