Hi,
I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong.
So here are the things I did so far:
1) I downloaded the Win-64 executable file from NCBI/blast/latest (2.2.26). Double-click and install the files under "C:\blast"
2) I went to Environmental Variables window and created variable BLAST with value "C:\blast\bin", BLASTDB with "C:\blast\db", BLASTMAT with "C:\Blast\data".
3) Under "C:\blast", I have three folders: bin, doc and db folder that I created to put the fasta database.
4) I downloaded pre-formatted non-redundant (nr) fasta database from NCBI ftp and put it under C:\blast\db
5) I used "formatdb -i c:\blast\db\nr -p T -o T" command to create index files.
6) Now C:\blast\db has the following files: nr.00.phr, nr.00.pin, nr.00.psq, [...], nr.08.phr, nr.08.pin, nr.08.psq an
7) Next I wanted to generate pssm file using this command:
C:>blastpgp -i c:\blast\O00257.fasta -j 2 -d c:\blast\db\nr -Q O0257.pssm
Unfortunately, I get the following error:
[blastall 2.2.24] WARNING: Unable to open nr.00.pin
[blastall 2.2.26] WARNING: Unable to open nr.00.pin
[blastall 2.2.26] WARNING: Unable to open nr.00.pin
[blastall 2.2.26] WARNING: Unable to open nr.01.pin
[blastall 2.2.26] WARNING: Unable to open nr.01.pin
[blastall 2.2.26] WARNING: Unable to open nr.01.pin
[blastall 2.2.26] WARNING: Unable to open nr.02.pin
[blastall 2.2.26] WARNING: Unable to op ...
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