[2024-02-17 00:33:39,022] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-17 00:33:39,023] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-17 00:33:39,023] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-17 00:33:39,025] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-17 00:33:39,025] 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}} [2024-02-17 00:33:39,026] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-17 00:33:39,196] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-17 00:33:39,196] multiqc [INFO ] This is MultiQC v1.9 [2024-02-17 00:33:39,196] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-17 00:33:39,196] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/f9/7a5010a3bc94080c66dbf03701617f/1 [2024-02-17 00:33:39,196] multiqc [INFO ] Template : default [2024-02-17 00:33:39,196] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-17 00:33:39,196] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/f9/7a5010a3bc94080c66dbf03701617f/1 [2024-02-17 00:33:39,197] 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 [2024-02-17 00:33:39,197] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43063975/tmplgxaboyv [2024-02-17 00:33:39,313] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.1_fastqc.html [2024-02-17 00:33:39,321] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.1_fastqc.html [2024-02-17 00:33:39,411] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.2_fastqc.html [2024-02-17 00:33:39,417] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.2_fastqc.html [2024-02-17 00:33:39,480] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.3_fastqc.html [2024-02-17 00:33:39,487] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LBY9B_l01.3_fastqc.html [2024-02-17 00:33:40,380] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-17 00:33:40,382] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-17 00:33:40,386] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-17 00:33:40,392] multiqc [DEBUG ] No samples found: conpair [2024-02-17 00:33:40,403] multiqc [DEBUG ] No samples found: peddy [2024-02-17 00:33:40,408] multiqc [DEBUG ] No samples found: somalier [2024-02-17 00:33:40,415] multiqc [DEBUG ] No samples found: methylQA [2024-02-17 00:33:40,426] multiqc [DEBUG ] No samples found: mosdepth [2024-02-17 00:33:40,431] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-17 00:33:40,435] multiqc [DEBUG ] No samples found: qualimap [2024-02-17 00:33:40,440] multiqc [DEBUG ] No samples found: preseq [2024-02-17 00:33:40,444] multiqc [DEBUG ] No samples found: quast [2024-02-17 00:33:40,450] multiqc [DEBUG ] No samples found: qorts [2024-02-17 00:33:40,459] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-17 00:33:40,463] multiqc [DEBUG ] No samples found: rockhopper [2024-02-17 00:33:40,468] multiqc [DEBUG ] No samples found: rsem [2024-02-17 00:33:40,481] multiqc [DEBUG ] No samples found: rseqc [2024-02-17 00:33:40,486] multiqc [DEBUG ] No samples found: busco [2024-02-17 00:33:40,491] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-17 00:33:40,496] multiqc [DEBUG ] No samples found: disambiguate [2024-02-17 00:33:40,500] multiqc [DEBUG ] No samples found: supernova [2024-02-17 00:33:40,514] multiqc [DEBUG ] No samples found: deeptools [2024-02-17 00:33:40,518] multiqc [DEBUG ] No samples found: sargasso [2024-02-17 00:33:40,524] multiqc [DEBUG ] No samples found: verifybamid [2024-02-17 00:33:40,529] multiqc [DEBUG ] No samples found: mirtrace [2024-02-17 00:33:40,534] multiqc [DEBUG ] No samples found: happy [2024-02-17 00:33:40,539] multiqc [DEBUG ] No samples found: mirtop [2024-02-17 00:33:40,546] multiqc [DEBUG ] No samples found: homer [2024-02-17 00:33:40,552] multiqc [DEBUG ] No samples found: macs2 [2024-02-17 00:33:40,560] multiqc [DEBUG ] No samples found: theta2 [2024-02-17 00:33:40,565] multiqc [DEBUG ] No samples found: snpeff [2024-02-17 00:33:40,582] multiqc [DEBUG ] No samples found: gatk [2024-02-17 00:33:40,587] multiqc [DEBUG ] No samples found: htseq [2024-02-17 00:33:40,594] multiqc [DEBUG ] No samples found: bcftools [2024-02-17 00:33:40,598] multiqc [DEBUG ] No samples found: featureCounts [2024-02-17 00:33:40,605] multiqc [DEBUG ] No samples found: fgbio [2024-02-17 00:33:40,631] multiqc [DEBUG ] No samples found: dragen [2024-02-17 00:33:40,636] multiqc [DEBUG ] No samples found: dedup [2024-02-17 00:33:40,641] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-17 