[2024-08-01 07:22:08,957] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-08-01 07:22:08,958] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-08-01 07:22:08,959] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-08-01 07:22:08,961] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-08-01 07:22:08,961] 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}} [2024-08-01 07:22:08,962] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-01 07:22:09,010] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-08-01 07:22:09,010] multiqc [INFO ] This is MultiQC v1.9 [2024-08-01 07:22:09,010] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-08-01 07:22:09,010] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/9b/373d6c75ba36ba2d8a9482c3acf929/1 [2024-08-01 07:22:09,010] multiqc [INFO ] Template : default [2024-08-01 07:22:09,010] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-08-01 07:22:09,010] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/9b/373d6c75ba36ba2d8a9482c3acf929/1 [2024-08-01 07:22:09,011] 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 [2024-08-01 07:22:09,011] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-49219884/tmp8a1hg74n [2024-08-01 07:22:09,150] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.1_fastqc.html [2024-08-01 07:22:09,160] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.1_fastqc.html [2024-08-01 07:22:09,255] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.2_fastqc.html [2024-08-01 07:22:09,263] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.2_fastqc.html [2024-08-01 07:22:09,328] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.3_fastqc.html [2024-08-01 07:22:09,335] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-DPHLP_l01.3_fastqc.html [2024-08-01 07:22:09,955] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-01 07:22:09,957] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-08-01 07:22:09,964] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-08-01 07:22:09,970] multiqc [DEBUG ] No samples found: conpair [2024-08-01 07:22:09,976] multiqc [DEBUG ] No samples found: peddy [2024-08-01 07:22:09,982] multiqc [DEBUG ] No samples found: somalier [2024-08-01 07:22:09,989] multiqc [DEBUG ] No samples found: methylQA [2024-08-01 07:22:09,999] multiqc [DEBUG ] No samples found: mosdepth [2024-08-01 07:22:10,005] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-08-01 07:22:10,009] multiqc [DEBUG ] No samples found: qualimap [2024-08-01 07:22:10,016] multiqc [DEBUG ] No samples found: preseq [2024-08-01 07:22:10,022] multiqc [DEBUG ] No samples found: quast [2024-08-01 07:22:10,029] multiqc [DEBUG ] No samples found: qorts [2024-08-01 07:22:10,035] multiqc [DEBUG ] No samples found: rna_seqc [2024-08-01 07:22:10,041] multiqc [DEBUG ] No samples found: rockhopper [2024-08-01 07:22:10,048] multiqc [DEBUG ] No samples found: rsem [2024-08-01 07:22:10,065] multiqc [DEBUG ] No samples found: rseqc [2024-08-01 07:22:10,071] multiqc [DEBUG ] No samples found: busco [2024-08-01 07:22:10,077] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-08-01 07:22:10,084] multiqc [DEBUG ] No samples found: disambiguate [2024-08-01 07:22:10,091] multiqc [DEBUG ] No samples found: supernova [2024-08-01 07:22:10,111] multiqc [DEBUG ] No samples found: deeptools [2024-08-01 07:22:10,118] multiqc [DEBUG ] No samples found: sargasso [2024-08-01 07:22:10,125] multiqc [DEBUG ] No samples found: verifybamid [2024-08-01 07:22:10,132] multiqc [DEBUG ] No samples found: mirtrace [2024-08-01 07:22:10,139] multiqc [DEBUG ] No samples found: happy [2024-08-01 07:22:10,145] multiqc [DEBUG ] No samples found: mirtop [2024-08-01 07:22:10,154] multiqc [DEBUG ] No samples found: homer [2024-08-01 07:22:10,160] multiqc [DEBUG ] No samples found: macs2 [2024-08-01 07:22:10,167] multiqc [DEBUG ] No samples found: theta2 [2024-08-01 07:22:10,173] multiqc [DEBUG ] No samples found: snpeff [2024-08-01 07:22:10,183] multiqc [DEBUG ] No samples found: gatk [2024-08-01 07:22:10,189] multiqc [DEBUG ] No samples found: htseq [2024-08-01 07:22:10,196] multiqc [DEBUG ] No samples found: bcftools [2024-08-01 07:22:10,203] multiqc [DEBUG ] No samples found: featureCounts [2024-08-01 07:22:10,212] multiqc [DEBUG ] No samples found: fgbio [2024-08-01 07:22:10,228] multiqc [DEBUG ] No samples found: dragen [2024-08-01 07:22:10,235] multiqc [DEBUG ] No samples found: dedup [2024-08-01 07:22:10,242] multiqc [DEBUG ] No samples found: damageprofiler [2024-08-01 