Question: Makeblastdb error: file does not match input format type, default input type is FASTA
0
gravatar for lessismore
17 months ago by
lessismore170
Mexico
lessismore170 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 • 787 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by lessismore170

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 17 months ago by genomax33k

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

ADD REPLYlink written 17 months ago by lessismore170

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 17 months ago • written 17 months ago by genomax33k

Already did, nothing changed.

ADD REPLYlink written 17 months ago by lessismore170
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 17 months ago by genomax33k

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

ADD REPLYlink written 17 months ago by 5heikki6.6k

it's linux ubuntu. Should probably update something?

ADD REPLYlink written 17 months ago by lessismore170
2

Update blast to the latest.

ADD REPLYlink written 17 months ago by genomax33k

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 17 months ago by 5heikki6.6k
1

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

ADD REPLYlink written 17 months ago by genomax33k
1
gravatar for lessismore
17 months ago by
lessismore170
Mexico
lessismore170 wrote:

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

ADD COMMENTlink modified 17 months ago • written 17 months ago by lessismore170
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