[2024-01-25 14:42:12,703] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-25 14:42:12,703] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-25 14:42:12,704] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-25 14:42:12,706] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-25 14:42:12,706] 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}} [2024-01-25 14:42:12,707] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-25 14:42:12,876] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-25 14:42:12,876] multiqc [INFO ] This is MultiQC v1.9 [2024-01-25 14:42:12,876] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-25 14:42:12,876] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/e8/861da8126f6f34f4f24295882081c0/1 [2024-01-25 14:42:12,876] multiqc [INFO ] Template : default [2024-01-25 14:42:12,876] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-25 14:42:12,876] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/e8/861da8126f6f34f4f24295882081c0/1 [2024-01-25 14:42:12,877] 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 [2024-01-25 14:42:12,877] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-42260696/tmp8bgymigf [2024-01-25 14:42:13,013] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.1_fastqc.html [2024-01-25 14:42:13,021] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.1_fastqc.html [2024-01-25 14:42:13,114] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.2_fastqc.html [2024-01-25 14:42:13,121] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.2_fastqc.html [2024-01-25 14:42:13,195] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.3_fastqc.html [2024-01-25 14:42:13,204] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 000000000-GKBG2_l01.3_fastqc.html [2024-01-25 14:42:13,628] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-25 14:42:13,631] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-25 14:42:13,636] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-25 14:42:13,642] multiqc [DEBUG ] No samples found: conpair [2024-01-25 14:42:13,648] multiqc [DEBUG ] No samples found: peddy [2024-01-25 14:42:13,653] multiqc [DEBUG ] No samples found: somalier [2024-01-25 14:42:13,659] multiqc [DEBUG ] No samples found: methylQA [2024-01-25 14:42:13,668] multiqc [DEBUG ] No samples found: mosdepth [2024-01-25 14:42:13,673] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-25 14:42:13,677] multiqc [DEBUG ] No samples found: qualimap [2024-01-25 14:42:13,682] multiqc [DEBUG ] No samples found: preseq [2024-01-25 14:42:13,687] multiqc [DEBUG ] No samples found: quast [2024-01-25 14:42:13,693] multiqc [DEBUG ] No samples found: qorts [2024-01-25 14:42:13,698] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-25 14:42:13,703] multiqc [DEBUG ] No samples found: rockhopper [2024-01-25 14:42:13,709] multiqc [DEBUG ] No samples found: rsem [2024-01-25 14:42:13,720] multiqc [DEBUG ] No samples found: rseqc [2024-01-25 14:42:13,725] multiqc [DEBUG ] No samples found: busco [2024-01-25 14:42:13,731] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-25 14:42:13,736] multiqc [DEBUG ] No samples found: disambiguate [2024-01-25 14:42:13,741] multiqc [DEBUG ] No samples found: supernova [2024-01-25 14:42:13,756] multiqc [DEBUG ] No samples found: deeptools [2024-01-25 14:42:13,761] multiqc [DEBUG ] No samples found: sargasso [2024-01-25 14:42:13,766] multiqc [DEBUG ] No samples found: verifybamid [2024-01-25 14:42:13,772] multiqc [DEBUG ] No samples found: mirtrace [2024-01-25 14:42:13,777] multiqc [DEBUG ] No samples found: happy [2024-01-25 14:42:13,782] multiqc [DEBUG ] No samples found: mirtop [2024-01-25 14:42:13,789] multiqc [DEBUG ] No samples found: homer [2024-01-25 14:42:13,794] multiqc [DEBUG ] No samples found: macs2 [2024-01-25 14:42:13,799] multiqc [DEBUG ] No samples found: theta2 [2024-01-25 14:42:13,804] multiqc [DEBUG ] No samples found: snpeff [2024-01-25 14:42:13,812] multiqc [DEBUG ] No samples found: gatk [2024-01-25 14:42:13,818] multiqc [DEBUG ] No samples found: htseq [2024-01-25 14:42:13,824] multiqc [DEBUG ] No samples found: bcftools [2024-01-25 14:42:13,830] multiqc [DEBUG ] No samples found: featureCounts [2024-01-25 14:42:13,836] multiqc [DEBUG ] No samples found: fgbio [2024-01-25 14:42:13,852] multiqc [DEBUG ] No samples found: dragen [2024-01-25 14:42:13,857] multiqc [DEBUG ] No samples found: dedup [2024-01-25 14:42:13,862] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-25 