Hey everyone,
Hope all is well! I was wondering if someone could help me with
another error I ran into. I recently downloaded the NCBI BLAST+
toolkit and it automatically installed itself into Galaxy. I'm just
wondering if anyone knows where I am supposed to put the directory
with the database files it needs to run correctly, or if it makes a
difference. I have configured the blastdb.loc file as shown below, and
the database now appears in the drop-down menu for the NCBI tools, but
when I try executing any of the BLASTs Galaxy returns the following
error, regardless of the path permutation I try:
When I tried putting the databases within the galaxy installation
(within galaxy_test) and I used the whole path:
BLAST Database error: No alias or index file found for nucleotide
database [/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/
tool-data/blastdb/refseq_rna] in search path [/Users/burtonigenomics/
Rosa_Files/bin/fastx_bin/galaxy_test/database/job_working_directory/
28::]
Return error code 2 from command: tblastx -query /Users/
burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/files/
000/dataset_27.dat -db /Users/burtonigenomics/Rosa_Files/bin/
fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna -evalue 0.001 -
out /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/
database/files/000/dataset_32.dat -outfmt 6 -num_threads 8
When I tried putting the databases within the galaxy installation
(within galaxy_test) and I used the path from the galaxy root:
BLAST Database error: No alias or index file found for nucleotide
database [/blastdb/refseq_rna] in search path`
[/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/
job_working_directory/24::] Return error code 2 from command: blastn -
query /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/
database/files/000/dataset_27.dat -db /blastdb/refseq_rna -task
megablast -evalue 0.001 -out
/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/
files/000/dataset_28.dat -outfmt 6 -num_threads 8
When I tried putting the databases outside of the galaxy installation:
BLAST Database error: No alias or index file found for nucleotide
database [/Users/burtonigenomics/Rosa_Files/data/BLAST_databases/
refseq_rna] in search path [/Users/burtonigenomics/Rosa_Files/bin/
fastx_bin/galaxy_test/database/job_working_directory/29::]
Return error code 2 from command:
tblastx -query /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/
galaxy_test/database/files/000/dataset_27.dat -db /Users/
burtonigenomics/Rosa_Files/data/BLAST_databases/refseq_rna -evalue
0.001 -out /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/
database/files/000/dataset_33.dat -outfmt 6 -num_threads 8
The index file is in the folder specified in the nucleotide database
[/blastdb/refseq_rna], but I don't know why/if the search path is
actually going to the right place. job_working_directory doesn't seem
to have any files, is it something that gets changed when galaxy
starts running? Do you know why it's looking there?
___
My current blastdb.loc file (which is supposed to point out the path)
currently reads:
#This is a sample file distributed with Galaxy that is used to define a
#list of nucleotide BLAST databases, using three columns tab separated
#(longer whitespace are TAB characters):
#
#unique_id database_caption base_name_path
#
#The captions typically contain spaces and might end with the build
date.
#It is important that the actual database name does not have a space
in it,
#and that the first tab that appears in the line is right before the
path.
#
#So, for example, if your database is nt and the path to your base name
#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry
#would look like this:
#
#nt_02_Dec_2009 nt 02 Dec 2009
/depot/data2/galaxy/blastdb/nt/nt.chunk
#
#and your /depot/data2/galaxy/blastdb/nt directory would contain all of
#your base names (e.g.):
#
#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr
#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin
#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
#...etc...
#
#Your blastdb.loc file should include an entry per line for each
base name
#you have stored. For example:
#
#nt_02_Dec_2009 nt 02 Dec 2009
/depot/data2/galaxy/blastdb/nt/nt.chunk
#wgs_30_Nov_2009 wgs 30 Nov 2009
/depot/data2/galaxy/blastdb/wgs/wgs.chunk
#test_20_Sep_2008test 20 Sep 2008
/depot/data2/galaxy/blastdb/test/test
#...etc...
#
#See also blastdb_p.loc which is for any protein BLAST database.
#
#Note that for backwards compatibility with workflows, the unique ID of
