[2024-06-13 05:45:58,440] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-13 05:45:58,440] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-13 05:45:58,440] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-13 05:45:58,443] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-13 05:45:58,443] 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}} [2024-06-13 05:45:58,443] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-13 05:45:58,478] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-13 05:45:58,478] multiqc [INFO ] This is MultiQC v1.9 [2024-06-13 05:45:58,478] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-13 05:45:58,478] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e8/a3bc85f40e2f73e619bc0a60243b12/merged [2024-06-13 05:45:58,478] multiqc [INFO ] Template : default [2024-06-13 05:45:58,478] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-13 05:45:58,478] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e8/a3bc85f40e2f73e619bc0a60243b12/merged [2024-06-13 05:45:58,479] 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 [2024-06-13 05:45:58,479] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47495860/tmplc8r9pis [2024-06-13 05:45:58,609] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_11_fastqc.html [2024-06-13 05:45:58,617] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_11_fastqc.html [2024-06-13 05:45:58,694] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_12_fastqc.html [2024-06-13 05:45:58,701] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_12_fastqc.html [2024-06-13 05:45:58,770] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_13_fastqc.html [2024-06-13 05:45:58,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_13_fastqc.html [2024-06-13 05:45:58,854] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_14_fastqc.html [2024-06-13 05:45:58,862] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n01_BS_5P_14_fastqc.html [2024-06-13 05:45:58,939] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n01_undetermined_fastqc.html [2024-06-13 05:45:58,946] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n01_undetermined_fastqc.html [2024-06-13 05:45:59,019] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_11_fastqc.html [2024-06-13 05:45:59,025] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_11_fastqc.html [2024-06-13 05:45:59,098] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_12_fastqc.html [2024-06-13 05:45:59,106] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_12_fastqc.html [2024-06-13 05:45:59,171] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_13_fastqc.html [2024-06-13 05:45:59,179] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_13_fastqc.html [2024-06-13 05:45:59,246] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_14_fastqc.html [2024-06-13 05:45:59,254] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n02_BS_5P_14_fastqc.html [2024-06-13 05:45:59,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H35YGAFX7_n02_undetermined_fastqc.html [2024-06-13 05:45:59,328] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H35YGAFX7_n02_undetermined_fastqc.html [2024-06-13 05:45:59,396] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 05:45:59,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-13 05:45:59,922] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-13 05:45:59,924] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-13 05:45:59,934] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2024-06-13 05:45:59,935] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-13 05:45:59,945] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-13 05:45:59,950] multiqc [DEBUG ] No samples found: conpair [2024-06-13 05:45:59,956] multiqc [DEBUG ] No samples found: peddy [2024-06-13 05:45:59,964] multiqc [DEBUG ] No samples found: somalier [2024-06-13 05:45:59,969] multiqc [DEBUG ] No samples found: methylQA [2024-06-13 05:45:59,979] multiqc [DEBUG ] No samples found: mosdepth [2024-06-13 05:45:59,984] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-13 05:45:59,987] multiqc [DEBUG ] No samples found: qualimap [2024-06-13 05:45:59,992] multiqc [DEBUG ] No samples found: preseq [2024-06-13 05:45:59,997] multiqc [DEBUG ] No samples found: quast [2024-06-13 05:46:00,002] multiqc [DEBUG ] No samples found: qorts [2024-06-13 05:46:00,006] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-13 05:46:00,011] multiqc [DEBUG ] No samples found: rockhopper [2024-06-13 05:46:00,016] multiqc [DEBUG ] No samples found: rsem [2024-06-13 05:46:00,028] multiqc [DEBUG ] No samples found: rseqc [2024-06-13 05:46:00,032] multiqc [DEBUG ] No samples found: busco [2024-06-13 05:46:00,037] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-13 05:46:00,041] multiqc [DEBUG ] No samples found: disambiguate [2024-06-13 05:46:00,046] multiqc [DEBUG ] No samples found: supernova [2024-06-13 05:46:00,060] multiqc [DEBUG ] No samples found: deeptools [2024-06-13 05:46:00,065] multiqc [DEBUG ] No samples found: sargasso [2024-06-13 05:46:00,069] multiqc [DEBUG ] No samples found: verifybamid [2024-06-13 05:46:00,074] multiqc [DEBUG ] No samples found: mirtrace [2024-06-13 05:46:00,079] multiqc [DEBUG ] No samples found: happy [2024-06-13 05:46:00,083] multiqc [DEBUG ] No samples found: mirtop [2024-06-13 05:46:00,090] multiqc [DEBUG ] No samples found: homer [2024-06-13 05:46:00,097] multiqc [DEBUG ] No samples found: macs2 [2024-06-13 05:46:00,105] multiqc [DEBUG ] No samples found: theta2 [2024-06-13 05:46:00,109] multiqc [DEBUG ] No samples found: snpeff [2024-06-13 05:46:00,117] multiqc [DEBUG ] No samples found: gatk [2024-06-13 05:46:00,121] multiqc [DEBUG ] No samples found: htseq [2024-06-13 05:46:00,127] multiqc [DEBUG ] No samples found: bcftools [2024-06-13 05:46:00,132] multiqc [DEBUG ] No samples found: featureCounts [2024-06-13 05:46:00,139] multiqc [DEBUG ] No samples found: fgbio [2024-06-13 05:46:00,153] multiqc [DEBUG ] No samples found: dragen [2024-06-13 05:46:00,157] multiqc [DEBUG ] No samples found: dedup [2024-06-13 05:46:00,162] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-13 05:46:00,185] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-13 05:46:00,190] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-13 05:46:00,192] multiqc [DEBUG ] No samples found: picard [2024-06-13 05:46:00,197] multiqc [DEBUG ] No samples found: prokka [2024-06-13 05:46:00,201] multiqc [DEBUG ] No samples found: samblaster [2024-06-13 05:46:00,211] multiqc [DEBUG ] No samples found: samtools [2024-06-13 05:46:00,215] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-13 05:46:00,221] multiqc [DEBUG ] No samples found: bamtools [2024-06-13 05:46:00,225] multiqc [DEBUG ] No samples found: jellyfish [2024-06-13 05:46:00,234] multiqc [DEBUG ] No samples found: vcftools [2024-06-13 05:46:00,238] multiqc [DEBUG ] No samples found: longranger [2024-06-13 05:46:00,243] multiqc [DEBUG ] No samples found: stacks [2024-06-13 05:46:00,248] multiqc [DEBUG ] No samples found: varscan2 [2024-06-13 05:46:00,263] multiqc [DEBUG ] No samples found: bbmap [2024-06-13 05:46:00,267] multiqc [DEBUG ] No samples found: bismark [2024-06-13 05:46:00,272] multiqc [DEBUG ] No samples found: biscuit [2024-06-13 05:46:00,277] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-13 05:46:00,282] multiqc [DEBUG ] No samples found: hicup [2024-06-13 05:46:00,287] multiqc [DEBUG ] No samples found: hicpro [2024-06-13 05:46:00,291] multiqc [DEBUG ] No samples found: salmon [2024-06-13 05:46:00,296] multiqc [DEBUG ] No samples found: kallisto [2024-06-13 05:46:00,300] multiqc [DEBUG ] No samples found: slamdunk [2024-06-13 05:46:00,305] multiqc [DEBUG ] No samples found: star [2024-06-13 05:46:00,310] multiqc [DEBUG ] No samples found: hisat2 [2024-06-13 05:46:00,314] multiqc [DEBUG ] No samples found: tophat [2024-06-13 05:46:00,319] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-13 05:46:00,324] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-13 05:46:00,328] multiqc [DEBUG ] No samples found: snpsplit [2024-06-13 05:46:00,333] multiqc [DEBUG ] No samples found: kat [2024-06-13 05:46:00,337] multiqc [DEBUG ] No samples found: leehom [2024-06-13 05:46:00,342] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-13 05:46:00,346] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-13 05:46:00,351] multiqc [DEBUG ] No samples found: cutadapt [2024-06-13 05:46:00,355] multiqc [DEBUG ] No samples found: flexbar [2024-06-13 05:46:00,360] multiqc [DEBUG ] No samples found: kaiju [2024-06-13 05:46:00,364] multiqc [DEBUG ] No samples found: kraken [2024-06-13 05:46:00,369] multiqc [DEBUG ] No samples found: malt [2024-06-13 05:46:00,373] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-13 05:46:00,378] multiqc [DEBUG ] No samples found: sickle [2024-06-13 05:46:00,382] multiqc [DEBUG ] No samples found: skewer [2024-06-13 05:46:00,387] multiqc [DEBUG ] No samples found: sortmerna [2024-06-13 05:46:00,391] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-13 05:46:00,396] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-13 05:46:00,400] multiqc [DEBUG ] No samples found: afterqc [2024-06-13 05:46:00,405] multiqc [DEBUG ] No samples found: fastp [2024-06-13 05:46:00,658] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2024-06-13 05:46:00,878] multiqc [DEBUG ] No samples found: pycoqc [2024-06-13 05:46:00,882] multiqc [DEBUG ] No samples found: minionqc [2024-06-13 05:46:00,887] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-13 05:46:00,892] multiqc [DEBUG ] No samples found: clusterflow [2024-06-13 05:46:00,897] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-13 05:46:00,902] multiqc [DEBUG ] No samples found: interop [2024-06-13 05:46:00,907] multiqc [DEBUG ] No samples found: ivar [2024-06-13 05:46:00,912] multiqc [DEBUG ] No samples found: flash [2024-06-13 05:46:00,916] multiqc [DEBUG ] No samples found: seqyclean [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,916] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-13 05:46:00,917] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-13 05:46:00,930] multiqc [INFO ] Compressing plot data [2024-06-13 05:46:01,132] multiqc [INFO ] Report : multiqc_report.html [2024-06-13 05:46:01,132] multiqc [INFO ] Data : multiqc_data [2024-06-13 05:46:01,132] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47495860/tmplc8r9pis/multiqc_data' to '/vast/gencore/GENEFLOW/work/e8/a3bc85f40e2f73e619bc0a60243b12/merged/multiqc_data' [2024-06-13 05:46:01,305] multiqc [INFO ] MultiQC complete