Makeblastdb error: file does not match input format type, default input type is FASTA
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
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lessismore
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Thank you guys. it was a problem of Blast version. With the latest one it worked.
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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.
blastn: 2.2.30+ Package: blast 2.2.30, build Aug 28 2015 11:17:27
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.
Otherwise try and upgrade blast to the latest version.
Already did, nothing changed.
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.
*nix or Windows? I imagine the file has *nix encoded linebreaks so it would look like >seqasassasa>seqsadsdsadsa>.. to Windows
it's linux ubuntu. Should probably update something?
Update blast to the latest.
Or if it's about the extra line on top, just
And then makeblastdb with that file. But really, keeping blast up-to-date is a rather good idea..
@lessismore tried that already and said that did not work.