[2024-02-21 22:02:45,781] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-21 22:02:45,781] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-21 22:02:45,781] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-21 22:02:45,784] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-21 22:02:45,784] 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}} [2024-02-21 22:02:45,784] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-21 22:02:45,944] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-21 22:02:45,944] multiqc [INFO ] This is MultiQC v1.9 [2024-02-21 22:02:45,944] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-21 22:02:45,944] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/a3/57d4516236fddd16fa14fe9a6f294f/merged [2024-02-21 22:02:45,944] multiqc [INFO ] Template : default [2024-02-21 22:02:45,944] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-21 22:02:45,944] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/a3/57d4516236fddd16fa14fe9a6f294f/merged [2024-02-21 22:02:45,945] 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 [2024-02-21 22:02:45,945] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43267382/tmp3_zl9jim [2024-02-21 22:02:46,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n01_2A-2C_240214_fastqc.html [2024-02-21 22:02:46,115] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n01_2A-2C_240214_fastqc.html [2024-02-21 22:02:46,188] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAH.96_240214_fastqc.html [2024-02-21 22:03:00,603] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAH.99_240214_fastqc.html [2024-02-21 22:03:00,609] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAH.99_240214_fastqc.html [2024-02-21 22:03:00,675] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAH.9_240214_fastqc.html [2024-02-21 22:03:00,682] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAH.9_240214_fastqc.html [2024-02-21 22:03:00,781] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v1_240214_fastqc.html [2024-02-21 22:03:00,788] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v1_240214_fastqc.html [2024-02-21 22:03:00,853] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v2_240214_fastqc.html [2024-02-21 22:03:00,860] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v2_240214_fastqc.html [2024-02-21 22:03:00,934] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v3_240214_fastqc.html [2024-02-21 22:03:00,941] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a1_v3_240214_fastqc.html [2024-02-21 22:03:01,011] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v1_240214_fastqc.html [2024-02-21 22:03:01,018] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v1_240214_fastqc.html [2024-02-21 22:03:01,086] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v2_240214_fastqc.html [2024-02-21 22:03:01,092] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v2_240214_fastqc.html [2024-02-21 22:03:01,157] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v3_240214_fastqc.html [2024-02-21 22:03:01,163] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_MAT0.a2_v3_240214_fastqc.html [2024-02-21 22:03:01,229] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVM72DRX3_n02_undetermined_fastqc.html [2024-02-21 22:03:01,237] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVM72DRX3_n02_undetermined_fastqc.html [2024-02-21 22:03:01,607] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-21 22:03:01,609] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-21 22:03:01,666] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 93 samples (table) [2024-02-21 22:03:01,668] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-21 22:03:01,677] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-21 22:03:01,683] multiqc [DEBUG ] No samples found: conpair [2024-02-21 22:03:01,689] multiqc [DEBUG ] No samples found: peddy [2024-02-21 22:03:01,694] multiqc [DEBUG ] No samples found: somalier [2024-02-21 22:03:01,698] multiqc [DEBUG ] No samples found: methylQA [2024-02-21 22:03:01,707] multiqc [DEBUG ] No samples found: mosdepth [2024-02-21 22:03:01,711] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-21 22:03:01,714] multiqc [DEBUG ] No samples found: qualimap [2024-02-21 22:03:01,719] multiqc [DEBUG ] No samples found: preseq [2024-02-21 22:03:01,724] multiqc [DEBUG ] No samples found: quast [2024-02-21 22:03:01,729] multiqc [DEBUG ] No samples found: qorts [2024-02-21 22:03:01,734] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-21 22:03:01,739] multiqc [DEBUG ] No samples found: rockhopper [2024-02-21 22:03:01,744] multiqc [DEBUG ] No samples found: rsem [2024-02-21 22:03:01,756] multiqc [DEBUG ] No samples found: rseqc [2024-02-21 22:03:01,761] multiqc [DEBUG ] No samples found: busco [2024-02-21 22:03:01,766] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-21 22:03:01,770] multiqc [DEBUG ] No samples found: disambiguate [2024-02-21 22:03:01,776] multiqc [DEBUG ] No samples found: supernova [2024-02-21 22:03:01,789] multiqc [DEBUG ] No samples found: deeptools [2024-02-21 22:03:01,794] multiqc [DEBUG ] No samples found: sargasso [2024-02-21 22:03:01,799] multiqc [DEBUG ] No samples found: verifybamid [2024-02-21 22:03:01,803] multiqc [DEBUG ] No samples found: mirtrace [2024-02-21 22:03:01,808] multiqc [DEBUG ] No samples found: happy [2024-02-21 