problem with samtools view -bS

[Giles]

I've been using samtools view -bS on tons of datasets with no problems at all. My workflow is to fastq-dump a .sra file, then clip with fastx-clipper, then map with bowtie, then convert .sam to .bam with samtools view. But this time, the script runs for about 1 minute and then outputs an empty .bam file; w/o any errors. Does anyone have any idea why this is happening? Its odd that it hasn't happened before.

[mastal]

problem with samtools view -bS

Have you looked at the sam file to see if it looks OK? How did the bowtie alignment go?
How large is the file?

[Giles]

Header looked fine. Size is ~3gb. Easily converted into interval using galaxy. I've used this workflow dozens of times, this is the first occurrence of empty bam with no error.

[Giles]

Should I sort

[Heisman]

I would try to run it on a file you know has worked in the past just to make sure there's a problem with the new file and not something else. If that works, then maybe try running it on the first 1000 lines of your file that isn't working and then you can probably pinpoint if the problem is with a specific read somewhere in the file or the header.