[2025-04-21 12:24:14,700] multiqc.config [INFO ] Loading config settings from: multiqc_config.yml [2025-04-21 12:24:14,701] multiqc.core.update_config [INFO ] Report title: Pmeandrina_RNAseq [2025-04-21 12:24:15,174] multiqc.core.version_check [WARNING] MultiQC Version v1.28 now available! [2025-04-21 12:24:15,175] multiqc.core.file_search [INFO ] Search path: /gscratch/scrubbed/srlab/nxf.Dw80wVKBQz [2025-04-21 12:24:15,176] multiqc.core.file_search [ERROR ] Module(s) in config.run_modules are unknown: bracken. Double check the case and dashes/underscores. Available modules IDs: adapterremoval, afterqc, anglerfish, bakta, bamdst, bamtools, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, minionqc, mirtop, mirtrace, mosdepth, motus, mtnucratio, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, somalier, sortmerna, sourmash, spaceranger, stacks, star, supernova, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenome [2025-04-21 12:24:15,176] multiqc.core.file_search [INFO ] Only using modules: custom_content, hisat2, kallisto, kraken, picard, preseq, qualimap, rsem, rseqc, salmon, samtools, sortmerna, star, umitools, fastqc, cutadapt, fastp, fastqc [2025-04-21 12:24:15,187] multiqc.report [INFO ] Skipping 6 file search patterns [2025-04-21 12:24:57,756] multiqc.modules.custom_content.custom_content [INFO ] DupInt: Found 39 General Statistics columns [2025-04-21 12:24:57,845] multiqc.validation [WARNING] custom_content/custom_content.py: warnings while parsing LinePlotConfig.FlatLine {'color': 'green', 'dash': 'longdash', 'label': {'text': '0.5 RPKM'}, 'value': 0.5, 'width': 1} (total: 1): • 'LongDash' is a deprecated dash style, use 'longdash' [2025-04-21 12:24:57,847] multiqc.validation [WARNING] custom_content/custom_content.py: warnings while parsing LinePlotConfig.FlatLine {'color': 'red', 'dash': 'longdash', 'label': {'text': '1 read/bp'}, 'value': 1000, 'width': 1} (total: 1): • 'LongDash' is a deprecated dash style, use 'longdash' [2025-04-21 12:24:57,848] multiqc.validation [WARNING] custom_content/custom_content.py: warnings while parsing LinePlotConfig.LinePlotConfig {'title': 'DupRadar General Linear Model', 'xlog': True, 'xlab': 'expression (reads/kbp)', 'ylab': '% duplicate reads', 'ymax': 100, 'ymin': 0, 'tt_label': '{point.x:.1f} reads/kbp: {point.y:,.2f}% duplicates', 'x_lines': [{'color': 'green', 'dash': 'LongDash', 'label': {'text': '0.5 RPKM'}, 'value': 0.5, 'width': 1}, {'color': 'red', 'dash': 'LongDash', 'label': {'text': '1 read/bp'}, 'value': 1000, 'width': 1}], 'anchor': 'dupradar-section-plot', 'id': 'dupradar'} (total: 1): • Line plot's x_lines or y_lines 'label' field is expected to be a string. Other fields other than 'text' are deprecated and will be ignored [2025-04-21 12:24:58,327] multiqc.modules.custom_content.custom_content [INFO ] dupradar: Found 1 samples (PlotType.LINE) [2025-04-21 12:24:58,339] multiqc.modules.custom_content.custom_content [INFO ] sample-relationships: Found 39 samples (PlotType.HEATMAP) [2025-04-21 12:24:58,354] multiqc.modules.custom_content.custom_content [INFO ] sample-status: Found 78 samples (PlotType.TABLE) [2025-04-21 12:24:58,354] multiqc.modules.custom_content.custom_content [WARNING] HTML plot type found with more than one dataset in nf-core-rnaseq-methods-description [2025-04-21 12:24:58,355] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnaseq-methods-description: Found 1 sample (html) [2025-04-21 12:24:58,355] multiqc.modules.custom_content.custom_content [WARNING] HTML plot type found with more than one dataset in nf-core-rnaseq-summary [2025-04-21 12:24:58,355] multiqc.modules.custom_content.custom_content [INFO ] nf-core-rnaseq-summary: Found 1 sample (html) [2025-04-21 12:24:58,357] multiqc.modules.custom_content.custom_content [INFO ] sample-relationships: Found 39 samples (PlotType.SCATTER) [2025-04-21 12:24:58,437] multiqc.modules.picard.picard [INFO ] Found 39 MarkDuplicates reports [2025-04-21 12:24:58,496] multiqc.modules.qualimap.qualimap [INFO ] Found 39 RNASeq reports [2025-04-21 12:24:58,515] multiqc.modules.rseqc.rseqc [INFO ] Found 39 read_distribution reports [2025-04-21 12:24:58,541] multiqc.modules.rseqc.rseqc [INFO ] Found 39 inner_distance reports [2025-04-21 12:24:58,580] multiqc.modules.rseqc.rseqc [INFO ] Found 39 read_duplication reports [2025-04-21 12:24:58,595] multiqc.modules.rseqc.rseqc [INFO ] Found 39 junction_annotation reports [2025-04-21 12:24:58,618] multiqc.modules.rseqc.rseqc [INFO ] Found 39 junction_saturation reports [2025-04-21 12:24:58,630] multiqc.modules.rseqc.rseqc [INFO ] Found 39 infer_experiment reports [2025-04-21 12:24:58,650] multiqc.modules.rseqc.rseqc [INFO ] Found 39 bam_stat reports [2025-04-21 12:24:59,637] multiqc.modules.samtools.samtools [INFO ] Found 39 stats reports [2025-04-21 12:24:59,676] multiqc.modules.samtools.samtools [INFO ] Found 39 flagstat reports [2025-04-21 12:24:59,724] multiqc.modules.samtools.samtools [INFO ] Found 39 idxstats reports [2025-04-21 12:24:59,736] multiqc.modules.star.star [INFO ] Found 39 reports [2025-04-21 12:25:06,150] multiqc.modules.fastqc.fastqc [INFO ] Found 78 reports [2025-04-21 12:25:06,336] multiqc.core.file_search [ERROR ] Module(s) in config.run_modules are unknown: bracken. Double check the case and dashes/underscores. Available modules IDs: adapterremoval, afterqc, anglerfish, bakta, bamdst, bamtools, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, minionqc, mirtop, mirtrace, mosdepth, motus, mtnucratio, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, somalier, sortmerna, sourmash, spaceranger, stacks, star, supernova, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenome [2025-04-21 12:25:06,336] multiqc.core.file_search [INFO ] Only using modules: picard, qualimap, rseqc, samtools, star, fastqc, dupradar, sample-relationships, sample-status, nf-core-rnaseq-methods-description, nf-core-rnaseq-summary [2025-04-21 12:25:06,337] multiqc.core.write_results [INFO ] Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag