Star RNA seq aligner issue:

Question

[play.tatha]

BAMoutput.cpp:27:BAMoutput: exiting because of OUTPUT FILE error: could not create output file /home/.../three_STARtmp//BAMsort/20/16

SOLUTION: check that the path exists and you have write permission for this file. Also check ulimit -n and increase it to allow more open files.

Can't figure out the actual issue.

[Bastien Hervé]

Did you try what's written in SOLUTION or is it your attempts ?

[play.tatha]

Yes, I checked that the path is valid.

The ulimit -n showed 1024 as output.

Still, the issue is not resolved.

[play.tatha]

It is related to the --outSAMtype BAM SortedByCoordinate command. The issue is automatically resolved if --outSAMtype BAM Unsorted is used.

https://github.com/alexdobin/STAR/issues/529

[Bastien Hervé]

We do not have your STAR command line but you can try to reduce the number of thread used and increase the ulimit even more. You can also sort your BAM file afterwards.

Answer 1

[Max]

ulimit -n 65535

it works!

https://www.cnblogs.com/xuexiaohun/articles/6233430.html