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Old 05-10-2016, 09:04 AM   #1
DL88
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Default Issue with BLAST database path!

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:

[email protected]:~$ export PATH=/home/gullived/ncbi-blast-2.3.0+/bin

and the Blast database:

[email protected]:~$ 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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Old 05-10-2016, 09:16 AM   #2
GenoMax
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Can you post a listing of

Code:
$ ls -lh /home/gullived/ncbi-blast-2.3.0+/db/env
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Old 05-10-2016, 09:25 AM   #3
DL88
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[email protected]:~$ ls -lh /home/gullived/ncbi-blast-2.3.0+/db/env
Command 'ls' is available in '/bin/ls'
The command could not be located because '/bin' is not included in the PATH environment variable.
ls: command not found
[email protected]:~$

This is what I get when I call the above line.

Thanks,

Daniel
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Old 05-10-2016, 09:32 AM   #4
GenoMax
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Looks like you messed up your default $PATH when you tried to change it. That should be fixable by a reboot. In mean time try /bin/ls and the rest of the command above and post the results.
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Old 05-10-2016, 09:43 AM   #5
DL88
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Do you mean adding /bin/ls to the path?

[email protected]:~$ ls -lh bin/ls/home/gullived/ncbi-blast-2.3.0+/db/env
Command 'ls' is available in '/bin/ls'
The command could not be located because '/bin' is not included in the PATH environment variable.
ls: command not found
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Old 05-10-2016, 09:52 AM   #6
GenoMax
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Try this.

Code:
$ /bin/ls -lh /home/gullived/ncbi-blast-2.3.0+/db/env
There should be 240 files for env_nt.NN.n**. You don't need to post the entire output, if you see a lot of files.

Last edited by GenoMax; 05-10-2016 at 09:56 AM.
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Old 05-10-2016, 10:28 AM   #7
DL88
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Restarted my computer:

Yes, there are a lot of files:

[email protected]:~$ /bin/ls -lh /home/gullived/ncbi-blast-2.3.0+/db/env
total 43G
-rw-r--r-- 1 gullived gullived 56M Nov 18 2012 env_nt.00.nhd
-rw-r--r-- 1 gullived gullived 1.3M Nov 18 2012 env_nt.00.nhi
-rw-rw-r-- 1 gullived gullived 416M Nov 18 2012 env_nt.00.nhr
-rw-rw-r-- 1 gullived gullived 37M Nov 18 2012 env_nt.00.nin
-rw-rw-r-- 1 gullived gullived 25M Nov 18 2012 env_nt.00.nnd
-rw-rw-r-- 1 gullived gullived 97K Nov 18 2012 env_nt.00.nni
-rw-r--r-- 1 gullived gullived 13M Nov 18 2012 env_nt.00.nog
-rw-rw-r-- 1 gullived gullived 137M Nov 18 2012 env_nt.00.nsd
-rw-rw-r-- 1 gullived gullived 2.8M Nov 18 2012 env_nt.00.nsi
-rw-rw-r-- 1 gullived gullived 745M Nov 18 2012 env_nt.00.nsq
.....
-rw-r--r-- 1 gullived gullived 954M Apr 19 14:04 env_nt.22.nsq
-rw-r--r-- 1 gullived gullived 378K May 2 13:54 env_nt.23.nhd
-rw-r--r-- 1 gullived gullived 8.9K May 2 13:54 env_nt.23.nhi
-rw-r--r-- 1 gullived gullived 3.4M May 2 13:54 env_nt.23.nhr
-rw-r--r-- 1 gullived gullived 279K May 2 13:54 env_nt.23.nin
-rw-r--r-- 1 gullived gullived 186K May 2 13:54 env_nt.23.nnd
-rw-r--r-- 1 gullived gullived 788 May 2 13:54 env_nt.23.nni
-rw-r--r-- 1 gullived gullived 93K May 2 13:54 env_nt.23.nog
-rw-r--r-- 1 gullived gullived 906K May 2 13:54 env_nt.23.nsd
-rw-r--r-- 1 gullived gullived 20K May 2 13:54 env_nt.23.nsi
-rw-r--r-- 1 gullived gullived 27M May 2 13:54 env_nt.23.nsq
-rw-r--r-- 1 gullived gullived 402 May 4 12:37 env_nt.nal
[email protected]:~$
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Old 05-10-2016, 12:02 PM   #8
GenoMax
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Great. Use the following. I suggest that you remove (and not use) any spaces in the file/dir names.


Code:
$ blastn -query '/home/gullived/Daniel_Data/MEtabat folders/documents-export-2016-05-10/July_5000_Hala_superspecific.1.fa' -db env_nt
if full path is required then
Code:
blastn -query '/home/gullived/Daniel_Data/MEtabat folders/documents-export-2016-05-10/July_5000_Hala_superspecific.1.fa' -db /home/gullived/ncbi-blast-2.3.0+/db/env/env_nt
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