[2024-02-19 06:38:52,652] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-19 06:38:52,652] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-19 06:38:52,653] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-19 06:38:52,655] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-19 06:38:52,655] 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}} [2024-02-19 06:38:52,655] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-19 06:38:52,816] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-19 06:38:52,816] multiqc [INFO ] This is MultiQC v1.9 [2024-02-19 06:38:52,816] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-19 06:38:52,816] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/7e/fc5ff43ded51a7ccc231423931e749/merged [2024-02-19 06:38:52,816] multiqc [INFO ] Template : default [2024-02-19 06:38:52,816] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-19 06:38:52,816] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/7e/fc5ff43ded51a7ccc231423931e749/merged [2024-02-19 06:38:52,817] 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 [2024-02-19 06:38:52,817] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43128235/tmpnjg9i13_ [2024-02-19 06:38:52,938] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n01_DEG_p17D_fastqc.html [2024-02-19 06:38:52,945] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n01_DEG_p17D_fastqc.html [2024-02-19 06:38:53,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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[2024-02-19 06:38:55,158] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17C_fastqc.html [2024-02-19 06:38:55,167] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17C_fastqc.html [2024-02-19 06:38:55,233] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17D_fastqc.html [2024-02-19 06:38:55,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17D_fastqc.html [2024-02-19 06:38:55,327] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17F_fastqc.html [2024-02-19 06:38:55,334] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17F_fastqc.html [2024-02-19 06:38:55,399] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17G_fastqc.html [2024-02-19 06:38:55,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n02_DEG_p9p17G_fastqc.html [2024-02-19 06:38:55,470] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H3VHMDSXC_n02_undetermined_fastqc.html [2024-02-19 06:38:55,476] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H3VHMDSXC_n02_undetermined_fastqc.html [2024-02-19 06:38:55,539] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-19 06:38:55,545] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-02-19 06:38:55,994] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-19 06:38:55,996] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-19 06:38:56,013] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 17 samples (table) [2024-02-19 06:38:56,014] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-19 06:38:56,025] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-02-19 06:38:56,030] multiqc [DEBUG ] No samples found: conpair [2024-02-19 06:38:56,036] multiqc [DEBUG ] No samples found: peddy [2024-02-19 06:38:56,044] multiqc [DEBUG ] No samples found: somalier [2024-02-19 06:38:56,049] multiqc [DEBUG ] No samples found: methylQA [2024-02-19 06:38:56,058] multiqc [DEBUG ] No samples found: mosdepth [2024-02-19 06:38:56,063] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-19 06:38:56,066] multiqc [DEBUG ] No samples found: qualimap [2024-02-19 06:38:56,071] multiqc [DEBUG ] No samples found: preseq [2024-02-19 06:38:56,076] multiqc [DEBUG ] No samples found: quast [2024-02-19 06:38:56,080] multiqc [DEBUG ] No samples found: qorts [2024-02-19 06:38:56,086] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-19 06:38:56,090] multiqc [DEBUG ] No samples found: rockhopper [2024-02-19 06:38:56,095] multiqc [DEBUG ] No samples found: rsem [2024-02-19 06:38:56,108] multiqc [DEBUG ] No samples found: rseqc [2024-02-19 06:38:56,113] multiqc [DEBUG ] No samples found: busco [2024-02-19 06:38:56,119] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-19 06:38:56,123] multiqc [DEBUG ] No samples found: disambiguate [2024-02-19 06:38:56,128] multiqc [DEBUG ] No samples found: supernova [2024-02-19 06:38:56,143] multiqc [DEBUG ] No samples found: deeptools [2024-02-19 06:38:56,148] multiqc [DEBUG ] No samples found: sargasso [2024-02-19 06:38:56,153] multiqc [DEBUG ] No samples found: verifybamid [2024-02-19 06:38:56,158] multiqc [DEBUG ] No samples found: mirtrace [2024-02-19 06:38:56,163] multiqc [DEBUG ] No samples found: happy [2024-02-19 06:38:56,167] multiqc [DEBUG ] No samples found: mirtop [2024-02-19 06:38:56,174] multiqc [DEBUG ] No samples found: homer [2024-02-19 06:38:56,179] multiqc [DEBUG ] No samples found: macs2 [2024-02-19 06:38:56,184] multiqc [DEBUG ] No samples found: theta2 [2024-02-19 06:38:56,188] multiqc [DEBUG ] No samples found: snpeff [2024-02-19 