Hi all,
I downloaded BLAST+ together with the env_nt pre-formatted database. All database files are under ../ncbi-blast-2.3.0+/db/env folder including the env_nt.nal folder.
Following compilation instructions online I also set the PATH for both the Blast executable:
gullived@PN0000044567:~$ export PATH=/home/gullived/ncbi-blast-2.3.0+/bin
and the Blast database:
gullived@PN0000044567:~$ export BLASTDB=/home/gullived/ncbi-blast-2.3.0+/db/env
However when I try to run a blast command blast does not find the database and I get an error like this:
blastn -query '/home/gullived/Daniel_Data/MEtabat folders/documents-export-2016-05-10/July_5000_Hala_superspecific.1.fa' -db env
BLAST Database error: No alias or index file found for nucleotide database [env] in search path [/home/gullived:/home/gullived/ncbi-blast-2.3.0+/db/env::]
It seems to add the path to the directory I call Blast from to the database path and a few additional colons. I tried to overcome this issue by adding a .ncbirc file and specifying the path to the database in that file, however that only made it worse and the error looked like this:
BLAST Database error: No alias or index file found for nucleotide database [env] in search path [/home/gullived:”/home/gullived/ncbi-blast-2.3.0+/db”:/home/gullived/ncbi-blast-2.3.0+/db/env:]
How can I tell the blast executable to only look for the database under the PATH I specify when setting the database path? and not add anything else to it?
Any help is appreciated!
Thank you!
I downloaded BLAST+ together with the env_nt pre-formatted database. All database files are under ../ncbi-blast-2.3.0+/db/env folder including the env_nt.nal folder.
Following compilation instructions online I also set the PATH for both the Blast executable:
gullived@PN0000044567:~$ export PATH=/home/gullived/ncbi-blast-2.3.0+/bin
and the Blast database:
gullived@PN0000044567:~$ export BLASTDB=/home/gullived/ncbi-blast-2.3.0+/db/env
However when I try to run a blast command blast does not find the database and I get an error like this:
blastn -query '/home/gullived/Daniel_Data/MEtabat folders/documents-export-2016-05-10/July_5000_Hala_superspecific.1.fa' -db env
BLAST Database error: No alias or index file found for nucleotide database [env] in search path [/home/gullived:/home/gullived/ncbi-blast-2.3.0+/db/env::]
It seems to add the path to the directory I call Blast from to the database path and a few additional colons. I tried to overcome this issue by adding a .ncbirc file and specifying the path to the database in that file, however that only made it worse and the error looked like this:
BLAST Database error: No alias or index file found for nucleotide database [env] in search path [/home/gullived:”/home/gullived/ncbi-blast-2.3.0+/db”:/home/gullived/ncbi-blast-2.3.0+/db/env:]
How can I tell the blast executable to only look for the database under the PATH I specify when setting the database path? and not add anything else to it?
Any help is appreciated!
Thank you!
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