[2024-02-10 07:29:44,936] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-10 07:29:44,937] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-10 07:29:44,939] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-10 07:29:44,942] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-10 07:29:44,942] 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}} [2024-02-10 07:29:44,942] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-10 07:29:45,138] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-02-10 07:29:45,138] multiqc [INFO ] This is MultiQC v1.9 [2024-02-10 07:29:45,138] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-10 07:29:45,138] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/7f/4f68a8a3cef28ab254dc48f0375737/1 [2024-02-10 07:29:45,138] multiqc [INFO ] Template : default [2024-02-10 07:29:45,139] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-10 07:29:45,139] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/7f/4f68a8a3cef28ab254dc48f0375737/1 [2024-02-10 07:29:45,139] 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 [2024-02-10 07:29:45,139] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42776625/tmpixbglsp3 [2024-02-10 07:29:45,276] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P01_fastqc.html [2024-02-10 07:29:45,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P01_fastqc.html [2024-02-10 07:29:45,359] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P02_fastqc.html [2024-02-10 07:29:45,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P02_fastqc.html [2024-02-10 07:29:45,437] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P03_fastqc.html [2024-02-10 07:29:45,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P03_fastqc.html [2024-02-10 07:29:45,516] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P04_fastqc.html [2024-02-10 07:29:45,523] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_Inoc_P04_fastqc.html [2024-02-10 07:29:45,593] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded 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hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_undetermined_fastqc.html [2024-02-10 07:29:45,842] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n01_undetermined_fastqc.html [2024-02-10 07:29:45,912] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P01_fastqc.html [2024-02-10 07:29:45,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P01_fastqc.html [2024-02-10 07:29:46,030] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P02_fastqc.html [2024-02-10 07:29:46,042] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P02_fastqc.html [2024-02-10 07:29:46,130] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P03_fastqc.html [2024-02-10 07:29:46,140] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P03_fastqc.html [2024-02-10 07:29:46,218] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P04_fastqc.html [2024-02-10 07:29:46,226] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P04_fastqc.html [2024-02-10 07:29:46,302] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P05_fastqc.html [2024-02-10 07:29:46,309] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_P05_fastqc.html [2024-02-10 07:29:46,385] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_X_fastqc.html [2024-02-10 07:29:46,392] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_X_fastqc.html [2024-02-10 07:29:46,468] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_Y_fastqc.html [2024-02-10 07:29:46,475] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_Inoc_Y_fastqc.html [2024-02-10 07:29:46,550] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_undetermined_fastqc.html [2024-02-10 07:29:46,557] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LFKD5_l01_n02_undetermined_fastqc.html [2024-02-10 07:29:46,622] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,629] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:46,690] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-10 07:29:49,927] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-10 07:29:49,931] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-10 07:29:49,946] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2024-02-10 07:29:49,947] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-10 07:29:49,957] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-10 07:29:49,964] multiqc [DEBUG ] No samples found: conpair [2024-02-10 07:29:49,971] multiqc [DEBUG ] No samples found: peddy [2024-02-10 07:29:49,978] multiqc [DEBUG ] No samples found: somalier [2024-02-10 07:29:49,984] multiqc [DEBUG ] No samples found: methylQA [2024-02-10 07:29:49,996] multiqc [DEBUG ] No samples found: mosdepth [2024-02-10 07:29:50,002] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-10 07:29:50,006] multiqc [DEBUG ] No samples found: qualimap [2024-02-10 07:29:50,013] multiqc [DEBUG ] No samples found: preseq [2024-02-10 07:29:50,020] multiqc [DEBUG ] No samples found: quast [2024-02-10 07:29:50,026] multiqc [DEBUG ] No samples found: qorts [2024-02-10 07:29:50,032] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-10 07:29:50,038] multiqc [DEBUG ] No samples found: rockhopper [2024-02-10 07:29:50,044] multiqc [DEBUG ] No samples found: rsem [2024-02-10 07:29:50,061] multiqc [DEBUG ] No samples found: rseqc [2024-02-10 07:29:50,068] multiqc [DEBUG ] No samples found: busco [2024-02-10 07:29:50,074] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-10 07:29:50,080] multiqc [DEBUG ] No samples found: disambiguate [2024-02-10 07:29:50,087] multiqc [DEBUG ] No samples found: supernova [2024-02-10 07:29:50,107] multiqc [DEBUG ] No samples found: deeptools [2024-02-10 