Makeblastdb error: file does not match input format type, default input type is FASTA

Question

[lessismore]

Hey all,

i have a problem in creating a database with this file. ftp://ftp.ncbi.nlm.nih.gov/repository/UniGene/Triticum_aestivum/Ta.seq.all.gz

i run

makeblastdb -in Ta.seq.all -title Ta_unigene -dbtype nucl -out Ta_database

it gives the error mentioned: file does not match input format type, default input type is FASTA

Could anybody help me ?

I checked if there are spaces after ">" I checked every entry starts with "^>"

Thank you in advance

[GenoMax]

What version of blast are you using?
I was able to make the database using the exact command you have above with blast v.2.3.0. No errors.

[lessismore]

blastn: 2.2.30+ Package: blast 2.2.30, build Aug 28 2015 11:17:27

[GenoMax]

Ta.seq.all file has this extra line up at the beginning of the file. You could try to remove it and then see if that works.

# Set containing 407 members  /gb=JP820949 /gi=359554132 /len=2058

Otherwise try and upgrade blast to the latest version.

[lessismore]

Already did, nothing changed.

[GenoMax]

I am able to reproduce the error with Blast v.2.2.30. But that does not help you.
Like I said above that file worked with a newer version of blast. I would suggest that you upgrade, if you can.

[5heikki]

*nix or Windows? I imagine the file has *nix encoded linebreaks so it would look like >seqasassasa>seqsadsdsadsa>.. to Windows

[lessismore]

it's linux ubuntu. Should probably update something?

[GenoMax]

Update blast to the latest.

[5heikki]

Or if it's about the extra line on top, just

tail -n +2 Ta.seq.all > Ta.seq.all.mod

And then makeblastdb with that file. But really, keeping blast up-to-date is a rather good idea..

[GenoMax]

@lessismore tried that already and said that did not work.

Answer 1

[lessismore]

Thank you guys. it was a problem of Blast version. With the latest one it worked.