[2024-07-29 15:19:52,676] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-07-29 15:19:52,676] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-07-29 15:19:52,676] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-07-29 15:19:52,679] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-07-29 15:19:52,679] 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}} [2024-07-29 15:19:52,679] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-29 15:19:52,717] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-07-29 15:19:52,717] multiqc [INFO ] This is MultiQC v1.9 [2024-07-29 15:19:52,717] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-29 15:19:52,717] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/11/e5e7b5fd6a5972dfe3bb986a663fa7/merged [2024-07-29 15:19:52,717] multiqc [INFO ] Template : default [2024-07-29 15:19:52,717] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-07-29 15:19:52,717] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/11/e5e7b5fd6a5972dfe3bb986a663fa7/merged [2024-07-29 15:19:52,717] 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 [2024-07-29 15:19:52,717] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49105742/tmppvw1l2b_ [2024-07-29 15:19:52,842] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKF3VBGXV_n01_HW50_fastqc.html [2024-07-29 15:19:52,853] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKF3VBGXV_n01_HW50_fastqc.html [2024-07-29 15:19:52,936] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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filesize limit: HKF3VBGXV_n01_YZ71_fastqc.html [2024-07-29 15:19:54,571] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKF3VBGXV_n01_YZ71_fastqc.html [2024-07-29 15:19:54,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKF3VBGXV_n01_undetermined_fastqc.html [2024-07-29 15:19:54,644] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKF3VBGXV_n01_undetermined_fastqc.html [2024-07-29 15:19:54,707] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-07-29 15:19:54,713] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-07-29 15:19:55,300] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-29 15:19:55,302] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-29 15:19:55,323] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 25 samples (table) [2024-07-29 15:19:55,324] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-07-29 15:19:55,334] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-07-29 15:19:55,341] multiqc [DEBUG ] No samples found: conpair [2024-07-29 15:19:55,347] multiqc [DEBUG ] No samples found: peddy [2024-07-29 15:19:55,353] multiqc [DEBUG ] No samples found: somalier [2024-07-29 15:19:55,359] multiqc [DEBUG ] No samples found: methylQA [2024-07-29 15:19:55,370] multiqc [DEBUG ] No samples found: mosdepth [2024-07-29 15:19:55,375] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-07-29 15:19:55,379] multiqc [DEBUG ] No samples found: qualimap [2024-07-29 15:19:55,385] multiqc [DEBUG ] No samples found: preseq [2024-07-29 15:19:55,391] multiqc [DEBUG ] No samples found: quast [2024-07-29 15:19:55,397] multiqc [DEBUG ] No samples found: qorts [2024-07-29 15:19:55,403] multiqc [DEBUG ] No samples found: rna_seqc [2024-07-29 15:19:55,408] multiqc [DEBUG ] No samples found: rockhopper [2024-07-29 15:19:55,414] multiqc [DEBUG ] No samples found: rsem [2024-07-29 15:19:55,428] multiqc [DEBUG ] No samples found: rseqc [2024-07-29 15:19:55,434] multiqc [DEBUG ] No samples found: busco [2024-07-29 15:19:55,440] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-07-29 15:19:55,446] multiqc [DEBUG ] No samples found: disambiguate [2024-07-29 15:19:55,452] multiqc [DEBUG ] No samples found: supernova [2024-07-29 15:19:55,470] multiqc [DEBUG ] No samples found: deeptools [2024-07-29 15:19:55,476] multiqc [DEBUG ] No samples found: sargasso [2024-07-29 15:19:55,482] multiqc [DEBUG ] No samples found: verifybamid [2024-07-29 15:19:55,488] multiqc [DEBUG ] No samples found: mirtrace [2024-07-29 15:19:55,493] multiqc [DEBUG ] No samples found: happy [2024-07-29 15:19:55,499] multiqc [DEBUG ] No samples found: mirtop [2024-07-29 15:19:55,507] multiqc [DEBUG ] No samples found: homer [2024-07-29 15:19:55,513] multiqc [DEBUG ] No samples found: macs2 [2024-07-29 15:19:55,518] multiqc [DEBUG ] No samples found: theta2 [2024-07-29 15:19:55,524] multiqc [DEBUG ] No samples found: snpeff [2024-07-29 15:19:55,533] multiqc [DEBUG ] No samples found: gatk [2024-07-29 15:19:55,539] multiqc [DEBUG ] No samples found: htseq [2024-07-29 15:19:55,545] multiqc [DEBUG ] No samples found: bcftools [2024-07-29 15:19:55,551] multiqc [DEBUG ] No samples found: featureCounts [2024-07-29 15:19:55,560] multiqc [DEBUG ] No samples found: fgbio [2024-07-29 15:19:55,576] multiqc [DEBUG ] No samples found: dragen [2024-07-29 15:19:55,582] multiqc [DEBUG ] No samples found: dedup [2024-07-29 15:19:55,588] multiqc [DEBUG ] No samples found: damageprofiler [2024-07-29 15:19:55,617] multiqc [DEBUG ] No samples found: biobambam2 [2024-07-29 15:19:55,622] multiqc [DEBUG ] No samples found: mtnucratio [2024-07-29 15:19:55,624] multiqc [DEBUG ] No samples found: picard [2024-07-29 15:19:55,630] multiqc [DEBUG ] No samples found: prokka [2024-07-29 15:19:55,635] multiqc [DEBUG ] No samples found: samblaster [2024-07-29 15:19:55,645] multiqc [DEBUG ] No samples found: samtools [2024-07-29 15:19:55,651] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-07-29 15:19:55,657] multiqc [DEBUG ] No samples found: bamtools [2024-07-29 15:19:55,662] multiqc [DEBUG ] No samples found: jellyfish [2024-07-29 15:19:55,671] multiqc [DEBUG ] No samples found: vcftools [2024-07-29 15:19:55,677] multiqc [DEBUG ] No samples found: longranger [2024-07-29 15:19:55,683] multiqc [DEBUG ] No samples found: stacks [2024-07-29 15:19:55,689] multiqc [DEBUG ] No samples found: varscan2 [2024-07-29 15:19:55,708] multiqc [DEBUG ] No samples found: bbmap [2024-07-29 15:19:55,713] multiqc [DEBUG ] No samples found: bismark [2024-07-29 15:19:55,720] multiqc [DEBUG ] No samples found: biscuit [2024-07-29 15:19:55,726] multiqc [DEBUG ] No samples found: hicexplorer [2024-07-29 15:19:55,732] multiqc [DEBUG ] No samples found: hicup [2024-07-29 15:19:55,737] multiqc [DEBUG ] No samples found: hicpro [2024-07-29 15:19:55,743] multiqc [DEBUG ] No samples found: salmon [2024-07-29 15:19:55,748] multiqc [DEBUG ] No samples found: kallisto [2024-07-29 15:19:55,754] multiqc [DEBUG ] No samples found: slamdunk [2024-07-29 15:19:55,760] multiqc [DEBUG ] No samples found: star [2024-07-29 15:19:55,765] multiqc [DEBUG ] No samples found: hisat2 [2024-07-29 15:19:55,771] multiqc [DEBUG ] No samples found: tophat [2024-07-29 15:19:55,776] multiqc [DEBUG ] No samples found: bowtie2 [2024-07-29 15:19:55,782] multiqc [DEBUG ] No samples found: bowtie1 [2024-07-29 15:19:55,787] multiqc [DEBUG ] No samples found: snpsplit [2024-07-29 15:19:55,793] multiqc [DEBUG ] No samples found: kat [2024-07-29 15:19:55,798] multiqc [DEBUG ] No samples found: leehom [2024-07-29 15:19:55,804] multiqc [DEBUG ] No samples found: adapterRemoval [2024-07-29 15:19:55,810] multiqc [DEBUG ] No samples found: clipandmerge [2024-07-29 15:19:55,815] multiqc [DEBUG ] No samples found: cutadapt [2024-07-29 15:19:55,821] multiqc [DEBUG ] No samples found: flexbar [2024-07-29 15:19:55,827] multiqc [DEBUG ] No samples found: kaiju [2024-07-29 15:19:55,832] multiqc [DEBUG ] No samples found: kraken [2024-07-29 15:19:55,838] multiqc [DEBUG ] No samples found: malt [2024-07-29 15:19:55,843] multiqc [DEBUG ] No samples found: trimmomatic [2024-07-29 15:19:55,848] multiqc [DEBUG ] No samples found: sickle [2024-07-29 15:19:55,853] multiqc [DEBUG ] No samples found: skewer [2024-07-29 15:19:55,859] multiqc [DEBUG ] No samples found: sortmerna [2024-07-29 15:19:55,864] multiqc [DEBUG ] No samples found: biobloomtools [2024-07-29 15:19:55,870] multiqc [DEBUG ] No samples found: fastq_screen [2024-07-29 15:19:55,876] multiqc [DEBUG ] No samples found: afterqc [2024-07-29 15:19:55,882] multiqc [DEBUG ] No samples found: fastp [2024-07-29 15:19:57,743] multiqc.modules.fastqc.fastqc [INFO ] Found 25 reports [2024-07-29 15:19:58,307] multiqc [DEBUG ] No samples found: pycoqc [2024-07-29 15:19:58,312] multiqc [DEBUG ] No samples found: minionqc [2024-07-29 15:19:58,318] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-07-29 15:19:58,324] multiqc [DEBUG ] No samples found: clusterflow [2024-07-29 15:19:58,329] multiqc [DEBUG ] No samples found: bcl2fastq [2024-07-29 15:19:58,335] multiqc [DEBUG ] No samples found: interop [2024-07-29 15:19:58,341] multiqc [DEBUG ] No samples found: ivar [2024-07-29 15:19:58,347] multiqc [DEBUG ] No samples found: flash [2024-07-29 15:19:58,352] multiqc [DEBUG ] No samples found: seqyclean [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,352] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-07-29 15:19:58,353] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-07-29 15:19:58,387] multiqc [INFO ] Compressing plot data [2024-07-29 15:19:58,863] multiqc [INFO ] Report : multiqc_report.html [2024-07-29 15:19:58,863] multiqc [INFO ] Data : multiqc_data [2024-07-29 15:19:58,864] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49105742/tmppvw1l2b_/multiqc_data' to '/vast/gencore/GENEFLOW/work/11/e5e7b5fd6a5972dfe3bb986a663fa7/merged/multiqc_data' [2024-07-29 15:19:59,070] multiqc [INFO ] MultiQC complete