Can'T Exec "Blastall":No Such File Or Directory...

Question

[jrymer1]

I'm trying to run a script that BLASTs against the pre-formated BLAST databases. When I run my script I get the error Can't exec "blastall." I'm using

blastall -p blastn -d database -i $i -o $1.out

When I unpack the NCBI tar there is no blastall.

Answer 1

[Arun]

There are two things I could think of, that usually is the reason in these scenarios:

1) You have downloaded the non-pre-compiled source, which means that you'll have to compile it yourself to obtain the executables ( ex: blastall is an executable script/file). If you haven't done this, then maybe your system administrator can help you installing it.
2) You don't have executable permissions for your blastall file. This can be obtained using this command in the terminal (assuming you're running linux:

> chmod 766 ./blastall  
> ./blastall <param>  ...

[Michael Schubert]

There is no blastall in NCBI's BLAST+. Only in the C branch (the one called "blast", not "blast+").

[Arun]

Yes, thank you. I edited my post to an even more general debugging one.

Answer 2

[pstew]

Are you following the instructions from http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node1.html ? Has blastall been successfully installed/compiled on the machine you are using?

The blastall directory might not be in your path. To check this (bash):

echo "$PATH"|grep -q blastall && echo "found it"

Replace blastall with the name of the directory if different (works for partial names too).

If you are a user on this machine and have used blastall before, then you might want to ask your sysadmin if anything happened to it.