[2024-03-04 19:11:58,404] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-03-04 19:11:58,404] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-03-04 19:11:58,405] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-03-04 19:11:58,407] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-03-04 19:11:58,407] 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}} [2024-03-04 19:11:58,407] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-04 19:11:58,773] multiqc [WARNING] MultiQC Version v1.21 now available! [2024-03-04 19:11:58,774] multiqc [INFO ] This is MultiQC v1.9 [2024-03-04 19:11:58,774] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-03-04 19:11:58,774] multiqc [DEBUG ] Working dir : /vast/gencore/GENEFLOW/work/c8/341f2e7a4a58e8921ecc6838692d74/merged [2024-03-04 19:11:58,774] multiqc [INFO ] Template : default [2024-03-04 19:11:58,774] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-03-04 19:11:58,774] multiqc [INFO ] Searching : /vast/gencore/GENEFLOW/work/c8/341f2e7a4a58e8921ecc6838692d74/merged [2024-03-04 19:11:58,774] 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 [2024-03-04 19:11:58,774] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-43671017/tmpkb73ji5r [2024-03-04 19:11:59,465] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-04 19:11:59,467] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-03-04 19:11:59,481] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 8 samples (table) [2024-03-04 19:11:59,483] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-03-04 19:11:59,493] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-03-04 19:11:59,500] multiqc [DEBUG ] No samples found: conpair [2024-03-04 19:11:59,507] multiqc [DEBUG ] No samples found: peddy [2024-03-04 19:11:59,514] multiqc [DEBUG ] No samples found: somalier [2024-03-04 19:11:59,521] multiqc [DEBUG ] No samples found: methylQA [2024-03-04 19:11:59,533] multiqc [DEBUG ] No samples found: mosdepth [2024-03-04 19:11:59,539] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-03-04 19:11:59,543] multiqc [DEBUG ] No samples found: qualimap [2024-03-04 19:11:59,550] multiqc [DEBUG ] No samples found: preseq [2024-03-04 19:11:59,557] multiqc [DEBUG ] No samples found: quast [2024-03-04 19:11:59,564] multiqc [DEBUG ] No samples found: qorts [2024-03-04 19:11:59,571] multiqc [DEBUG ] No samples found: rna_seqc [2024-03-04 19:11:59,578] multiqc [DEBUG ] No samples found: rockhopper [2024-03-04 19:11:59,584] multiqc [DEBUG ] No samples found: rsem [2024-03-04 19:11:59,600] multiqc [DEBUG ] No samples found: rseqc [2024-03-04 19:11:59,606] multiqc [DEBUG ] No samples found: busco [2024-03-04 19:11:59,613] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-03-04 19:11:59,619] multiqc [DEBUG ] No samples found: disambiguate [2024-03-04 19:11:59,626] multiqc [DEBUG ] No samples found: supernova [2024-03-04 19:11:59,646] multiqc [DEBUG ] No samples found: deeptools [2024-03-04 19:11:59,654] multiqc [DEBUG ] No samples found: sargasso [2024-03-04 19:11:59,661] multiqc [DEBUG ] No samples found: verifybamid [2024-03-04 19:11:59,667] multiqc [DEBUG ] No samples found: mirtrace [2024-03-04 19:11:59,674] multiqc [DEBUG ] No samples found: happy [2024-03-04 19:11:59,680] multiqc [DEBUG ] No samples found: mirtop [2024-03-04 19:11:59,690] multiqc [DEBUG ] No samples found: homer [2024-03-04 19:11:59,697] multiqc [DEBUG ] No samples found: macs2 [2024-03-04 19:11:59,703] multiqc [DEBUG ] No samples found: theta2 [2024-03-04 19:11:59,709] multiqc [DEBUG ] No samples found: snpeff [2024-03-04 19:11:59,719] multiqc [DEBUG ] No samples found: gatk [2024-03-04 19:11:59,726] multiqc [DEBUG ] No samples found: htseq [2024-03-04 19:11:59,734] multiqc [DEBUG ] No samples found: bcftools [2024-03-04 19:11:59,740] multiqc [DEBUG ] No samples found: featureCounts [2024-03-04 19:11:59,749] multiqc [DEBUG ] No samples found: fgbio [2024-03-04 19:11:59,769] multiqc [DEBUG ] No samples found: dragen [2024-03-04 19:11:59,777] multiqc [DEBUG ] No samples found: dedup [2024-03-04 19:11:59,783] multiqc [DEBUG ] No samples found: damageprofiler [2024-03-04 19:11:59,823] multiqc [DEBUG ] No samples found: biobambam2 [2024-03-04 19:11:59,829] multiqc [DEBUG ] No samples found: