[2023-12-15 15:54:47,592] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2023-12-15 15:54:47,592] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2023-12-15 15:54:47,592] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-12-15 15:54:47,595] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2023-12-15 15:54:47,595] 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}} [2023-12-15 15:54:47,595] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-15 15:54:47,798] multiqc [WARNING] MultiQC Version v1.17 now available! [2023-12-15 15:54:47,799] multiqc [INFO ] This is MultiQC v1.9 [2023-12-15 15:54:47,799] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2023-12-15 15:54:47,799] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/64/76bd444f06ef3b3c2165263c729260/merged [2023-12-15 15:54:47,799] multiqc [INFO ] Template : default [2023-12-15 15:54:47,799] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2023-12-15 15:54:47,799] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/64/76bd444f06ef3b3c2165263c729260/merged [2023-12-15 15:54:47,799] 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 [2023-12-15 15:54:47,799] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-40862310/tmp_f4kcy2m [2023-12-15 15:54:47,910] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_1_fastqc.html [2023-12-15 15:54:47,918] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_1_fastqc.html [2023-12-15 15:54:48,018] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_2_fastqc.html [2023-12-15 15:54:48,026] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_2_fastqc.html [2023-12-15 15:54:48,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKVTJDRX3_3_fastqc.html [2023-12-15 15:54:48,101] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKVTJDRX3_3_fastqc.html [2023-12-15 15:54:48,595] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 15:54:48,595] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2023-12-15 15:54:48,600] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2023-12-15 15:54:48,603] multiqc [DEBUG ] No samples found: conpair [2023-12-15 15:54:48,606] multiqc [DEBUG ] No samples found: peddy [2023-12-15 15:54:48,609] multiqc [DEBUG ] No samples found: somalier [2023-12-15 15:54:48,612] multiqc [DEBUG ] No samples found: methylQA [2023-12-15 15:54:48,616] multiqc [DEBUG ] No samples found: mosdepth [2023-12-15 15:54:48,619] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-12-15 15:54:48,621] multiqc [DEBUG ] No samples found: qualimap [2023-12-15 15:54:48,624] multiqc [DEBUG ] No samples found: preseq [2023-12-15 15:54:48,627] multiqc [DEBUG ] No samples found: quast [2023-12-15 15:54:48,630] multiqc [DEBUG ] No samples found: qorts [2023-12-15 15:54:48,633] multiqc [DEBUG ] No samples found: rna_seqc [2023-12-15 15:54:48,636] multiqc [DEBUG ] No samples found: rockhopper [2023-12-15 15:54:48,639] multiqc [DEBUG ] No samples found: rsem [2023-12-15 15:54:48,643] multiqc [DEBUG ] No samples found: rseqc [2023-12-15 15:54:48,646] multiqc [DEBUG ] No samples found: busco [2023-12-15 15:54:48,649] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-12-15 15:54:48,652] multiqc [DEBUG ] No samples found: disambiguate [2023-12-15 15:54:48,655] multiqc [DEBUG ] No samples found: supernova [2023-12-15 15:54:48,661] multiqc [DEBUG ] No samples found: deeptools [2023-12-15 15:54:48,663] multiqc [DEBUG ] No samples found: sargasso [2023-12-15 15:54:48,666] multiqc [DEBUG ] No samples found: verifybamid [2023-12-15 15:54:48,669] multiqc [DEBUG ] No samples found: mirtrace [2023-12-15 15:54:48,672] multiqc [DEBUG ] No samples found: happy [2023-12-15 15:54:48,675] multiqc [DEBUG ] No samples found: mirtop [2023-12-15 15:54:48,678] multiqc [DEBUG ] No samples found: homer [2023-12-15 15:54:48,681] multiqc [DEBUG ] No samples found: macs2 [2023-12-15 15:54:48,684] multiqc [DEBUG ] No samples found: theta2 [2023-12-15 15:54:48,687] multiqc [DEBUG ] No samples found: snpeff [2023-12-15 15:54:48,690] multiqc [DEBUG ] No samples found: gatk [2023-12-15 15:54:48,694] multiqc [DEBUG ] No samples found: htseq [2023-12-15 15:54:48,697] multiqc [DEBUG ] No samples found: bcftools [2023-12-15 15:54:48,700] multiqc [DEBUG ] No samples found: featureCounts [2023-12-15 15:54:48,703] multiqc [DEBUG ] No samples found: fgbio [2023-12-15 15:54:48,709] multiqc [DEBUG ] No samples found: dragen [2023-12-15 15:54:48,712] multiqc [DEBUG ] No samples found: dedup [2023-12-15 15:54:48,716] multiqc [DEBUG ] No samples found: damageprofiler [2023-12-15 15:54:48,725] multiqc [DEBUG ] No samples found: biobambam2 [2023-12-15 15:54:48,728] multiqc [DEBUG ] No samples found: mtnucratio [2023-12-15 15:54:48,731] multiqc [DEBUG ] No samples found: picard [2023-12-15 15:54:48,734] multiqc [DEBUG ] No samples found: prokka [2023-12-15 15:54:48,736] multiqc [DEBUG ] No samples found: samblaster [2023-12-15 15:54:48,741] multiqc [DEBUG ] No samples found: samtools [2023-12-15 15:54:48,744] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-12-15 15:54:48,747] multiqc [DEBUG ] No samples found: bamtools [2023-12-15 15:54:48,749] multiqc [DEBUG ] No samples found: jellyfish [2023-12-15 15:54:48,753] multiqc [DEBUG ] No samples found: vcftools [2023-12-15 15:54:48,756] multiqc [DEBUG ] No samples found: longranger [2023-12-15 15:54:48,759] multiqc [DEBUG ] No samples found: stacks [2023-12-15 15:54:48,762] multiqc [DEBUG ] No samples found: varscan2 [2023-12-15 15:54:48,767] multiqc [DEBUG ] No samples found: bbmap [2023-12-15 15:54:48,771] multiqc [DEBUG ] No samples found: bismark [2023-12-15 15:54:48,774] multiqc [DEBUG ] No samples found: biscuit [2023-12-15 15:54:48,777] multiqc [DEBUG ] No samples found: hicexplorer [2023-12-15 15:54:48,780] multiqc [DEBUG ] No samples found: hicup [2023-12-15 15:54:48,783] multiqc [DEBUG ] No samples found: hicpro [2023-12-15 15:54:48,786] multiqc [DEBUG ] No samples found: salmon [2023-12-15 15:54:48,789] multiqc [DEBUG ] No samples found: kallisto [2023-12-15 15:54:48,792] multiqc [DEBUG ] No samples found: slamdunk [2023-12-15 15:54:48,795] multiqc [DEBUG ] No samples found: star [2023-12-15 15:54:48,798] multiqc [DEBUG ] No samples found: hisat2 [2023-12-15 15:54:48,801] multiqc [DEBUG ] No samples found: tophat [2023-12-15 15:54:48,804] multiqc [DEBUG ] No samples found: bowtie2 [2023-12-15 15:54:48,806] multiqc [DEBUG ] No samples found: bowtie1 [2023-12-15 15:54:48,810] multiqc [DEBUG ] No samples found: snpsplit [2023-12-15 15:54:48,812] multiqc [DEBUG ] No samples found: kat [2023-12-15 15:54:48,815] multiqc [DEBUG ] No samples found: leehom [2023-12-15 15:54:48,818] multiqc [DEBUG ] No samples found: adapterRemoval [2023-12-15 15:54:48,821] multiqc [DEBUG ] No samples found: clipandmerge [2023-12-15 15:54:48,824] multiqc [DEBUG ] No samples found: cutadapt [2023-12-15 15:54:48,826] multiqc [DEBUG ] No samples found: flexbar [2023-12-15 15:54:48,829] multiqc [DEBUG ] No samples found: kaiju [2023-12-15 15:54:48,832] multiqc [DEBUG ] No samples found: kraken [2023-12-15 15:54:48,835] multiqc [DEBUG ] No samples found: malt [2023-12-15 15:54:48,838] multiqc [DEBUG ] No samples found: trimmomatic [2023-12-15 15:54:48,842] multiqc [DEBUG ] No samples found: sickle [2023-12-15 15:54:48,845] multiqc [DEBUG ] No samples found: skewer [2023-12-15 15:54:48,848] multiqc [DEBUG ] No samples found: sortmerna [2023-12-15 15:54:48,850] multiqc [DEBUG ] No samples found: biobloomtools [2023-12-15 15:54:48,853] multiqc [DEBUG ] No samples found: fastq_screen [2023-12-15 15:54:48,856] multiqc [DEBUG ] No samples found: afterqc [2023-12-15 15:54:48,859] multiqc [DEBUG ] No samples found: fastp [2023-12-15 15:54:48,923] multiqc.modules.fastqc.fastqc [INFO ] Found 3 reports [2023-12-15 15:54:48,975] multiqc [DEBUG ] No samples found: pycoqc [2023-12-15 15:54:48,978] multiqc [DEBUG ] No samples found: minionqc [2023-12-15 15:54:48,981] multiqc [DEBUG ] No samples found: multivcfanalyzer [2023-12-15 15:54:48,985] multiqc [DEBUG ] No samples found: clusterflow [2023-12-15 15:54:48,988] multiqc [DEBUG ] No samples found: bcl2fastq [2023-12-15 15:54:48,991] multiqc [DEBUG ] No samples found: interop [2023-12-15 15:54:48,994] multiqc [DEBUG ] No samples found: ivar [2023-12-15 15:54:48,997] multiqc [DEBUG ] No samples found: flash [2023-12-15 15:54:49,000] multiqc [DEBUG ] No samples found: seqyclean [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2023-12-15 15:54:49,000] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2023-12-15 15:54:49,005] multiqc [INFO ] Compressing plot data [2023-12-15 15:54:49,069] multiqc [INFO ] Report : multiqc_report.html [2023-12-15 15:54:49,069] multiqc [INFO ] Data : multiqc_data [2023-12-15 15:54:49,069] multiqc [DEBUG ] Moving data file from '/state/partition1/job-40862310/tmp_f4kcy2m/multiqc_data' to '/vast/gencore/GENEFLOW/work/64/76bd444f06ef3b3c2165263c729260/merged/multiqc_data' [2023-12-15 15:54:49,204] multiqc [INFO ] MultiQC complete