[2023-05-13 22:30:27,556] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-05-13 22:30:27,556] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-05-13 22:30:27,556] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-13 22:30:27,559] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2023-05-13 22:30:27,559] 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}} [2023-05-13 22:30:27,559] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHWYGAFX5/merged [2023-05-13 22:30:27,727] multiqc [WARNING] MultiQC Version v1.14 now available! [2023-05-13 22:30:27,727] multiqc [INFO ] This is MultiQC v1.9 [2023-05-13 22:30:27,728] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HHWYGAFX5/merged [2023-05-13 22:30:27,728] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HHWYGAFX5/merged [2023-05-13 22:30:27,728] multiqc [INFO ] Template : default [2023-05-13 22:30:27,728] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-05-13 22:30:27,728] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HHWYGAFX5/merged [2023-05-13 22:30:27,728] 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 [2023-05-13 22:30:27,728] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-33323056/tmpquz3e5ri [2023-05-13 22:30:27,841] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN114_hs_fastqc.html [2023-05-13 22:30:27,843] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded 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HHWYGAFX5_n01_EN118_hs_fastqc.html [2023-05-13 22:30:31,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN139_hs_fastqc.html [2023-05-13 22:30:31,782] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN139_hs_fastqc.html [2023-05-13 22:30:31,824] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN151_hs_fastqc.html [2023-05-13 22:30:31,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN151_hs_fastqc.html [2023-05-13 22:30:31,866] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN119_hs_fastqc.html [2023-05-13 22:30:31,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 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HHWYGAFX5_n01_EN121_hs_fastqc.html [2023-05-13 22:30:32,040] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n01_EN154_hs_fastqc.html [2023-05-13 22:30:32,041] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n01_EN154_hs_fastqc.html [2023-05-13 22:30:32,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN147_hs_fastqc.html [2023-05-13 22:30:32,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN147_hs_fastqc.html [2023-05-13 22:30:32,129] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN123_hs_fastqc.html [2023-05-13 22:30:32,131] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN123_hs_fastqc.html [2023-05-13 22:30:32,173] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN126_hs_fastqc.html [2023-05-13 22:30:32,175] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HHWYGAFX5_n02_EN126_hs_fastqc.html [2023-05-13 22:30:32,789] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-13 22:30:32,791] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-05-13 22:30:32,820] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 49 samples (table) [2023-05-13 22:30:32,821] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-05-13 22:30:32,831] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-05-13 22:30:32,835] multiqc [DEBUG ] No samples found: conpair [2023-05-13 22:30:32,840] multiqc [DEBUG ] No samples found: peddy [2023-05-13 22:30:32,844] multiqc [DEBUG ] No samples found: somalier [2023-05-13 22:30:32,848] multiqc [DEBUG ] No samples found: methylQA [2023-05-13 22:30:32,855] multiqc [DEBUG ] No samples found: mosdepth [2023-05-13 22:30:32,859] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-13 22:30:32,863] multiqc [DEBUG ] No samples found: qualimap [2023-05-13 22:30:32,867] multiqc [DEBUG ] No samples found: preseq [2023-05-13 22:30:32,871] multiqc [DEBUG ] No samples found: quast [2023-05-13 22:30:32,875] multiqc [DEBUG ] No samples found: qorts [2023-05-13 22:30:32,879] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-13 22:30:32,884] multiqc [DEBUG ] No samples found: rockhopper [2023-05-13 22:30:32,888] multiqc [DEBUG ] No samples found: rsem [2023-05-13 22:30:32,897] multiqc [DEBUG ] No samples found: rseqc [2023-05-13 22:30:32,901] multiqc [DEBUG ] No samples found: busco [2023-05-13 22:30:32,905] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-13 22:30:32,909] multiqc [DEBUG ] No samples found: disambiguate [2023-05-13 22:30:32,913] multiqc [DEBUG ] No samples found: supernova [2023-05-13 22:30:32,923] multiqc [DEBUG ] No samples found: deeptools [2023-05-13 22:30:32,928] multiqc [DEBUG ] No samples found: sargasso [2023-05-13 22:30:32,932] multiqc [DEBUG ] No samples found: verifybamid [2023-05-13 22:30:32,936] multiqc [DEBUG ] No samples found: mirtrace [2023-05-13 22:30:32,940] multiqc [DEBUG ] No samples found: happy [2023-05-13 22:30:32,944] multiqc [DEBUG ] No samples found: mirtop [2023-05-13 22:30:32,950] multiqc [DEBUG ] No samples found: homer [2023-05-13 22:30:32,954] multiqc [DEBUG ] No samples found: macs2 [2023-05-13 22:30:32,958] multiqc [DEBUG ] No samples found: theta2 [2023-05-13 