[2023-12-13 13:57:17,005] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-13 13:57:17,005] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-13 13:57:17,007] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-13 13:57:17,009] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-12-13 13:57:17,009] 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}} [2023-12-13 13:57:17,010] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-13 13:57:17,410] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-13 13:57:17,410] multiqc [INFO ] This is MultiQC v1.9 [2023-12-13 13:57:17,410] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-13 13:57:17,410] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/03/956d433f098bda7ec1f4b635c547a3/merged [2023-12-13 13:57:17,411] multiqc [INFO ] Template : default [2023-12-13 13:57:17,411] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-13 13:57:17,411] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/03/956d433f098bda7ec1f4b635c547a3/merged [2023-12-13 13:57:17,411] 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 [2023-12-13 13:57:17,411] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40818719/tmpod5ltzgr [2023-12-13 13:57:17,549] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_01_fastqc.html [2023-12-13 13:57:17,557] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n01_NMD_01_fastqc.html [2023-12-13 13:57:17,624] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HF3T2DRX3_n02_SF_12_fastqc.html [2023-12-13 13:57:22,350] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n02_SF_12_fastqc.html [2023-12-13 13:57:22,424] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HF3T2DRX3_n02_undetermined_fastqc.html [2023-12-13 13:57:22,433] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HF3T2DRX3_n02_undetermined_fastqc.html [2023-12-13 13:57:22,520] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:22,527] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-12-13 13:57:23,884] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 13:57:23,886] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-13 13:57:23,910] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 31 samples (table) [2023-12-13 13:57:23,911] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-13 13:57:23,921] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-12-13 13:57:23,927] multiqc [DEBUG ] No samples found: conpair [2023-12-13 13:57:23,932] multiqc [DEBUG ] No samples found: peddy [2023-12-13 13:57:23,938] multiqc [DEBUG ] No samples found: somalier [2023-12-13 13:57:23,944] multiqc [DEBUG ] No samples found: methylQA [2023-12-13 13:57:23,953] multiqc [DEBUG ] No samples found: mosdepth [2023-12-13 13:57:23,958] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-13 13:57:23,962] multiqc [DEBUG ] No samples found: qualimap [2023-12-13 13:57:23,968] multiqc [DEBUG ] No samples found: preseq [2023-12-13 13:57:23,973] multiqc [DEBUG ] No samples found: quast [2023-12-13 13:57:23,978] multiqc [DEBUG ] No samples found: qorts [2023-12-13 13:57:23,984] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-13 13:57:23,989] multiqc [DEBUG ] No samples found: rockhopper [2023-12-13 13:57:23,994] multiqc [DEBUG ] No samples found: rsem [2023-12-13 13:57:24,012] multiqc [DEBUG ] No samples found: rseqc [2023-12-13 13:57:24,017] multiqc [DEBUG ] No samples found: busco [2023-12-13 13:57:24,023] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-13 13:57:24,028] multiqc [DEBUG ] No samples found: disambiguate [2023-12-13 13:57:24,033] multiqc [DEBUG ] No samples found: supernova [2023-12-13 13:57:24,053] multiqc [DEBUG ] No samples found: deeptools [2023-12-13 13:57:24,059] multiqc [DEBUG ] No samples found: sargasso [2023-12-13 13:57:24,064] multiqc [DEBUG ] No samples found: verifybamid [2023-12-13 13:57:24,070] multiqc [DEBUG ] No samples found: mirtrace [2023-12-13 13:57:24,075] multiqc [DEBUG ] No samples found: happy [2023-12-13 13:57:24,080] multiqc [DEBUG ] No samples found: mirtop [2023-12-13 13:57:24,088] multiqc [DEBUG ] No samples found: homer [2023-12-13 13:57:24,093] multiqc [DEBUG ] No samples found: macs2 [2023-12-13 13:57:24,098] multiqc [DEBUG ] No samples found: theta2 [2023-12-13 13:57:24,103] multiqc [DEBUG ] No samples found: snpeff [2023-12-13 13:57:24,112] multiqc [DEBUG ] No samples found: gatk [2023-12-13 13:57:24,118] multiqc [DEBUG ] No samples found: htseq [2023-12-13 13:57:24,124] multiqc [DEBUG ] No samples found: bcftools [2023-12-13 13:57:24,129] multiqc [DEBUG ] No samples found: featureCounts [2023-12-13 13:57:24,136] multiqc [DEBUG ] No samples found: fgbio [2023-12-13 