Question: Error: legacy_blast.pl command not found
0
gravatar for venura
11 months ago by
venura30
venura30 wrote:

Hi,

I am trying to run the following command

legacy_blast.pl blastall -i test.fa -d StDB –p blastp –e 1e-10 –b 5 –v 5 –m 8 –o Sol.blast

but getting following error ;

legact_blast.pl: command not found

I am using ncbi-blast+ 2.2.25 . Can someone help me on this regard? Thank you!

blast • 220 views
ADD COMMENTlink modified 11 months ago by ATpoint38k • written 11 months ago by venura30

Hello venura!

We believe that this post does not fit the main topic of this site.

found a solution.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 11 months ago by venura30

You don't need to close a post to indicate closure. You accepted the answer which signals closure. Closing post is an action for mods to deal with off-topic/incomplete posts.

ADD REPLYlink written 11 months ago by genomax89k
2
gravatar for ATpoint
11 months ago by
ATpoint38k
Germany
ATpoint38k wrote:

It is not in PATH. Please google what PATH is in Unix systems and how to add executables to it. Alternatively, it it not executable, so chmod +x your.pl might help.

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint38k

blast is already in the PATH and perl script is executable. Still I am getting the same error :(.

ADD REPLYlink written 11 months ago by venura30

What happens if you just run legacy_blast.pl? That should print the help dialog to screen.

ADD REPLYlink written 11 months ago by genomax89k

Getting the same error . legacy_blast.pl command not found

ADD REPLYlink written 11 months ago by venura30

Interesting. So something is not properly set up.

I see

$ legacy_blast.pl 
NAME
    legacy_blast.pl - Convert BLAST command line invocations from NCBI C
    toolkit's implementation to NCBI C++ toolkit's implementation. 

(truncated)

What does which legacy_blast.pl produce?

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax89k

No output. nothing at all:|

ADD REPLYlink written 11 months ago by venura30

I suggest you check your $PATH and the location of where the bin directory is in the blast package. Reconcile those if needed. Otherwise use full path to legacy_blast.pl location and see if you can get the in-line help to show up.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax89k

When I use the full path as you suggested, I get the help file.

When I echo, i get the following #path/home/venura/miniconda3/bin:/home/venura/miniconda3/condabin:/home/venura/bin:/home/venura/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

ADD REPLYlink modified 11 months ago • written 11 months ago by venura30
2

That tells us that your blast bin directory is not in your $PATH. Add it by doing export PATH=$PATH:/full_path_to_blast_bin and you should be all set.

ADD REPLYlink written 11 months ago by genomax89k

Thank you! I know its not possible. But, I am darn sure that blast was there in the $PATH earlier :(.

ADD REPLYlink written 11 months ago by venura30
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