[2024-01-26 00:50:42,970] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-26 00:50:42,970] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-26 00:50:42,970] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-26 00:50:42,973] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-26 00:50:42,973] 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}} [2024-01-26 00:50:42,973] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-26 00:50:43,146] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-26 00:50:43,146] multiqc [INFO ] This is MultiQC v1.9 [2024-01-26 00:50:43,146] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-26 00:50:43,146] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/fb/2cac5aab766e967c1dcbad540308ce/merged [2024-01-26 00:50:43,146] multiqc [INFO ] Template : default [2024-01-26 00:50:43,146] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-26 00:50:43,146] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/fb/2cac5aab766e967c1dcbad540308ce/merged [2024-01-26 00:50:43,147] 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 [2024-01-26 00:50:43,147] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42286341/tmpkggion7g [2024-01-26 00:50:43,275] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-EV_fastqc.html [2024-01-26 00:50:43,284] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-EV_fastqc.html [2024-01-26 00:50:43,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-26 00:50:43,366] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-GBF2-1_fastqc.html [2024-01-26 00:50:43,435] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-26 00:50:43,442] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-GBF2-2_fastqc.html [2024-01-26 00:50:43,513] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-26 00:50:43,521] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-NLP7-1_fastqc.html [2024-01-26 00:50:43,592] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-26 00:50:43,600] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR-NLP7-2_fastqc.html [2024-01-26 00:50:43,672] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-26 00:50:43,679] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR_bZIP1-1_fastqc.html [2024-01-26 00:50:43,750] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-26 00:50:43,758] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_DAM-GR_bZIP1-2_fastqc.html [2024-01-26 00:50:43,828] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVF32AFX5_n01_undetermined_fastqc.html [2024-01-26 00:50:43,835] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVF32AFX5_n01_undetermined_fastqc.html [2024-01-26 00:50:43,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 00:50:43,908] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-26 00:50:45,110] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-26 00:50:45,112] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-26 00:50:45,125] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2024-01-26 00:50:45,127] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-26 00:50:45,138] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-26 00:50:45,144] multiqc [DEBUG ] No samples found: conpair [2024-01-26 00:50:45,150] multiqc [DEBUG ] No samples found: peddy [2024-01-26 00:50:45,157] multiqc [DEBUG ] No samples found: somalier [2024-01-26 00:50:45,162] multiqc [DEBUG ] No samples found: methylQA [2024-01-26 00:50:45,172] multiqc [DEBUG ] No samples found: mosdepth [2024-01-26 00:50:45,178] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-26 00:50:45,182] multiqc [DEBUG ] No samples found: qualimap [2024-01-26 00:50:45,188] multiqc [DEBUG ] No samples found: preseq [2024-01-26 00:50:45,194] multiqc [DEBUG ] No samples found: quast [2024-01-26 00:50:45,199] multiqc [DEBUG ] No samples found: qorts [2024-01-26 00:50:45,205] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-26 00:50:45,211] multiqc [DEBUG ] No samples found: rockhopper [2024-01-26 00:50:45,216] multiqc [DEBUG ] No samples found: rsem [2024-01-26 00:50:45,230] multiqc [DEBUG ] No samples found: rseqc [2024-01-26 00:50:45,236] multiqc [DEBUG ] No samples found: busco [2024-01-26 00:50:45,241] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-26 00:50:45,247] multiqc [DEBUG ] No samples found: disambiguate [2024-01-26 00:50:45,253] multiqc [DEBUG ] No samples found: supernova [2024-01-26 00:50:45,269] multiqc [DEBUG ] No samples found: deeptools [2024-01-26 00:50:45,274] multiqc [DEBUG ] No samples found: sargasso [2024-01-26 00:50:45,280] multiqc [DEBUG ] No samples found: verifybamid [2024-01-26 00:50:45,286] multiqc [DEBUG ] No samples found: mirtrace [2024-01-26 00:50:45,291] multiqc [DEBUG ] No samples found: happy [2024-01-26 00:50:45,297] multiqc [DEBUG ] No samples found: mirtop [2024-01-26 00:50:45,305] multiqc [DEBUG ] No samples found: homer [2024-01-26 00:50:45,310] multiqc [DEBUG ] No samples found: macs2 [2024-01-26 00:50:45,316] multiqc [DEBUG ] No samples found: theta2 [2024-01-26 00:50:45,322] multiqc [DEBUG ] No samples found: snpeff [2024-01-26 