[2024-02-15 18:40:16,001] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-15 18:40:16,001] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-15 18:40:16,004] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-15 18:40:16,006] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-15 18:40:16,006] 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}} [2024-02-15 18:40:16,006] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-15 18:40:16,172] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-15 18:40:16,172] multiqc [INFO ] This is MultiQC v1.9 [2024-02-15 18:40:16,172] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-15 18:40:16,172] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/ae/f5efdf129e9e16b5aa8d09ce06264f/merged [2024-02-15 18:40:16,172] multiqc [INFO ] Template : default [2024-02-15 18:40:16,172] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-15 18:40:16,172] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/ae/f5efdf129e9e16b5aa8d09ce06264f/merged [2024-02-15 18:40:16,172] 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 [2024-02-15 18:40:16,172] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43020859/tmpso7u3v_j [2024-02-15 18:40:16,291] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG3TDMXY_n01_O8_351_B_2_fastqc.html [2024-02-15 18:40:16,300] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG3TDMXY_n01_O8_351_B_2_fastqc.html [2024-02-15 18:40:16,376] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HTG3TDMXY_n01_W8_D2_C_2_fastqc.html [2024-02-15 18:40:18,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG3TDMXY_n01_W8_D2_C_2_fastqc.html [2024-02-15 18:40:18,999] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG3TDMXY_n01_W8_D2_E_2_fastqc.html [2024-02-15 18:40:19,006] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG3TDMXY_n01_W8_D2_E_2_fastqc.html [2024-02-15 18:40:19,075] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HTG3TDMXY_n01_undetermined_fastqc.html [2024-02-15 18:40:19,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HTG3TDMXY_n01_undetermined_fastqc.html [2024-02-15 18:40:19,458] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-15 18:40:19,459] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-15 18:40:19,487] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 37 samples (table) [2024-02-15 18:40:19,489] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-15 18:40:19,499] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-15 18:40:19,502] multiqc [DEBUG ] No samples found: conpair [2024-02-15 18:40:19,506] multiqc [DEBUG ] No samples found: peddy [2024-02-15 18:40:19,509] multiqc [DEBUG ] No samples found: somalier [2024-02-15 18:40:19,512] multiqc [DEBUG ] No samples found: methylQA [2024-02-15 18:40:19,516] multiqc [DEBUG ] No samples found: mosdepth [2024-02-15 18:40:19,519] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-15 18:40:19,521] multiqc [DEBUG ] No samples found: qualimap [2024-02-15 18:40:19,524] multiqc [DEBUG ] No samples found: preseq [2024-02-15 18:40:19,527] multiqc [DEBUG ] No samples found: quast [2024-02-15 18:40:19,530] multiqc [DEBUG ] No samples found: qorts [2024-02-15 18:40:19,533] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-15 18:40:19,536] multiqc [DEBUG ] No samples found: rockhopper [2024-02-15 18:40:19,539] multiqc [DEBUG ] No samples found: rsem [2024-02-15 18:40:19,544] multiqc [DEBUG ] No samples found: rseqc [2024-02-15 18:40:19,559] multiqc [DEBUG ] No samples found: busco [2024-02-15 18:40:19,562] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-15 18:40:19,565] multiqc [DEBUG ] No samples found: disambiguate [2024-02-15 18:40:19,568] multiqc [DEBUG ] No samples found: supernova [2024-02-15 18:40:19,573] multiqc [DEBUG ] No samples found: deeptools [2024-02-15 18:40:19,576] multiqc [DEBUG ] No samples found: sargasso [2024-02-15 18:40:19,579] multiqc [DEBUG ] No samples found: verifybamid [2024-02-15 18:40:19,582] multiqc [DEBUG ] No samples found: mirtrace [2024-02-15 18:40:19,585] multiqc [DEBUG ] No samples found: happy [2024-02-15 18:40:19,588] multiqc [DEBUG ] No samples found: mirtop [2024-02-15 18:40:19,591] multiqc [DEBUG ] No samples found: homer [2024-02-15 18:40:19,594] multiqc [DEBUG ] No samples found: macs2 [2024-02-15 18:40:19,598] multiqc [DEBUG ] No samples found: theta2 [2024-02-15 18:40:19,601] multiqc [DEBUG ] No samples found: snpeff [2024-02-15 18:40:19,604] multiqc [DEBUG ] No samples found: gatk [2024-02-15 18:40:19,607] multiqc [DEBUG ] No samples found: htseq [2024-02-15 18:40:19,610] multiqc [DEBUG ] No samples found: bcftools [2024-02-15 18:40:19,613] multiqc [DEBUG ] No samples found: featureCounts [2024-02-15 