BiocParallel errors when running bambu

[lyj95618]

Hi,

I am running bambu with the following command and I got this error. What does this error mean?
My bambu version is 3.4.0 and my R is 4.3.3

bamlist <- opt$sample #just one bam here
bambuAnnotations <- prepareAnnotations(opt$gtf)

se <- bambu(trackReads=TRUE, returnDistTable=FALSE,NDR=1, reads = bamlist, annotations = bambuAnnotations, genome = fa.file, ncore = 4,
    opt.discovery = list(min.exonDistance = 1,min.readFractionByGene=0.04, remove.subsetTx=FALSE))
sampleID <- basename(dirname(opt$sample))
writeBambuOutput(se, path = opt$output, prefix=sampleID)

WARNING - If you change the number of cores (ncore) between Bambu runs and there is no progress please restart your R session to resolve the issue that originates from the XGboost package.
--- Start generating read class files ---
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'splitAsList': subscript contains NAs
Execution halted

Thanks for the help!
Laur

[cying111]

Hi @lyj95618 ,

sorry for getting back lately. Based on a brief read, it looks to me this error suggests there is some issue in reads processing. have you checked that if your gtf file, reads are using the same seqlevelstyles, for example, chr1 vs 1?

Best,
Ying