Indexing error with local blast

Question

[ando.kelli]

Hi all,

I'm trying to do a blast to local NCBI nt database in Linux. The code I've used to download and decompress the DB is:

cd /volume/BlastDBs

update_blastdb.pl nt
update_blastdb.pl taxdb

gunzip *tar.g*

ls *.tar |xargs -n1 tar -xvf

Notes: I needed to do a loop as tar will only do one file at a time I noticed that the .md5 suffix files not recognised -> was ignored by gunzip This folder has files with the following extensions for each 'piece' of the DB:

.tar
.tar.gz.md5
.nhd
.nhi
.nhr
.nin
.nnd
.nni
.nog
.nsd
.nsi
.nsq

There is also an nt.nal file

The taxdb has:

.tar
.tar.gz.md5
.btd
.bti

Doing the blast (I tried with the full path to the DB, and using the -nt parameter, got the same error message both times):

blastn -db /volume/BlastDBs -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

I get the error message:

BLAST Database error: No alias or index file found for nucleotide database [/volume/BlastDBs] in search path [/volume/Assembly_data/Test:$/volume/BlastDBs:]

As a way of troubleshooting, I created a small DB from a fasta file using the following script:

cd /volume/Assembly_data/Test/TestDB

makeblastdb -dbtype nucl -in /volume/Assembly_data/Test/Test.fasta -title Test_db -out Test_db

It seemed to work and created 3 output files in the TestDB directory: Test_db.nhr Test_db.nin Test_db.nsq

Then ran the blast using:

blastn -db /volume/Assembly_data/Test/TestDB -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

Got the same error message. ..............................

I don't know if it's important, but I installed blast using:

conda install blast

Any suggestions about what could be going wrong are greatly appreciated. It's doing my head in.

Cheers, Kelli

Answer 1

[GenoMax]

You need to use the basename of the blast index in your command line for the -db option. Since you are using nt database (which also is the basename) your command needs to be

blastn -db /volume/BlastDBs/nt -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

Also in other test case use the basename Test_db.

blastn -db /volume/Assembly_data/Test/TestDB/Test_db -query /volume/Assembly_data/Test/Test.fasta -outfmt 6 -out TEST_blastn.tabular

[ando.kelli]

Wow. I can't believe that's what the issue was. Thank you so much Genomax!!

[ando.kelli]

Hi again Genomax,

I split my assembly so that I can do the annotation in parallel. When I run the following code, the output is missing sscinames sskingdom

ls trinity_out_dir.Trinity.*.fasta | parallel --eta -j 10 --load 80% --noswap 'blastn -db /volume/BlastDBs/nt -query {} -out blastn_outfiles/{.}.tabular -evalue 1e-5 -outfmt "6 std stitle staxids sscinames sskingdom" -max_target_seqs 1 -max_hsps 1 -num_threads 2'

I get the error message: Warning: [blastn] Taxonomy name lookup from taxid requires installation of taxdb database with ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz

The taxdb .btd and .bti files are in the same directory as the nt db files. How can I get Blast to find them properly?

[GenoMax]

Do this: A: getting sscinames in viral blastx query

[ando.kelli]

Thanks again Genomax :-)