[2024-01-16 23:00:59,121] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-01-16 23:00:59,121] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-01-16 23:00:59,121] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-01-16 23:00:59,124] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-01-16 23:00:59,124] 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}} [2024-01-16 23:00:59,125] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-16 23:00:59,296] multiqc [WARNING] MultiQC Version v1.19 now available! [2024-01-16 23:00:59,296] multiqc [INFO ] This is MultiQC v1.9 [2024-01-16 23:00:59,296] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-01-16 23:00:59,296] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/4f/59c5c5b78699d905910b95290027f5/merged [2024-01-16 23:00:59,296] multiqc [INFO ] Template : default [2024-01-16 23:00:59,296] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-01-16 23:00:59,296] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/4f/59c5c5b78699d905910b95290027f5/merged [2024-01-16 23:00:59,296] 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 [2024-01-16 23:00:59,297] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-41897245/tmpc4sis7ha [2024-01-16 23:00:59,472] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_10X_fastqc.html [2024-01-16 23:00:59,482] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_10X_fastqc.html [2024-01-16 23:00:59,555] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_dialout_fastqc.html [2024-01-16 23:00:59,563] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_JAY_dialout_fastqc.html [2024-01-16 23:00:59,637] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n01_undetermined_fastqc.html [2024-01-16 23:00:59,645] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n01_undetermined_fastqc.html [2024-01-16 23:00:59,736] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_10X_fastqc.html [2024-01-16 23:00:59,751] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_10X_fastqc.html [2024-01-16 23:00:59,865] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_dialout_fastqc.html [2024-01-16 23:00:59,873] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_JAY_dialout_fastqc.html [2024-01-16 23:00:59,993] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HT2VYDRX3_n02_undetermined_fastqc.html [2024-01-16 23:01:00,003] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HT2VYDRX3_n02_undetermined_fastqc.html [2024-01-16 23:01:00,070] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,077] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,078] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,078] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,078] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,078] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,078] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:00,101] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2024-01-16 23:01:01,767] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-16 23:01:01,769] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-01-16 23:01:01,783] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 3 samples (table) [2024-01-16 23:01:01,785] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-01-16 23:01:01,795] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-01-16 23:01:01,803] multiqc [DEBUG ] No samples found: conpair [2024-01-16 23:01:01,810] multiqc [DEBUG ] No samples found: peddy [2024-01-16 23:01:01,817] multiqc [DEBUG ] No samples found: somalier [2024-01-16 23:01:01,825] multiqc [DEBUG ] No samples found: methylQA [2024-01-16 23:01:01,836] multiqc [DEBUG ] No samples found: mosdepth [2024-01-16 23:01:01,842] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-01-16 23:01:01,847] multiqc [DEBUG ] No samples found: qualimap [2024-01-16 23:01:01,855] multiqc [DEBUG ] No samples found: preseq [2024-01-16 23:01:01,866] multiqc [DEBUG ] No samples found: quast [2024-01-16 23:01:01,873] multiqc [DEBUG ] No samples found: qorts [2024-01-16 23:01:01,880] multiqc [DEBUG ] No samples found: rna_seqc [2024-01-16 23:01:01,887] multiqc [DEBUG ] No samples found: rockhopper [2024-01-16 23:01:01,894] multiqc [DEBUG ] No samples found: rsem [2024-01-16 23:01:01,912] multiqc [DEBUG ] No samples found: rseqc [2024-01-16 23:01:01,918] multiqc [DEBUG ] No samples found: busco [2024-01-16 23:01:01,930] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-01-16 23:01:01,937] multiqc [DEBUG ] No samples found: disambiguate [2024-01-16 23:01:01,945] multiqc [DEBUG ] No samples found: supernova [2024-01-16 23:01:01,964] multiqc [DEBUG ] No samples found: deeptools [2024-01-16 23:01:01,970] multiqc [DEBUG ] No samples found: sargasso [2024-01-16 23:01:01,977] multiqc [DEBUG ] No samples found: verifybamid [2024-01-16 23:01:01,985] multiqc [DEBUG ] No samples found: mirtrace [2024-01-16 23:01:01,992] multiqc [DEBUG ] No samples found: happy [2024-01-16 23:01:01,998] multiqc [DEBUG ] No samples found: mirtop [2024-01-16 23:01:02,007] multiqc [DEBUG ] No samples found: homer [2024-01-16 23:01:02,016] multiqc [DEBUG ] No samples found: macs2 [2024-01-16 23:01:02,023] multiqc [DEBUG ] No samples found: theta2 [2024-01-16 23:01:02,029] multiqc [DEBUG ] No samples found: snpeff [2024-01-16 23:01:02,039] multiqc [DEBUG ] No samples found: gatk [2024-01-16 23:01:02,046] multiqc [DEBUG ] No samples found: htseq [2024-01-16 23:01:02,063] multiqc [DEBUG ] No samples found: bcftools [2024-01-16 23:01:02,074] multiqc [DEBUG ] No samples found: featureCounts [2024-01-16 23:01:02,087] multiqc [DEBUG ] No samples found: fgbio [2024-01-16 23:01:02,106] multiqc [DEBUG ] No samples found: dragen [2024-01-16 23:01:02,113] multiqc [DEBUG ] No samples found: dedup [2024-01-16 23:01:02,120] multiqc [DEBUG ] No samples found: damageprofiler [2024-01-16 23:01:02,153] multiqc [DEBUG ] No samples found: biobambam2 [2024-01-16 23:01:02,159] multiqc [DEBUG ] No samples found: mtnucratio [2024-01-16 23:01:02,161] multiqc [DEBUG ] No samples found: picard [2024-01-16 23:01:02,169] multiqc [DEBUG ] No samples found: prokka [2024-01-16 23:01:02,175] multiqc [DEBUG ] No samples found: samblaster [2024-01-16 23:01:02,188] multiqc [DEBUG ] No samples found: samtools [2024-01-16 23:01:02,195] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-01-16 23:01:02,203] multiqc [DEBUG ] No samples found: bamtools [2024-01-16 23:01:02,209] multiqc [DEBUG ] No samples found: jellyfish [2024-01-16 23:01:02,220] multiqc [DEBUG ] No samples found: vcftools [2024-01-16 23:01:02,228] multiqc [DEBUG ] No samples found: longranger [2024-01-16 23:01:02,234] multiqc [DEBUG ] No samples found: stacks [2024-01-16 23:01:02,241] multiqc [DEBUG ] No samples found: varscan2 [2024-01-16 23:01:02,261] multiqc [DEBUG ] No samples found: bbmap [2024-01-16 23:01:02,271] multiqc [DEBUG ] No samples found: bismark [2024-01-16 23:01:02,278] multiqc [DEBUG ] No samples found: biscuit [2024-01-16 23:01:02,284] multiqc [DEBUG ] No samples found: hicexplorer [2024-01-16 23:01:02,292] multiqc [DEBUG ] No samples found: hicup [2024-01-16 23:01:02,299] multiqc [DEBUG ] No samples found: hicpro [2024-01-16 23:01:02,305] multiqc [DEBUG ] No samples found: salmon [2024-01-16 23:01:02,312] multiqc [DEBUG ] No samples found: kallisto [2024-01-16 23:01:02,319] multiqc [DEBUG ] No samples found: slamdunk [2024-01-16 23:01:02,327] multiqc [DEBUG ] No samples found: star [2024-01-16 23:01:02,336] multiqc [DEBUG ] No samples found: hisat2 [2024-01-16 23:01:02,343] multiqc [DEBUG ] No samples found: tophat [2024-01-16 23:01:02,349] multiqc [DEBUG ] No samples found: bowtie2 [2024-01-16 23:01:02,356] multiqc [DEBUG ] No samples found: bowtie1 [2024-01-16 23:01:02,363] multiqc [DEBUG ] No samples found: snpsplit [2024-01-16 23:01:02,369] multiqc [DEBUG ] No samples found: kat [2024-01-16 23:01:02,375] multiqc [DEBUG ] No samples found: leehom [2024-01-16 23:01:02,382] multiqc [DEBUG ] No samples found: adapterRemoval [2024-01-16 23:01:02,388] multiqc [DEBUG ] No samples found: clipandmerge [2024-01-16 23:01:02,395] multiqc [DEBUG ] No samples found: cutadapt [2024-01-16 23:01:02,401] multiqc [DEBUG ] No samples found: flexbar [2024-01-16 23:01:02,408] multiqc [DEBUG ] No samples found: kaiju [2024-01-16 23:01:02,415] multiqc [DEBUG ] No samples found: kraken [2024-01-16 23:01:02,421] multiqc [DEBUG ] No samples found: malt [2024-01-16 23:01:02,428] multiqc [DEBUG ] No samples found: trimmomatic [2024-01-16 23:01:02,435] multiqc [DEBUG ] No samples found: sickle [2024-01-16 23:01:02,442] multiqc [DEBUG ] No samples found: skewer [2024-01-16 23:01:02,449] multiqc [DEBUG ] No samples found: sortmerna [2024-01-16 23:01:02,456] multiqc [DEBUG ] No samples found: biobloomtools [2024-01-16 23:01:02,462] multiqc [DEBUG ] No samples found: fastq_screen [2024-01-16 23:01:02,469] multiqc [DEBUG ] No samples found: afterqc [2024-01-16 23:01:02,480] multiqc [DEBUG ] No samples found: fastp [2024-01-16 23:01:02,685] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2024-01-16 23:01:02,762] multiqc [DEBUG ] No samples found: pycoqc [2024-01-16 23:01:02,769] multiqc [DEBUG ] No samples found: minionqc [2024-01-16 23:01:02,775] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-01-16 23:01:02,782] multiqc [DEBUG ] No samples found: clusterflow [2024-01-16 23:01:02,790] multiqc [DEBUG ] No samples found: bcl2fastq [2024-01-16 23:01:02,796] multiqc [DEBUG ] No samples found: interop [2024-01-16 23:01:02,803] multiqc [DEBUG ] No samples found: ivar [2024-01-16 23:01:02,815] multiqc [DEBUG ] No samples found: flash [2024-01-16 23:01:02,822] multiqc [DEBUG ] No samples found: seqyclean [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-01-16 23:01:02,822] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-01-16 23:01:02,823] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-01-16 23:01:02,831] multiqc [INFO ] Compressing plot data [2024-01-16 23:01:02,942] multiqc [INFO ] Report : multiqc_report.html [2024-01-16 23:01:02,943] multiqc [INFO ] Data : multiqc_data [2024-01-16 23:01:02,943] multiqc [DEBUG ] Moving data file from '/state/partition1/job-41897245/tmpc4sis7ha/multiqc_data' to '/vast/gencore/GENEFLOW/work/4f/59c5c5b78699d905910b95290027f5/merged/multiqc_data' [2024-01-16 23:01:03,129] multiqc [INFO ] MultiQC complete