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asapp 10-03-2015 11:49 AM

STAR segmentation fault (--genomeSAindexNbases not reassigning?)

I have used STAR successfully in the past to align with large reference genomes. I am now trying to align with a small genome (~3230 bases). I am using STAR v. 2.4.1d (and have tried the older v. 2.3.0e) and have tried to set the --genomeSAIndexNbases parameter so as to accommodate the small genome. However, I am still receiving segmentation fault (core dumped) errors and when looking at the Log.out file, see that the --genomeSAIndexNbases is being recognized as 14 (the default) rather than the 4 or 5 I have tried to set it to based on log2(numBases)/2 -1 (the formula STAR provides).

Any suggestions would be much appreciated! And thanks in advance.


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