bambu discovery not working

[imilenkovic]

When choosing bambu for de novo transcript discovery, I run into the following error:

Error: BiocParallel errors
element index: 5
first error: missing value where TRUE/FALSE needed
In addition: Warning message:
stop worker failed:
attempt to select less than one element in OneIndex
Execution halted

[soniacruciani]

Hi, I get the same error:

`Command error:

The following objects are masked from ‘package:stats’:

  IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

  anyDuplicated, append, as.data.frame, basename, cbind, colnames,
  dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
  grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
  order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
  rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
  union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

  expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

  Vignettes contain introductory material; view with
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

  rowMedians

The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians

Start generating read class files
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: missing value where TRUE/FALSE needed
In addition: Warning message:
stop worker failed:
attempt to select less than one element in OneIndex
Execution halted`

[lucacozzuto]

Hi, this seems a bambu related problem. Try to dig in the temporary folder and check what is happening. I just google it and it seems more people are complaining sometime:
https://stackoverflow.com/questions/68703020/biocparallel-error-cannot-open-the-connection-how-do-i-fix-it