[2024-01-17 21:57:49,838] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-17 21:57:49,839] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-17 21:57:49,839] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-17 21:57:49,841] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2024-01-17 21:57:49,841] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2024-01-17 21:57:49,841] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNTFHDMXY/merged [2024-01-17 21:57:50,012] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-17 21:57:50,012] multiqc [INFO ] This is MultiQC v1.9 [2024-01-17 21:57:50,012] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HNTFHDMXY/merged [2024-01-17 21:57:50,012] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HNTFHDMXY/merged [2024-01-17 21:57:50,012] multiqc [INFO ] Template : default [2024-01-17 21:57:50,012] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-17 21:57:50,013] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HNTFHDMXY/merged [2024-01-17 21:57:50,013] 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 [2024-01-17 21:57:50,013] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41936435/tmpic80ydm2 [2024-01-17 21:57:50,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-033_r2_fastqc.html [2024-01-17 21:57:50,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HNTFHDMXY_n02_MTH-039_r2_fastqc.html [2024-01-17 21:58:09,201] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n01_MTH-028_r2_fastqc.html [2024-01-17 21:58:09,203] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n01_MTH-028_r2_fastqc.html [2024-01-17 21:58:09,279] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MTH-027_r2_fastqc.html [2024-01-17 21:58:09,282] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MTH-027_r2_fastqc.html [2024-01-17 21:58:09,352] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-051_r2_fastqc.html [2024-01-17 21:58:09,354] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-051_r2_fastqc.html [2024-01-17 21:58:09,404] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n01_MTH-015_r2_fastqc.html [2024-01-17 21:58:09,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n01_MTH-015_r2_fastqc.html [2024-01-17 21:58:09,478] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MTH-031_r2_fastqc.html [2024-01-17 21:58:09,480] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MTH-031_r2_fastqc.html [2024-01-17 21:58:09,532] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-052_r2_fastqc.html [2024-01-17 21:58:09,534] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-052_r2_fastqc.html [2024-01-17 21:58:09,601] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-018_r2_fastqc.html [2024-01-17 21:58:09,603] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-018_r2_fastqc.html [2024-01-17 21:58:09,709] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-006_r2_fastqc.html [2024-01-17 21:58:09,711] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-006_r2_fastqc.html [2024-01-17 21:58:09,772] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-084_r2_fastqc.html [2024-01-17 21:58:09,774] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HNTFHDMXY_n02_MHC-084_r2_fastqc.html [2024-01-17 21:58:10,527] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-17 21:58:10,529] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-17 21:58:10,539] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-17 21:58:10,613] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 149 samples (table) [2024-01-17 21:58:10,623] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-17 21:58:10,628] multiqc [DEBUG ] No samples found: conpair [2024-01-17 21:58:10,633] multiqc [DEBUG ] No samples found: peddy [2024-01-17 21:58:10,640] multiqc [DEBUG ] No samples found: somalier [2024-01-17 21:58:10,650] multiqc [DEBUG ] No samples found: methylQA [2024-01-17 21:58:10,661] multiqc [DEBUG ] No samples found: mosdepth [2024-01-17 21:58:10,666] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-17 21:58:10,670] multiqc [DEBUG ] No samples found: qualimap [2024-01-17 21:58:10,677] multiqc [DEBUG ] No samples found: preseq [2024-01-17 21:58:10,682] multiqc [DEBUG ] No samples found: quast [2024-01-17 21:58:10,687] multiqc [DEBUG ] No samples found: qorts [2024-01-17 21:58:10,692] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-17 21:58:10,721] multiqc [DEBUG ] No samples found: rockhopper [2024-01-17 21:58:10,727] multiqc [DEBUG ] No samples found: rsem [2024-01-17 21:58:10,750] multiqc [DEBUG ] No samples found: rseqc [2024-01-17 21:58:10,755] multiqc [DEBUG ] No samples found: busco [2024-01-17 21:58:10,769] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-17 21:58:10,775] multiqc [DEBUG ] No samples found: disambiguate [2024-01-17 21:58:10,780] multiqc [DEBUG ] No samples found: supernova [2024-01-17 21:58:10,800] multiqc [DEBUG ] No samples found: deeptools [2024-01-17 21:58:10,811] multiqc [DEBUG ] No samples found: sargasso [2024-01-17 21:58:10,821] multiqc [DEBUG ] No samples found: verifybamid [2024-01-17 21:58:10,833] multiqc [DEBUG ] No samples found: mirtrace [2024-01-17 21:58:10,844] multiqc [DEBUG ] No samples found: happy [2024-01-17 21:58:10,855] multiqc [DEBUG ] No samples found: