[2024-10-19 03:46:31,011] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-10-19 03:46:31,011] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-10-19 03:46:31,011] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-10-19 03:46:31,014] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-10-19 03:46:31,014] 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}} [2024-10-19 03:46:31,014] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-19 03:46:31,050] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-10-19 03:46:31,050] multiqc [INFO ] This is MultiQC v1.9 [2024-10-19 03:46:31,050] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-19 03:46:31,050] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/ab/3fa9292be84bc0cf0eac2cadbb85fe/merged [2024-10-19 03:46:31,050] multiqc [INFO ] Template : default [2024-10-19 03:46:31,050] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-10-19 03:46:31,050] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/ab/3fa9292be84bc0cf0eac2cadbb85fe/merged [2024-10-19 03:46:31,051] 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 [2024-10-19 03:46:31,051] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52414087/tmpnlf8l5po [2024-10-19 03:46:31,166] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-10-19 03:46:31,169] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-10-19 03:46:31,292] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_undetermined_fastqc.html [2024-10-19 03:46:32,223] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_undetermined_fastqc.html [2024-10-19 03:46:32,272] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA95_fastqc.html [2024-10-19 03:46:32,274] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA95_fastqc.html [2024-10-19 03:46:32,324] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_DO149_fastqc.html [2024-10-19 03:46:32,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_DO149_fastqc.html [2024-10-19 03:46:32,371] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_DO134_fastqc.html [2024-10-19 03:46:32,373] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_DO134_fastqc.html [2024-10-19 03:46:32,419] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA89_fastqc.html [2024-10-19 03:46:32,421] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA89_fastqc.html [2024-10-19 03:46:32,469] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA93_fastqc.html [2024-10-19 03:46:32,471] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5GFVBGYW_n01_AA93_fastqc.html [2024-10-19 03:46:32,864] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-19 03:46:32,866] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-19 03:46:32,887] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-10-19 03:46:32,897] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-10-19 03:46:32,899] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-10-19 03:46:32,906] multiqc [DEBUG ] No samples found: conpair [2024-10-19 03:46:32,912] multiqc [DEBUG ] No samples found: peddy [2024-10-19 03:46:32,919] multiqc [DEBUG ] No samples found: somalier [2024-10-19 03:46:32,928] multiqc [DEBUG ] No samples found: methylQA [2024-10-19 03:46:32,941] multiqc [DEBUG ] No samples found: mosdepth [2024-10-19 03:46:32,947] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-10-19 03:46:32,952] multiqc [DEBUG ] No samples found: qualimap [2024-10-19 03:46:32,958] multiqc [DEBUG ] No samples found: preseq [2024-10-19 03:46:32,965] multiqc [DEBUG ] No samples found: quast [2024-10-19 03:46:32,972] multiqc [DEBUG ] No samples found: qorts [2024-10-19 03:46:32,979] multiqc [DEBUG ] No samples found: rna_seqc [2024-10-19 03:46:32,986] multiqc [DEBUG ] No samples found: rockhopper [2024-10-19 03:46:32,992] multiqc [DEBUG ] No samples found: rsem [2024-10-19 03:46:33,011] multiqc [DEBUG ] No samples found: rseqc [2024-10-19 03:46:33,017] multiqc [DEBUG ] No samples found: busco [2024-10-19 03:46:33,024] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-10-19 03:46:33,030] multiqc [DEBUG ] No samples found: disambiguate [2024-10-19 03:46:33,038] multiqc [DEBUG ] No samples found: supernova [2024-10-19 03:46:33,060] multiqc [DEBUG ] No samples found: deeptools [2024-10-19 03:46:33,067] multiqc [DEBUG ] No samples found: sargasso [2024-10-19 03:46:33,074] multiqc [DEBUG ] No samples found: verifybamid [2024-10-19 03:46:33,081] multiqc [DEBUG ] No samples found: mirtrace [2024-10-19 03:46:33,087] multiqc [DEBUG ] No samples found: happy [2024-10-19 03:46:33,095] multiqc [DEBUG ] No samples found: mirtop [2024-10-19 03:46:33,104] multiqc [DEBUG ] No samples found: homer [2024-10-19 03:46:33,111] multiqc [DEBUG ] No samples found: macs2 [2024-10-19 03:46:33,118] multiqc [DEBUG ] No samples found: theta2 [2024-10-19 03:46:33,125] multiqc [DEBUG ] No samples found: snpeff [2024-10-19 03:46:33,135] multiqc [DEBUG ] No samples found: gatk [2024-10-19 03:46:33,141] multiqc [DEBUG ] No samples found: htseq [2024-10-19 03:46:33,149] multiqc [DEBUG ] No samples found: bcftools [2024-10-19 03:46:33,157] multiqc [DEBUG ] No samples found: