Paired-end BAM files recognized as single end

[gaynora7]

Hi everyone,

I am having an issue when trying to create my fds table. Below is my Rscript:

library(FRASER)

sampleTable <- fread(system.file(
"scripts_objects", "fraser_settings_object.tsv", package="FRASER", mustWork=TRUE))

bamFiles <- sampleTable[ ,bamFile]
sampleTable[,bamFile:=bamFiles]

settings <- FraserDataSet(colData=sampleTable,
workingDir=tempdir())

if(.Platform$OS.type == "unix") {
register(MulticoreParam(workers=multicoreWorkers()))
} else {
register(SnowParam(workers=multicoreWorkers()))
}

fds <- countRNAData(settings)

write.table(fds, "fds.txt")

I get the following error:

ERROR: Paired-end reads were detected in single-end read library : /HOME/BAM_files/STAR_1010Aligned.sortedByCoord.out.bam
No counts were generated.
Error: BiocParallel errors
  element index: 1
  first error: 
In addition: Warning message:
stop worker failed:
  attempt to select less than one element in OneIndex 
Execution halted

I have run the code a couple times with different iterations of MulticoreParam() and everytime a different BAM file is flagged as being "paired-end reads detected in single-end read library". I checked my BAMs and they are definitely paired-end, so I am not sure why the BAMs are being recognized as single-ended. Is there additional syntax I have to add to specify the BAMs are paired-end? I couldn't find anything in the vignette.

That seems to be my main issue-- however if there are any suggestions on how to solve the "stop worker failed" issue, that would be appreciated as well! I believe it has to do with my memory not being comparable for all the BAM files I have, but I am not sure.

thank you very much,

Alison