[2024-04-27 13:56:56,659] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-04-27 13:56:56,659] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-04-27 13:56:56,660] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-04-27 13:56:56,662] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-04-27 13:56:56,662] 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}} [2024-04-27 13:56:56,662] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-27 13:56:56,694] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-04-27 13:56:56,694] multiqc [INFO ] This is MultiQC v1.9 [2024-04-27 13:56:56,694] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-04-27 13:56:56,694] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/3c/b0d78458e80e12888b7a06bfcc4a97/merged [2024-04-27 13:56:56,694] multiqc [INFO ] Template : default [2024-04-27 13:56:56,694] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-04-27 13:56:56,694] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/3c/b0d78458e80e12888b7a06bfcc4a97/merged [2024-04-27 13:56:56,694] 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 [2024-04-27 13:56:56,694] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-45718699/tmpb_jt10qn [2024-04-27 13:56:56,810] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5N3TDSXC_1_fastqc.html [2024-04-27 13:56:56,816] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5N3TDSXC_1_fastqc.html [2024-04-27 13:56:56,895] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5N3TDSXC_2_fastqc.html [2024-04-27 13:56:56,903] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5N3TDSXC_2_fastqc.html [2024-04-27 13:56:56,980] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5N3TDSXC_3_fastqc.html [2024-04-27 13:56:56,987] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5N3TDSXC_3_fastqc.html [2024-04-27 13:56:57,069] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H5N3TDSXC_4_fastqc.html [2024-04-27 13:56:57,075] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H5N3TDSXC_4_fastqc.html [2024-04-27 13:56:57,553] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-27 13:56:57,554] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-04-27 13:56:57,559] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-04-27 13:56:57,563] multiqc [DEBUG ] No samples found: conpair [2024-04-27 13:56:57,568] multiqc [DEBUG ] No samples found: peddy [2024-04-27 13:56:57,572] multiqc [DEBUG ] No samples found: somalier [2024-04-27 13:56:57,576] multiqc [DEBUG ] No samples found: methylQA [2024-04-27 13:56:57,583] multiqc [DEBUG ] No samples found: mosdepth [2024-04-27 13:56:57,587] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-04-27 13:56:57,591] multiqc [DEBUG ] No samples found: qualimap [2024-04-27 13:56:57,595] multiqc [DEBUG ] No samples found: preseq [2024-04-27 13:56:57,599] multiqc [DEBUG ] No samples found: quast [2024-04-27 13:56:57,604] multiqc [DEBUG ] No samples found: qorts [2024-04-27 13:56:57,608] multiqc [DEBUG ] No samples found: rna_seqc [2024-04-27 13:56:57,612] multiqc [DEBUG ] No samples found: rockhopper [2024-04-27 13:56:57,616] multiqc [DEBUG ] No samples found: rsem [2024-04-27 13:56:57,627] multiqc [DEBUG ] No samples found: rseqc [2024-04-27 13:56:57,630] multiqc [DEBUG ] No samples found: busco [2024-04-27 13:56:57,635] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-04-27 13:56:57,639] multiqc [DEBUG ] No samples found: disambiguate [2024-04-27 13:56:57,643] multiqc [DEBUG ] No samples found: supernova [2024-04-27 13:56:57,654] multiqc [DEBUG ] No samples found: deeptools [2024-04-27 13:56:57,658] multiqc [DEBUG ] No samples found: sargasso [2024-04-27 13:56:57,663] multiqc [DEBUG ] No samples found: verifybamid [2024-04-27 13:56:57,667] multiqc [DEBUG ] No samples found: mirtrace [2024-04-27 13:56:57,671] multiqc [DEBUG ] No samples found: happy [2024-04-27 13:56:57,675] multiqc [DEBUG ] No samples found: mirtop [2024-04-27 13:56:57,681] multiqc [DEBUG ] No samples found: homer [2024-04-27 13:56:57,685] multiqc [DEBUG ] No samples found: macs2 [2024-04-27 13:56:57,689] multiqc [DEBUG ] No samples found: theta2 [2024-04-27 13:56:57,694] multiqc [DEBUG ] No samples found: snpeff [2024-04-27 13:56:57,700] multiqc [DEBUG ] No samples found: gatk [2024-04-27 13:56:57,704] multiqc [DEBUG ] No samples found: htseq [2024-04-27 13:56:57,709] multiqc [DEBUG ] No samples found: bcftools [2024-04-27 13:56:57,713] multiqc [DEBUG ] No samples found: featureCounts [2024-04-27 13:56:57,718] multiqc [DEBUG ] No samples found: fgbio [2024-04-27 13:56:57,730] multiqc [DEBUG ] No samples found: