Question: NCBI BLAST+ on local Galaxy and associated .loc file entries
1
gravatar for lp.vandergouw
5 months ago by
lp.vandergouw10 wrote:

Hi,

I recently downloaded a local instance of galaxy and added the NCBI BLAST+ tool from the toolshed. Now I downloaded both the nt and the nr databases from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ but when installed, only the nr database shows up. The databases are intsalled as followed:

nt(tab)NCBI nt 01 Nov 2016(tab)/media/lucas/Verbatim_2TB/BLAST/nt/nt in blastdb.loc
nr(tab)NCBI nr 01 Nov 2016(tab)/media/lucas/Verbatim_2TB/BLAST/nr/nr in blastdb_p.loc

Does anyone know how I can fix this?

Kind regards, Lucas van der Gouw

tool blast+ galaxy local index • 176 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson22k • written 5 months ago by lp.vandergouw10

Hello,

Few things to check:

  • Indexes are uncompressed
  • Differences between with the "base name" for the nr indexes and what is in the loc file
  • Do not use symbolic links - avoid these and use the direct full path
  • Restart after changes to see the effect

If you still have trouble after that, run the command below, then post the results, along with the exact lines from the blastdb.loc for the target database and we can help with syntax.

% ls -alh /media/lucas/Verbatim_2TB/BLAST/nt | head 20 > out
ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson22k

Hi Jennefer,

The indexes are all uncompressed, are all called nt..* and the path given in the blastdb.loc file is the absolute path. The output of the command is as follows:

 total 42G
drwx------ 1 lucas lucas  192K Nov 20 17:50 .
drwx------ 1 lucas lucas  512K Nov 18 12:38 ..
-rw------- 2 lucas lucas   14M Oct 28 13:09 nt.00.nhd
-rw------- 2 lucas lucas  311K Oct 28 13:09 nt.00.nhi
-rw------- 2 lucas lucas  136M Oct 28 23:07 nt.00.nhr
-rw------- 2 lucas lucas  9,1M Oct 28 23:07 nt.00.nin
-rw------- 2 lucas lucas  7,1M Oct 28 13:09 nt.00.nnd
-rw------- 2 lucas lucas   29K Oct 28 13:09 nt.00.nni
-rw------- 2 lucas lucas  3,1M Oct 28 13:09 nt.00.nog

and here is the content of the bastdb.loc file:

  (bunch of commented lines)

nt  NCBI nt 01 Nov 2016 /media/lucas/Verbatim_2TB/BLAST/nt/nt

note that I used the exact same syntax for the nr database in bastdb_p.loc (replaced nt with nr) and that works like a charm

ADD REPLYlink modified 5 months ago • written 5 months ago by lp.vandergouw10

What happens if you change the file permissions so that they are user, group, world readable/executable? Restart Galaxy after the change.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson22k

so for some reason my file won't change: neither via GUI nor via

sudo chmod -R 777 /media/lucas/Verbatim_2TB/BLAST/nt

the nr files have the same permissions as the nt files

I decided to try and get my taxonomic profiles some other way, so I downloaden MetaPhlAn2 from the toolshed. However, same as blastn, it can not find the database even after changing the .loc file to contain:

mpa_v20_m200    Defaut database with clade-specific marker genes /media/lucas/Verbatim_2TB/metaphlan2/db_v20/mpa_v20_m200
ADD REPLYlink written 5 months ago by lp.vandergouw10

Lucas, isn't nt & nr both Nucleotides?

ADD REPLYlink written 4 months ago by Bjoern Gruening4.5k

from the NCBI BLAST readme:

nr.*tar.gz                    | Non-redundant protein sequences from GenPept, 
                                Swissprot, PIR, PDF, PDB, and NCBI RefSeq
nt.*tar.gz                    | Partially non-redundant nucleotide sequences from 
                                all traditional divisions of GenBank, EMBL, and DDBJ 
                                excluding GSS,STS, PAT, EST, HTG, and WGS.
ADD REPLYlink modified 4 months ago • written 4 months ago by lp.vandergouw10
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