[2024-07-30 12:23:10,520] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-07-30 12:23:10,521] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-07-30 12:23:10,521] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-07-30 12:23:10,524] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-07-30 12:23:10,524] 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}} [2024-07-30 12:23:10,524] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-30 12:23:10,608] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-07-30 12:23:10,608] multiqc [INFO ] This is MultiQC v1.9 [2024-07-30 12:23:10,608] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-07-30 12:23:10,608] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/1d/66a50deb0fe8d25183f9063ec5046e/1 [2024-07-30 12:23:10,608] multiqc [INFO ] Template : default [2024-07-30 12:23:10,609] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-07-30 12:23:10,609] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/1d/66a50deb0fe8d25183f9063ec5046e/1 [2024-07-30 12:23:10,609] 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 [2024-07-30 12:23:10,609] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49143825/tmpsmupig79 [2024-07-30 12:23:10,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.1_fastqc.html [2024-07-30 12:23:10,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.1_fastqc.html [2024-07-30 12:23:10,830] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.2_fastqc.html [2024-07-30 12:23:10,839] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.2_fastqc.html [2024-07-30 12:23:10,912] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.3_fastqc.html [2024-07-30 12:23:10,919] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.3_fastqc.html [2024-07-30 12:23:10,991] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.4_fastqc.html [2024-07-30 12:23:11,000] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GLVJ8_l01.4_fastqc.html [2024-07-30 12:23:11,382] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-30 12:23:11,384] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-07-30 12:23:11,389] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-07-30 12:23:11,394] multiqc [DEBUG ] No samples found: conpair [2024-07-30 12:23:11,400] multiqc [DEBUG ] No samples found: peddy [2024-07-30 12:23:11,410] multiqc [DEBUG ] No samples found: somalier [2024-07-30 12:23:11,415] multiqc [DEBUG ] No samples found: methylQA [2024-07-30 12:23:11,424] multiqc [DEBUG ] No samples found: mosdepth [2024-07-30 12:23:11,428] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-07-30 12:23:11,432] multiqc [DEBUG ] No samples found: qualimap [2024-07-30 12:23:11,437] multiqc [DEBUG ] No samples found: preseq [2024-07-30 12:23:11,442] multiqc [DEBUG ] No samples found: quast [2024-07-30 12:23:11,448] multiqc [DEBUG ] No samples found: qorts [2024-07-30 12:23:11,453] multiqc [DEBUG ] No samples found: rna_seqc [2024-07-30 12:23:11,458] multiqc [DEBUG ] No samples found: rockhopper [2024-07-30 12:23:11,463] multiqc [DEBUG ] No samples found: rsem [2024-07-30 12:23:11,476] multiqc [DEBUG ] No samples found: rseqc [2024-07-30 12:23:11,481] multiqc [DEBUG ] No samples found: busco [2024-07-30 12:23:11,486] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-07-30 12:23:11,491] multiqc [DEBUG ] No samples found: disambiguate [2024-07-30 12:23:11,496] multiqc [DEBUG ] No samples found: supernova [2024-07-30 12:23:11,511] multiqc [DEBUG ] No samples found: deeptools [2024-07-30 12:23:11,519] multiqc [DEBUG ] No samples found: sargasso [2024-07-30 12:23:11,525] multiqc [DEBUG ] No samples found: verifybamid [2024-07-30 12:23:11,530] multiqc [DEBUG ] No samples found: mirtrace [2024-07-30 12:23:11,535] multiqc [DEBUG ] No samples found: happy [2024-07-30 12:23:11,540] multiqc [DEBUG ] No samples found: mirtop [2024-07-30 12:23:11,547] multiqc [DEBUG ] No samples found: homer [2024-07-30 12:23:11,552] multiqc [DEBUG ] No samples found: macs2 [2024-07-30 12:23:11,557] multiqc [DEBUG ] No samples found: theta2 [2024-07-30 12:23:11,562] multiqc [DEBUG ] No samples found: snpeff [2024-07-30 12:23:11,570] multiqc [DEBUG ] No samples found: gatk [2024-07-30 12:23:11,574] multiqc [DEBUG ] No samples found: htseq [2024-07-30 12:23:11,581] multiqc [DEBUG ] No samples found: bcftools [2024-07-30 12:23:11,586] multiqc [DEBUG ] No samples found: featureCounts [2024-07-30 12:23:11,593] multiqc [DEBUG ] No samples found: fgbio [2024-07-30 12:23:11,609] multiqc [DEBUG ] No samples found: dragen [2024-07-30 