bedtools2: Non-writable IO device error when intersecting BAM and BED files
I have a sorted BAM file that I want to filter for reads not overlapping regions in a BED file. However, the following error occurs:
bedtools intersect -a sample.bam -b regions.bed -v > reads.not.in.regions.bam
terminate called after throwing an instance of 'std::runtime_error'
what(): BgzfStream::Write() - trying to write to non-writable IO device
I have plenty of space to write the files, and if I do not specify an output file it prints to the console.
About this issue
- Original URL
- State: closed
- Created 9 years ago
- Comments: 24 (11 by maintainers)
Same problem here, cannot directly output bam to NFS storage, only bed. Local storage is fine. My current workaround is pipe to stdout and then use samtools view.