07:22:10,272] multiqc [DEBUG ] No samples found: biobambam2 [2024-08-01 07:22:10,280] multiqc [DEBUG ] No samples found: mtnucratio [2024-08-01 07:22:10,282] multiqc [DEBUG ] No samples found: picard [2024-08-01 07:22:10,289] multiqc [DEBUG ] No samples found: prokka [2024-08-01 07:22:10,294] multiqc [DEBUG ] No samples found: samblaster [2024-08-01 07:22:10,305] multiqc [DEBUG ] No samples found: samtools [2024-08-01 07:22:10,312] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-08-01 07:22:10,319] multiqc [DEBUG ] No samples found: bamtools [2024-08-01 07:22:10,326] multiqc [DEBUG ] No samples found: jellyfish [2024-08-01 07:22:10,335] multiqc [DEBUG ] No samples found: vcftools [2024-08-01 07:22:10,341] multiqc [DEBUG ] No samples found: longranger [2024-08-01 07:22:10,347] multiqc [DEBUG ] No samples found: stacks [2024-08-01 07:22:10,354] multiqc [DEBUG ] No samples found: varscan2 [2024-08-01 07:22:10,371] multiqc [DEBUG ] No samples found: bbmap [2024-08-01 07:22:10,378] multiqc [DEBUG ] No samples found: bismark [2024-08-01 07:22:10,384] multiqc [DEBUG ] No samples found: biscuit [2024-08-01 07:22:10,391] multiqc [DEBUG ] No samples found: hicexplorer [2024-08-01 07:22:10,397] multiqc [DEBUG ] No samples found: hicup [2024-08-01 07:22:10,404] multiqc [DEBUG ] No samples found: hicpro [2024-08-01 07:22:10,410] multiqc [DEBUG ] No samples found: salmon [2024-08-01 07:22:10,416] multiqc [DEBUG ] No samples found: kallisto [2024-08-01 07:22:10,422] multiqc [DEBUG ] No samples found: slamdunk [2024-08-01 07:22:10,429] multiqc [DEBUG ] No samples found: star [2024-08-01 07:22:10,440] multiqc [DEBUG ] No samples found: hisat2 [2024-08-01 07:22:10,449] multiqc [DEBUG ] No samples found: tophat [2024-08-01 07:22:10,470] multiqc [DEBUG ] No samples found: bowtie2 [2024-08-01 07:22:10,476] multiqc [DEBUG ] No samples found: bowtie1 [2024-08-01 07:22:10,489] multiqc [DEBUG ] No samples found: snpsplit [2024-08-01 07:22:10,496] multiqc [DEBUG ] No samples found: kat [2024-08-01 07:22:10,506] multiqc [DEBUG ] No samples found: leehom [2024-08-01 07:22:10,512] multiqc [DEBUG ] No samples found: adapterRemoval [2024-08-01 07:22:10,519] multiqc [DEBUG ] No samples found: clipandmerge [2024-08-01 07:22:10,526] multiqc [DEBUG ] No samples found: cutadapt [2024-08-01 07:22:10,532] multiqc [DEBUG ] No samples found: flexbar [2024-08-01 07:22:10,538] multiqc [DEBUG ] No samples found: kaiju [2024-08-01 07:22:10,544] multiqc [DEBUG ] No samples found: kraken [2024-08-01 07:22:10,550] multiqc [DEBUG ] No samples found: malt [2024-08-01 07:22:10,556] multiqc [DEBUG ] No samples found: trimmomatic [2024-08-01 07:22:10,562] multiqc [DEBUG ] No samples found: sickle [2024-08-01 07:22:10,569] multiqc [DEBUG ] No samples found: skewer [2024-08-01 07:22:10,575] multiqc [DEBUG ] No samples found: sortmerna [2024-08-01 07:22:10,581] multiqc [DEBUG ] No samples found: biobloomtools [2024-08-01 07:22:10,588] multiqc [DEBUG ] No samples found: fastq_screen [2024-08-01 07:22:10,595] multiqc [DEBUG ] No samples found: afterqc [2024-08-01 07:22:10,601] multiqc [DEBUG ] No samples found: fastp [2024-08-01 07:22:10,616] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-08-01 07:22:10,679] multiqc [DEBUG ] No samples found: pycoqc [2024-08-01 07:22:10,686] multiqc [DEBUG ] No samples found: minionqc [2024-08-01 07:22:10,692] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-08-01 07:22:10,699] multiqc [DEBUG ] No samples found: clusterflow [2024-08-01 07:22:10,706] multiqc [DEBUG ] No samples found: bcl2fastq [2024-08-01 07:22:10,713] multiqc [DEBUG ] No samples found: interop [2024-08-01 07:22:10,719] multiqc [DEBUG ] No samples found: ivar [2024-08-01 07:22:10,725] multiqc [DEBUG ] No samples found: flash [2024-08-01 07:22:10,731] multiqc [DEBUG ] No samples found: seqyclean [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-08-01 07:22:10,731] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-08-01 07:22:10,732] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-08-01 07:22:10,737] multiqc [INFO ] Compressing plot data [2024-08-01 07:22:10,796] multiqc [INFO ] Report : multiqc_report.html [2024-08-01 07:22:10,796] multiqc [INFO ] Data : multiqc_data [2024-08-01 07:22:10,797] multiqc [DEBUG ] Moving data file from '/state/partition1/job-49219884/tmp8a1hg74n/multiqc_data' to '/vast/gencore/GENEFLOW/work/9b/373d6c75ba36ba2d8a9482c3acf929/1/multiqc_data' [2024-08-01 07:22:10,971] multiqc [INFO ] MultiQC complete