[2024-05-03 08:20:58,550] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-05-03 08:20:58,550] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-05-03 08:20:58,550] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-05-03 08:20:58,553] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-05-03 08:20:58,553] 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}} [2024-05-03 08:20:58,553] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-03 08:20:58,584] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-05-03 08:20:58,584] multiqc [INFO ] This is MultiQC v1.9 [2024-05-03 08:20:58,584] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-05-03 08:20:58,584] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/52/36f7c0587767754f3bdd53e13e5d8f/merged [2024-05-03 08:20:58,584] multiqc [INFO ] Template : default [2024-05-03 08:20:58,584] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-05-03 08:20:58,584] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/52/36f7c0587767754f3bdd53e13e5d8f/merged [2024-05-03 08:20:58,585] 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 [2024-05-03 08:20:58,585] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-46012658/tmpzdob6di8 [2024-05-03 08:20:58,712] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n01_KO_H2AZ_1_fastqc.html [2024-05-03 08:20:58,720] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n01_KO_H2AZ_1_fastqc.html [2024-05-03 08:20:58,787] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HYJMJDRX3_n02_KO_SOX2_1_fastqc.html [2024-05-03 08:21:00,276] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_KO_SOX2_1_fastqc.html [2024-05-03 08:21:00,339] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n02_KO_SOX2_2_fastqc.html [2024-05-03 08:21:00,345] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_KO_SOX2_2_fastqc.html [2024-05-03 08:21:00,408] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_H2AZ_1_fastqc.html [2024-05-03 08:21:00,414] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_H2AZ_1_fastqc.html [2024-05-03 08:21:00,474] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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HYJMJDRX3_n02_NT_K4Me3_1_fastqc.html [2024-05-03 08:21:00,694] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_K4Me3_1_fastqc.html [2024-05-03 08:21:00,756] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_K4Me3_2_fastqc.html [2024-05-03 08:21:00,762] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_K4Me3_2_fastqc.html [2024-05-03 08:21:00,823] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_ZNHIT_1_fastqc.html [2024-05-03 08:21:00,830] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_NT_ZNHIT_1_fastqc.html [2024-05-03 08:21:00,891] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HYJMJDRX3_n02_undetermined_fastqc.html [2024-05-03 08:21:00,899] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HYJMJDRX3_n02_undetermined_fastqc.html [2024-05-03 08:21:00,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-03 08:21:00,965] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-05-03 08:21:01,671] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-03 08:21:01,673] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-05-03 08:21:01,692] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 16 samples (table) [2024-05-03 08:21:01,694] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-05-03 08:21:01,704] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-05-03 08:21:01,709] multiqc [DEBUG ] No samples found: conpair [2024-05-03 08:21:01,715] multiqc [DEBUG ] No samples found: peddy [2024-05-03 08:21:01,720] multiqc [DEBUG ] No samples found: somalier [2024-05-03 08:21:01,726] multiqc [DEBUG ] No samples found: methylQA [2024-05-03 08:21:01,735] multiqc [DEBUG ] No samples found: mosdepth [2024-05-03 08:21:01,740] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-05-03 08:21:01,744] multiqc [DEBUG ] No samples found: qualimap [2024-05-03 08:21:01,749] multiqc [DEBUG ] No samples found: preseq [2024-05-03 08:21:01,755] multiqc [DEBUG ] No samples found: quast [2024-05-03 08:21:01,760] multiqc [DEBUG ] No samples found: qorts [2024-05-03 08:21:01,766] multiqc [DEBUG ] No samples found: rna_seqc [2024-05-03 08:21:01,771] multiqc [DEBUG ] No samples found: rockhopper [2024-05-03 08:21:01,776] multiqc [DEBUG ] No samples found: rsem [2024-05-03 08:21:01,789] multiqc [DEBUG ] No samples found: rseqc [2024-05-03 08:21:01,794] multiqc [DEBUG ] No samples found: busco [2024-05-03 08:21:01,800] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-05-03 08:21:01,805] multiqc [DEBUG ] No samples found: disambiguate [2024-05-03 08:21:01,810] multiqc [DEBUG ] No samples found: supernova [2024-05-03 08:21:01,825] multiqc [DEBUG ] No samples found: deeptools [2024-05-03 08:21:01,830] multiqc [DEBUG ] No samples found: sargasso [2024-05-03 08:21:01,836] multiqc [DEBUG ] No samples found: verifybamid [2024-05-03 08:21:01,841] multiqc [DEBUG ] No samples found: mirtrace [2024-05-03 08:21:01,846] multiqc [DEBUG ] No samples found: happy [2024-05-03 08:21:01,852] multiqc [DEBUG ] No samples found: mirtop [2024-05-03 08:21:01,858] multiqc [DEBUG ] No samples found: homer [2024-05-03 08:21:01,864] multiqc [DEBUG ] No samples found: macs2 [2024-05-03 08:21:01,869] multiqc [DEBUG ] No samples found: theta2 [2024-05-03 08:21:01,874] multiqc [DEBUG ] No samples found: snpeff [2024-05-03 08:21:01,882] multiqc [DEBUG ] No samples found: gatk [2024-05-03 08:21:01,887] multiqc [DEBUG ] No samples found: htseq [2024-05-03 08:21:01,894] multiqc [DEBUG ] No samples found: bcftools [2024-05-03 08:21:01,899] multiqc [DEBUG ] No samples found: featureCounts [2024-05-03 08:21:01,907] multiqc [DEBUG ] No samples found: fgbio [2024-05-03 08:21:01,924] multiqc [DEBUG ] No samples found: dragen [2024-05-03 08:21:01,930] multiqc [DEBUG ] No samples found: dedup [2024-05-03 08:21:01,935] multiqc [DEBUG ] No samples found: damageprofiler [2024-05-03 08:21:01,961] multiqc [DEBUG ] No samples found: biobambam2 [2024-05-03 08:21:01,967] multiqc [DEBUG ] No samples found: mtnucratio [2024-05-03 08:21:01,969] multiqc [DEBUG ] No samples found: picard [2024-05-03 08:21:01,975] multiqc [DEBUG ] No samples found: prokka [2024-05-03 08:21:01,979] multiqc [DEBUG ] No samples found: samblaster [2024-05-03 08:21:01,989] multiqc [DEBUG ] No samples found: samtools [2024-05-03 08:21:01,994] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-05-03 08:21:02,001] multiqc [DEBUG ] No samples found: bamtools [2024-05-03 08:21:02,006] multiqc [DEBUG ] No samples found: jellyfish [2024-05-03 08:21:02,014] multiqc [DEBUG ] No samples found: vcftools [2024-05-03 08:21:02,019] multiqc [DEBUG ] No samples found: longranger [2024-05-03 08:21:02,025] multiqc [DEBUG ] No samples found: stacks [2024-05-03 08:21:02,030] multiqc [DEBUG ] No samples found: varscan2 [2024-05-03 08:21:02,045] multiqc [DEBUG ] No samples found: bbmap [2024-05-03 08:21:02,050] multiqc [DEBUG ] No samples found: bismark [2024-05-03 08:21:02,056] multiqc [DEBUG ] No samples found: biscuit [2024-05-03 08:21:02,061] multiqc [DEBUG ] No samples found: hicexplorer [2024-05-03 08:21:02,066] multiqc [DEBUG ] No samples found: hicup [2024-05-03 08:21:02,071] multiqc [DEBUG ] No samples found: hicpro [2024-05-03 08:21:02,076] multiqc [DEBUG ] No samples found: salmon [2024-05-03 08:21:02,081] multiqc [DEBUG ] No samples found: kallisto [2024-05-03 08:21:02,086] multiqc [DEBUG ] No samples found: slamdunk [2024-05-03 08:21:02,091] multiqc [DEBUG ] No samples found: star [2024-05-03 08:21:02,096] multiqc [DEBUG ] No samples found: hisat2 [2024-05-03 08:21:02,100] multiqc [DEBUG ] No samples found: tophat [2024-05-03 08:21:02,105] multiqc [DEBUG ] No samples found: bowtie2 [2024-05-03 08:21:02,111] multiqc [DEBUG ] No samples found: bowtie1 [2024-05-03 08:21:02,116] multiqc [DEBUG ] No samples found: snpsplit [2024-05-03 08:21:02,121] multiqc [DEBUG ] No samples found: kat [2024-05-03 08:21:02,126] multiqc [DEBUG ] No samples found: leehom [2024-05-03 08:21:02,131] multiqc [DEBUG ] No samples found: adapterRemoval [2024-05-03 08:21:02,136] multiqc [DEBUG ] No samples found: clipandmerge [2024-05-03 08:21:02,142] multiqc [DEBUG ] No samples found: cutadapt [2024-05-03 08:21:02,147] multiqc [DEBUG ] No samples found: flexbar [2024-05-03 08:21:02,152] multiqc [DEBUG ] No samples found: kaiju [2024-05-03 08:21:02,157] multiqc [DEBUG ] No samples found: kraken [2024-05-03 08:21:02,162] multiqc [DEBUG ] No samples found: malt [2024-05-03 08:21:02,168] multiqc [DEBUG ] No samples found: trimmomatic [2024-05-03 08:21:02,173] multiqc [DEBUG ] No samples found: sickle [2024-05-03 08:21:02,178] multiqc [DEBUG ] No samples found: skewer [2024-05-03 08:21:02,182] multiqc [DEBUG ] No samples found: sortmerna [2024-05-03 08:21:02,187] multiqc [DEBUG ] No samples found: biobloomtools [2024-05-03 08:21:02,192] multiqc [DEBUG ] No samples found: fastq_screen [2024-05-03 08:21:02,197] multiqc [DEBUG ] No samples found: afterqc [2024-05-03 08:21:02,201] multiqc [DEBUG ] No samples found: fastp [2024-05-03 08:21:03,115] multiqc.modules.fastqc.fastqc [INFO ] Found 32 reports [2024-05-03 08:21:03,436] multiqc [DEBUG ] No samples found: pycoqc [2024-05-03 08:21:03,441] multiqc [DEBUG ] No samples found: minionqc [2024-05-03 08:21:03,446] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-05-03 08:21:03,452] multiqc [DEBUG ] No samples found: clusterflow [2024-05-03 08:21:03,458] multiqc [DEBUG ] No samples found: bcl2fastq [2024-05-03 08:21:03,463] multiqc [DEBUG ] No samples found: interop [2024-05-03 08:21:03,468] multiqc [DEBUG ] No samples found: ivar [2024-05-03 08:21:03,476] multiqc [DEBUG ] No samples found: flash [2024-05-03 08:21:03,481] multiqc [DEBUG ] No samples found: seqyclean [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-05-03 08:21:03,481] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-05-03 08:21:03,482] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-05-03 08:21:03,520] multiqc [INFO ] Compressing plot data [2024-05-03 08:21:04,105] multiqc [INFO ] Report : multiqc_report.html [2024-05-03 08:21:04,105] multiqc [INFO ] Data : multiqc_data [2024-05-03 08:21:04,105] multiqc [DEBUG ] Moving data file from '/state/partition1/job-46012658/tmpzdob6di8/multiqc_data' to '/vast/gencore/GENEFLOW/work/52/36f7c0587767754f3bdd53e13e5d8f/merged/multiqc_data' [2024-05-03 08:21:04,277] multiqc [INFO ] MultiQC complete