[2024-04-04 18:12:58,532] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-04-04 18:12:58,532] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-04-04 18:12:58,532] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-04-04 18:12:58,535] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-04-04 18:12:58,535] 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}} [2024-04-04 18:12:58,535] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-04 18:12:58,567] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-04-04 18:12:58,567] multiqc [INFO ] This is MultiQC v1.9 [2024-04-04 18:12:58,567] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-04 18:12:58,567] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/2b/db62a996e1737a065ea2c39c14751b/merged [2024-04-04 18:12:58,567] multiqc [INFO ] Template : default [2024-04-04 18:12:58,567] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-04-04 18:12:58,567] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/2b/db62a996e1737a065ea2c39c14751b/merged [2024-04-04 18:12:58,567] 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 [2024-04-04 18:12:58,567] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45033452/tmpz0bjxbmb [2024-04-04 18:12:58,701] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H25J7AFX7_n01_11281_ChIP_fastqc.html [2024-04-04 18:12:58,709] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H25J7AFX7_n01_11281_ChIP_fastqc.html [2024-04-04 18:12:58,779] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H25J7AFX7_n02_7797_Spikein_ChIP_fastqc.html [2024-04-04 18:13:01,095] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H25J7AFX7_n02_7797_Spikein_ChIP_fastqc.html [2024-04-04 18:13:01,172] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H25J7AFX7_n02_7797_Spikein_Input_fastqc.html [2024-04-04 18:13:01,181] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H25J7AFX7_n02_7797_Spikein_Input_fastqc.html [2024-04-04 18:13:01,251] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H25J7AFX7_n02_undetermined_fastqc.html [2024-04-04 18:13:01,258] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H25J7AFX7_n02_undetermined_fastqc.html [2024-04-04 18:13:01,326] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-04 18:13:01,331] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-04-04 18:13:01,925] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-04 18:13:01,927] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-04 18:13:01,945] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2024-04-04 18:13:01,946] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-04-04 18:13:01,956] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-04-04 18:13:01,963] multiqc [DEBUG ] No samples found: conpair [2024-04-04 18:13:01,970] multiqc [DEBUG ] No samples found: peddy [2024-04-04 18:13:01,976] multiqc [DEBUG ] No samples found: somalier [2024-04-04 18:13:01,983] multiqc [DEBUG ] No samples found: methylQA [2024-04-04 18:13:01,995] multiqc [DEBUG ] No samples found: mosdepth [2024-04-04 18:13:02,001] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-04-04 18:13:02,005] multiqc [DEBUG ] No samples found: qualimap [2024-04-04 18:13:02,011] multiqc [DEBUG ] No samples found: preseq [2024-04-04 18:13:02,018] multiqc [DEBUG ] No samples found: quast [2024-04-04 18:13:02,025] multiqc [DEBUG ] No samples found: qorts [2024-04-04 18:13:02,031] multiqc [DEBUG ] No samples found: rna_seqc [2024-04-04 18:13:02,037] multiqc [DEBUG ] No samples found: rockhopper [2024-04-04 18:13:02,043] multiqc [DEBUG ] No samples found: rsem [2024-04-04 18:13:02,059] multiqc [DEBUG ] No samples found: rseqc [2024-04-04 18:13:02,064] multiqc [DEBUG ] No samples found: busco [2024-04-04 18:13:02,072] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-04-04 18:13:02,079] multiqc [DEBUG ] No samples found: disambiguate [2024-04-04 18:13:02,086] multiqc [DEBUG ] No samples found: supernova [2024-04-04 18:13:02,105] multiqc [DEBUG ] No samples found: deeptools [2024-04-04 18:13:02,112] multiqc [DEBUG ] No samples found: sargasso [2024-04-04 18:13:02,118] multiqc [DEBUG ] No samples found: verifybamid [2024-04-04 18:13:02,125] multiqc [DEBUG ] No samples found: mirtrace [2024-04-04 18:13:02,131] multiqc [DEBUG ] No samples found: happy [2024-04-04 18:13:02,137] multiqc [DEBUG ] No samples found: mirtop [2024-04-04 18:13:02,145] multiqc [DEBUG ] No samples found: homer [2024-04-04 18:13:02,152] multiqc [DEBUG ] No samples found: macs2 [2024-04-04 18:13:02,158] multiqc [DEBUG ] No samples found: theta2 [2024-04-04 18:13:02,164] multiqc [DEBUG ] No samples found: snpeff [2024-04-04 18:13:02,174] multiqc [DEBUG ] No samples found: gatk [2024-04-04 18:13:02,179] multiqc [DEBUG ] No samples found: htseq [2024-04-04 18:13:02,187] multiqc [DEBUG ] No samples found: bcftools [2024-04-04 