[2024-06-07 16:48:39,993] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-07 16:48:39,994] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-07 16:48:39,994] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-07 16:48:39,997] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-07 16:48:39,997] 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}} [2024-06-07 16:48:39,997] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-07 16:48:40,034] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-07 16:48:40,034] multiqc [INFO ] This is MultiQC v1.9 [2024-06-07 16:48:40,035] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-07 16:48:40,035] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/9f/9941c3d821e38e02cc7e0a0779d460/1 [2024-06-07 16:48:40,035] multiqc [INFO ] Template : default [2024-06-07 16:48:40,035] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-07 16:48:40,035] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/9f/9941c3d821e38e02cc7e0a0779d460/1 [2024-06-07 16:48:40,035] 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 [2024-06-07 16:48:40,035] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47325665/tmphpbntf7q [2024-06-07 16:48:40,169] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA86_fastqc.html [2024-06-07 16:48:40,177] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA86_fastqc.html [2024-06-07 16:48:40,259] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA87_fastqc.html [2024-06-07 16:48:40,266] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA87_fastqc.html [2024-06-07 16:48:40,331] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA88_fastqc.html [2024-06-07 16:48:40,337] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AA88_fastqc.html [2024-06-07 16:48:40,401] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AS02_fastqc.html [2024-06-07 16:48:40,408] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AS02_fastqc.html [2024-06-07 16:48:40,483] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AS03_fastqc.html [2024-06-07 16:48:40,494] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_NYUEB_HiC_AS03_fastqc.html [2024-06-07 16:48:40,561] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_undetermined_fastqc.html [2024-06-07 16:48:40,568] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n01_undetermined_fastqc.html [2024-06-07 16:48:40,639] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA86_fastqc.html [2024-06-07 16:48:40,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA86_fastqc.html [2024-06-07 16:48:40,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA87_fastqc.html [2024-06-07 16:48:40,736] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA87_fastqc.html [2024-06-07 16:48:40,799] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA88_fastqc.html [2024-06-07 16:48:40,806] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AA88_fastqc.html [2024-06-07 16:48:40,879] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AS02_fastqc.html [2024-06-07 16:48:40,890] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AS02_fastqc.html [2024-06-07 16:48:40,964] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AS03_fastqc.html [2024-06-07 16:48:40,970] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_NYUEB_HiC_AS03_fastqc.html [2024-06-07 16:48:41,041] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_undetermined_fastqc.html [2024-06-07 16:48:41,048] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LG6KY_l01_n02_undetermined_fastqc.html [2024-06-07 16:48:41,122] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,135] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:41,183] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-06-07 16:48:42,851] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-07 16:48:42,853] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-07 16:48:42,866] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 6 samples (table) [2024-06-07 16:48:42,867] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-07 16:48:42,878] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-06-07 16:48:42,888] multiqc [DEBUG ] No samples found: conpair [2024-06-07 16:48:42,895] multiqc [DEBUG ] No samples found: peddy [2024-06-07 16:48:42,905] multiqc [DEBUG ] No samples found: somalier [2024-06-07 16:48:42,910] multiqc [DEBUG ] No samples found: methylQA [2024-06-07 16:48:42,923] multiqc [DEBUG ] No samples found: mosdepth [2024-06-07 16:48:42,930] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-07 16:48:42,933] multiqc [DEBUG ] No samples found: qualimap [2024-06-07 16:48:42,939] multiqc [DEBUG ] No samples found: preseq [2024-06-07 16:48:42,945] multiqc [DEBUG ] No samples found: quast [2024-06-07 16:48:42,951] multiqc [DEBUG ] No samples found: qorts [2024-06-07 16:48:42,956] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-07 16:48:42,962] multiqc [DEBUG ] No samples found: rockhopper [2024-06-07 16:48:42,971] multiqc [DEBUG ] No samples found: rsem [2024-06-07 16:48:42,988] multiqc [DEBUG ] No samples found: rseqc [2024-06-07 16:48:42,998] multiqc [DEBUG ] No samples found: busco [2024-06-07 16:48:43,005] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-07 16:48:43,011] multiqc [DEBUG ] No samples found: disambiguate [2024-06-07 16:48:43,020] multiqc [DEBUG ] No samples found: supernova [2024-06-07 16:48:43,038] multiqc [DEBUG ] No samples found: deeptools [2024-06-07 16:48:43,043] multiqc [DEBUG ] No samples found: sargasso [2024-06-07 16:48:43,051] multiqc [DEBUG ] No samples found: verifybamid [2024-06-07 16:48:43,056] multiqc [DEBUG ] No samples found: mirtrace [2024-06-07 16:48:43,061] multiqc [DEBUG ] No samples found: happy [2024-06-07 16:48:43,067] multiqc [DEBUG ] No samples found: mirtop [2024-06-07 16:48:43,075] multiqc [DEBUG ] No samples found: homer [2024-06-07 16:48:43,081] multiqc [DEBUG ] No samples found: macs2 [2024-06-07 16:48:43,086] multiqc [DEBUG ] No samples found: theta2 [2024-06-07 16:48:43,091] multiqc [DEBUG ] No samples found: snpeff [2024-06-07 16:48:43,101] multiqc [DEBUG ] No samples found: gatk [2024-06-07 16:48:43,109] multiqc [DEBUG ] No samples found: htseq [2024-06-07 16:48:43,117] multiqc [DEBUG ] No samples found: bcftools [2024-06-07 16:48:43,124] multiqc [DEBUG ] No samples found: featureCounts [2024-06-07 16:48:43,134] multiqc [DEBUG ] No samples found: fgbio [2024-06-07 16:48:43,155] multiqc [DEBUG ] No samples found: dragen [2024-06-07 16:48:43,161] multiqc [DEBUG ] No samples found: dedup [2024-06-07 16:48:43,166] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-07 16:48:43,198] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-07 16:48:43,205] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-07 16:48:43,208] multiqc [DEBUG ] No samples found: picard [2024-06-07 16:48:43,215] multiqc [DEBUG ] No samples found: prokka [2024-06-07 16:48:43,220] multiqc [DEBUG ] No samples found: samblaster [2024-06-07 16:48:43,237] multiqc [DEBUG ] No samples found: samtools [2024-06-07 16:48:43,242] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-07 16:48:43,250] multiqc [DEBUG ] No samples found: bamtools [2024-06-07 16:48:43,255] multiqc [DEBUG ] No samples found: jellyfish [2024-06-07 16:48:43,265] multiqc [DEBUG ] No samples found: vcftools [2024-06-07 16:48:43,272] multiqc [DEBUG ] No samples found: longranger [2024-06-07 16:48:43,278] multiqc [DEBUG ] No samples found: stacks [2024-06-07 16:48:43,285] multiqc [DEBUG ] No samples found: varscan2 [2024-06-07 16:48:43,307] multiqc [DEBUG ] No samples found: bbmap [2024-06-07 16:48:43,312] multiqc [DEBUG ] No samples found: bismark [2024-06-07 16:48:43,318] multiqc [DEBUG ] No samples found: biscuit [2024-06-07 16:48:43,326] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-07 16:48:43,332] multiqc [DEBUG ] No samples found: hicup [2024-06-07 16:48:43,338] multiqc [DEBUG ] No samples found: hicpro [2024-06-07 16:48:43,343] multiqc [DEBUG ] No samples found: salmon [2024-06-07 16:48:43,350] multiqc [DEBUG ] No samples found: kallisto [2024-06-07 16:48:43,356] multiqc [DEBUG ] No samples found: slamdunk [2024-06-07 16:48:43,362] multiqc [DEBUG ] No samples found: star [2024-06-07 16:48:43,367] multiqc [DEBUG ] No samples found: hisat2 [2024-06-07 16:48:43,376] multiqc [DEBUG ] No samples found: tophat [2024-06-07 16:48:43,382] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-07 16:48:43,389] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-07 16:48:43,395] multiqc [DEBUG ] No samples found: snpsplit [2024-06-07 16:48:43,402] multiqc [DEBUG ] No samples found: kat [2024-06-07 16:48:43,406] multiqc [DEBUG ] No samples found: leehom [2024-06-07 16:48:43,412] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-07 16:48:43,420] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-07 16:48:43,426] multiqc [DEBUG ] No samples found: cutadapt [2024-06-07 16:48:43,432] multiqc [DEBUG ] No samples found: flexbar [2024-06-07 16:48:43,438] multiqc [DEBUG ] No samples found: kaiju [2024-06-07 16:48:43,444] multiqc [DEBUG ] No samples found: kraken [2024-06-07 16:48:43,451] multiqc [DEBUG ] No samples found: malt [2024-06-07 16:48:43,457] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-07 16:48:43,463] multiqc [DEBUG ] No samples found: sickle [2024-06-07 16:48:43,469] multiqc [DEBUG ] No samples found: skewer [2024-06-07 16:48:43,474] multiqc [DEBUG ] No samples found: sortmerna [2024-06-07 16:48:43,482] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-07 16:48:43,489] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-07 16:48:43,495] multiqc [DEBUG ] No samples found: afterqc [2024-06-07 16:48:43,501] multiqc [DEBUG ] No samples found: fastp [2024-06-07 16:48:43,602] multiqc.modules.fastqc.fastqc [INFO ] Found 12 reports [2024-06-07 16:48:43,724] multiqc [DEBUG ] No samples found: pycoqc [2024-06-07 16:48:43,730] multiqc [DEBUG ] No samples found: minionqc [2024-06-07 16:48:43,737] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-07 16:48:43,744] multiqc [DEBUG ] No samples found: clusterflow [2024-06-07 16:48:43,750] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-07 16:48:43,756] multiqc [DEBUG ] No samples found: interop [2024-06-07 16:48:43,761] multiqc [DEBUG ] No samples found: ivar [2024-06-07 16:48:43,769] multiqc [DEBUG ] No samples found: flash [2024-06-07 16:48:43,774] multiqc [DEBUG ] No samples found: seqyclean [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-07 16:48:43,775] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-07 16:48:43,791] multiqc [INFO ] Compressing plot data [2024-06-07 16:48:43,998] multiqc [INFO ] Report : multiqc_report.html [2024-06-07 16:48:43,998] multiqc [INFO ] Data : multiqc_data [2024-06-07 16:48:43,998] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47325665/tmphpbntf7q/multiqc_data' to '/vast/gencore/GENEFLOW/work/9f/9941c3d821e38e02cc7e0a0779d460/1/multiqc_data' [2024-06-07 16:48:44,195] multiqc [INFO ] MultiQC complete