Error running blastdbaliastool

nupurgupta · 06-12-2012, 10:45 AM

SOLVED: The makedb tool was not creating index files. I directly downloaded the database from NCBI and it is working.

Hi,
I am running command line blastplus, and need to blast against bacteria. I have downloaded databases nr and nt, but need to create a subset for faster searching. I have followed the method in
http://www.biostars.org/post/show/65...-build-my-own/
where I have downloaded a list of accession numbers for bacteria, and am trying to create a subset database based on this. I have tried the command

blastdb_aliastool -gilist bacteria.gilist.txt -db nr -out nr_bacter -title nr_bacteria
but I get an error
"BLAST Database error: GI list specified but no ISAM file found for GI."

Any idea what this is?
Thanks so much

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06-12-2012, 10:45 AM	#1
nupurgupta Member Location: New Jersey Join Date: Aug 2010 Posts: 29	Error running blastdbaliastool SOLVED: The makedb tool was not creating index files. I directly downloaded the database from NCBI and it is working. Hi, I am running command line blastplus, and need to blast against bacteria. I have downloaded databases nr and nt, but need to create a subset for faster searching. I have followed the method in http://www.biostars.org/post/show/65...-build-my-own/ where I have downloaded a list of accession numbers for bacteria, and am trying to create a subset database based on this. I have tried the command blastdb_aliastool -gilist bacteria.gilist.txt -db nr -out nr_bacter -title nr_bacteria but I get an error "BLAST Database error: GI list specified but no ISAM file found for GI." Any idea what this is? Thanks so much Last edited by nupurgupta; 06-14-2012 at 10:37 AM.