[2024-06-18 18:48:29,641] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-06-18 18:48:29,641] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-06-18 18:48:29,641] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-06-18 18:48:29,644] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-06-18 18:48:29,644] 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}} [2024-06-18 18:48:29,644] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-18 18:48:29,681] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-06-18 18:48:29,681] multiqc [INFO ] This is MultiQC v1.9 [2024-06-18 18:48:29,681] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-06-18 18:48:29,681] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/1a/8c23e1515f4758e219c58c80d73206/1 [2024-06-18 18:48:29,681] multiqc [INFO ] Template : default [2024-06-18 18:48:29,681] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-06-18 18:48:29,681] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/1a/8c23e1515f4758e219c58c80d73206/1 [2024-06-18 18:48:29,681] 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 [2024-06-18 18:48:29,681] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-47648432/tmpny3dm4e5 [2024-06-18 18:48:29,817] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.1_fastqc.html [2024-06-18 18:48:29,826] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.1_fastqc.html [2024-06-18 18:48:29,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.2_fastqc.html [2024-06-18 18:48:29,916] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.2_fastqc.html [2024-06-18 18:48:29,981] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.3_fastqc.html [2024-06-18 18:48:29,989] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-LJVBV_l01.3_fastqc.html [2024-06-18 18:48:30,576] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-18 18:48:30,578] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-06-18 18:48:30,584] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-06-18 18:48:30,591] multiqc [DEBUG ] No samples found: conpair [2024-06-18 18:48:30,598] multiqc [DEBUG ] No samples found: peddy [2024-06-18 18:48:30,605] multiqc [DEBUG ] No samples found: somalier [2024-06-18 18:48:30,611] multiqc [DEBUG ] No samples found: methylQA [2024-06-18 18:48:30,623] multiqc [DEBUG ] No samples found: mosdepth [2024-06-18 18:48:30,628] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-06-18 18:48:30,632] multiqc [DEBUG ] No samples found: qualimap [2024-06-18 18:48:30,639] multiqc [DEBUG ] No samples found: preseq [2024-06-18 18:48:30,645] multiqc [DEBUG ] No samples found: quast [2024-06-18 18:48:30,652] multiqc [DEBUG ] No samples found: qorts [2024-06-18 18:48:30,658] multiqc [DEBUG ] No samples found: rna_seqc [2024-06-18 18:48:30,664] multiqc [DEBUG ] No samples found: rockhopper [2024-06-18 18:48:30,670] multiqc [DEBUG ] No samples found: rsem [2024-06-18 18:48:30,685] multiqc [DEBUG ] No samples found: rseqc [2024-06-18 18:48:30,691] multiqc [DEBUG ] No samples found: busco [2024-06-18 18:48:30,698] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-06-18 18:48:30,704] multiqc [DEBUG ] No samples found: disambiguate [2024-06-18 18:48:30,710] multiqc [DEBUG ] No samples found: supernova [2024-06-18 18:48:30,729] multiqc [DEBUG ] No samples found: deeptools [2024-06-18 18:48:30,736] multiqc [DEBUG ] No samples found: sargasso [2024-06-18 18:48:30,743] multiqc [DEBUG ] No samples found: verifybamid [2024-06-18 18:48:30,749] multiqc [DEBUG ] No samples found: mirtrace [2024-06-18 18:48:30,755] multiqc [DEBUG ] No samples found: happy [2024-06-18 18:48:30,762] multiqc [DEBUG ] No samples found: mirtop [2024-06-18 18:48:30,771] multiqc [DEBUG ] No samples found: homer [2024-06-18 18:48:30,777] multiqc [DEBUG ] No samples found: macs2 [2024-06-18 18:48:30,783] multiqc [DEBUG ] No samples found: theta2 [2024-06-18 18:48:30,789] multiqc [DEBUG ] No samples found: snpeff [2024-06-18 18:48:30,800] multiqc [DEBUG ] No samples found: gatk [2024-06-18 18:48:30,806] multiqc [DEBUG ] No samples found: htseq [2024-06-18 18:48:30,813] multiqc [DEBUG ] No samples found: bcftools [2024-06-18 18:48:30,820] multiqc [DEBUG ] No samples found: featureCounts [2024-06-18 18:48:30,828] multiqc [DEBUG ] No samples found: fgbio [2024-06-18 18:48:30,848] multiqc [DEBUG ] No samples found: dragen [2024-06-18 18:48:30,856] multiqc [DEBUG ] No samples found: dedup [2024-06-18 18:48:30,863] multiqc [DEBUG ] No samples found: damageprofiler [2024-06-18 