[2024-05-25 20:19:39,694] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-25 20:19:39,694] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-25 20:19:39,694] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-25 20:19:39,697] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-25 20:19:39,697] 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}} [2024-05-25 20:19:39,697] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-25 20:19:39,745] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-25 20:19:39,745] multiqc [INFO ] This is MultiQC v1.9 [2024-05-25 20:19:39,746] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-25 20:19:39,746] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/4e/ca1f791bb8e115145f04c9e3713386/merged [2024-05-25 20:19:39,746] multiqc [INFO ] Template : default [2024-05-25 20:19:39,746] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-25 20:19:39,746] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/4e/ca1f791bb8e115145f04c9e3713386/merged [2024-05-25 20:19:39,746] 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 [2024-05-25 20:19:39,746] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-46993706/tmp0nwuapei [2024-05-25 20:19:39,892] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n01_WGS_D_verna_173_fastqc.html [2024-05-25 20:19:39,901] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n01_WGS_D_verna_173_fastqc.html [2024-05-25 20:19:39,970] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize 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because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_257_fastqc.html [2024-05-25 20:19:53,440] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_258_fastqc.html [2024-05-25 20:19:53,447] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_258_fastqc.html [2024-05-25 20:19:53,517] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_259_fastqc.html [2024-05-25 20:19:53,524] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_259_fastqc.html [2024-05-25 20:19:53,596] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_260_fastqc.html [2024-05-25 20:19:53,602] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_260_fastqc.html [2024-05-25 20:19:53,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_261_fastqc.html [2024-05-25 20:19:53,763] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n02_WGS_D_verna_261_fastqc.html [2024-05-25 20:19:53,890] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVN2MDMXY_n02_undetermined_fastqc.html [2024-05-25 20:19:53,897] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVN2MDMXY_n02_undetermined_fastqc.html [2024-05-25 20:19:54,429] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-25 20:19:54,431] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-25 20:19:54,482] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 90 samples (table) [2024-05-25 20:19:54,483] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-25 20:19:54,493] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-25 20:19:54,499] multiqc [DEBUG ] No samples found: conpair [2024-05-25 20:19:54,505] multiqc [DEBUG ] No samples found: peddy [2024-05-25 20:19:54,511] multiqc [DEBUG ] No samples found: somalier [2024-05-25 20:19:54,517] multiqc [DEBUG ] No samples found: methylQA [2024-05-25 20:19:54,527] multiqc [DEBUG ] No samples found: mosdepth [2024-05-25 20:19:54,532] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-25 20:19:54,536] multiqc [DEBUG ] No samples found: qualimap [2024-05-25 20:19:54,541] multiqc [DEBUG ] No samples found: preseq [2024-05-25 20:19:54,547] multiqc [DEBUG ] No samples found: quast [2024-05-25 20:19:54,552] multiqc [DEBUG ] No samples found: qorts [2024-05-25 20:19:54,558] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-25 20:19:54,563] multiqc [DEBUG ] No samples found: rockhopper [2024-05-25 20:19:54,568] multiqc [DEBUG ] No samples found: rsem [2024-05-25 20:19:54,581] multiqc [DEBUG ] No samples found: rseqc [2024-05-25 20:19:54,587] multiqc [DEBUG ] No samples found: busco [2024-05-25 20:19:54,592] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-25 20:19:54,598] multiqc [DEBUG ] No samples found: disambiguate [2024-05-25 20:19:54,604] multiqc [DEBUG ] No samples found: supernova [2024-05-25 20:19:54,618] multiqc [DEBUG ] No samples found: deeptools [2024-05-25 20:19:54,623] multiqc [DEBUG ] No samples found: sargasso [2024-05-25 20:19:54,629] multiqc [DEBUG ] No samples found: verifybamid [2024-05-25 20:19:54,634] multiqc [DEBUG ] No samples found: mirtrace [2024-05-25 20:19:54,639] multiqc [DEBUG ] No samples found: happy [2024-05-25 20:19:54,645] multiqc [DEBUG ] No samples found: mirtop [2024-05-25 20:19:54,652] multiqc [DEBUG ] No samples found: homer [2024-05-25 20:19:54,657] multiqc [DEBUG ] No samples found: macs2 [2024-05-25 20:19:54,662] multiqc [DEBUG ] No samples found: theta2 [2024-05-25 20:19:54,668] multiqc [DEBUG ] No samples found: snpeff [2024-05-25 20:19:54,675] multiqc [DEBUG ] No samples found: gatk [2024-05-25 20:19:54,680] multiqc [DEBUG ] No samples found: htseq [2024-05-25 20:19:54,687] multiqc [DEBUG ] No samples found: bcftools [2024-05-25 20:19:54,692] multiqc [DEBUG ] No samples found: featureCounts [2024-05-25 20:19:54,700] multiqc [DEBUG ] No samples found: fgbio [2024-05-25 20:19:54,714] multiqc [DEBUG ] No samples found: dragen [2024-05-25 20:19:54,719] multiqc [DEBUG ] No samples found: dedup [2024-05-25 20:19:54,725] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-25 20:19:54,750] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-25 20:19:54,756] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-25 20:19:54,758] multiqc [DEBUG ] No samples found: picard [2024-05-25 20:19:54,764] multiqc [DEBUG ] No samples found: prokka [2024-05-25 20:19:54,769] multiqc [DEBUG ] No samples found: samblaster [2024-05-25 20:19:54,779] multiqc [DEBUG ] No samples found: samtools [2024-05-25 20:19:54,784] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-25 20:19:54,790] multiqc [DEBUG ] No samples found: bamtools [2024-05-25 20:19:54,795] multiqc [DEBUG ] No samples found: jellyfish [2024-05-25 20:19:54,804] multiqc [DEBUG ] No samples found: vcftools [2024-05-25 20:19:54,809] multiqc [DEBUG ] No samples found: longranger [2024-05-25 20:19:54,815] multiqc [DEBUG ] No samples found: stacks [2024-05-25 20:19:54,821] multiqc [DEBUG ] No samples found: varscan2 [2024-05-25 20:19:54,836] multiqc [DEBUG ] No samples found: bbmap [2024-05-25 20:19:54,843] multiqc [DEBUG ] No samples found: bismark [2024-05-25 20:19:54,848] multiqc [DEBUG ] No samples found: biscuit [2024-05-25 20:19:54,854] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-25 20:19:54,860] multiqc [DEBUG ] No samples found: hicup [2024-05-25 20:19:54,866] multiqc [DEBUG ] No samples found: hicpro [2024-05-25 20:19:54,871] multiqc [DEBUG ] No samples found: salmon [2024-05-25 20:19:54,877] multiqc [DEBUG ] No samples found: kallisto [2024-05-25 20:19:54,882] multiqc [DEBUG ] No samples found: slamdunk [2024-05-25 20:19:54,887] multiqc [DEBUG ] No samples found: star [2024-05-25 20:19:54,893] multiqc [DEBUG ] No samples found: hisat2 [2024-05-25 20:19:54,898] multiqc [DEBUG ] No samples found: tophat [2024-05-25 20:19:54,904] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-25 20:19:54,909] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-25 20:19:54,914] multiqc [DEBUG ] No samples found: snpsplit [2024-05-25 20:19:54,920] multiqc [DEBUG ] No samples found: kat [2024-05-25 20:19:54,924] multiqc [DEBUG ] No samples found: leehom [2024-05-25 20:19:54,930] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-25 20:19:54,936] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-25 20:19:54,941] multiqc [DEBUG ] No samples found: cutadapt [2024-05-25 20:19:54,947] multiqc [DEBUG ] No samples found: flexbar [2024-05-25 20:19:54,952] multiqc [DEBUG ] No samples found: kaiju [2024-05-25 20:19:54,957] multiqc [DEBUG ] No samples found: kraken [2024-05-25 20:19:54,963] multiqc [DEBUG ] No samples found: malt [2024-05-25 20:19:54,969] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-25 20:19:54,974] multiqc [DEBUG ] No samples found: sickle [2024-05-25 20:19:54,979] multiqc [DEBUG ] No samples found: skewer [2024-05-25 20:19:54,985] multiqc [DEBUG ] No samples found: sortmerna [2024-05-25 20:19:54,990] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-25 20:19:54,995] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-25 20:19:55,001] multiqc [DEBUG ] No samples found: afterqc [2024-05-25 20:19:55,006] multiqc [DEBUG ] No samples found: fastp [2024-05-25 20:20:12,493] multiqc.modules.fastqc.fastqc [INFO ] Found 180 reports [2024-05-25 20:20:12,497] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HVN2MDMXY_n01_WGS_D_verna_197' [2024-05-25 20:20:12,498] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HVN2MDMXY_n01_WGS_D_verna_255' [2024-05-25 20:20:12,498] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HVN2MDMXY_n02_WGS_D_verna_197' [2024-05-25 20:20:12,498] multiqc.modules.fastqc.fastqc [WARNING] Sample had zero reads: 'HVN2MDMXY_n02_WGS_D_verna_255' [2024-05-25 20:20:33,497] multiqc [DEBUG ] No samples found: pycoqc [2024-05-25 20:20:33,502] multiqc [DEBUG ] No samples found: minionqc [2024-05-25 20:20:33,508] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-25 20:20:33,514] multiqc [DEBUG ] No samples found: clusterflow [2024-05-25 20:20:33,520] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-25 20:20:33,526] multiqc [DEBUG ] No samples found: interop [2024-05-25 20:20:33,531] multiqc [DEBUG ] No samples found: ivar [2024-05-25 20:20:33,536] multiqc [DEBUG ] No samples found: flash [2024-05-25 20:20:33,542] multiqc [DEBUG ] No samples found: seqyclean [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-25 20:20:33,543] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-25 20:20:33,753] multiqc [INFO ] Compressing plot data [2024-05-25 20:20:33,839] multiqc [INFO ] Report : multiqc_report.html [2024-05-25 20:20:33,839] multiqc [INFO ] Data : multiqc_data [2024-05-25 20:20:33,839] multiqc [DEBUG ] Moving data file from '/state/partition1/job-46993706/tmp0nwuapei/multiqc_data' to '/vast/gencore/GENEFLOW/work/4e/ca1f791bb8e115145f04c9e3713386/merged/multiqc_data' [2024-05-25 20:20:34,071] multiqc [INFO ] MultiQC complete