Makeblast Db Problem

Question

[Christiank]

I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txt

I put the ecoli.fnn I downloaded as CP000948.ffn into the bin folder. I get the error:

C:\Users\Christian\Desktop\AlBioU\bin>makeblastdb -in ecoli.fnn -dbtype nucl  -out ecolidb.db

Building a new DB, current time: 10/24/2010 17:18:23
New DB name:   ecolidb.db
New DB title:  ecoli.fnn
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Error: Unable to open input ecoli.fnn as either FASTA file or BLAST db

Are there any gotchas that might have caused my problem?

Answer 1

[Michael Schubert]

I suppose your command was C:UsersChristianDesktopAlBioUbinmakeblastdb (backslash in front of makeblastdb instead of a >)

There are 2 things that might have gone wrong:

1. Your FASTA file is not in your current working directory (type "dir" -w/o the quotes- in Windows' cmd to see where you're at)
2. It is not valid FASTA format

[Niek De Klein]

Or he did do the > and that's what went wront

Answer 2

[Neilfws]

"Unable to open input ecoli.fnn" means what it says - the makeblastdb command cannot see the file. Perhaps try specifying the full file path, using "-in C:UsersChristianDesktopAlBioUbinecoli.ffn".

Answer 3

[Christiank]

The problem was that Cygwin wasn't installed.

[Neilfws]

If you're comfortable installing and using Cygwin, take my advice and just move to Linux. Annoyances like file paths will just melt away and you'll become much more productive :-)

[Michael Schubert]

I don't see how missing Cygwin could produce this kind of error. Any ideas on that one?