bfast local align (putAlnReadBase)

[nisha]

Hi,

I am running bfast localalign on basespace data and I get the following error:

Reads processed: 0bfast: AlignedEntry.c:59: putAlnReadBase: Assertion `1==0' failed

Has someone seen this error before? When I look into the code it seems like the base is something other than A,C,G,T,N and - which is why it's failing.

Thanks
-N

[nilshomer]

Could it be a corrupt file? Try re-running "bfast match" and "bfast localalign" to see if you can repeat the error. If you can, try narrowing down the read in the input FASTQ. Then when you have a small test case that reproducibly causes the error, post here or email [email protected].