00:33:40,666] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-17 00:33:40,672] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-17 00:33:40,675] multiqc [DEBUG ] No samples found: picard [2024-02-17 00:33:40,679] multiqc [DEBUG ] No samples found: prokka [2024-02-17 00:33:40,683] multiqc [DEBUG ] No samples found: samblaster [2024-02-17 00:33:40,692] multiqc [DEBUG ] No samples found: samtools [2024-02-17 00:33:40,697] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-17 00:33:40,702] multiqc [DEBUG ] No samples found: bamtools [2024-02-17 00:33:40,707] multiqc [DEBUG ] No samples found: jellyfish [2024-02-17 00:33:40,718] multiqc [DEBUG ] No samples found: vcftools [2024-02-17 00:33:40,723] multiqc [DEBUG ] No samples found: longranger [2024-02-17 00:33:40,728] multiqc [DEBUG ] No samples found: stacks [2024-02-17 00:33:40,734] multiqc [DEBUG ] No samples found: varscan2 [2024-02-17 00:33:40,755] multiqc [DEBUG ] No samples found: bbmap [2024-02-17 00:33:40,760] multiqc [DEBUG ] No samples found: bismark [2024-02-17 00:33:40,765] multiqc [DEBUG ] No samples found: biscuit [2024-02-17 00:33:40,770] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-17 00:33:40,775] multiqc [DEBUG ] No samples found: hicup [2024-02-17 00:33:40,779] multiqc [DEBUG ] No samples found: hicpro [2024-02-17 00:33:40,783] multiqc [DEBUG ] No samples found: salmon [2024-02-17 00:33:40,789] multiqc [DEBUG ] No samples found: kallisto [2024-02-17 00:33:40,794] multiqc [DEBUG ] No samples found: slamdunk [2024-02-17 00:33:40,798] multiqc [DEBUG ] No samples found: star [2024-02-17 00:33:40,803] multiqc [DEBUG ] No samples found: hisat2 [2024-02-17 00:33:40,808] multiqc [DEBUG ] No samples found: tophat [2024-02-17 00:33:40,813] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-17 00:33:40,818] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-17 00:33:40,822] multiqc [DEBUG ] No samples found: snpsplit [2024-02-17 00:33:40,827] multiqc [DEBUG ] No samples found: kat [2024-02-17 00:33:40,831] multiqc [DEBUG ] No samples found: leehom [2024-02-17 00:33:40,836] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-17 00:33:40,844] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-17 00:33:40,849] multiqc [DEBUG ] No samples found: cutadapt [2024-02-17 00:33:40,855] multiqc [DEBUG ] No samples found: flexbar [2024-02-17 00:33:40,860] multiqc [DEBUG ] No samples found: kaiju [2024-02-17 00:33:40,864] multiqc [DEBUG ] No samples found: kraken [2024-02-17 00:33:40,872] multiqc [DEBUG ] No samples found: malt [2024-02-17 00:33:40,880] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-17 00:33:40,885] multiqc [DEBUG ] No samples found: sickle [2024-02-17 00:33:40,889] multiqc [DEBUG ] No samples found: skewer [2024-02-17 00:33:40,893] multiqc [DEBUG ] No samples found: sortmerna [2024-02-17 00:33:40,899] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-17 00:33:40,903] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-17 00:33:40,908] multiqc [DEBUG ] No samples found: afterqc [2024-02-17 00:33:40,913] multiqc [DEBUG ] No samples found: fastp [2024-02-17 00:33:40,938] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-02-17 00:33:40,992] multiqc [DEBUG ] No samples found: pycoqc [2024-02-17 00:33:40,996] multiqc [DEBUG ] No samples found: minionqc [2024-02-17 00:33:41,003] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-17 00:33:41,025] multiqc [DEBUG ] No samples found: clusterflow [2024-02-17 00:33:41,030] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-17 00:33:41,047] multiqc [DEBUG ] No samples found: interop [2024-02-17 00:33:41,052] multiqc [DEBUG ] No samples found: ivar [2024-02-17 00:33:41,056] multiqc [DEBUG ] No samples found: flash [2024-02-17 00:33:41,060] multiqc [DEBUG ] No samples found: seqyclean [2024-02-17 00:33:41,060] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-17 00:33:41,060] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-17 00:33:41,061] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-17 00:33:41,065] multiqc [INFO ] Compressing plot data [2024-02-17 00:33:41,121] multiqc [INFO ] Report : multiqc_report.html [2024-02-17 00:33:41,121] multiqc [INFO ] Data : multiqc_data [2024-02-17 00:33:41,121] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43063975/tmplgxaboyv/multiqc_data' to '/vast/gencore/GENEFLOW/work/f9/7a5010a3bc94080c66dbf03701617f/1/multiqc_data' [2024-02-17 00:33:41,270] multiqc [INFO ] MultiQC complete