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blastall with a GI list to limit the search


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#1 neokao

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Posted 14 June 2009 - 10:38 AM

I setup a standalone blast server on Windows vista. It seems to work well except that I could not do a restricted search with a GI list.
The database is nr downloaded from NCBI and I formatdb it myself.
I also got the GI list (as attached) from NCBI entrez for Drosophila proteins and I put that file in the same folder with the nr and input file.

Somehow whenever I used -l Dm.gi.txt in the blastall command, I always got error messages " [NULL_Caption] ERROR: [000.000] ...omited... Unable to open file Dm.gi.txt"
...then some other warnings."


Could somebody give me some suggestions?

Thanks a lot.

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#2 HomeBrew

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Posted 14 June 2009 - 12:44 PM

Try providing the full path to the file after the command line switch -- you may have to quote it if there's spaces in the path. Or, try putting Dm.gi.txt in the same directory as the blastall executable.

#3 neokao

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Posted 14 June 2009 - 12:59 PM

Try providing the full path to the file after the command line switch -- you may have to quote it if there's spaces in the path. Or, try putting Dm.gi.txt in the same directory as the blastall executable.


I did. Actually, Dm.gi.txt is in the same directory with blastall.exe and nr data base. I still have no clue to fix it.




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