[2024-02-29 20:08:57,267] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-02-29 20:08:57,267] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-02-29 20:08:57,268] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-02-29 20:08:57,270] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-02-29 20:08:57,270] 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}} [2024-02-29 20:08:57,270] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-29 20:08:57,640] multiqc [WARNING] MultiQC Version v1.21 now available! [2024-02-29 20:08:57,641] multiqc [INFO ] This is MultiQC v1.9 [2024-02-29 20:08:57,641] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-02-29 20:08:57,641] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/78/bd6adf5a7052e5756ab8aa9cdefb27/merged [2024-02-29 20:08:57,641] multiqc [INFO ] Template : default [2024-02-29 20:08:57,641] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-02-29 20:08:57,641] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/78/bd6adf5a7052e5756ab8aa9cdefb27/merged [2024-02-29 20:08:57,641] 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 [2024-02-29 20:08:57,641] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43528957/tmp5sa935k7 [2024-02-29 20:08:57,770] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ5VDRX3_1_fastqc.html [2024-02-29 20:08:57,778] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ5VDRX3_1_fastqc.html [2024-02-29 20:08:57,845] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ5VDRX3_2_fastqc.html [2024-02-29 20:08:57,852] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ5VDRX3_2_fastqc.html [2024-02-29 20:08:57,923] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ5VDRX3_3_fastqc.html [2024-02-29 20:08:57,930] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ5VDRX3_3_fastqc.html [2024-02-29 20:08:58,001] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HVJ5VDRX3_4_fastqc.html [2024-02-29 20:08:58,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HVJ5VDRX3_4_fastqc.html [2024-02-29 20:08:58,433] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-29 20:08:58,435] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-02-29 20:08:58,440] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-02-29 20:08:58,447] multiqc [DEBUG ] No samples found: conpair [2024-02-29 20:08:58,453] multiqc [DEBUG ] No samples found: peddy [2024-02-29 20:08:58,459] multiqc [DEBUG ] No samples found: somalier [2024-02-29 20:08:58,465] multiqc [DEBUG ] No samples found: methylQA [2024-02-29 20:08:58,477] multiqc [DEBUG ] No samples found: mosdepth [2024-02-29 20:08:58,482] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-02-29 20:08:58,486] multiqc [DEBUG ] No samples found: qualimap [2024-02-29 20:08:58,493] multiqc [DEBUG ] No samples found: preseq [2024-02-29 20:08:58,499] multiqc [DEBUG ] No samples found: quast [2024-02-29 20:08:58,506] multiqc [DEBUG ] No samples found: qorts [2024-02-29 20:08:58,512] multiqc [DEBUG ] No samples found: rna_seqc [2024-02-29 20:08:58,518] multiqc [DEBUG ] No samples found: rockhopper [2024-02-29 20:08:58,524] multiqc [DEBUG ] No samples found: rsem [2024-02-29 20:08:58,539] multiqc [DEBUG ] No samples found: rseqc [2024-02-29 20:08:58,544] multiqc [DEBUG ] No samples found: busco [2024-02-29 20:08:58,551] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-02-29 20:08:58,557] multiqc [DEBUG ] No samples found: disambiguate [2024-02-29 20:08:58,562] multiqc [DEBUG ] No samples found: supernova [2024-02-29 20:08:58,579] multiqc [DEBUG ] No samples found: deeptools [2024-02-29 20:08:58,585] multiqc [DEBUG ] No samples found: sargasso [2024-02-29 20:08:58,591] multiqc [DEBUG ] No samples found: verifybamid [2024-02-29 20:08:58,598] multiqc [DEBUG ] No samples found: mirtrace [2024-02-29 20:08:58,604] multiqc [DEBUG ] No samples found: happy [2024-02-29 20:08:58,610] multiqc [DEBUG ] No samples found: mirtop [2024-02-29 20:08:58,618] multiqc [DEBUG ] No samples found: homer [2024-02-29 20:08:58,625] multiqc [DEBUG ] No samples found: macs2 [2024-02-29 20:08:58,631] multiqc [DEBUG ] No samples found: theta2 [2024-02-29 20:08:58,636] multiqc [DEBUG ] No samples found: snpeff [2024-02-29 20:08:58,645] multiqc [DEBUG ] No samples found: gatk [2024-02-29 20:08:58,652] multiqc [DEBUG ] No samples found: htseq [2024-02-29 20:08:58,659] multiqc [DEBUG ] No samples found: bcftools [2024-02-29 20:08:58,665] multiqc [DEBUG ] No samples found: featureCounts [2024-02-29 20:08:58,673] multiqc [DEBUG ] No samples found: fgbio [2024-02-29 20:08:58,691] multiqc [DEBUG ] No samples found: dragen [2024-02-29 20:08:58,697] multiqc [DEBUG ] No samples found: dedup [2024-02-29 20:08:58,704] multiqc [DEBUG ] No samples found: damageprofiler [2024-02-29 20:08:58,732] multiqc [DEBUG ] No samples found: biobambam2 [2024-02-29 20:08:58,739] multiqc [DEBUG ] No samples found: mtnucratio [2024-02-29 20:08:58,742] multiqc [DEBUG ] No samples found: picard [2024-02-29 20:08:58,748] multiqc [DEBUG ] No samples found: prokka [2024-02-29 20:08:58,754] multiqc [DEBUG ] No samples found: samblaster [2024-02-29 20:08:58,765] multiqc [DEBUG ] No samples found: samtools [2024-02-29 20:08:58,771] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-02-29 20:08:58,777] multiqc [DEBUG ] No samples found: bamtools [2024-02-29 20:08:58,783] multiqc [DEBUG ] No samples found: jellyfish [2024-02-29 20:08:58,793] multiqc [DEBUG ] No samples found: vcftools [2024-02-29 20:08:58,799] multiqc [DEBUG ] No samples found: longranger [2024-02-29 20:08:58,805] multiqc [DEBUG ] No samples found: stacks [2024-02-29 20:08:58,811] multiqc [DEBUG ] No samples found: varscan2 [2024-02-29 20:08:58,830] multiqc [DEBUG ] No samples found: bbmap [2024-02-29 20:08:58,836] multiqc [DEBUG ] No samples found: bismark [2024-02-29 20:08:58,842] multiqc [DEBUG ] No samples found: biscuit [2024-02-29 20:08:58,849] multiqc [DEBUG ] No samples found: hicexplorer [2024-02-29 20:08:58,855] multiqc [DEBUG ] No samples found: hicup [2024-02-29 20:08:58,862] multiqc [DEBUG ] No samples found: hicpro [2024-02-29 20:08:58,867] multiqc [DEBUG ] No samples found: salmon [2024-02-29 20:08:58,873] multiqc [DEBUG ] No samples found: kallisto [2024-02-29 20:08:58,880] multiqc [DEBUG ] No samples found: slamdunk [2024-02-29 20:08:58,887] multiqc [DEBUG ] No samples found: star [2024-02-29 20:08:58,893] multiqc [DEBUG ] No samples found: hisat2 [2024-02-29 20:08:58,899] multiqc [DEBUG ] No samples found: tophat [2024-02-29 20:08:58,904] multiqc [DEBUG ] No samples found: bowtie2 [2024-02-29 20:08:58,910] multiqc [DEBUG ] No samples found: bowtie1 [2024-02-29 20:08:58,916] multiqc [DEBUG ] No samples found: snpsplit [2024-02-29 20:08:58,921] multiqc [DEBUG ] No samples found: kat [2024-02-29 20:08:58,926] multiqc [DEBUG ] No samples found: leehom [2024-02-29 20:08:58,932] multiqc [DEBUG ] No samples found: adapterRemoval [2024-02-29 20:08:58,938] multiqc [DEBUG ] No samples found: clipandmerge [2024-02-29 20:08:58,943] multiqc [DEBUG ] No samples found: cutadapt [2024-02-29 20:08:58,949] multiqc [DEBUG ] No samples found: flexbar [2024-02-29 20:08:58,955] multiqc [DEBUG ] No samples found: kaiju [2024-02-29 20:08:58,960] multiqc [DEBUG ] No samples found: kraken [2024-02-29 20:08:58,966] multiqc [DEBUG ] No samples found: malt [2024-02-29 20:08:58,972] multiqc [DEBUG ] No samples found: trimmomatic [2024-02-29 20:08:58,977] multiqc [DEBUG ] No samples found: sickle [2024-02-29 20:08:58,983] multiqc [DEBUG ] No samples found: skewer [2024-02-29 20:08:58,988] multiqc [DEBUG ] No samples found: sortmerna [2024-02-29 20:08:58,993] multiqc [DEBUG ] No samples found: biobloomtools [2024-02-29 20:08:58,999] multiqc [DEBUG ] No samples found: fastq_screen [2024-02-29 20:08:59,004] multiqc [DEBUG ] No samples found: afterqc [2024-02-29 20:08:59,010] multiqc [DEBUG ] No samples found: fastp [2024-02-29 20:08:59,084] multiqc.modules.fastqc.fastqc [INFO ] Found 4 reports [2024-02-29 20:08:59,135] multiqc [DEBUG ] No samples found: pycoqc [2024-02-29 20:08:59,143] multiqc [DEBUG ] No samples found: minionqc [2024-02-29 20:08:59,149] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-02-29 20:08:59,156] multiqc [DEBUG ] No samples found: clusterflow [2024-02-29 20:08:59,165] multiqc [DEBUG ] No samples found: bcl2fastq [2024-02-29 20:08:59,175] multiqc [DEBUG ] No samples found: interop [2024-02-29 20:08:59,187] multiqc [DEBUG ] No samples found: ivar [2024-02-29 20:08:59,193] multiqc [DEBUG ] No samples found: flash [2024-02-29 20:08:59,200] multiqc [DEBUG ] No samples found: seqyclean [2024-02-29 20:08:59,200] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-02-29 20:08:59,201] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-02-29 20:08:59,207] multiqc [INFO ] Compressing plot data [2024-02-29 20:08:59,280] multiqc [INFO ] Report : multiqc_report.html [2024-02-29 20:08:59,280] multiqc [INFO ] Data : multiqc_data [2024-02-29 20:08:59,280] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43528957/tmp5sa935k7/multiqc_data' to '/vast/gencore/GENEFLOW/work/78/bd6adf5a7052e5756ab8aa9cdefb27/merged/multiqc_data' [2024-02-29 20:08:59,444] multiqc [INFO ] MultiQC complete