13:57:24,156] multiqc [DEBUG ] No samples found: dragen [2023-12-13 13:57:24,161] multiqc [DEBUG ] No samples found: dedup [2023-12-13 13:57:24,167] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-13 13:57:24,198] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-13 13:57:24,203] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-13 13:57:24,206] multiqc [DEBUG ] No samples found: picard [2023-12-13 13:57:24,211] multiqc [DEBUG ] No samples found: prokka [2023-12-13 13:57:24,216] multiqc [DEBUG ] No samples found: samblaster [2023-12-13 13:57:24,233] multiqc [DEBUG ] No samples found: samtools [2023-12-13 13:57:24,238] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-13 13:57:24,245] multiqc [DEBUG ] No samples found: bamtools [2023-12-13 13:57:24,250] multiqc [DEBUG ] No samples found: jellyfish [2023-12-13 13:57:24,265] multiqc [DEBUG ] No samples found: vcftools [2023-12-13 13:57:24,271] multiqc [DEBUG ] No samples found: longranger [2023-12-13 13:57:24,276] multiqc [DEBUG ] No samples found: stacks [2023-12-13 13:57:24,282] multiqc [DEBUG ] No samples found: varscan2 [2023-12-13 13:57:24,303] multiqc [DEBUG ] No samples found: bbmap [2023-12-13 13:57:24,308] multiqc [DEBUG ] No samples found: bismark [2023-12-13 13:57:24,313] multiqc [DEBUG ] No samples found: biscuit [2023-12-13 13:57:24,319] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-13 13:57:24,325] multiqc [DEBUG ] No samples found: hicup [2023-12-13 13:57:24,330] multiqc [DEBUG ] No samples found: hicpro [2023-12-13 13:57:24,334] multiqc [DEBUG ] No samples found: salmon [2023-12-13 13:57:24,339] multiqc [DEBUG ] No samples found: kallisto [2023-12-13 13:57:24,345] multiqc [DEBUG ] No samples found: slamdunk [2023-12-13 13:57:24,350] multiqc [DEBUG ] No samples found: star [2023-12-13 13:57:24,355] multiqc [DEBUG ] No samples found: hisat2 [2023-12-13 13:57:24,360] multiqc [DEBUG ] No samples found: tophat [2023-12-13 13:57:24,365] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-13 13:57:24,370] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-13 13:57:24,375] multiqc [DEBUG ] No samples found: snpsplit [2023-12-13 13:57:24,379] multiqc [DEBUG ] No samples found: kat [2023-12-13 13:57:24,384] multiqc [DEBUG ] No samples found: leehom [2023-12-13 13:57:24,389] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-13 13:57:24,394] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-13 13:57:24,399] multiqc [DEBUG ] No samples found: cutadapt [2023-12-13 13:57:24,404] multiqc [DEBUG ] No samples found: flexbar [2023-12-13 13:57:24,409] multiqc [DEBUG ] No samples found: kaiju [2023-12-13 13:57:24,414] multiqc [DEBUG ] No samples found: kraken [2023-12-13 13:57:24,419] multiqc [DEBUG ] No samples found: malt [2023-12-13 13:57:24,424] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-13 13:57:24,429] multiqc [DEBUG ] No samples found: sickle [2023-12-13 13:57:24,434] multiqc [DEBUG ] No samples found: skewer [2023-12-13 13:57:24,439] multiqc [DEBUG ] No samples found: sortmerna [2023-12-13 13:57:24,443] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-13 13:57:24,448] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-13 13:57:24,453] multiqc [DEBUG ] No samples found: afterqc [2023-12-13 13:57:24,459] multiqc [DEBUG ] No samples found: fastp [2023-12-13 13:57:26,786] multiqc.modules.fastqc.fastqc [INFO ] Found 62 reports [2023-12-13 13:57:27,632] multiqc [DEBUG ] No samples found: pycoqc [2023-12-13 13:57:27,639] multiqc [DEBUG ] No samples found: minionqc [2023-12-13 13:57:27,645] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-13 13:57:27,651] multiqc [DEBUG ] No samples found: clusterflow [2023-12-13 13:57:27,660] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-13 13:57:27,665] multiqc [DEBUG ] No samples found: interop [2023-12-13 13:57:27,670] multiqc [DEBUG ] No samples found: ivar [2023-12-13 13:57:27,676] multiqc [DEBUG ] No samples found: flash [2023-12-13 13:57:27,681] multiqc [DEBUG ] No samples found: seqyclean [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,681] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-13 13:57:27,682] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-13 13:57:27,755] multiqc [INFO ] Compressing plot data [2023-12-13 13:57:28,993] multiqc [INFO ] Report : multiqc_report.html [2023-12-13 13:57:28,993] multiqc [INFO ] Data : multiqc_data [2023-12-13 13:57:28,993] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40818719/tmpod5ltzgr/multiqc_data' to '/vast/gencore/GENEFLOW/work/03/956d433f098bda7ec1f4b635c547a3/merged/multiqc_data' [2023-12-13 13:57:29,226] multiqc [INFO ] MultiQC complete