22:30:32,962] multiqc [DEBUG ] No samples found: snpeff [2023-05-13 22:30:32,968] multiqc [DEBUG ] No samples found: gatk [2023-05-13 22:30:32,972] multiqc [DEBUG ] No samples found: htseq [2023-05-13 22:30:32,976] multiqc [DEBUG ] No samples found: bcftools [2023-05-13 22:30:32,980] multiqc [DEBUG ] No samples found: featureCounts [2023-05-13 22:30:32,985] multiqc [DEBUG ] No samples found: fgbio [2023-05-13 22:30:32,996] multiqc [DEBUG ] No samples found: dragen [2023-05-13 22:30:33,000] multiqc [DEBUG ] No samples found: dedup [2023-05-13 22:30:33,005] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-13 22:30:33,023] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-13 22:30:33,027] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-13 22:30:33,029] multiqc [DEBUG ] No samples found: picard [2023-05-13 22:30:33,034] multiqc [DEBUG ] No samples found: prokka [2023-05-13 22:30:33,037] multiqc [DEBUG ] No samples found: samblaster [2023-05-13 22:30:33,045] multiqc [DEBUG ] No samples found: samtools [2023-05-13 22:30:33,049] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-13 22:30:33,053] multiqc [DEBUG ] No samples found: bamtools [2023-05-13 22:30:33,057] multiqc [DEBUG ] No samples found: jellyfish [2023-05-13 22:30:33,063] multiqc [DEBUG ] No samples found: vcftools [2023-05-13 22:30:33,068] multiqc [DEBUG ] No samples found: longranger [2023-05-13 22:30:33,072] multiqc [DEBUG ] No samples found: stacks [2023-05-13 22:30:33,076] multiqc [DEBUG ] No samples found: varscan2 [2023-05-13 22:30:33,087] multiqc [DEBUG ] No samples found: bbmap [2023-05-13 22:30:33,092] multiqc [DEBUG ] No samples found: bismark [2023-05-13 22:30:33,096] multiqc [DEBUG ] No samples found: biscuit [2023-05-13 22:30:33,101] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-13 22:30:33,105] multiqc [DEBUG ] No samples found: hicup [2023-05-13 22:30:33,109] multiqc [DEBUG ] No samples found: hicpro [2023-05-13 22:30:33,113] multiqc [DEBUG ] No samples found: salmon [2023-05-13 22:30:33,117] multiqc [DEBUG ] No samples found: kallisto [2023-05-13 22:30:33,121] multiqc [DEBUG ] No samples found: slamdunk [2023-05-13 22:30:33,125] multiqc [DEBUG ] No samples found: star [2023-05-13 22:30:33,129] multiqc [DEBUG ] No samples found: hisat2 [2023-05-13 22:30:33,133] multiqc [DEBUG ] No samples found: tophat [2023-05-13 22:30:33,137] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-13 22:30:33,141] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-13 22:30:33,145] multiqc [DEBUG ] No samples found: snpsplit [2023-05-13 22:30:33,149] multiqc [DEBUG ] No samples found: kat [2023-05-13 22:30:33,153] multiqc [DEBUG ] No samples found: leehom [2023-05-13 22:30:33,157] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-13 22:30:33,161] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-13 22:30:33,165] multiqc [DEBUG ] No samples found: cutadapt [2023-05-13 22:30:33,169] multiqc [DEBUG ] No samples found: flexbar [2023-05-13 22:30:33,173] multiqc [DEBUG ] No samples found: kaiju [2023-05-13 22:30:33,177] multiqc [DEBUG ] No samples found: kraken [2023-05-13 22:30:33,181] multiqc [DEBUG ] No samples found: malt [2023-05-13 22:30:33,185] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-13 22:30:33,189] multiqc [DEBUG ] No samples found: sickle [2023-05-13 22:30:33,193] multiqc [DEBUG ] No samples found: skewer [2023-05-13 22:30:33,197] multiqc [DEBUG ] No samples found: sortmerna [2023-05-13 22:30:33,200] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-13 22:30:33,204] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-13 22:30:33,208] multiqc [DEBUG ] No samples found: afterqc [2023-05-13 22:30:33,213] multiqc [DEBUG ] No samples found: fastp [2023-05-13 22:30:35,839] multiqc.modules.fastqc.fastqc [INFO ] Found 98 reports [2023-05-13 22:30:37,717] multiqc [DEBUG ] No samples found: pycoqc [2023-05-13 22:30:37,721] multiqc [DEBUG ] No samples found: minionqc [2023-05-13 22:30:37,725] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-05-13 22:30:37,729] multiqc [DEBUG ] No samples found: clusterflow [2023-05-13 22:30:37,734] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-13 22:30:37,738] multiqc [DEBUG ] No samples found: interop [2023-05-13 22:30:37,742] multiqc [DEBUG ] No samples found: ivar [2023-05-13 22:30:37,746] multiqc [DEBUG ] No samples found: flash [2023-05-13 22:30:37,751] multiqc [DEBUG ] No samples found: seqyclean [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-05-13 22:30:37,751] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-05-13 22:30:37,752] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-05-13 22:30:37,752] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-05-13 22:30:37,752] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-05-13 22:30:37,863] multiqc [INFO ] Compressing plot data [2023-05-13 22:30:39,570] multiqc [INFO ] Report : multiqc_report.html [2023-05-13 22:30:39,570] multiqc [INFO ] Data : multiqc_data [2023-05-13 22:30:39,570] multiqc [DEBUG ] Moving data file from '/state/partition1/job-33323056/tmpquz3e5ri/multiqc_data' to '/scratch/gencore/logs/html/HHWYGAFX5/merged/multiqc_data' [2023-05-13 22:30:39,696] multiqc [INFO ] MultiQC complete