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Bus Error #614

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radh1ka opened this issue Apr 9, 2019 · 4 comments
Closed

Bus Error #614

radh1ka opened this issue Apr 9, 2019 · 4 comments
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@radh1ka
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radh1ka commented Apr 9, 2019

Bus error when aligning with STAR-2.6.1b

Input file is 91M Aligning this to a bacterial genome (1.7M)
I have 32GB of RAM available. Can't figure out why I am getting this error....

Fusobacterium_sp_obrc1.FspOBRC1v1.0
Apr 09 14:01:52 ..... started STAR run
Apr 09 14:01:52 ..... loading genome
Apr 09 14:02:30 ..... started mapping
Bus error (core dumped)

BusERROR.txt
@alexdobin
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Hi @radh1ka

have you reduced --genomeSAindexNbases (to ~10 in your case), as is required for the small genomes.
If you did, and it still does not work, please send me the Log.out file.

Cheers
Alex

@radh1ka
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radh1ka commented Apr 10, 2019

Thank you so much Alex, This worked!

@radh1ka radh1ka closed this as completed Apr 10, 2019
@thoelken
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Ran into the same problem. Adding --genomeSAindexNbases 10 during index generation fixed the problem. I'd love to reopen the issue and suggest throwing an error or warning, if that is possible.

@alexdobin
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Hi @thoelken

it is described in the manual... but I agree that a warning would be the best.
Also, I am still hoping to solve the underlying problem.

Cheers
Alex

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@thoelken @alexdobin @radh1ka