Question: local blast on ubuntu 17.04 using refseq_genomic
0
gravatar for jf
5 weeks ago by
jf0
jf0 wrote:

Hello I am trying to run local blast on ubuntu 17.04.

I have blast installed: ncbi-blast+ is already the newest version (2.6.0-1).

then export BLASTDB=path/to/blastdb/folder

Then cd into blastdb and I ran: update_blastdb refseq_genomic

to download all 289 files.

Now I want to be able to screen all refseq files against a .fa file so I run:
blastn -query path/to/.fa -db refseq_genomic -out somename -outfmt "10 score staxids sscinames stitle" and I get this error:

BLAST Database error: No alias or index file found for nucleotide database [refseq_genomic] in search path [./blastdb::]

What I would like to do is compress all 289 files so I can search all of them at once, and figure out how to create the index so I can run the blast.

while cded into the blastdb folder If I run: makeblastdb in refseq_genomic -dbtype nucl -out refseq_db -title refseq_db

I get this error Error: Too many positional arguments (1), the offending value: in Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: in

if I run this command for a specific file: makeblastdb in some/path/refseq_genomic.99.tar.gz -dbtype nucl -out refseq_db -title refseq_db

I get the same error: Error: Too many positional arguments (1), the offending value: in Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: in

if I gzip the refseq_genomic.99 into that folder and run this: makeblastdb in refseq_genomic.99 -dbtype nucl -out refseq_db -title refseq_db

I get this error: Error: Too many positional arguments (1), the offending value: in Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: in

Any assistance that can be provided would be greatly appreciated.

blast refseq • 195 views
ADD COMMENTlink written 5 weeks ago by jf0
1

"in" must be "-in", I think.

ADD REPLYlink written 5 weeks ago by yamule100

yamule, thank you for catching that oversight on my part, that did fix the issue.

ADD REPLYlink written 4 weeks ago by jf0
1

After you "update_blastdb" all you should need to do is unzip the tar files. There should also be a refseq_genomic.nal file in that contains a listing of all the 289 files. It will look something like this.

#
# Alias file created: Oct 13, 2017  3:00 PM
#
TITLE NCBI Genomic Reference Sequences
DBLIST refseq_genomic.00 refseq_genomic.01 refseq_genomic.02 refseq_genomic.03 refseq_genomic.04 
refseq_genomic.05 refseq_genomic.06 refseq_genomic.07 refseq_genomic.08 refseq_genomic.09 refseq_
genomic.10 refseq_genomic.11 refseq_genomic.12 and so on

There is no need to run makeblastdb.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax37k

genomax, I just ran: update_blastdb refseq_genomic and got: Connected to NCBI Downloading refseq_genomic (291 volumes) ... and all volumes were up to date, I do have the .nal file in my db directory

I then gunzip every .tar.gz file <- do I have to extract the .tar files?

Then run blast from there what should the next command look like? this: blastn -query some/file/.fa -db path/to/refseq_genomic.nal -out somename -outfmt "10 score staxids sscinames stitle"

That command gives me this error: BLAST Database error: No alias or index file found for nucleotide database [path/to/refseq_genomic.nal] in search path [path/blastdb::] <- I dont know if it has something to do with the two colons at the end of blastdb.

and the .nal file does have a list just like you depict.

yet I am still getting that no alias or index error.

ADD REPLYlink written 4 weeks ago by jf0

Yes you do need to extract the tar files before you can use them. You should not use .nal at the end of the database name. Try blastn -query some/file/.fa -db path/to/refseq_genomic -out somename -outfmt "10 score staxids sscinames stitle"

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax37k

Thank you I got it to run based on your recommendations

ADD REPLYlink written 4 weeks ago by jf0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 616 users visited in the last hour