dragen [2024-04-27 13:56:57,734] multiqc [DEBUG ] No samples found: dedup [2024-04-27 13:56:57,738] multiqc [DEBUG ] No samples found: damageprofiler [2024-04-27 13:56:57,758] multiqc [DEBUG ] No samples found: biobambam2 [2024-04-27 13:56:57,762] multiqc [DEBUG ] No samples found: mtnucratio [2024-04-27 13:56:57,764] multiqc [DEBUG ] No samples found: picard [2024-04-27 13:56:57,769] multiqc [DEBUG ] No samples found: prokka [2024-04-27 13:56:57,773] multiqc [DEBUG ] No samples found: samblaster [2024-04-27 13:56:57,780] multiqc [DEBUG ] No samples found: samtools [2024-04-27 13:56:57,784] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-04-27 13:56:57,789] multiqc [DEBUG ] No samples found: bamtools [2024-04-27 13:56:57,793] multiqc [DEBUG ] No samples found: jellyfish [2024-04-27 13:56:57,800] multiqc [DEBUG ] No samples found: vcftools [2024-04-27 13:56:57,804] multiqc [DEBUG ] No samples found: longranger [2024-04-27 13:56:57,808] multiqc [DEBUG ] No samples found: stacks [2024-04-27 13:56:57,812] multiqc [DEBUG ] No samples found: varscan2 [2024-04-27 13:56:57,824] multiqc [DEBUG ] No samples found: bbmap [2024-04-27 13:56:57,829] multiqc [DEBUG ] No samples found: bismark [2024-04-27 13:56:57,833] multiqc [DEBUG ] No samples found: biscuit [2024-04-27 13:56:57,838] multiqc [DEBUG ] No samples found: hicexplorer [2024-04-27 13:56:57,842] multiqc [DEBUG ] No samples found: hicup [2024-04-27 13:56:57,846] multiqc [DEBUG ] No samples found: hicpro [2024-04-27 13:56:57,850] multiqc [DEBUG ] No samples found: salmon [2024-04-27 13:56:57,854] multiqc [DEBUG ] No samples found: kallisto [2024-04-27 13:56:57,859] multiqc [DEBUG ] No samples found: slamdunk [2024-04-27 13:56:57,863] multiqc [DEBUG ] No samples found: star [2024-04-27 13:56:57,867] multiqc [DEBUG ] No samples found: hisat2 [2024-04-27 13:56:57,871] multiqc [DEBUG ] No samples found: tophat [2024-04-27 13:56:57,876] multiqc [DEBUG ] No samples found: bowtie2 [2024-04-27 13:56:57,880] multiqc [DEBUG ] No samples found: bowtie1 [2024-04-27 13:56:57,884] multiqc [DEBUG ] No samples found: snpsplit [2024-04-27 13:56:57,888] multiqc [DEBUG ] No samples found: kat [2024-04-27 13:56:57,892] multiqc [DEBUG ] No samples found: leehom [2024-04-27 13:56:57,896] multiqc [DEBUG ] No samples found: adapterRemoval [2024-04-27 13:56:57,900] multiqc [DEBUG ] No samples found: clipandmerge [2024-04-27 13:56:57,905] multiqc [DEBUG ] No samples found: cutadapt [2024-04-27 13:56:57,909] multiqc [DEBUG ] No samples found: flexbar [2024-04-27 13:56:57,913] multiqc [DEBUG ] No samples found: kaiju [2024-04-27 13:56:57,917] multiqc [DEBUG ] No samples found: kraken [2024-04-27 13:56:57,921] multiqc [DEBUG ] No samples found: malt [2024-04-27 13:56:57,926] multiqc [DEBUG ] No samples found: trimmomatic [2024-04-27 13:56:57,930] multiqc [DEBUG ] No samples found: sickle [2024-04-27 13:56:57,934] multiqc [DEBUG ] No samples found: skewer [2024-04-27 13:56:57,938] multiqc [DEBUG ] No samples found: sortmerna [2024-04-27 13:56:57,942] multiqc [DEBUG ] No samples found: biobloomtools [2024-04-27 13:56:57,946] multiqc [DEBUG ] No samples found: fastq_screen [2024-04-27 13:56:57,951] multiqc [DEBUG ] No samples found: afterqc [2024-04-27 13:56:57,955] multiqc [DEBUG ] No samples found: fastp [2024-04-27 13:56:58,605] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-04-27 13:56:58,679] multiqc [DEBUG ] No samples found: pycoqc [2024-04-27 13:56:58,683] multiqc [DEBUG ] No samples found: minionqc [2024-04-27 13:56:58,688] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-04-27 13:56:58,692] multiqc [DEBUG ] No samples found: clusterflow [2024-04-27 13:56:58,697] multiqc [DEBUG ] No samples found: bcl2fastq [2024-04-27 13:56:58,701] multiqc [DEBUG ] No samples found: interop [2024-04-27 13:56:58,705] multiqc [DEBUG ] No samples found: ivar [2024-04-27 13:56:58,710] multiqc [DEBUG ] No samples found: flash [2024-04-27 13:56:58,714] multiqc [DEBUG ] No samples found: seqyclean [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-04-27 13:56:58,714] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-04-27 13:56:58,720] multiqc [INFO ] Compressing plot data [2024-04-27 13:56:58,808] multiqc [INFO ] Report : multiqc_report.html [2024-04-27 13:56:58,808] multiqc [INFO ] Data : multiqc_data [2024-04-27 13:56:58,808] multiqc [DEBUG ] Moving data file from '/state/partition1/job-45718699/tmpb_jt10qn/multiqc_data' to '/vast/gencore/GENEFLOW/work/3c/b0d78458e80e12888b7a06bfcc4a97/merged/multiqc_data' [2024-04-27 13:56:58,950] multiqc [INFO ] MultiQC complete