07:29:50,114] multiqc [DEBUG ] No samples found: sargasso [2024-02-10 07:29:50,121] multiqc [DEBUG ] No samples found: verifybamid [2024-02-10 07:29:50,128] multiqc [DEBUG ] No samples found: mirtrace [2024-02-10 07:29:50,135] multiqc [DEBUG ] No samples found: happy [2024-02-10 07:29:50,145] multiqc [DEBUG ] No samples found: mirtop [2024-02-10 07:29:50,155] multiqc [DEBUG ] No samples found: homer [2024-02-10 07:29:50,162] multiqc [DEBUG ] No samples found: macs2 [2024-02-10 07:29:50,169] multiqc [DEBUG ] No samples found: theta2 [2024-02-10 07:29:50,175] multiqc [DEBUG ] No samples found: snpeff [2024-02-10 07:29:50,191] multiqc [DEBUG ] No samples found: gatk [2024-02-10 07:29:50,197] multiqc [DEBUG ] No samples found: htseq [2024-02-10 07:29:50,204] multiqc [DEBUG ] No samples found: bcftools [2024-02-10 07:29:50,211] multiqc [DEBUG ] No samples found: featureCounts [2024-02-10 07:29:50,222] multiqc [DEBUG ] No samples found: fgbio [2024-02-10 07:29:50,241] multiqc [DEBUG ] No samples found: dragen [2024-02-10 07:29:50,247] multiqc [DEBUG ] No samples found: dedup [2024-02-10 07:29:50,254] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-10 07:29:50,286] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-10 07:29:50,292] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-10 07:29:50,294] multiqc [DEBUG ] No samples found: picard [2024-02-10 07:29:50,300] multiqc [DEBUG ] No samples found: prokka [2024-02-10 07:29:50,306] multiqc [DEBUG ] No samples found: samblaster [2024-02-10 07:29:50,317] multiqc [DEBUG ] No samples found: samtools [2024-02-10 07:29:50,323] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-10 07:29:50,329] multiqc [DEBUG ] No samples found: bamtools [2024-02-10 07:29:50,335] multiqc [DEBUG ] No samples found: jellyfish [2024-02-10 07:29:50,345] multiqc [DEBUG ] No samples found: vcftools [2024-02-10 07:29:50,351] multiqc [DEBUG ] No samples found: longranger [2024-02-10 07:29:50,357] multiqc [DEBUG ] No samples found: stacks [2024-02-10 07:29:50,363] multiqc [DEBUG ] No samples found: varscan2 [2024-02-10 07:29:50,382] multiqc [DEBUG ] No samples found: bbmap [2024-02-10 07:29:50,388] multiqc [DEBUG ] No samples found: bismark [2024-02-10 07:29:50,395] multiqc [DEBUG ] No samples found: biscuit [2024-02-10 07:29:50,401] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-10 07:29:50,408] multiqc [DEBUG ] No samples found: hicup [2024-02-10 07:29:50,414] multiqc [DEBUG ] No samples found: hicpro [2024-02-10 07:29:50,420] multiqc [DEBUG ] No samples found: salmon [2024-02-10 07:29:50,426] multiqc [DEBUG ] No samples found: kallisto [2024-02-10 07:29:50,432] multiqc [DEBUG ] No samples found: slamdunk [2024-02-10 07:29:50,439] multiqc [DEBUG ] No samples found: star [2024-02-10 07:29:50,444] multiqc [DEBUG ] No samples found: hisat2 [2024-02-10 07:29:50,453] multiqc [DEBUG ] No samples found: tophat [2024-02-10 07:29:50,461] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-10 07:29:50,468] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-10 07:29:50,474] multiqc [DEBUG ] No samples found: snpsplit [2024-02-10 07:29:50,484] multiqc [DEBUG ] No samples found: kat [2024-02-10 07:29:50,493] multiqc [DEBUG ] No samples found: leehom [2024-02-10 07:29:50,504] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-10 07:29:50,514] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-10 07:29:50,523] multiqc [DEBUG ] No samples found: cutadapt [2024-02-10 07:29:50,535] multiqc [DEBUG ] No samples found: flexbar [2024-02-10 07:29:50,546] multiqc [DEBUG ] No samples found: kaiju [2024-02-10 07:29:50,553] multiqc [DEBUG ] No samples found: kraken [2024-02-10 07:29:50,560] multiqc [DEBUG ] No samples found: malt [2024-02-10 07:29:50,567] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-10 07:29:50,574] multiqc [DEBUG ] No samples found: sickle [2024-02-10 07:29:50,580] multiqc [DEBUG ] No samples found: skewer [2024-02-10 07:29:50,590] multiqc [DEBUG ] No samples found: sortmerna [2024-02-10 07:29:50,595] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-10 07:29:50,601] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-10 07:29:50,613] multiqc [DEBUG ] No samples found: afterqc [2024-02-10 07:29:50,628] multiqc [DEBUG ] No samples found: fastp [2024-02-10 07:29:50,788] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2024-02-10 07:29:51,136] multiqc [DEBUG ] No samples found: pycoqc [2024-02-10 07:29:51,142] multiqc [DEBUG ] No samples found: minionqc [2024-02-10 07:29:51,148] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-10 07:29:51,155] multiqc [DEBUG ] No samples found: clusterflow [2024-02-10 07:29:51,161] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-10 07:29:51,168] multiqc [DEBUG ] No samples found: interop [2024-02-10 07:29:51,174] multiqc [DEBUG ] No samples found: ivar [2024-02-10 07:29:51,181] multiqc [DEBUG ] No samples found: flash [2024-02-10 07:29:51,187] multiqc [DEBUG ] No samples found: seqyclean [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-10 07:29:51,187] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-10 07:29:51,188] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-10 07:29:51,188] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-10 07:29:51,208] multiqc [INFO ] Compressing plot data [2024-02-10 07:29:51,457] multiqc [INFO ] Report : multiqc_report.html [2024-02-10 07:29:51,457] multiqc [INFO ] Data : multiqc_data [2024-02-10 07:29:51,457] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42776625/tmpixbglsp3/multiqc_data' to '/vast/gencore/GENEFLOW/work/7f/4f68a8a3cef28ab254dc48f0375737/1/multiqc_data' [2024-02-10 07:29:51,653] multiqc [INFO ] MultiQC complete