12:23:11,614] multiqc [DEBUG ] No samples found: dedup [2024-07-30 12:23:11,620] multiqc [DEBUG ] No samples found: damageprofiler [2024-07-30 12:23:11,645] multiqc [DEBUG ] No samples found: biobambam2 [2024-07-30 12:23:11,650] multiqc [DEBUG ] No samples found: mtnucratio [2024-07-30 12:23:11,653] multiqc [DEBUG ] No samples found: picard [2024-07-30 12:23:11,658] multiqc [DEBUG ] No samples found: prokka [2024-07-30 12:23:11,662] multiqc [DEBUG ] No samples found: samblaster [2024-07-30 12:23:11,673] multiqc [DEBUG ] No samples found: samtools [2024-07-30 12:23:11,678] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-07-30 12:23:11,683] multiqc [DEBUG ] No samples found: bamtools [2024-07-30 12:23:11,688] multiqc [DEBUG ] No samples found: jellyfish [2024-07-30 12:23:11,697] multiqc [DEBUG ] No samples found: vcftools [2024-07-30 12:23:11,702] multiqc [DEBUG ] No samples found: longranger [2024-07-30 12:23:11,707] multiqc [DEBUG ] No samples found: stacks [2024-07-30 12:23:11,712] multiqc [DEBUG ] No samples found: varscan2 [2024-07-30 12:23:11,728] multiqc [DEBUG ] No samples found: bbmap [2024-07-30 12:23:11,733] multiqc [DEBUG ] No samples found: bismark [2024-07-30 12:23:11,739] multiqc [DEBUG ] No samples found: biscuit [2024-07-30 12:23:11,744] multiqc [DEBUG ] No samples found: hicexplorer [2024-07-30 12:23:11,749] multiqc [DEBUG ] No samples found: hicup [2024-07-30 12:23:11,754] multiqc [DEBUG ] No samples found: hicpro [2024-07-30 12:23:11,759] multiqc [DEBUG ] No samples found: salmon [2024-07-30 12:23:11,764] multiqc [DEBUG ] No samples found: kallisto [2024-07-30 12:23:11,769] multiqc [DEBUG ] No samples found: slamdunk [2024-07-30 12:23:11,774] multiqc [DEBUG ] No samples found: star [2024-07-30 12:23:11,779] multiqc [DEBUG ] No samples found: hisat2 [2024-07-30 12:23:11,786] multiqc [DEBUG ] No samples found: tophat [2024-07-30 12:23:11,791] multiqc [DEBUG ] No samples found: bowtie2 [2024-07-30 12:23:11,796] multiqc [DEBUG ] No samples found: bowtie1 [2024-07-30 12:23:11,801] multiqc [DEBUG ] No samples found: snpsplit [2024-07-30 12:23:11,806] multiqc [DEBUG ] No samples found: kat [2024-07-30 12:23:11,810] multiqc [DEBUG ] No samples found: leehom [2024-07-30 12:23:11,815] multiqc [DEBUG ] No samples found: adapterRemoval [2024-07-30 12:23:11,820] multiqc [DEBUG ] No samples found: clipandmerge [2024-07-30 12:23:11,825] multiqc [DEBUG ] No samples found: cutadapt [2024-07-30 12:23:11,830] multiqc [DEBUG ] No samples found: flexbar [2024-07-30 12:23:11,835] multiqc [DEBUG ] No samples found: kaiju [2024-07-30 12:23:11,840] multiqc [DEBUG ] No samples found: kraken [2024-07-30 12:23:11,845] multiqc [DEBUG ] No samples found: malt [2024-07-30 12:23:11,850] multiqc [DEBUG ] No samples found: trimmomatic [2024-07-30 12:23:11,855] multiqc [DEBUG ] No samples found: sickle [2024-07-30 12:23:11,860] multiqc [DEBUG ] No samples found: skewer [2024-07-30 12:23:11,865] multiqc [DEBUG ] No samples found: sortmerna [2024-07-30 12:23:11,869] multiqc [DEBUG ] No samples found: biobloomtools [2024-07-30 12:23:11,875] multiqc [DEBUG ] No samples found: fastq_screen [2024-07-30 12:23:11,880] multiqc [DEBUG ] No samples found: afterqc [2024-07-30 12:23:11,885] multiqc [DEBUG ] No samples found: fastp [2024-07-30 12:23:11,908] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-07-30 12:23:11,960] multiqc [DEBUG ] No samples found: pycoqc [2024-07-30 12:23:11,967] multiqc [DEBUG ] No samples found: minionqc [2024-07-30 12:23:11,972] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-07-30 12:23:11,977] multiqc [DEBUG ] No samples found: clusterflow [2024-07-30 12:23:11,982] multiqc [DEBUG ] No samples found: bcl2fastq [2024-07-30 12:23:11,988] multiqc [DEBUG ] No samples found: interop [2024-07-30 12:23:11,993] multiqc [DEBUG ] No samples found: ivar [2024-07-30 12:23:11,998] multiqc [DEBUG ] No samples found: flash [2024-07-30 12:23:12,003] multiqc [DEBUG ] No samples found: seqyclean [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-07-30 12:23:12,003] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-07-30 12:23:12,010] multiqc [INFO ] Compressing plot data [2024-07-30 12:23:12,088] multiqc [INFO ] Report : multiqc_report.html [2024-07-30 12:23:12,089] multiqc [INFO ] Data : multiqc_data [2024-07-30 12:23:12,089] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49143825/tmpsmupig79/multiqc_data' to '/vast/gencore/GENEFLOW/work/1d/66a50deb0fe8d25183f9063ec5046e/1/multiqc_data' [2024-07-30 12:23:12,272] multiqc [INFO ] MultiQC complete