mirtop [2024-01-17 21:58:10,861] multiqc [DEBUG ] No samples found: homer [2024-01-17 21:58:10,866] multiqc [DEBUG ] No samples found: macs2 [2024-01-17 21:58:10,872] multiqc [DEBUG ] No samples found: theta2 [2024-01-17 21:58:10,877] multiqc [DEBUG ] No samples found: snpeff [2024-01-17 21:58:10,884] multiqc [DEBUG ] No samples found: gatk [2024-01-17 21:58:10,888] multiqc [DEBUG ] No samples found: htseq [2024-01-17 21:58:10,894] multiqc [DEBUG ] No samples found: bcftools [2024-01-17 21:58:10,900] multiqc [DEBUG ] No samples found: featureCounts [2024-01-17 21:58:10,933] multiqc [DEBUG ] No samples found: fgbio [2024-01-17 21:58:10,986] multiqc [DEBUG ] No samples found: dragen [2024-01-17 21:58:10,991] multiqc [DEBUG ] No samples found: dedup [2024-01-17 21:58:10,996] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-17 21:58:11,093] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-17 21:58:11,097] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-17 21:58:11,100] multiqc [DEBUG ] No samples found: picard [2024-01-17 21:58:11,106] multiqc [DEBUG ] No samples found: prokka [2024-01-17 21:58:11,111] multiqc [DEBUG ] No samples found: samblaster [2024-01-17 21:58:11,130] multiqc [DEBUG ] No samples found: samtools [2024-01-17 21:58:11,139] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-17 21:58:11,144] multiqc [DEBUG ] No samples found: bamtools [2024-01-17 21:58:11,151] multiqc [DEBUG ] No samples found: jellyfish [2024-01-17 21:58:11,183] multiqc [DEBUG ] No samples found: vcftools [2024-01-17 21:58:11,188] multiqc [DEBUG ] No samples found: longranger [2024-01-17 21:58:11,193] multiqc [DEBUG ] No samples found: stacks [2024-01-17 21:58:11,198] multiqc [DEBUG ] No samples found: varscan2 [2024-01-17 21:58:11,220] multiqc [DEBUG ] No samples found: bbmap [2024-01-17 21:58:11,226] multiqc [DEBUG ] No samples found: bismark [2024-01-17 21:58:11,232] multiqc [DEBUG ] No samples found: biscuit [2024-01-17 21:58:11,246] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-17 21:58:11,251] multiqc [DEBUG ] No samples found: hicup [2024-01-17 21:58:11,256] multiqc [DEBUG ] No samples found: hicpro [2024-01-17 21:58:11,267] multiqc [DEBUG ] No samples found: salmon [2024-01-17 21:58:11,272] multiqc [DEBUG ] No samples found: kallisto [2024-01-17 21:58:11,277] multiqc [DEBUG ] No samples found: slamdunk [2024-01-17 21:58:11,282] multiqc [DEBUG ] No samples found: star [2024-01-17 21:58:11,288] multiqc [DEBUG ] No samples found: hisat2 [2024-01-17 21:58:11,293] multiqc [DEBUG ] No samples found: tophat [2024-01-17 21:58:11,300] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-17 21:58:11,311] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-17 21:58:11,323] multiqc [DEBUG ] No samples found: snpsplit [2024-01-17 21:58:11,332] multiqc [DEBUG ] No samples found: kat [2024-01-17 21:58:11,336] multiqc [DEBUG ] No samples found: leehom [2024-01-17 21:58:11,355] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-17 21:58:11,359] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-17 21:58:11,365] multiqc [DEBUG ] No samples found: cutadapt [2024-01-17 21:58:11,377] multiqc [DEBUG ] No samples found: flexbar [2024-01-17 21:58:11,387] multiqc [DEBUG ] No samples found: kaiju [2024-01-17 21:58:11,399] multiqc [DEBUG ] No samples found: kraken [2024-01-17 21:58:11,404] multiqc [DEBUG ] No samples found: malt [2024-01-17 21:58:11,408] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-17 21:58:11,413] multiqc [DEBUG ] No samples found: sickle [2024-01-17 21:58:11,418] multiqc [DEBUG ] No samples found: skewer [2024-01-17 21:58:11,422] multiqc [DEBUG ] No samples found: sortmerna [2024-01-17 21:58:11,428] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-17 21:58:11,450] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-17 21:58:11,469] multiqc [DEBUG ] No samples found: afterqc [2024-01-17 21:58:11,474] multiqc [DEBUG ] No samples found: fastp [2024-01-17 21:59:06,349] multiqc.modules.fastqc.fastqc [INFO ] Found 298 reports [2024-01-17 21:59:41,385] multiqc [DEBUG ] No samples found: pycoqc [2024-01-17 21:59:41,390] multiqc [DEBUG ] No samples found: minionqc [2024-01-17 21:59:41,394] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-17 21:59:41,399] multiqc [DEBUG ] No samples found: clusterflow [2024-01-17 21:59:41,410] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-17 21:59:41,415] multiqc [DEBUG ] No samples found: interop [2024-01-17 21:59:41,432] multiqc [DEBUG ] No samples found: ivar [2024-01-17 21:59:41,436] multiqc [DEBUG ] No samples found: flash [2024-01-17 21:59:41,443] multiqc [DEBUG ] No samples found: seqyclean [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,443] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-17 21:59:41,444] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-17 21:59:41,812] multiqc [INFO ] Compressing plot data [2024-01-17 21:59:41,918] multiqc [INFO ] Report : multiqc_report.html [2024-01-17 21:59:41,918] multiqc [INFO ] Data : multiqc_data [2024-01-17 21:59:41,918] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41936435/tmpic80ydm2/multiqc_data' to '/scratch/gencore/logs/html/HNTFHDMXY/merged/multiqc_data' [2024-01-17 21:59:42,148] multiqc [INFO ] MultiQC complete