ERROR: Paired-end reads were detected in single-end read library

[deb0612]

Dear sir,
I tried to use fds<- countRNAData(fds) to count my bam file.
There are something wrong when running Subread:
ERROR: Paired-end reads were detected in single-end read library : /NGS_Storage/Debbie/Tumor/A3060/arriba/Aligned.sortedByCoord.out.bam
No counts were generated.
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:

Should I add any option? or I should direct use Subread?