[2023-10-13 15:58:46,830] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-10-13 15:58:46,830] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-10-13 15:58:46,831] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-10-13 15:58:46,833] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-10-13 15:58:46,833] 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}} [2023-10-13 15:58:46,833] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-13 15:58:47,010] multiqc [WARNING] MultiQC Version v1.16 now available! [2023-10-13 15:58:47,010] multiqc [INFO ] This is MultiQC v1.9 [2023-10-13 15:58:47,010] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-10-13 15:58:47,010] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/b2/9e6f471691d43a1b8c1e48bd8435f7/merged [2023-10-13 15:58:47,010] multiqc [INFO ] Template : default [2023-10-13 15:58:47,010] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-10-13 15:58:47,010] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/b2/9e6f471691d43a1b8c1e48bd8435f7/merged [2023-10-13 15:58:47,011] 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 [2023-10-13 15:58:47,011] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-38856325/tmp5omoncvy [2023-10-13 15:58:47,140] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n01_2331_fastqc.html [2023-10-13 15:58:47,148] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n01_2331_fastqc.html [2023-10-13 15:58:47,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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filesize limit: HJMF7AFX5_n02_DGY_3220_fastqc.html [2023-10-13 15:58:51,490] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_3220_fastqc.html [2023-10-13 15:58:51,559] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_3221_fastqc.html [2023-10-13 15:58:51,566] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_3221_fastqc.html [2023-10-13 15:58:51,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_3222_fastqc.html [2023-10-13 15:58:51,644] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_DGY_3222_fastqc.html [2023-10-13 15:58:51,721] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HJMF7AFX5_n02_undetermined_fastqc.html [2023-10-13 15:58:51,729] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HJMF7AFX5_n02_undetermined_fastqc.html [2023-10-13 15:58:51,794] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,802] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,802] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,802] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,802] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,802] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,803] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:51,844] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2023-10-13 15:58:53,971] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-13 15:58:53,973] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-10-13 15:58:53,997] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 29 samples (table) [2023-10-13 15:58:53,999] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-10-13 15:58:54,008] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2023-10-13 15:58:54,014] multiqc [DEBUG ] No samples found: conpair [2023-10-13 15:58:54,020] multiqc [DEBUG ] No samples found: peddy [2023-10-13 15:58:54,029] multiqc [DEBUG ] No samples found: somalier [2023-10-13 15:58:54,034] multiqc [DEBUG ] No samples found: methylQA [2023-10-13 15:58:54,044] multiqc [DEBUG ] No samples found: mosdepth [2023-10-13 15:58:54,049] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-10-13 15:58:54,053] multiqc [DEBUG ] No samples found: qualimap [2023-10-13 15:58:54,058] multiqc [DEBUG ] No samples found: preseq [2023-10-13 15:58:54,064] multiqc [DEBUG ] No samples found: quast [2023-10-13 15:58:54,069] multiqc [DEBUG ] No samples found: qorts [2023-10-13 15:58:54,075] multiqc [DEBUG ] No samples found: rna_seqc [2023-10-13 15:58:54,080] multiqc [DEBUG ] No samples found: rockhopper [2023-10-13 15:58:54,085] multiqc [DEBUG ] No samples found: rsem [2023-10-13 15:58:54,099] multiqc [DEBUG ] No samples found: rseqc [2023-10-13 15:58:54,104] multiqc [DEBUG ] No samples found: busco [2023-10-13 15:58:54,110] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-10-13 15:58:54,115] multiqc [DEBUG ] No samples found: disambiguate [2023-10-13 15:58:54,121] multiqc [DEBUG ] No samples found: supernova [2023-10-13 15:58:54,138] multiqc [DEBUG ] No samples found: deeptools [2023-10-13 15:58:54,143] multiqc [DEBUG ] No samples found: sargasso [2023-10-13 15:58:54,149] multiqc [DEBUG ] No samples found: verifybamid [2023-10-13 15:58:54,154] multiqc [DEBUG ] No samples found: mirtrace [2023-10-13 15:58:54,160] multiqc [DEBUG ] No samples found: happy [2023-10-13 15:58:54,165] multiqc [DEBUG ] No samples found: mirtop [2023-10-13 15:58:54,173] multiqc [DEBUG ] No samples found: homer [2023-10-13 15:58:54,178] multiqc [DEBUG ] No samples found: macs2 [2023-10-13 15:58:54,183] multiqc [DEBUG ] No samples found: theta2 [2023-10-13 15:58:54,188] multiqc [DEBUG ] No samples found: snpeff [2023-10-13 15:58:54,197] multiqc [DEBUG ] No samples found: gatk [2023-10-13 15:58:54,202] multiqc [DEBUG ] No samples found: htseq [2023-10-13 15:58:54,208] multiqc [DEBUG ] No samples found: bcftools [2023-10-13 15:58:54,214] multiqc [DEBUG ] No samples found: featureCounts [2023-10-13 15:58:54,221] multiqc [DEBUG ] No samples found: fgbio [2023-10-13 15:58:54,239] multiqc [DEBUG ] No samples found: dragen [2023-10-13 15:58:54,244] multiqc [DEBUG ] No samples found: dedup [2023-10-13 15:58:54,250] multiqc [DEBUG ] No samples found: damageprofiler [2023-10-13 15:58:54,277] multiqc [DEBUG ] No samples found: biobambam2 [2023-10-13 15:58:54,282] multiqc [DEBUG ] No samples found: mtnucratio [2023-10-13 15:58:54,284] multiqc [DEBUG ] No samples found: picard [2023-10-13 15:58:54,289] multiqc [DEBUG ] No samples found: prokka [2023-10-13 15:58:54,294] multiqc [DEBUG ] No samples found: samblaster [2023-10-13 15:58:54,307] multiqc [DEBUG ] No samples found: samtools [2023-10-13 15:58:54,313] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-10-13 15:58:54,318] multiqc [DEBUG ] No samples found: bamtools [2023-10-13 15:58:54,323] multiqc [DEBUG ] No samples found: jellyfish [2023-10-13 15:58:54,335] multiqc [DEBUG ] No samples found: vcftools [2023-10-13 15:58:54,340] multiqc [DEBUG ] No samples found: longranger [2023-10-13 15:58:54,346] multiqc [DEBUG ] No samples found: stacks [2023-10-13 15:58:54,351] multiqc [DEBUG ] No samples found: varscan2 [2023-10-13 15:58:54,406] multiqc [DEBUG ] No samples found: bbmap [2023-10-13 15:58:54,412] multiqc [DEBUG ] No samples found: bismark [2023-10-13 15:58:54,418] multiqc [DEBUG ] No samples found: biscuit [2023-10-13 15:58:54,426] multiqc [DEBUG ] No samples found: hicexplorer [2023-10-13 15:58:54,443] multiqc [DEBUG ] No samples found: hicup [2023-10-13 15:58:54,458] multiqc [DEBUG ] No samples found: hicpro [2023-10-13 15:58:54,471] multiqc [DEBUG ] No samples found: salmon [2023-10-13 15:58:54,478] multiqc [DEBUG ] No samples found: kallisto [2023-10-13 15:58:54,486] multiqc [DEBUG ] No samples found: slamdunk [2023-10-13 15:58:54,491] multiqc [DEBUG ] No samples found: star [2023-10-13 15:58:54,496] multiqc [DEBUG ] No samples found: hisat2 [2023-10-13 15:58:54,502] multiqc [DEBUG ] No samples found: tophat [2023-10-13 15:58:54,507] multiqc [DEBUG ] No samples found: bowtie2 [2023-10-13 15:58:54,512] multiqc [DEBUG ] No samples found: bowtie1 [2023-10-13 15:58:54,517] multiqc [DEBUG ] No samples found: snpsplit [2023-10-13 15:58:54,522] multiqc [DEBUG ] No samples found: kat [2023-10-13 15:58:54,527] multiqc [DEBUG ] No samples found: leehom [2023-10-13 15:58:54,532] multiqc [DEBUG ] No samples found: adapterRemoval [2023-10-13 15:58:54,537] multiqc [DEBUG ] No samples found: clipandmerge [2023-10-13 15:58:54,542] multiqc [DEBUG ] No samples found: cutadapt [2023-10-13 15:58:54,547] multiqc [DEBUG ] No samples found: flexbar [2023-10-13 15:58:54,552] multiqc [DEBUG ] No samples found: kaiju [2023-10-13 15:58:54,558] multiqc [DEBUG ] No samples found: kraken [2023-10-13 15:58:54,563] multiqc [DEBUG ] No samples found: malt [2023-10-13 15:58:54,568] multiqc [DEBUG ] No samples found: trimmomatic [2023-10-13 15:58:54,573] multiqc [DEBUG ] No samples found: sickle [2023-10-13 15:58:54,579] multiqc [DEBUG ] No samples found: skewer [2023-10-13 15:58:54,583] multiqc [DEBUG ] No samples found: sortmerna [2023-10-13 15:58:54,588] multiqc [DEBUG ] No samples found: biobloomtools [2023-10-13 15:58:54,594] multiqc [DEBUG ] No samples found: fastq_screen [2023-10-13 15:58:54,599] multiqc [DEBUG ] No samples found: afterqc [2023-10-13 15:58:54,604] multiqc [DEBUG ] No samples found: fastp [2023-10-13 15:58:55,992] multiqc.modules.fastqc.fastqc [INFO ] Found 58 reports [2023-10-13 15:58:56,459] multiqc [DEBUG ] No samples found: pycoqc [2023-10-13 15:58:56,464] multiqc [DEBUG ] No samples found: minionqc [2023-10-13 15:58:56,469] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-10-13 15:58:56,475] multiqc [DEBUG ] No samples found: clusterflow [2023-10-13 15:58:56,480] multiqc [DEBUG ] No samples found: bcl2fastq [2023-10-13 15:58:56,486] multiqc [DEBUG ] No samples found: interop [2023-10-13 15:58:56,491] multiqc [DEBUG ] No samples found: ivar [2023-10-13 15:58:56,496] multiqc [DEBUG ] No samples found: flash [2023-10-13 15:58:56,501] multiqc [DEBUG ] No samples found: seqyclean [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,501] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-10-13 15:58:56,502] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-10-13 15:58:56,570] multiqc [INFO ] Compressing plot data [2023-10-13 15:58:57,495] multiqc [INFO ] Report : multiqc_report.html [2023-10-13 15:58:57,495] multiqc [INFO ] Data : multiqc_data [2023-10-13 15:58:57,495] multiqc [DEBUG ] Moving data file from '/state/partition1/job-38856325/tmp5omoncvy/multiqc_data' to '/vast/gencore/GENEFLOW/work/b2/9e6f471691d43a1b8c1e48bd8435f7/merged/multiqc_data' [2023-10-13 15:58:57,730] multiqc [INFO ] MultiQC complete