BlastX Database: output search is empty

Question

[marongiu.luigi]

Dear all,

I am running a blastx search using a cluster. I uploaded the nr database as well as the taxon indices taxdb.btd and taxdb.bti into a local folder and ran a script as

blastx -db <path_to_nr_database/nr> -num_threads 30 -max_target_seqs 10 -outfmt '6 sskingdoms' -query <file>

I also exported the variable for the database

export BLASTDB="<path_to_nr_database/nr>"

but the output is empty. Is there something wrong in the syntax?

[GenoMax]

How about just

export BLASTDB="<path_to_nr_database>"

[marongiu.luigi]

the same, it is still empty, as is in "N/A"

[lieven.sterck]

does that cmdline provide any feedback/errors/warnings ?

on the other hand if there are no hits, then with the -outfmt 6 you will indeed get an empty file (as it only prints hits info to the output in that case)

[marongiu.luigi]

no errors, but when I ran a check on my machine I got a hit, thus I am afraid something is not right when running in the cluster...

[GenoMax]

Is $BLASTDB directory available on all cluster nodes? Sometimes parts of a cluster may not be able to access all storage.

[marongiu.luigi]

I am using bsub ... -env "all, BLASTDB=<path>" and export BLASTDB=<path in the shell script but when I do echo $BLASTDB the result is emtpy...

[GenoMax]

If your $BLASTDB variable is not propagating correctly in your shell script then that is the problem. It is not clear how you submit these jobs so once you figure out why that is happening the problem should be fixed.

[marongiu.luigi]

clearly blastx does not find a hit in the taxon database. Is there a way to force blastx to find the taxon database more directly than with the environmental variable BLASTDB? Also, are taxdb.btd and taxdb.bti the correct databases for protein hits? Thanks

[lieven.sterck]

can you first check if you have the taxon part of the DB? I seem to remember you had to download that one separately, it was (is?) not part of the default blastdb release.

from the NCBI blast website:

The BLAST taxonomy database is required in order to print the scientific name, common name, blast name, or super kingdom as part of the BLAST report or in a report with blastdbcmd. The BLAST database contains only the taxid (an integer) for each entry, and the taxonomy database allow BLAST to retrieve the scientific name etc. from a taxid. The BLAST taxonomy database consists of a pair of files (taxdb.bti and taxdb.btd) that are available as a compressed archive from the NCBI BLAST FTP site (ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz).

[marongiu.luigi]

The md5sum of the files in the link is different from those of the files I had, I guess it is only a different update, but I will try to see if there is a difference. Thank you