00:50:45,331] multiqc [DEBUG ] No samples found: gatk [2024-01-26 00:50:45,342] multiqc [DEBUG ] No samples found: htseq [2024-01-26 00:50:45,352] multiqc [DEBUG ] No samples found: bcftools [2024-01-26 00:50:45,358] multiqc [DEBUG ] No samples found: featureCounts [2024-01-26 00:50:45,367] multiqc [DEBUG ] No samples found: fgbio [2024-01-26 00:50:45,409] multiqc [DEBUG ] No samples found: dragen [2024-01-26 00:50:45,415] multiqc [DEBUG ] No samples found: dedup [2024-01-26 00:50:45,426] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-26 00:50:45,454] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-26 00:50:45,461] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-26 00:50:45,463] multiqc [DEBUG ] No samples found: picard [2024-01-26 00:50:45,469] multiqc [DEBUG ] No samples found: prokka [2024-01-26 00:50:45,475] multiqc [DEBUG ] No samples found: samblaster [2024-01-26 00:50:45,485] multiqc [DEBUG ] No samples found: samtools [2024-01-26 00:50:45,491] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-26 00:50:45,497] multiqc [DEBUG ] No samples found: bamtools [2024-01-26 00:50:45,502] multiqc [DEBUG ] No samples found: jellyfish [2024-01-26 00:50:45,511] multiqc [DEBUG ] No samples found: vcftools [2024-01-26 00:50:45,517] multiqc [DEBUG ] No samples found: longranger [2024-01-26 00:50:45,523] multiqc [DEBUG ] No samples found: stacks [2024-01-26 00:50:45,529] multiqc [DEBUG ] No samples found: varscan2 [2024-01-26 00:50:45,546] multiqc [DEBUG ] No samples found: bbmap [2024-01-26 00:50:45,551] multiqc [DEBUG ] No samples found: bismark [2024-01-26 00:50:45,558] multiqc [DEBUG ] No samples found: biscuit [2024-01-26 00:50:45,563] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-26 00:50:45,569] multiqc [DEBUG ] No samples found: hicup [2024-01-26 00:50:45,575] multiqc [DEBUG ] No samples found: hicpro [2024-01-26 00:50:45,580] multiqc [DEBUG ] No samples found: salmon [2024-01-26 00:50:45,586] multiqc [DEBUG ] No samples found: kallisto [2024-01-26 00:50:45,592] multiqc [DEBUG ] No samples found: slamdunk [2024-01-26 00:50:45,598] multiqc [DEBUG ] No samples found: star [2024-01-26 00:50:45,604] multiqc [DEBUG ] No samples found: hisat2 [2024-01-26 00:50:45,609] multiqc [DEBUG ] No samples found: tophat [2024-01-26 00:50:45,615] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-26 00:50:45,620] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-26 00:50:45,626] multiqc [DEBUG ] No samples found: snpsplit [2024-01-26 00:50:45,631] multiqc [DEBUG ] No samples found: kat [2024-01-26 00:50:45,636] multiqc [DEBUG ] No samples found: leehom [2024-01-26 00:50:45,642] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-26 00:50:45,647] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-26 00:50:45,653] multiqc [DEBUG ] No samples found: cutadapt [2024-01-26 00:50:45,658] multiqc [DEBUG ] No samples found: flexbar [2024-01-26 00:50:45,663] multiqc [DEBUG ] No samples found: kaiju [2024-01-26 00:50:45,669] multiqc [DEBUG ] No samples found: kraken [2024-01-26 00:50:45,675] multiqc [DEBUG ] No samples found: malt [2024-01-26 00:50:45,680] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-26 00:50:45,686] multiqc [DEBUG ] No samples found: sickle [2024-01-26 00:50:45,691] multiqc [DEBUG ] No samples found: skewer [2024-01-26 00:50:45,697] multiqc [DEBUG ] No samples found: sortmerna [2024-01-26 00:50:45,702] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-26 00:50:45,707] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-26 00:50:45,713] multiqc [DEBUG ] No samples found: afterqc [2024-01-26 00:50:45,718] multiqc [DEBUG ] No samples found: fastp [2024-01-26 00:50:45,925] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2024-01-26 00:50:46,015] multiqc [DEBUG ] No samples found: pycoqc [2024-01-26 00:50:46,021] multiqc [DEBUG ] No samples found: minionqc [2024-01-26 00:50:46,026] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-26 00:50:46,032] multiqc [DEBUG ] No samples found: clusterflow [2024-01-26 00:50:46,038] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-26 00:50:46,044] multiqc [DEBUG ] No samples found: interop [2024-01-26 00:50:46,049] multiqc [DEBUG ] No samples found: ivar [2024-01-26 00:50:46,055] multiqc [DEBUG ] No samples found: flash [2024-01-26 00:50:46,061] multiqc [DEBUG ] No samples found: seqyclean [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-26 00:50:46,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-26 00:50:46,062] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-26 00:50:46,062] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-26 00:50:46,073] multiqc [INFO ] Compressing plot data [2024-01-26 00:50:46,225] multiqc [INFO ] Report : multiqc_report.html [2024-01-26 00:50:46,225] multiqc [INFO ] Data : multiqc_data [2024-01-26 00:50:46,225] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42286341/tmpkggion7g/multiqc_data' to '/vast/gencore/GENEFLOW/work/fb/2cac5aab766e967c1dcbad540308ce/merged/multiqc_data' [2024-01-26 00:50:46,445] multiqc [INFO ] MultiQC complete