Segmentation fault

[GoogleCodeExporter]

Hello,

I'm getting a segmentation fault while trying to align reads to a bacterial 
genome. I was able to isolate the problem to the following read:

@M01793:3:000000000-A5GLB:1:1101:14294:3045 1:N:0:4
CCGAAGGACATTGCAGCACCGTTCTGAGACTTAACAGCAGCCAGGTAGCCGAAGTAAGTCCACTGGATAGCTTCTGTCTC
TTATACACATCTCCGAGCCCACGAGACTCCTGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA
+
ABB?ADBFFFBFGGFG4GGGGGGHGGHFFHHHGHHHHFHGHHHHH3DGFGEEFGAGHEHFHHHHFHHHGFBBGHGHDGGH
HHHHHHHHGGHHHHGGGGGGHGGCEGDFHHHGF2FFEHEE0??EBBHFDFGGGHGFHGGFGGFG//>A@-

My guess is that it has something to do with the run of A at the end of the 
read. I'd like to use the aligner, but would like to refrain from diving into 
the code. Perhaps this case would easy to debug and fix given the single read 
on which it fails.

Cheers,
Alexey

Original issue reported on code.google.com by [email protected] on 15 Nov 2013 at 12:22

[GoogleCodeExporter]

Hi Alexey,

I think this problem may have been already reported, please check the following 
post:
https://groups.google.com/d/msg/rna-star/YL5oztckayQ/AeH7HDNgwEoJ

Please try to generate the genome with --genomeSAindexNbases 8 or smaller. If 
this does not work, please send me your genome and I will have a closer look. 

Please post at https://groups.google.com/forum/#!forum/rna-star for a quicker 
turn-around.

Cheers
Alex

Original comment by [email protected] on 15 Nov 2013 at 4:13