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Vivianstats / AIDE

AIDE: annotation-assisted isoform discovery and quantification from RNA-seq data
https://genome.cshlp.org/content/29/12/2056
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Fatal error after "Make the TxDb object" #8

Open astulaaa opened 2 years ago

astulaaa commented 2 years ago

Hello,

I am encountering this error, and I am not sure why. Has anyone have an idea how to deal with this?

aide(gtf_path = "./Homo_sapiens.GRCh38.105.gtf", bam_path = "./KUKS10_Aligned.sortedByCoord.out.bam", fasta_path = "./Homo_sapiens.GRCh38.dna.primary_assembly.fa", out_dir = "./", readLen = 100, strandmode = 0, ncores = 20) [1] "extracting gene models from GTF " Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK...

[1] "estimating fragment length ..." [1] "start estimating mean and sd of fragment length ..." [1] "number of genes used: 11529" *Error in (1 - h) qs[i] : non-numeric argument to binary operator**

Thank you! Asta

THccaa commented 1 year ago

Hi Asta,

any chance that you figured out what the problem was? I ran into the same error.