Question: Makeblastdb error: file does not match input format type, default input type is FASTA
0
gravatar for lessismore
2.2 years ago by
lessismore490
Mexico
lessismore490 wrote:

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

blast • 1.3k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by lessismore490

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.

ADD REPLYlink written 2.2 years ago by genomax49k

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

ADD REPLYlink written 2.2 years ago by lessismore490

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax49k

Already did, nothing changed.

ADD REPLYlink written 2.2 years ago by lessismore490
1

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.

ADD REPLYlink written 2.2 years ago by genomax49k

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

ADD REPLYlink written 2.2 years ago by 5heikki7.3k

it's linux ubuntu. Should probably update something?

ADD REPLYlink written 2.2 years ago by lessismore490
2

Update blast to the latest.

ADD REPLYlink written 2.2 years ago by genomax49k

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..

ADD REPLYlink written 2.2 years ago by 5heikki7.3k
1

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

ADD REPLYlink written 2.2 years ago by genomax49k
1
gravatar for lessismore
2.2 years ago by
lessismore490
Mexico
lessismore490 wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by lessismore490
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