22:03:01,812] multiqc [DEBUG ] No samples found: mirtop [2024-02-21 22:03:01,819] multiqc [DEBUG ] No samples found: homer [2024-02-21 22:03:01,823] multiqc [DEBUG ] No samples found: macs2 [2024-02-21 22:03:01,828] multiqc [DEBUG ] No samples found: theta2 [2024-02-21 22:03:01,834] multiqc [DEBUG ] No samples found: snpeff [2024-02-21 22:03:01,840] multiqc [DEBUG ] No samples found: gatk [2024-02-21 22:03:01,844] multiqc [DEBUG ] No samples found: htseq [2024-02-21 22:03:01,850] multiqc [DEBUG ] No samples found: bcftools [2024-02-21 22:03:01,854] multiqc [DEBUG ] No samples found: featureCounts [2024-02-21 22:03:01,860] multiqc [DEBUG ] No samples found: fgbio [2024-02-21 22:03:01,872] multiqc [DEBUG ] No samples found: dragen [2024-02-21 22:03:01,877] multiqc [DEBUG ] No samples found: dedup [2024-02-21 22:03:01,882] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-21 22:03:01,906] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-21 22:03:01,910] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-21 22:03:01,912] multiqc [DEBUG ] No samples found: picard [2024-02-21 22:03:01,917] multiqc [DEBUG ] No samples found: prokka [2024-02-21 22:03:01,921] multiqc [DEBUG ] No samples found: samblaster [2024-02-21 22:03:01,931] multiqc [DEBUG ] No samples found: samtools [2024-02-21 22:03:01,936] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-21 22:03:01,942] multiqc [DEBUG ] No samples found: bamtools [2024-02-21 22:03:01,948] multiqc [DEBUG ] No samples found: jellyfish [2024-02-21 22:03:01,957] multiqc [DEBUG ] No samples found: vcftools [2024-02-21 22:03:01,967] multiqc [DEBUG ] No samples found: longranger [2024-02-21 22:03:01,974] multiqc [DEBUG ] No samples found: stacks [2024-02-21 22:03:01,979] multiqc [DEBUG ] No samples found: varscan2 [2024-02-21 22:03:01,996] multiqc [DEBUG ] No samples found: bbmap [2024-02-21 22:03:02,001] multiqc [DEBUG ] No samples found: bismark [2024-02-21 22:03:02,008] multiqc [DEBUG ] No samples found: biscuit [2024-02-21 22:03:02,014] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-21 22:03:02,019] multiqc [DEBUG ] No samples found: hicup [2024-02-21 22:03:02,025] multiqc [DEBUG ] No samples found: hicpro [2024-02-21 22:03:02,030] multiqc [DEBUG ] No samples found: salmon [2024-02-21 22:03:02,036] multiqc [DEBUG ] No samples found: kallisto [2024-02-21 22:03:02,042] multiqc [DEBUG ] No samples found: slamdunk [2024-02-21 22:03:02,047] multiqc [DEBUG ] No samples found: star [2024-02-21 22:03:02,052] multiqc [DEBUG ] No samples found: hisat2 [2024-02-21 22:03:02,057] multiqc [DEBUG ] No samples found: tophat [2024-02-21 22:03:02,062] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-21 22:03:02,068] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-21 22:03:02,074] multiqc [DEBUG ] No samples found: snpsplit [2024-02-21 22:03:02,079] multiqc [DEBUG ] No samples found: kat [2024-02-21 22:03:02,083] multiqc [DEBUG ] No samples found: leehom [2024-02-21 22:03:02,088] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-21 22:03:02,094] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-21 22:03:02,099] multiqc [DEBUG ] No samples found: cutadapt [2024-02-21 22:03:02,103] multiqc [DEBUG ] No samples found: flexbar [2024-02-21 22:03:02,109] multiqc [DEBUG ] No samples found: kaiju [2024-02-21 22:03:02,115] multiqc [DEBUG ] No samples found: kraken [2024-02-21 22:03:02,120] multiqc [DEBUG ] No samples found: malt [2024-02-21 22:03:02,125] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-21 22:03:02,130] multiqc [DEBUG ] No samples found: sickle [2024-02-21 22:03:02,137] multiqc [DEBUG ] No samples found: skewer [2024-02-21 22:03:02,142] multiqc [DEBUG ] No samples found: sortmerna [2024-02-21 22:03:02,147] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-21 22:03:02,152] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-21 22:03:02,157] multiqc [DEBUG ] No samples found: afterqc [2024-02-21 22:03:02,162] multiqc [DEBUG ] No samples found: fastp [2024-02-21 22:03:07,039] multiqc.modules.fastqc.fastqc [INFO ] Found 186 reports [2024-02-21 22:03:22,142] multiqc [DEBUG ] No samples found: pycoqc [2024-02-21 22:03:22,150] multiqc [DEBUG ] No samples found: minionqc [2024-02-21 22:03:22,156] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-21 22:03:22,178] multiqc [DEBUG ] No samples found: clusterflow [2024-02-21 22:03:22,186] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-21 22:03:22,204] multiqc [DEBUG ] No samples found: interop [2024-02-21 22:03:22,210] multiqc [DEBUG ] No samples found: ivar [2024-02-21 22:03:22,218] multiqc [DEBUG ] No samples found: flash [2024-02-21 22:03:22,224] multiqc [DEBUG ] No samples found: seqyclean [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-21 22:03:22,224] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-21 22:03:22,225] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-21 22:03:22,441] multiqc [INFO ] Compressing plot data [2024-02-21 22:03:22,528] multiqc [INFO ] Report : multiqc_report.html [2024-02-21 22:03:22,528] multiqc [INFO ] Data : multiqc_data [2024-02-21 22:03:22,528] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43267382/tmp3_zl9jim/multiqc_data' to '/vast/gencore/GENEFLOW/work/a3/57d4516236fddd16fa14fe9a6f294f/merged/multiqc_data' [2024-02-21 22:03:22,853] multiqc [INFO ] MultiQC complete