[2024-01-22 23:45:53,220] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-22 23:45:53,220] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-22 23:45:53,220] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-22 23:45:53,223] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-22 23:45:53,223] 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}} [2024-01-22 23:45:53,223] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-22 23:45:53,387] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-22 23:45:53,387] multiqc [INFO ] This is MultiQC v1.9 [2024-01-22 23:45:53,387] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-22 23:45:53,387] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/b3/656da8398cbafdb66f564b0fd01dfa/merged [2024-01-22 23:45:53,387] multiqc [INFO ] Template : default [2024-01-22 23:45:53,387] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-22 23:45:53,387] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/b3/656da8398cbafdb66f564b0fd01dfa/merged [2024-01-22 23:45:53,388] 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 [2024-01-22 23:45:53,388] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42173223/tmpis9s78c7 [2024-01-22 23:45:53,612] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-EV_fastqc.html [2024-01-22 23:45:53,624] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-EV_fastqc.html [2024-01-22 23:45:53,708] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-22 23:45:53,718] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-22 23:45:53,796] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-22 23:45:53,804] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-22 23:45:53,886] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-22 23:45:53,896] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-22 23:45:53,974] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-22 23:45:53,984] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-22 23:45:54,071] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-22 23:45:54,080] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-22 23:45:54,179] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-22 23:45:54,190] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-22 23:45:54,309] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HN2GGAFX5_n01_undetermined_fastqc.html [2024-01-22 23:45:54,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HN2GGAFX5_n01_undetermined_fastqc.html [2024-01-22 23:45:54,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-22 23:45:54,452] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-22 23:45:55,342] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-22 23:45:55,345] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-22 23:45:55,363] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2024-01-22 23:45:55,365] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-22 23:45:55,375] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-22 23:45:55,394] multiqc [DEBUG ] No samples found: conpair [2024-01-22 23:45:55,418] multiqc [DEBUG ] No samples found: peddy [2024-01-22 23:45:55,439] multiqc [DEBUG ] No samples found: somalier [2024-01-22 23:45:55,461] multiqc [DEBUG ] No samples found: methylQA [2024-01-22 23:45:55,514] multiqc [DEBUG ] No samples found: mosdepth [2024-01-22 23:45:55,533] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-22 23:45:55,539] multiqc [DEBUG ] No samples found: qualimap [2024-01-22 23:45:55,565] multiqc [DEBUG ] No samples found: preseq [2024-01-22 23:45:55,587] multiqc [DEBUG ] No samples found: quast [2024-01-22 23:45:55,610] multiqc [DEBUG ] No samples found: qorts [2024-01-22 23:45:55,622] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-22 23:45:55,646] multiqc [DEBUG ] No samples found: rockhopper [2024-01-22 23:45:55,659] multiqc [DEBUG ] No samples found: rsem [2024-01-22 23:45:55,740] multiqc [DEBUG ] No samples found: rseqc [2024-01-22 23:45:55,756] multiqc [DEBUG ] No samples found: busco [2024-01-22 23:45:55,796] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-22 23:45:55,815] multiqc [DEBUG ] No samples found: disambiguate [2024-01-22 23:45:55,853] multiqc [DEBUG ] No samples found: supernova [2024-01-22 23:45:55,950] multiqc [DEBUG ] No samples found: deeptools [2024-01-22 23:45:55,963] multiqc [DEBUG ] No samples found: sargasso [2024-01-22 23:45:55,987] multiqc [DEBUG ] No samples found: verifybamid [2024-01-22 23:45:56,020] multiqc [DEBUG ] No samples found: mirtrace [2024-01-22 23:45:56,042] multiqc [DEBUG ] No samples found: happy [2024-01-22 23:45:56,061] multiqc [DEBUG ] No samples found: mirtop [2024-01-22 23:45:56,106] multiqc [DEBUG ] No samples found: homer [2024-01-22 23:45:56,133] multiqc [DEBUG ] No samples found: macs2 [2024-01-22 23:45:56,149] multiqc [DEBUG ] No samples found: theta2 [2024-01-22 23:45:56,174] multiqc [DEBUG ] No samples found: snpeff [2024-01-22 23:45:56,209] multiqc [DEBUG ] No samples found: gatk [2024-01-22 23:45:56,242] multiqc [DEBUG ] No samples found: htseq [2024-01-22 23:45:56,268] multiqc [DEBUG ] No samples found: bcftools [2024-01-22 23:45:56,287] multiqc [DEBUG ] No samples found: featureCounts [2024-01-22 23:45:56,320] multiqc [DEBUG ] No samples found: fgbio [2024-01-22 23:45:56,429] multiqc [DEBUG ] No samples found: dragen [2024-01-22 23:45:56,465] multiqc [DEBUG ] No samples found: dedup [2024-01-22 23:45:56,485] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-22 23:45:56,687] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-22 23:45:56,699] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-22 23:45:56,702] multiqc [DEBUG ] No samples found: picard [2024-01-22 23:45:56,723] multiqc [DEBUG ] No samples found: prokka [2024-01-22 23:45:56,742] multiqc [DEBUG ] No samples found: samblaster [2024-01-22 23:45:56,805] multiqc [DEBUG ] No samples found: samtools [2024-01-22 23:45:56,840] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-22 23:45:56,848] multiqc [DEBUG ] No samples found: bamtools [2024-01-22 23:45:56,868] multiqc [DEBUG ] No samples found: jellyfish [2024-01-22 23:45:56,911] multiqc [DEBUG ] No samples found: vcftools [2024-01-22 23:45:56,932] multiqc [DEBUG ] No samples found: longranger [2024-01-22 23:45:56,963] multiqc [DEBUG ] No samples found: stacks [2024-01-22 23:45:56,984] multiqc [DEBUG ] No samples found: varscan2 [2024-01-22 23:45:57,087] multiqc [DEBUG ] No samples found: bbmap [2024-01-22 23:45:57,109] multiqc [DEBUG ] No samples found: bismark [2024-01-22 23:45:57,133] multiqc [DEBUG ] No samples found: biscuit [2024-01-22 23:45:57,155] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-22 23:45:57,183] multiqc [DEBUG ] No samples found: hicup [2024-01-22 23:45:57,205] multiqc [DEBUG ] No samples found: hicpro [2024-01-22 23:45:57,224] multiqc [DEBUG ] No samples found: salmon [2024-01-22 23:45:57,253] multiqc [DEBUG ] No samples found: kallisto [2024-01-22 23:45:57,285] multiqc [DEBUG ] No samples found: slamdunk [2024-01-22 23:45:57,314] multiqc [DEBUG ] No samples found: star [2024-01-22 23:45:57,336] multiqc [DEBUG ] No samples found: hisat2 [2024-01-22 23:45:57,380] multiqc [DEBUG ] No samples found: tophat [2024-01-22 23:45:57,403] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-22 23:45:57,425] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-22 23:45:57,446] multiqc [DEBUG ] No samples found: snpsplit [2024-01-22 23:45:57,462] multiqc [DEBUG ] No samples found: kat [2024-01-22 23:45:57,480] multiqc [DEBUG ] No samples found: leehom [2024-01-22 23:45:57,502] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-22 23:45:57,519] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-22 23:45:57,541] multiqc [DEBUG ] No samples found: cutadapt [2024-01-22 23:45:57,570] multiqc [DEBUG ] No samples found: flexbar [2024-01-22 23:45:57,592] multiqc [DEBUG ] No samples found: kaiju [2024-01-22 23:45:57,619] multiqc [DEBUG ] No samples found: kraken [2024-01-22 23:45:57,648] multiqc [DEBUG ] No samples found: malt [2024-01-22 23:45:57,676] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-22 23:45:57,709] multiqc [DEBUG ] No samples found: sickle [2024-01-22 23:45:57,731] multiqc [DEBUG ] No samples found: skewer [2024-01-22 23:45:57,743] multiqc [DEBUG ] No samples found: sortmerna [2024-01-22 23:45:57,764] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-22 23:45:57,782] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-22 23:45:57,815] multiqc [DEBUG ] No samples found: afterqc [2024-01-22 23:45:57,843] multiqc [DEBUG ] No samples found: fastp [2024-01-22 23:45:58,141] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2024-01-22 23:45:58,352] multiqc [DEBUG ] No samples found: pycoqc [2024-01-22 23:45:58,374] multiqc [DEBUG ] No samples found: minionqc [2024-01-22 23:45:58,396] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-22 23:45:58,418] multiqc [DEBUG ] No samples found: clusterflow [2024-01-22 23:45:58,440] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-22 23:45:58,473] multiqc [DEBUG ] No samples found: interop [2024-01-22 23:45:58,500] multiqc [DEBUG ] No samples found: ivar [2024-01-22 23:45:58,529] multiqc [DEBUG ] No samples found: flash [2024-01-22 23:45:58,556] multiqc [DEBUG ] No samples found: seqyclean [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-22 23:45:58,556] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-22 23:45:58,557] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-22 23:45:58,557] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-22 23:45:58,557] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-22 23:45:58,567] multiqc [INFO ] Compressing plot data [2024-01-22 23:45:58,745] multiqc [INFO ] Report : multiqc_report.html [2024-01-22 23:45:58,745] multiqc [INFO ] Data : multiqc_data [2024-01-22 23:45:58,745] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42173223/tmpis9s78c7/multiqc_data' to '/vast/gencore/GENEFLOW/work/b3/656da8398cbafdb66f564b0fd01dfa/merged/multiqc_data' [2024-01-22 23:45:59,282] multiqc [INFO ] MultiQC complete