mtnucratio [2024-03-04 19:11:59,831] multiqc [DEBUG ] No samples found: picard [2024-03-04 19:11:59,837] multiqc [DEBUG ] No samples found: prokka [2024-03-04 19:11:59,843] multiqc [DEBUG ] No samples found: samblaster [2024-03-04 19:11:59,854] multiqc [DEBUG ] No samples found: samtools [2024-03-04 19:11:59,861] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-03-04 19:11:59,868] multiqc [DEBUG ] No samples found: bamtools [2024-03-04 19:11:59,875] multiqc [DEBUG ] No samples found: jellyfish [2024-03-04 19:11:59,885] multiqc [DEBUG ] No samples found: vcftools [2024-03-04 19:11:59,891] multiqc [DEBUG ] No samples found: longranger [2024-03-04 19:11:59,899] multiqc [DEBUG ] No samples found: stacks [2024-03-04 19:11:59,906] multiqc [DEBUG ] No samples found: varscan2 [2024-03-04 19:11:59,926] multiqc [DEBUG ] No samples found: bbmap [2024-03-04 19:11:59,932] multiqc [DEBUG ] No samples found: bismark [2024-03-04 19:11:59,939] multiqc [DEBUG ] No samples found: biscuit [2024-03-04 19:11:59,946] multiqc [DEBUG ] No samples found: hicexplorer [2024-03-04 19:11:59,952] multiqc [DEBUG ] No samples found: hicup [2024-03-04 19:11:59,959] multiqc [DEBUG ] No samples found: hicpro [2024-03-04 19:11:59,965] multiqc [DEBUG ] No samples found: salmon [2024-03-04 19:11:59,971] multiqc [DEBUG ] No samples found: kallisto [2024-03-04 19:11:59,977] multiqc [DEBUG ] No samples found: slamdunk [2024-03-04 19:11:59,984] multiqc [DEBUG ] No samples found: star [2024-03-04 19:11:59,989] multiqc [DEBUG ] No samples found: hisat2 [2024-03-04 19:11:59,995] multiqc [DEBUG ] No samples found: tophat [2024-03-04 19:12:00,002] multiqc [DEBUG ] No samples found: bowtie2 [2024-03-04 19:12:00,008] multiqc [DEBUG ] No samples found: bowtie1 [2024-03-04 19:12:00,017] multiqc [DEBUG ] No samples found: snpsplit [2024-03-04 19:12:00,024] multiqc [DEBUG ] No samples found: kat [2024-03-04 19:12:00,029] multiqc [DEBUG ] No samples found: leehom [2024-03-04 19:12:00,036] multiqc [DEBUG ] No samples found: adapterRemoval [2024-03-04 19:12:00,044] multiqc [DEBUG ] No samples found: clipandmerge [2024-03-04 19:12:00,060] multiqc [DEBUG ] No samples found: cutadapt [2024-03-04 19:12:00,071] multiqc [DEBUG ] No samples found: flexbar [2024-03-04 19:12:00,081] multiqc [DEBUG ] No samples found: kaiju [2024-03-04 19:12:00,090] multiqc [DEBUG ] No samples found: kraken [2024-03-04 19:12:00,099] multiqc [DEBUG ] No samples found: malt [2024-03-04 19:12:00,106] multiqc [DEBUG ] No samples found: trimmomatic [2024-03-04 19:12:00,113] multiqc [DEBUG ] No samples found: sickle [2024-03-04 19:12:00,119] multiqc [DEBUG ] No samples found: skewer [2024-03-04 19:12:00,125] multiqc [DEBUG ] No samples found: sortmerna [2024-03-04 19:12:00,130] multiqc [DEBUG ] No samples found: biobloomtools [2024-03-04 19:12:00,137] multiqc [DEBUG ] No samples found: fastq_screen [2024-03-04 19:12:00,143] multiqc [DEBUG ] No samples found: afterqc [2024-03-04 19:12:00,149] multiqc [DEBUG ] No samples found: fastp [2024-03-04 19:12:00,157] multiqc [DEBUG ] No samples found: fastqc [2024-03-04 19:12:00,163] multiqc [DEBUG ] No samples found: pycoqc [2024-03-04 19:12:00,170] multiqc [DEBUG ] No samples found: minionqc [2024-03-04 19:12:00,176] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-03-04 19:12:00,183] multiqc [DEBUG ] No samples found: clusterflow [2024-03-04 19:12:00,189] multiqc [DEBUG ] No samples found: bcl2fastq [2024-03-04 19:12:00,196] multiqc [DEBUG ] No samples found: interop [2024-03-04 19:12:00,202] multiqc [DEBUG ] No samples found: ivar [2024-03-04 19:12:00,208] multiqc [DEBUG ] No samples found: flash [2024-03-04 19:12:00,213] multiqc [DEBUG ] No samples found: seqyclean [2024-03-04 19:12:00,213] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-03-04 19:12:00,214] multiqc [INFO ] Compressing plot data [2024-03-04 19:12:00,216] multiqc [INFO ] Report : multiqc_report.html [2024-03-04 19:12:00,216] multiqc [INFO ] Data : multiqc_data [2024-03-04 19:12:00,216] multiqc [DEBUG ] Moving data file from '/state/partition1/job-43671017/tmpkb73ji5r/multiqc_data' to '/vast/gencore/GENEFLOW/work/c8/341f2e7a4a58e8921ecc6838692d74/merged/multiqc_data' [2024-03-04 19:12:00,392] multiqc [INFO ] MultiQC complete