[2024-04-09 04:23:56,278] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-04-09 04:23:56,278] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-04-09 04:23:56,278] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-04-09 04:23:56,281] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-04-09 04:23:56,281] 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}} [2024-04-09 04:23:56,281] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-09 04:23:56,313] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-04-09 04:23:56,313] multiqc [INFO ] This is MultiQC v1.9 [2024-04-09 04:23:56,313] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-09 04:23:56,313] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/cd/93077f4f65b082f1af2d6ca6612f70/merged [2024-04-09 04:23:56,313] multiqc [INFO ] Template : default [2024-04-09 04:23:56,313] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-04-09 04:23:56,313] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/cd/93077f4f65b082f1af2d6ca6612f70/merged [2024-04-09 04:23:56,314] 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 [2024-04-09 04:23:56,314] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45126376/tmpl8tmql4t [2024-04-09 04:23:56,481] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n01_MDA_01_fastqc.html [2024-04-09 04:23:56,512] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n01_MDA_01_fastqc.html [2024-04-09 04:23:56,640] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-04-09 04:23:59,357] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_04_fastqc.html [2024-04-09 04:23:59,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_04_fastqc.html [2024-04-09 04:23:59,506] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_05_fastqc.html [2024-04-09 04:23:59,530] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_05_fastqc.html [2024-04-09 04:23:59,670] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_06_fastqc.html [2024-04-09 04:23:59,679] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_06_fastqc.html [2024-04-09 04:23:59,804] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_07_fastqc.html [2024-04-09 04:23:59,822] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_07_fastqc.html [2024-04-09 04:23:59,925] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_08_fastqc.html [2024-04-09 04:23:59,953] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_08_fastqc.html [2024-04-09 04:24:00,073] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_09_fastqc.html [2024-04-09 04:24:00,087] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_09_fastqc.html [2024-04-09 04:24:00,187] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_10_fastqc.html [2024-04-09 04:24:00,200] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_10_fastqc.html [2024-04-09 04:24:00,314] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_11_fastqc.html [2024-04-09 04:24:00,326] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_11_fastqc.html [2024-04-09 04:24:00,450] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_12_fastqc.html [2024-04-09 04:24:00,469] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_12_fastqc.html [2024-04-09 04:24:00,575] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_13_fastqc.html [2024-04-09 04:24:00,588] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_13_fastqc.html [2024-04-09 04:24:00,681] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_14_fastqc.html [2024-04-09 04:24:00,690] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_14_fastqc.html [2024-04-09 04:24:00,858] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_15_fastqc.html [2024-04-09 04:24:00,893] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_15_fastqc.html [2024-04-09 04:24:01,058] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_16_fastqc.html [2024-04-09 04:24:01,078] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_MDA_16_fastqc.html [2024-04-09 04:24:01,190] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HLM3KBGXV_n02_undetermined_fastqc.html [2024-04-09 04:24:01,201] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HLM3KBGXV_n02_undetermined_fastqc.html [2024-04-09 04:24:01,669] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-09 04:24:01,672] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-09 04:24:01,694] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2024-04-09 04:24:01,696] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-04-09 04:24:01,706] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-04-09 04:24:01,712] multiqc [DEBUG ] No samples found: conpair [2024-04-09 04:24:01,718] multiqc [DEBUG ] No samples found: peddy [2024-04-09 04:24:01,727] multiqc [DEBUG ] No samples found: somalier [2024-04-09 04:24:01,732] multiqc [DEBUG ] No samples found: methylQA [2024-04-09 04:24:01,741] multiqc [DEBUG ] No samples found: mosdepth [2024-04-09 04:24:01,747] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-04-09 04:24:01,751] multiqc [DEBUG ] No samples found: qualimap [2024-04-09 04:24:01,756] multiqc [DEBUG ] No samples found: preseq [2024-04-09 04:24:01,761] multiqc [DEBUG ] No samples found: quast [2024-04-09 04:24:01,767] multiqc [DEBUG ] No samples found: qorts [2024-04-09 04:24:01,772] multiqc [DEBUG ] No samples found: rna_seqc [2024-04-09 04:24:01,778] multiqc [DEBUG ] No samples found: rockhopper [2024-04-09 04:24:01,783] multiqc [DEBUG ] No samples found: rsem [2024-04-09 04:24:01,797] multiqc [DEBUG ] No samples found: rseqc [2024-04-09 04:24:01,802] multiqc [DEBUG ] No samples found: busco [2024-04-09 04:24:01,807] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-04-09 04:24:01,812] multiqc [DEBUG ] No samples found: disambiguate [2024-04-09 04:24:01,818] multiqc [DEBUG ] No samples found: supernova [2024-04-09 04:24:01,833] multiqc [DEBUG ] No samples found: deeptools [2024-04-09 04:24:01,838] multiqc [DEBUG ] No samples found: sargasso [2024-04-09 04:24:01,843] multiqc [DEBUG ] No samples found: verifybamid [2024-04-09 04:24:01,849] multiqc [DEBUG ] No samples found: mirtrace [2024-04-09 04:24:01,854] multiqc [DEBUG ] No samples found: happy [2024-04-09 04:24:01,859] multiqc [DEBUG ] No samples found: mirtop [2024-04-09 04:24:01,867] multiqc [DEBUG ] No samples found: homer [2024-04-09 04:24:01,872] multiqc [DEBUG ] No samples found: macs2 [2024-04-09 04:24:01,877] multiqc [DEBUG ] No samples found: theta2 [2024-04-09 04:24:01,882] multiqc [DEBUG ] No samples found: snpeff [2024-04-09 04:24:01,890] multiqc [DEBUG ] No samples found: gatk [2024-04-09 04:24:01,895] multiqc [DEBUG ] No samples found: htseq [2024-04-09 04:24:01,901] multiqc [DEBUG ] No samples found: bcftools [2024-04-09 04:24:01,906] multiqc [DEBUG ] No samples found: featureCounts [2024-04-09 04:24:01,913] multiqc [DEBUG ] No samples found: fgbio [2024-04-09 04:24:01,929] multiqc [DEBUG ] No samples found: dragen [2024-04-09 04:24:01,935] multiqc [DEBUG ] No samples found: dedup [2024-04-09 04:24:01,940] multiqc [DEBUG ] No samples found: damageprofiler [2024-04-09 04:24:01,965] multiqc [DEBUG ] No samples found: biobambam2 [2024-04-09 04:24:01,971] multiqc [DEBUG ] No samples found: mtnucratio [2024-04-09 04:24:01,973] multiqc [DEBUG ] No samples found: picard [2024-04-09 04:24:01,979] multiqc [DEBUG ] No samples found: prokka [2024-04-09 04:24:01,984] multiqc [DEBUG ] No samples found: samblaster [2024-04-09 04:24:01,995] multiqc [DEBUG ] No samples found: samtools [2024-04-09 04:24:02,000] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-04-09 04:24:02,006] multiqc [DEBUG ] No samples found: bamtools [2024-04-09 04:24:02,011] multiqc [DEBUG ] No samples found: jellyfish [2024-04-09 