[2024-02-22 11:45:17,402] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-22 11:45:17,402] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-22 11:45:17,402] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-22 11:45:17,405] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-22 11:45:17,405] 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}} [2024-02-22 11:45:17,405] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-22 11:45:17,599] multiqc [WARNING] MultiQC Version v1.20 now available! [2024-02-22 11:45:17,599] multiqc [INFO ] This is MultiQC v1.9 [2024-02-22 11:45:17,599] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-22 11:45:17,600] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e3/fd05f11a85ae49acbe2485adf7db0a/merged [2024-02-22 11:45:17,600] multiqc [INFO ] Template : default [2024-02-22 11:45:17,600] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-22 11:45:17,600] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e3/fd05f11a85ae49acbe2485adf7db0a/merged [2024-02-22 11:45:17,600] 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 [2024-02-22 11:45:17,600] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43283558/tmp8wm2knuo [2024-02-22 11:45:17,732] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3FDRX3_1_fastqc.html [2024-02-22 11:45:17,741] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3FDRX3_1_fastqc.html [2024-02-22 11:45:17,821] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3FDRX3_2_fastqc.html [2024-02-22 11:45:17,827] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3FDRX3_2_fastqc.html [2024-02-22 11:45:17,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3FDRX3_3_fastqc.html [2024-02-22 11:45:17,907] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3FDRX3_3_fastqc.html [2024-02-22 11:45:17,978] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVH3FDRX3_4_fastqc.html [2024-02-22 11:45:17,986] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVH3FDRX3_4_fastqc.html [2024-02-22 11:45:18,608] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-22 11:45:18,609] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-22 11:45:18,613] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-22 11:45:18,617] multiqc [DEBUG ] No samples found: conpair [2024-02-22 11:45:18,620] multiqc [DEBUG ] No samples found: peddy [2024-02-22 11:45:18,623] multiqc [DEBUG ] No samples found: somalier [2024-02-22 11:45:18,626] multiqc [DEBUG ] No samples found: methylQA [2024-02-22 11:45:18,631] multiqc [DEBUG ] No samples found: mosdepth [2024-02-22 11:45:18,634] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-22 11:45:18,636] multiqc [DEBUG ] No samples found: qualimap [2024-02-22 11:45:18,639] multiqc [DEBUG ] No samples found: preseq [2024-02-22 11:45:18,643] multiqc [DEBUG ] No samples found: quast [2024-02-22 11:45:18,646] multiqc [DEBUG ] No samples found: qorts [2024-02-22 11:45:18,649] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-22 11:45:18,652] multiqc [DEBUG ] No samples found: rockhopper [2024-02-22 11:45:18,655] multiqc [DEBUG ] No samples found: rsem [2024-02-22 11:45:18,660] multiqc [DEBUG ] No samples found: rseqc [2024-02-22 11:45:18,663] multiqc [DEBUG ] No samples found: busco [2024-02-22 11:45:18,666] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-22 11:45:18,669] multiqc [DEBUG ] No samples found: disambiguate [2024-02-22 11:45:18,672] multiqc [DEBUG ] No samples found: supernova [2024-02-22 11:45:18,678] multiqc [DEBUG ] No samples found: deeptools [2024-02-22 11:45:18,681] multiqc [DEBUG ] No samples found: sargasso [2024-02-22 11:45:18,684] multiqc [DEBUG ] No samples found: verifybamid [2024-02-22 11:45:18,687] multiqc [DEBUG ] No samples found: mirtrace [2024-02-22 11:45:18,690] multiqc [DEBUG ] No samples found: happy [2024-02-22 11:45:18,693] multiqc [DEBUG ] No samples found: mirtop [2024-02-22 11:45:18,697] multiqc [DEBUG ] No samples found: homer [2024-02-22 11:45:18,700] multiqc [DEBUG ] No samples found: macs2 [2024-02-22 11:45:18,703] multiqc [DEBUG ] No samples found: theta2 [2024-02-22 11:45:18,706] multiqc [DEBUG ] No samples found: snpeff [2024-02-22 11:45:18,709] multiqc [DEBUG ] No samples found: gatk [2024-02-22 11:45:18,712] multiqc [DEBUG ] No samples found: htseq [2024-02-22 11:45:18,715] multiqc [DEBUG ] No samples found: bcftools [2024-02-22 11:45:18,718] multiqc [DEBUG ] No samples found: featureCounts [2024-02-22 11:45:18,722] multiqc [DEBUG ] No samples found: fgbio [2024-02-22 11:45:18,727] multiqc [DEBUG ] No samples found: dragen [2024-02-22 11:45:18,730] multiqc [DEBUG ] No samples found: dedup [2024-02-22 