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Makeblast Db Problem

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?

makeblastdb ncbi blast
• 5,268 views • link
updated by Biostar Biostar • written by Christiank • Christiank

3 answers

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
• 2 views • link
updated by Ram Ram • written by Michael Schubert Michael Schubert

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

• 0 views • link
written by Niek De Klein Niek De Klein

"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".

• 1 views • link
written by Neilfws Neilfws

The problem was that Cygwin wasn't installed.

• 1 views • link
written by Christiank • Christiank

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 :-)

• 0 views • link
written by Neilfws Neilfws

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

• 0 views • link
written by Michael Schubert Michael Schubert

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