18:48:30,893] multiqc [DEBUG ] No samples found: biobambam2 [2024-06-18 18:48:30,898] multiqc [DEBUG ] No samples found: mtnucratio [2024-06-18 18:48:30,902] multiqc [DEBUG ] No samples found: picard [2024-06-18 18:48:30,908] multiqc [DEBUG ] No samples found: prokka [2024-06-18 18:48:30,914] multiqc [DEBUG ] No samples found: samblaster [2024-06-18 18:48:30,926] multiqc [DEBUG ] No samples found: samtools [2024-06-18 18:48:30,933] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-06-18 18:48:30,940] multiqc [DEBUG ] No samples found: bamtools [2024-06-18 18:48:30,946] multiqc [DEBUG ] No samples found: jellyfish [2024-06-18 18:48:30,958] multiqc [DEBUG ] No samples found: vcftools [2024-06-18 18:48:30,964] multiqc [DEBUG ] No samples found: longranger [2024-06-18 18:48:30,970] multiqc [DEBUG ] No samples found: stacks [2024-06-18 18:48:30,977] multiqc [DEBUG ] No samples found: varscan2 [2024-06-18 18:48:30,996] multiqc [DEBUG ] No samples found: bbmap [2024-06-18 18:48:31,002] multiqc [DEBUG ] No samples found: bismark [2024-06-18 18:48:31,010] multiqc [DEBUG ] No samples found: biscuit [2024-06-18 18:48:31,017] multiqc [DEBUG ] No samples found: hicexplorer [2024-06-18 18:48:31,023] multiqc [DEBUG ] No samples found: hicup [2024-06-18 18:48:31,030] multiqc [DEBUG ] No samples found: hicpro [2024-06-18 18:48:31,035] multiqc [DEBUG ] No samples found: salmon [2024-06-18 18:48:31,042] multiqc [DEBUG ] No samples found: kallisto [2024-06-18 18:48:31,048] multiqc [DEBUG ] No samples found: slamdunk [2024-06-18 18:48:31,054] multiqc [DEBUG ] No samples found: star [2024-06-18 18:48:31,060] multiqc [DEBUG ] No samples found: hisat2 [2024-06-18 18:48:31,066] multiqc [DEBUG ] No samples found: tophat [2024-06-18 18:48:31,072] multiqc [DEBUG ] No samples found: bowtie2 [2024-06-18 18:48:31,078] multiqc [DEBUG ] No samples found: bowtie1 [2024-06-18 18:48:31,085] multiqc [DEBUG ] No samples found: snpsplit [2024-06-18 18:48:31,091] multiqc [DEBUG ] No samples found: kat [2024-06-18 18:48:31,097] multiqc [DEBUG ] No samples found: leehom [2024-06-18 18:48:31,103] multiqc [DEBUG ] No samples found: adapterRemoval [2024-06-18 18:48:31,109] multiqc [DEBUG ] No samples found: clipandmerge [2024-06-18 18:48:31,115] multiqc [DEBUG ] No samples found: cutadapt [2024-06-18 18:48:31,121] multiqc [DEBUG ] No samples found: flexbar [2024-06-18 18:48:31,128] multiqc [DEBUG ] No samples found: kaiju [2024-06-18 18:48:31,133] multiqc [DEBUG ] No samples found: kraken [2024-06-18 18:48:31,140] multiqc [DEBUG ] No samples found: malt [2024-06-18 18:48:31,146] multiqc [DEBUG ] No samples found: trimmomatic [2024-06-18 18:48:31,151] multiqc [DEBUG ] No samples found: sickle [2024-06-18 18:48:31,157] multiqc [DEBUG ] No samples found: skewer [2024-06-18 18:48:31,163] multiqc [DEBUG ] No samples found: sortmerna [2024-06-18 18:48:31,169] multiqc [DEBUG ] No samples found: biobloomtools [2024-06-18 18:48:31,175] multiqc [DEBUG ] No samples found: fastq_screen [2024-06-18 18:48:31,182] multiqc [DEBUG ] No samples found: afterqc [2024-06-18 18:48:31,189] multiqc [DEBUG ] No samples found: fastp [2024-06-18 18:48:31,219] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-06-18 18:48:31,278] multiqc [DEBUG ] No samples found: pycoqc [2024-06-18 18:48:31,284] multiqc [DEBUG ] No samples found: minionqc [2024-06-18 18:48:31,290] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-06-18 18:48:31,296] multiqc [DEBUG ] No samples found: clusterflow [2024-06-18 18:48:31,303] multiqc [DEBUG ] No samples found: bcl2fastq [2024-06-18 18:48:31,309] multiqc [DEBUG ] No samples found: interop [2024-06-18 18:48:31,315] multiqc [DEBUG ] No samples found: ivar [2024-06-18 18:48:31,321] multiqc [DEBUG ] No samples found: flash [2024-06-18 18:48:31,327] multiqc [DEBUG ] No samples found: seqyclean [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-06-18 18:48:31,327] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-06-18 18:48:31,328] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-06-18 18:48:31,333] multiqc [INFO ] Compressing plot data [2024-06-18 18:48:31,394] multiqc [INFO ] Report : multiqc_report.html [2024-06-18 18:48:31,395] multiqc [INFO ] Data : multiqc_data [2024-06-18 18:48:31,395] multiqc [DEBUG ] Moving data file from '/state/partition1/job-47648432/tmpny3dm4e5/multiqc_data' to '/vast/gencore/GENEFLOW/work/1a/8c23e1515f4758e219c58c80d73206/1/multiqc_data' [2024-06-18 18:48:31,567] multiqc [INFO ] MultiQC complete