14:42:13,887] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-25 14:42:13,893] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-25 14:42:13,895] multiqc [DEBUG ] No samples found: picard [2024-01-25 14:42:13,901] multiqc [DEBUG ] No samples found: prokka [2024-01-25 14:42:13,905] multiqc [DEBUG ] No samples found: samblaster [2024-01-25 14:42:13,916] multiqc [DEBUG ] No samples found: samtools [2024-01-25 14:42:13,921] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-25 14:42:13,927] multiqc [DEBUG ] No samples found: bamtools [2024-01-25 14:42:13,932] multiqc [DEBUG ] No samples found: jellyfish [2024-01-25 14:42:13,941] multiqc [DEBUG ] No samples found: vcftools [2024-01-25 14:42:13,946] multiqc [DEBUG ] No samples found: longranger [2024-01-25 14:42:13,952] multiqc [DEBUG ] No samples found: stacks [2024-01-25 14:42:13,958] multiqc [DEBUG ] No samples found: varscan2 [2024-01-25 14:42:13,973] multiqc [DEBUG ] No samples found: bbmap [2024-01-25 14:42:13,979] multiqc [DEBUG ] No samples found: bismark [2024-01-25 14:42:13,985] multiqc [DEBUG ] No samples found: biscuit [2024-01-25 14:42:13,990] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-25 14:42:13,996] multiqc [DEBUG ] No samples found: hicup [2024-01-25 14:42:14,002] multiqc [DEBUG ] No samples found: hicpro [2024-01-25 14:42:14,007] multiqc [DEBUG ] No samples found: salmon [2024-01-25 14:42:14,012] multiqc [DEBUG ] No samples found: kallisto [2024-01-25 14:42:14,018] multiqc [DEBUG ] No samples found: slamdunk [2024-01-25 14:42:14,023] multiqc [DEBUG ] No samples found: star [2024-01-25 14:42:14,029] multiqc [DEBUG ] No samples found: hisat2 [2024-01-25 14:42:14,034] multiqc [DEBUG ] No samples found: tophat [2024-01-25 14:42:14,039] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-25 14:42:14,044] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-25 14:42:14,050] multiqc [DEBUG ] No samples found: snpsplit [2024-01-25 14:42:14,055] multiqc [DEBUG ] No samples found: kat [2024-01-25 14:42:14,059] multiqc [DEBUG ] No samples found: leehom [2024-01-25 14:42:14,065] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-25 14:42:14,070] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-25 14:42:14,075] multiqc [DEBUG ] No samples found: cutadapt [2024-01-25 14:42:14,080] multiqc [DEBUG ] No samples found: flexbar [2024-01-25 14:42:14,085] multiqc [DEBUG ] No samples found: kaiju [2024-01-25 14:42:14,091] multiqc [DEBUG ] No samples found: kraken [2024-01-25 14:42:14,097] multiqc [DEBUG ] No samples found: malt [2024-01-25 14:42:14,102] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-25 14:42:14,107] multiqc [DEBUG ] No samples found: sickle [2024-01-25 14:42:14,114] multiqc [DEBUG ] No samples found: skewer [2024-01-25 14:42:14,119] multiqc [DEBUG ] No samples found: sortmerna [2024-01-25 14:42:14,123] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-25 14:42:14,129] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-25 14:42:14,134] multiqc [DEBUG ] No samples found: afterqc [2024-01-25 14:42:14,140] multiqc [DEBUG ] No samples found: fastp [2024-01-25 14:42:14,159] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2024-01-25 14:42:14,216] multiqc [DEBUG ] No samples found: pycoqc [2024-01-25 14:42:14,222] multiqc [DEBUG ] No samples found: minionqc [2024-01-25 14:42:14,227] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-25 14:42:14,233] multiqc [DEBUG ] No samples found: clusterflow [2024-01-25 14:42:14,239] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-25 14:42:14,244] multiqc [DEBUG ] No samples found: interop [2024-01-25 14:42:14,250] multiqc [DEBUG ] No samples found: ivar [2024-01-25 14:42:14,255] multiqc [DEBUG ] No samples found: flash [2024-01-25 14:42:14,260] multiqc [DEBUG ] No samples found: seqyclean [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-25 14:42:14,260] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-25 14:42:14,261] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-25 14:42:14,265] multiqc [INFO ] Compressing plot data [2024-01-25 14:42:14,326] multiqc [INFO ] Report : multiqc_report.html [2024-01-25 14:42:14,326] multiqc [INFO ] Data : multiqc_data [2024-01-25 14:42:14,326] multiqc [DEBUG ] Moving data file from '/state/partition1/job-42260696/tmp8bgymigf/multiqc_data' to '/vast/gencore/GENEFLOW/work/e8/861da8126f6f34f4f24295882081c0/1/multiqc_data' [2024-01-25 14:42:14,493] multiqc [INFO ] MultiQC complete