06:38:56,196] multiqc [DEBUG ] No samples found: gatk [2024-02-19 06:38:56,201] multiqc [DEBUG ] No samples found: htseq [2024-02-19 06:38:56,207] multiqc [DEBUG ] No samples found: bcftools [2024-02-19 06:38:56,212] multiqc [DEBUG ] No samples found: featureCounts [2024-02-19 06:38:56,218] multiqc [DEBUG ] No samples found: fgbio [2024-02-19 06:38:56,234] multiqc [DEBUG ] No samples found: dragen [2024-02-19 06:38:56,239] multiqc [DEBUG ] No samples found: dedup [2024-02-19 06:38:56,244] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-19 06:38:56,267] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-19 06:38:56,273] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-19 06:38:56,276] multiqc [DEBUG ] No samples found: picard [2024-02-19 06:38:56,280] multiqc [DEBUG ] No samples found: prokka [2024-02-19 06:38:56,285] multiqc [DEBUG ] No samples found: samblaster [2024-02-19 06:38:56,296] multiqc [DEBUG ] No samples found: samtools [2024-02-19 06:38:56,301] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-19 06:38:56,307] multiqc [DEBUG ] No samples found: bamtools [2024-02-19 06:38:56,311] multiqc [DEBUG ] No samples found: jellyfish [2024-02-19 06:38:56,319] multiqc [DEBUG ] No samples found: vcftools [2024-02-19 06:38:56,325] multiqc [DEBUG ] No samples found: longranger [2024-02-19 06:38:56,330] multiqc [DEBUG ] No samples found: stacks [2024-02-19 06:38:56,337] multiqc [DEBUG ] No samples found: varscan2 [2024-02-19 06:38:56,362] multiqc [DEBUG ] No samples found: bbmap [2024-02-19 06:38:56,368] multiqc [DEBUG ] No samples found: bismark [2024-02-19 06:38:56,375] multiqc [DEBUG ] No samples found: biscuit [2024-02-19 06:38:56,381] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-19 06:38:56,386] multiqc [DEBUG ] No samples found: hicup [2024-02-19 06:38:56,391] multiqc [DEBUG ] No samples found: hicpro [2024-02-19 06:38:56,396] multiqc [DEBUG ] No samples found: salmon [2024-02-19 06:38:56,401] multiqc [DEBUG ] No samples found: kallisto [2024-02-19 06:38:56,406] multiqc [DEBUG ] No samples found: slamdunk [2024-02-19 06:38:56,411] multiqc [DEBUG ] No samples found: star [2024-02-19 06:38:56,416] multiqc [DEBUG ] No samples found: hisat2 [2024-02-19 06:38:56,421] multiqc [DEBUG ] No samples found: tophat [2024-02-19 06:38:56,426] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-19 06:38:56,431] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-19 06:38:56,436] multiqc [DEBUG ] No samples found: snpsplit [2024-02-19 06:38:56,440] multiqc [DEBUG ] No samples found: kat [2024-02-19 06:38:56,445] multiqc [DEBUG ] No samples found: leehom [2024-02-19 06:38:56,449] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-19 06:38:56,454] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-19 06:38:56,459] multiqc [DEBUG ] No samples found: cutadapt [2024-02-19 06:38:56,463] multiqc [DEBUG ] No samples found: flexbar [2024-02-19 06:38:56,468] multiqc [DEBUG ] No samples found: kaiju [2024-02-19 06:38:56,473] multiqc [DEBUG ] No samples found: kraken [2024-02-19 06:38:56,478] multiqc [DEBUG ] No samples found: malt [2024-02-19 06:38:56,483] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-19 06:38:56,488] multiqc [DEBUG ] No samples found: sickle [2024-02-19 06:38:56,493] multiqc [DEBUG ] No samples found: skewer [2024-02-19 06:38:56,497] multiqc [DEBUG ] No samples found: sortmerna [2024-02-19 06:38:56,502] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-19 06:38:56,506] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-19 06:38:56,511] multiqc [DEBUG ] No samples found: afterqc [2024-02-19 06:38:56,516] multiqc [DEBUG ] No samples found: fastp [2024-02-19 06:39:03,074] multiqc.modules.fastqc.fastqc [INFO ] Found 34 reports [2024-02-19 06:39:03,602] multiqc [DEBUG ] No samples found: pycoqc [2024-02-19 06:39:03,607] multiqc [DEBUG ] No samples found: minionqc [2024-02-19 06:39:03,612] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-19 06:39:03,617] multiqc [DEBUG ] No samples found: clusterflow [2024-02-19 06:39:03,622] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-19 06:39:03,627] multiqc [DEBUG ] No samples found: interop [2024-02-19 06:39:03,632] multiqc [DEBUG ] No samples found: ivar [2024-02-19 06:39:03,637] multiqc [DEBUG ] No samples found: flash [2024-02-19 06:39:03,641] multiqc [DEBUG ] No samples found: seqyclean [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,641] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-19 06:39:03,642] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-19 06:39:03,683] multiqc [INFO ] Compressing plot data [2024-02-19 06:39:04,421] multiqc [INFO ] Report : multiqc_report.html [2024-02-19 06:39:04,422] multiqc [INFO ] Data : multiqc_data [2024-02-19 06:39:04,422] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43128235/tmpnjg9i13_/multiqc_data' to '/vast/gencore/GENEFLOW/work/7e/fc5ff43ded51a7ccc231423931e749/merged/multiqc_data' [2024-02-19 06:39:04,600] multiqc [INFO ] MultiQC complete