local blast on ubuntu 17.04 using refseq_genomic

Question

[jf]

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.

[fishgolden]

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

[jf]

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

[GenoMax]

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.

[jf]

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.

[GenoMax]

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"

[jf]

Thank you I got it to run based on your recommendations