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.
Hi everyone,
I am having an issue when trying to create my fds table. Below is my Rscript:
I get the following error:
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