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Star RNA seq aligner issue:

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.

rna-seq star bam
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updated by Max • Max • written by play.tatha • play.tatha

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

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written by Bastien Hervé Bastien Hervé

Yes, I checked that the path is valid.

The ulimit -n showed 1024 as output.

Still, the issue is not resolved.

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written by play.tatha • play.tatha

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.

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written by Bastien Hervé Bastien Hervé

1 answer

ulimit -n 65535

it works!

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

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written by Max • Max

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