18:40:19,616] multiqc [DEBUG ] No samples found: fgbio [2024-02-15 18:40:19,622] multiqc [DEBUG ] No samples found: dragen [2024-02-15 18:40:19,625] multiqc [DEBUG ] No samples found: dedup [2024-02-15 18:40:19,628] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-15 18:40:19,636] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-15 18:40:19,639] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-15 18:40:19,642] multiqc [DEBUG ] No samples found: picard [2024-02-15 18:40:19,644] multiqc [DEBUG ] No samples found: prokka [2024-02-15 18:40:19,647] multiqc [DEBUG ] No samples found: samblaster [2024-02-15 18:40:19,651] multiqc [DEBUG ] No samples found: samtools [2024-02-15 18:40:19,654] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-15 18:40:19,657] multiqc [DEBUG ] No samples found: bamtools [2024-02-15 18:40:19,661] multiqc [DEBUG ] No samples found: jellyfish [2024-02-15 18:40:19,665] multiqc [DEBUG ] No samples found: vcftools [2024-02-15 18:40:19,667] multiqc [DEBUG ] No samples found: longranger [2024-02-15 18:40:19,670] multiqc [DEBUG ] No samples found: stacks [2024-02-15 18:40:19,673] multiqc [DEBUG ] No samples found: varscan2 [2024-02-15 18:40:19,679] multiqc [DEBUG ] No samples found: bbmap [2024-02-15 18:40:19,682] multiqc [DEBUG ] No samples found: bismark [2024-02-15 18:40:19,685] multiqc [DEBUG ] No samples found: biscuit [2024-02-15 18:40:19,688] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-15 18:40:19,690] multiqc [DEBUG ] No samples found: hicup [2024-02-15 18:40:19,693] multiqc [DEBUG ] No samples found: hicpro [2024-02-15 18:40:19,696] multiqc [DEBUG ] No samples found: salmon [2024-02-15 18:40:19,699] multiqc [DEBUG ] No samples found: kallisto [2024-02-15 18:40:19,702] multiqc [DEBUG ] No samples found: slamdunk [2024-02-15 18:40:19,705] multiqc [DEBUG ] No samples found: star [2024-02-15 18:40:19,708] multiqc [DEBUG ] No samples found: hisat2 [2024-02-15 18:40:19,710] multiqc [DEBUG ] No samples found: tophat [2024-02-15 18:40:19,714] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-15 18:40:19,717] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-15 18:40:19,720] multiqc [DEBUG ] No samples found: snpsplit [2024-02-15 18:40:19,723] multiqc [DEBUG ] No samples found: kat [2024-02-15 18:40:19,726] multiqc [DEBUG ] No samples found: leehom [2024-02-15 18:40:19,729] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-15 18:40:19,732] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-15 18:40:19,735] multiqc [DEBUG ] No samples found: cutadapt [2024-02-15 18:40:19,738] multiqc [DEBUG ] No samples found: flexbar [2024-02-15 18:40:19,741] multiqc [DEBUG ] No samples found: kaiju [2024-02-15 18:40:19,745] multiqc [DEBUG ] No samples found: kraken [2024-02-15 18:40:19,748] multiqc [DEBUG ] No samples found: malt [2024-02-15 18:40:19,750] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-15 18:40:19,753] multiqc [DEBUG ] No samples found: sickle [2024-02-15 18:40:19,756] multiqc [DEBUG ] No samples found: skewer [2024-02-15 18:40:19,759] multiqc [DEBUG ] No samples found: sortmerna [2024-02-15 18:40:19,762] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-15 18:40:19,765] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-15 18:40:19,768] multiqc [DEBUG ] No samples found: afterqc [2024-02-15 18:40:19,771] multiqc [DEBUG ] No samples found: fastp [2024-02-15 18:40:25,441] multiqc.modules.fastqc.fastqc [INFO ] Found 37 reports [2024-02-15 18:40:26,014] multiqc [DEBUG ] No samples found: pycoqc [2024-02-15 18:40:26,018] multiqc [DEBUG ] No samples found: minionqc [2024-02-15 18:40:26,021] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-15 18:40:26,024] multiqc [DEBUG ] No samples found: clusterflow [2024-02-15 18:40:26,027] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-15 18:40:26,032] multiqc [DEBUG ] No samples found: interop [2024-02-15 18:40:26,035] multiqc [DEBUG ] No samples found: ivar [2024-02-15 18:40:26,038] multiqc [DEBUG ] No samples found: flash [2024-02-15 18:40:26,041] multiqc [DEBUG ] No samples found: seqyclean [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-15 18:40:26,041] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-15 18:40:26,042] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-15 18:40:26,087] multiqc [INFO ] Compressing plot data [2024-02-15 18:40:26,837] multiqc [INFO ] Report : multiqc_report.html [2024-02-15 18:40:26,837] multiqc [INFO ] Data : multiqc_data [2024-02-15 18:40:26,837] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43020859/tmpso7u3v_j/multiqc_data' to '/vast/gencore/GENEFLOW/work/ae/f5efdf129e9e16b5aa8d09ce06264f/merged/multiqc_data' [2024-02-15 18:40:26,986] multiqc [INFO ] MultiQC complete