makeblastdb error

[ML1975]

Dear all,

I hope you can help. I'm trying to use to create a database to BLAST against. I use the makeblastdb command of:

makeblastdb -in BacMet_PRE.40556.fasta -title PRE -dbtype prot -out PRE -parse_seqids

I got the following result:

Building a new DB, current time: 12/03/2017 00:24:24
New DB name: PRE
New DB title: PRE
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 40556 sequences in 1.71942 seconds.

A number of files with PRE.* are produced (PRE.phr PRE.pnd PRE.pog PRE.psi PRE.pin PRE.pni PRE.psd PRE.psq) however, there is no PRE.pal file.

When I attempt to BLAST against the db - I get the following error:

BLAST Database error: Could not find volume or alias file (.pal) referenced in alias file (-).

I really have no idea how to proceed. Have spent hours looking at forums and other sources. I am reasonably new at using UNIX and command line but know enough to get around. Any suggestions please?

[neavemj]

Hi ML1975,

I just checked my latest protein BLAST databases. They also do not create a *.pal file, but they work fine with blastp or blastx. I think the *.pal files are only created if you have a large database.

- what is your exact BLAST command?
- are you using the latest BLAST version?

Cheers,

Matt.

[ML1975]

Thanks Matt. You are right. I got the BLAST command incorrect by not giving the correct name of the database. It now works using BLASt. I do have the latest version of BLAST.

To be honest, I am trying to use a program called BacMet (http://bacmet.biomedicine.gu.se/index.html) which incorporates BLAST and that allows me to scan an input file against a curated heavy metal/biocide database but their website has little information on getting the database set up. This is what I'm struggling with. If you have any expertise in this software then that would be great otherwise, I'll battle on!

[neavemj]

hmm, I'm afraid I haven't heard of that program.

Good luck!

Matt.