18:13:02,194] multiqc [DEBUG ] No samples found: featureCounts [2024-04-04 18:13:02,203] multiqc [DEBUG ] No samples found: fgbio [2024-04-04 18:13:02,220] multiqc [DEBUG ] No samples found: dragen [2024-04-04 18:13:02,226] multiqc [DEBUG ] No samples found: dedup [2024-04-04 18:13:02,235] multiqc [DEBUG ] No samples found: damageprofiler [2024-04-04 18:13:02,275] multiqc [DEBUG ] No samples found: biobambam2 [2024-04-04 18:13:02,285] multiqc [DEBUG ] No samples found: mtnucratio [2024-04-04 18:13:02,287] multiqc [DEBUG ] No samples found: picard [2024-04-04 18:13:02,295] multiqc [DEBUG ] No samples found: prokka [2024-04-04 18:13:02,301] multiqc [DEBUG ] No samples found: samblaster [2024-04-04 18:13:02,313] multiqc [DEBUG ] No samples found: samtools [2024-04-04 18:13:02,319] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-04-04 18:13:02,327] multiqc [DEBUG ] No samples found: bamtools [2024-04-04 18:13:02,333] multiqc [DEBUG ] No samples found: jellyfish [2024-04-04 18:13:02,344] multiqc [DEBUG ] No samples found: vcftools [2024-04-04 18:13:02,351] multiqc [DEBUG ] No samples found: longranger [2024-04-04 18:13:02,358] multiqc [DEBUG ] No samples found: stacks [2024-04-04 18:13:02,365] multiqc [DEBUG ] No samples found: varscan2 [2024-04-04 18:13:02,387] multiqc [DEBUG ] No samples found: bbmap [2024-04-04 18:13:02,394] multiqc [DEBUG ] No samples found: bismark [2024-04-04 18:13:02,401] multiqc [DEBUG ] No samples found: biscuit [2024-04-04 18:13:02,407] multiqc [DEBUG ] No samples found: hicexplorer [2024-04-04 18:13:02,413] multiqc [DEBUG ] No samples found: hicup [2024-04-04 18:13:02,420] multiqc [DEBUG ] No samples found: hicpro [2024-04-04 18:13:02,425] multiqc [DEBUG ] No samples found: salmon [2024-04-04 18:13:02,432] multiqc [DEBUG ] No samples found: kallisto [2024-04-04 18:13:02,438] multiqc [DEBUG ] No samples found: slamdunk [2024-04-04 18:13:02,444] multiqc [DEBUG ] No samples found: star [2024-04-04 18:13:02,450] multiqc [DEBUG ] No samples found: hisat2 [2024-04-04 18:13:02,456] multiqc [DEBUG ] No samples found: tophat [2024-04-04 18:13:02,461] multiqc [DEBUG ] No samples found: bowtie2 [2024-04-04 18:13:02,468] multiqc [DEBUG ] No samples found: bowtie1 [2024-04-04 18:13:02,473] multiqc [DEBUG ] No samples found: snpsplit [2024-04-04 18:13:02,479] multiqc [DEBUG ] No samples found: kat [2024-04-04 18:13:02,484] multiqc [DEBUG ] No samples found: leehom [2024-04-04 18:13:02,491] multiqc [DEBUG ] No samples found: adapterRemoval [2024-04-04 18:13:02,496] multiqc [DEBUG ] No samples found: clipandmerge [2024-04-04 18:13:02,502] multiqc [DEBUG ] No samples found: cutadapt [2024-04-04 18:13:02,508] multiqc [DEBUG ] No samples found: flexbar [2024-04-04 18:13:02,514] multiqc [DEBUG ] No samples found: kaiju [2024-04-04 18:13:02,520] multiqc [DEBUG ] No samples found: kraken [2024-04-04 18:13:02,526] multiqc [DEBUG ] No samples found: malt [2024-04-04 18:13:02,531] multiqc [DEBUG ] No samples found: trimmomatic [2024-04-04 18:13:02,537] multiqc [DEBUG ] No samples found: sickle [2024-04-04 18:13:02,543] multiqc [DEBUG ] No samples found: skewer [2024-04-04 18:13:02,548] multiqc [DEBUG ] No samples found: sortmerna [2024-04-04 18:13:02,554] multiqc [DEBUG ] No samples found: biobloomtools [2024-04-04 18:13:02,560] multiqc [DEBUG ] No samples found: fastq_screen [2024-04-04 18:13:02,566] multiqc [DEBUG ] No samples found: afterqc [2024-04-04 18:13:02,572] multiqc [DEBUG ] No samples found: fastp [2024-04-04 18:13:03,398] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2024-04-04 18:13:03,708] multiqc [DEBUG ] No samples found: pycoqc [2024-04-04 18:13:03,714] multiqc [DEBUG ] No samples found: minionqc [2024-04-04 18:13:03,720] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-04-04 18:13:03,726] multiqc [DEBUG ] No samples found: clusterflow [2024-04-04 18:13:03,732] multiqc [DEBUG ] No samples found: bcl2fastq [2024-04-04 18:13:03,739] multiqc [DEBUG ] No samples found: interop [2024-04-04 18:13:03,745] multiqc [DEBUG ] No samples found: ivar [2024-04-04 18:13:03,751] multiqc [DEBUG ] No samples found: flash [2024-04-04 18:13:03,757] multiqc [DEBUG ] No samples found: seqyclean [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,757] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-04-04 18:13:03,758] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-04-04 18:13:03,799] multiqc [INFO ] Compressing plot data [2024-04-04 18:13:04,394] multiqc [INFO ] Report : multiqc_report.html [2024-04-04 18:13:04,394] multiqc [INFO ] Data : multiqc_data [2024-04-04 18:13:04,395] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45033452/tmpz0bjxbmb/multiqc_data' to '/vast/gencore/GENEFLOW/work/2b/db62a996e1737a065ea2c39c14751b/merged/multiqc_data' [2024-04-04 18:13:04,589] multiqc [INFO ] MultiQC complete