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Old 10-28-2016, 05:36 AM   #8
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,178
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Quote:
Originally Posted by rvgill View Post
No, when you end with a slash it created a separate folder with all of my output files within it names MV1SDB_a. That is not my issue here. But thank you for trying to trouble shoot that.

From a different posting i was looking at I found out that I have to now figure out how to combine my individual databases into one larger database that is then the .nal
Did you try running it with the command I suggested, in the same directory you were in when you ran makeblastdb with the "-out MV1SDB_a/MV1SDB_a"?

I understand that the database has been created in it's own directory and that is the problem, when you then try to run blastn it can't find the database because it isn't in the same directory you are running the command from and you don't provide the full path to the database with the "-db" parameter.

Look again at the error message

Quote:
BLAST Database error: No alias or index file found for nucleotide database [MV1SDB/] in search path
It says it can't find an alias OR index file. Your makeblastdb command did create an index file but blastn can't find it because you are not specifying the correct path and db name in your blastn command.

You appear to have gotten hung up on the idea that you need an alias (.nal) file. You do not. alias files are only needed if your database is very large and therefore been broken up into several smaller chunks, or if you are want blast to perform a search by combining two or more separate databases.

Pay attention to properly specifying the path/dbname when you run blastn and that should solve your problem.
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