featureCounts [2024-10-19 03:46:33,167] multiqc [DEBUG ] No samples found: fgbio [2024-10-19 03:46:33,188] multiqc [DEBUG ] No samples found: dragen [2024-10-19 03:46:33,194] multiqc [DEBUG ] No samples found: dedup [2024-10-19 03:46:33,202] multiqc [DEBUG ] No samples found: damageprofiler [2024-10-19 03:46:33,240] multiqc [DEBUG ] No samples found: biobambam2 [2024-10-19 03:46:33,246] multiqc [DEBUG ] No samples found: mtnucratio [2024-10-19 03:46:33,249] multiqc [DEBUG ] No samples found: picard [2024-10-19 03:46:33,256] multiqc [DEBUG ] No samples found: prokka [2024-10-19 03:46:33,263] multiqc [DEBUG ] No samples found: samblaster [2024-10-19 03:46:33,277] multiqc [DEBUG ] No samples found: samtools [2024-10-19 03:46:33,284] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-10-19 03:46:33,292] multiqc [DEBUG ] No samples found: bamtools [2024-10-19 03:46:33,298] multiqc [DEBUG ] No samples found: jellyfish [2024-10-19 03:46:33,310] multiqc [DEBUG ] No samples found: vcftools [2024-10-19 03:46:33,318] multiqc [DEBUG ] No samples found: longranger [2024-10-19 03:46:33,325] multiqc [DEBUG ] No samples found: stacks [2024-10-19 03:46:33,332] multiqc [DEBUG ] No samples found: varscan2 [2024-10-19 03:46:33,354] multiqc [DEBUG ] No samples found: bbmap [2024-10-19 03:46:33,361] multiqc [DEBUG ] No samples found: bismark [2024-10-19 03:46:33,368] multiqc [DEBUG ] No samples found: biscuit [2024-10-19 03:46:33,374] multiqc [DEBUG ] No samples found: hicexplorer [2024-10-19 03:46:33,381] multiqc [DEBUG ] No samples found: hicup [2024-10-19 03:46:33,389] multiqc [DEBUG ] No samples found: hicpro [2024-10-19 03:46:33,395] multiqc [DEBUG ] No samples found: salmon [2024-10-19 03:46:33,402] multiqc [DEBUG ] No samples found: kallisto [2024-10-19 03:46:33,409] multiqc [DEBUG ] No samples found: slamdunk [2024-10-19 03:46:33,415] multiqc [DEBUG ] No samples found: star [2024-10-19 03:46:33,421] multiqc [DEBUG ] No samples found: hisat2 [2024-10-19 03:46:33,428] multiqc [DEBUG ] No samples found: tophat [2024-10-19 03:46:33,436] multiqc [DEBUG ] No samples found: bowtie2 [2024-10-19 03:46:33,443] multiqc [DEBUG ] No samples found: bowtie1 [2024-10-19 03:46:33,450] multiqc [DEBUG ] No samples found: snpsplit [2024-10-19 03:46:33,456] multiqc [DEBUG ] No samples found: kat [2024-10-19 03:46:33,462] multiqc [DEBUG ] No samples found: leehom [2024-10-19 03:46:33,471] multiqc [DEBUG ] No samples found: adapterRemoval [2024-10-19 03:46:33,477] multiqc [DEBUG ] No samples found: clipandmerge [2024-10-19 03:46:33,483] multiqc [DEBUG ] No samples found: cutadapt [2024-10-19 03:46:33,490] multiqc [DEBUG ] No samples found: flexbar [2024-10-19 03:46:33,497] multiqc [DEBUG ] No samples found: kaiju [2024-10-19 03:46:33,503] multiqc [DEBUG ] No samples found: kraken [2024-10-19 03:46:33,510] multiqc [DEBUG ] No samples found: malt [2024-10-19 03:46:33,518] multiqc [DEBUG ] No samples found: trimmomatic [2024-10-19 03:46:33,524] multiqc [DEBUG ] No samples found: sickle [2024-10-19 03:46:33,531] multiqc [DEBUG ] No samples found: skewer [2024-10-19 03:46:33,538] multiqc [DEBUG ] No samples found: sortmerna [2024-10-19 03:46:33,544] multiqc [DEBUG ] No samples found: biobloomtools [2024-10-19 03:46:33,552] multiqc [DEBUG ] No samples found: fastq_screen [2024-10-19 03:46:33,558] multiqc [DEBUG ] No samples found: afterqc [2024-10-19 03:46:33,565] multiqc [DEBUG ] No samples found: fastp [2024-10-19 03:46:35,367] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2024-10-19 03:46:35,937] multiqc [DEBUG ] No samples found: pycoqc [2024-10-19 03:46:35,943] multiqc [DEBUG ] No samples found: minionqc [2024-10-19 03:46:35,948] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-10-19 03:46:35,955] multiqc [DEBUG ] No samples found: clusterflow [2024-10-19 03:46:35,961] multiqc [DEBUG ] No samples found: bcl2fastq [2024-10-19 03:46:35,968] multiqc [DEBUG ] No samples found: interop [2024-10-19 03:46:35,974] multiqc [DEBUG ] No samples found: ivar [2024-10-19 03:46:35,980] multiqc [DEBUG ] No samples found: flash [2024-10-19 03:46:35,986] multiqc [DEBUG ] No samples found: seqyclean [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-10-19 03:46:35,986] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-10-19 03:46:35,987] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-10-19 03:46:35,987] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-10-19 03:46:35,987] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-10-19 03:46:35,987] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-10-19 03:46:35,987] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-10-19 03:46:36,018] multiqc [INFO ] Compressing plot data [2024-10-19 03:46:36,510] multiqc [INFO ] Report : multiqc_report.html [2024-10-19 03:46:36,511] multiqc [INFO ] Data : multiqc_data [2024-10-19 03:46:36,511] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52414087/tmpnlf8l5po/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/ab/3fa9292be84bc0cf0eac2cadbb85fe/merged/multiqc_data' [2024-10-19 03:46:36,663] multiqc [INFO ] MultiQC complete