11:45:18,734] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-22 11:45:18,741] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-22 11:45:18,746] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-22 11:45:18,748] multiqc [DEBUG ] No samples found: picard [2024-02-22 11:45:18,751] multiqc [DEBUG ] No samples found: prokka [2024-02-22 11:45:18,754] multiqc [DEBUG ] No samples found: samblaster [2024-02-22 11:45:18,758] multiqc [DEBUG ] No samples found: samtools [2024-02-22 11:45:18,761] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-22 11:45:18,765] multiqc [DEBUG ] No samples found: bamtools [2024-02-22 11:45:18,768] multiqc [DEBUG ] No samples found: jellyfish [2024-02-22 11:45:18,772] multiqc [DEBUG ] No samples found: vcftools [2024-02-22 11:45:18,775] multiqc [DEBUG ] No samples found: longranger [2024-02-22 11:45:18,778] multiqc [DEBUG ] No samples found: stacks [2024-02-22 11:45:18,781] multiqc [DEBUG ] No samples found: varscan2 [2024-02-22 11:45:18,787] multiqc [DEBUG ] No samples found: bbmap [2024-02-22 11:45:18,790] multiqc [DEBUG ] No samples found: bismark [2024-02-22 11:45:18,793] multiqc [DEBUG ] No samples found: biscuit [2024-02-22 11:45:18,796] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-22 11:45:18,799] multiqc [DEBUG ] No samples found: hicup [2024-02-22 11:45:18,802] multiqc [DEBUG ] No samples found: hicpro [2024-02-22 11:45:18,805] multiqc [DEBUG ] No samples found: salmon [2024-02-22 11:45:18,808] multiqc [DEBUG ] No samples found: kallisto [2024-02-22 11:45:18,811] multiqc [DEBUG ] No samples found: slamdunk [2024-02-22 11:45:18,814] multiqc [DEBUG ] No samples found: star [2024-02-22 11:45:18,818] multiqc [DEBUG ] No samples found: hisat2 [2024-02-22 11:45:18,821] multiqc [DEBUG ] No samples found: tophat [2024-02-22 11:45:18,823] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-22 11:45:18,826] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-22 11:45:18,829] multiqc [DEBUG ] No samples found: snpsplit [2024-02-22 11:45:18,835] multiqc [DEBUG ] No samples found: kat [2024-02-22 11:45:18,840] multiqc [DEBUG ] No samples found: leehom [2024-02-22 11:45:18,846] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-22 11:45:18,850] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-22 11:45:18,854] multiqc [DEBUG ] No samples found: cutadapt [2024-02-22 11:45:18,861] multiqc [DEBUG ] No samples found: flexbar [2024-02-22 11:45:18,864] multiqc [DEBUG ] No samples found: kaiju [2024-02-22 11:45:18,868] multiqc [DEBUG ] No samples found: kraken [2024-02-22 11:45:18,871] multiqc [DEBUG ] No samples found: malt [2024-02-22 11:45:18,874] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-22 11:45:18,878] multiqc [DEBUG ] No samples found: sickle [2024-02-22 11:45:18,883] multiqc [DEBUG ] No samples found: skewer [2024-02-22 11:45:18,886] multiqc [DEBUG ] No samples found: sortmerna [2024-02-22 11:45:18,893] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-22 11:45:18,897] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-22 11:45:18,900] multiqc [DEBUG ] No samples found: afterqc [2024-02-22 11:45:18,904] multiqc [DEBUG ] No samples found: fastp [2024-02-22 11:45:18,979] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-02-22 11:45:19,022] multiqc [DEBUG ] No samples found: pycoqc [2024-02-22 11:45:19,026] multiqc [DEBUG ] No samples found: minionqc [2024-02-22 11:45:19,029] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-22 11:45:19,032] multiqc [DEBUG ] No samples found: clusterflow [2024-02-22 11:45:19,035] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-22 11:45:19,038] multiqc [DEBUG ] No samples found: interop [2024-02-22 11:45:19,041] multiqc [DEBUG ] No samples found: ivar [2024-02-22 11:45:19,044] multiqc [DEBUG ] No samples found: flash [2024-02-22 11:45:19,047] multiqc [DEBUG ] No samples found: seqyclean [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-22 11:45:19,047] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-22 11:45:19,048] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-22 11:45:19,048] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-22 11:45:19,048] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-22 11:45:19,053] multiqc [INFO ] Compressing plot data [2024-02-22 11:45:19,124] multiqc [INFO ] Report : multiqc_report.html [2024-02-22 11:45:19,125] multiqc [INFO ] Data : multiqc_data [2024-02-22 11:45:19,125] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43283558/tmp8wm2knuo/multiqc_data' to '/vast/gencore/GENEFLOW/work/e3/fd05f11a85ae49acbe2485adf7db0a/merged/multiqc_data' [2024-02-22 11:45:19,256] multiqc [INFO ] MultiQC complete