04:24:02,021] multiqc [DEBUG ] No samples found: vcftools [2024-04-09 04:24:02,026] multiqc [DEBUG ] No samples found: longranger [2024-04-09 04:24:02,032] multiqc [DEBUG ] No samples found: stacks [2024-04-09 04:24:02,037] multiqc [DEBUG ] No samples found: varscan2 [2024-04-09 04:24:02,053] multiqc [DEBUG ] No samples found: bbmap [2024-04-09 04:24:02,058] multiqc [DEBUG ] No samples found: bismark [2024-04-09 04:24:02,064] multiqc [DEBUG ] No samples found: biscuit [2024-04-09 04:24:02,070] multiqc [DEBUG ] No samples found: hicexplorer [2024-04-09 04:24:02,075] multiqc [DEBUG ] No samples found: hicup [2024-04-09 04:24:02,081] multiqc [DEBUG ] No samples found: hicpro [2024-04-09 04:24:02,085] multiqc [DEBUG ] No samples found: salmon [2024-04-09 04:24:02,091] multiqc [DEBUG ] No samples found: kallisto [2024-04-09 04:24:02,096] multiqc [DEBUG ] No samples found: slamdunk [2024-04-09 04:24:02,102] multiqc [DEBUG ] No samples found: star [2024-04-09 04:24:02,107] multiqc [DEBUG ] No samples found: hisat2 [2024-04-09 04:24:02,112] multiqc [DEBUG ] No samples found: tophat [2024-04-09 04:24:02,118] multiqc [DEBUG ] No samples found: bowtie2 [2024-04-09 04:24:02,123] multiqc [DEBUG ] No samples found: bowtie1 [2024-04-09 04:24:02,129] multiqc [DEBUG ] No samples found: snpsplit [2024-04-09 04:24:02,134] multiqc [DEBUG ] No samples found: kat [2024-04-09 04:24:02,140] multiqc [DEBUG ] No samples found: leehom [2024-04-09 04:24:02,146] multiqc [DEBUG ] No samples found: adapterRemoval [2024-04-09 04:24:02,151] multiqc [DEBUG ] No samples found: clipandmerge [2024-04-09 04:24:02,157] multiqc [DEBUG ] No samples found: cutadapt [2024-04-09 04:24:02,162] multiqc [DEBUG ] No samples found: flexbar [2024-04-09 04:24:02,167] multiqc [DEBUG ] No samples found: kaiju [2024-04-09 04:24:02,173] multiqc [DEBUG ] No samples found: kraken [2024-04-09 04:24:02,178] multiqc [DEBUG ] No samples found: malt [2024-04-09 04:24:02,184] multiqc [DEBUG ] No samples found: trimmomatic [2024-04-09 04:24:02,189] multiqc [DEBUG ] No samples found: sickle [2024-04-09 04:24:02,194] multiqc [DEBUG ] No samples found: skewer [2024-04-09 04:24:02,200] multiqc [DEBUG ] No samples found: sortmerna [2024-04-09 04:24:02,205] multiqc [DEBUG ] No samples found: biobloomtools [2024-04-09 04:24:02,210] multiqc [DEBUG ] No samples found: fastq_screen [2024-04-09 04:24:02,216] multiqc [DEBUG ] No samples found: afterqc [2024-04-09 04:24:02,221] multiqc [DEBUG ] No samples found: fastp [2024-04-09 04:24:04,245] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2024-04-09 04:24:04,459] multiqc [DEBUG ] No samples found: pycoqc [2024-04-09 04:24:04,465] multiqc [DEBUG ] No samples found: minionqc [2024-04-09 04:24:04,470] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-04-09 04:24:04,475] multiqc [DEBUG ] No samples found: clusterflow [2024-04-09 04:24:04,481] multiqc [DEBUG ] No samples found: bcl2fastq [2024-04-09 04:24:04,486] multiqc [DEBUG ] No samples found: interop [2024-04-09 04:24:04,492] multiqc [DEBUG ] No samples found: ivar [2024-04-09 04:24:04,497] multiqc [DEBUG ] No samples found: flash [2024-04-09 04:24:04,502] multiqc [DEBUG ] No samples found: seqyclean [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,502] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-04-09 04:24:04,503] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-04-09 04:24:04,546] multiqc [INFO ] Compressing plot data [2024-04-09 04:24:05,066] multiqc [INFO ] Report : multiqc_report.html [2024-04-09 04:24:05,067] multiqc [INFO ] Data : multiqc_data [2024-04-09 04:24:05,067] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45126376/tmpl8tmql4t/multiqc_data' to '/vast/gencore/GENEFLOW/work/cd/93077f4f65b082f1af2d6ca6612f70/merged/multiqc_data' [2024-04-09 04:24:05,364] multiqc [INFO ] MultiQC complete