Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

Loading required package: BiocIO
Loading required package: rtracklayer
Loading required package: dbplyr
[1] "Directory already exists"
--- per sample warnings during read class construction ---
Warnings for:

Attaching package: ‘Biostrings’

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

Loading required package: BiocIO
Loading required package: rtracklayer
Loading required package: dbplyr
[1] "Directory already exists"
--- per sample warnings during read class construction ---
Warnings for:
not all chromosomes present in reference annotations, annotations might be incomplete. Please compare objects on the same reference
26926 reads are mapped outside the provided genomic regions. These reads will be dropped. Check you are using the same genome used for the alignment
--- Start extending annotations ---
combing spliced feature tibble objects across all samples in 14.8 mins.
extract new unspliced ranges object for all samples in 1.3 mins.
reduce new unspliced ranges object across all samples in 1 mins.
combine new unspliced tibble object across all samples in 0.8 mins.
combining transcripts in 17.9 mins.
extended annotations for spliced reads in 0.2 mins.
extended annotations for unspliced reads in 0 mins.
-- Predicting annotation completeness to determine NDR threshold --
Recommended NDR for baseline FDR of 0.1 = 0.181
Using a novel discovery rate (NDR) of: 0.181
transcript filtering in 0.4 mins.
extend annotations in 0.8 mins.
--- Start isoform quantification ---
calculated distance table in 14.8 mins.
Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in left_join(refGenExonMap, exonTxMap, by = "newExonId"): This join would result in more rows than dplyr can handle.
In addition: Warning message:
There was 1 warning in `filter()`.
ℹ In argument: `newGeneId == min(newGeneId)`.
Caused by warning in `min()`:
! no non-missing arguments to min; returning Inf
Execution halted

se.NDR_default <- bambu(reads = rds, annotations = annotations, ncore = ncores,
            genome = fa.file, verbose=TRUE, yieldSize = yieldSize, lowMemory=TRUE,
            fusionMode=FALSE)