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Error: legacy_blast.pl command not found

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
• 2,023 views • link
updated by ATpoint ATpoint • written by venura venura

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!

• 0 views • link
written by venura venura

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.

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written by GenoMax GenoMax

1 answer

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.

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written by ATpoint ATpoint

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

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written by venura venura

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

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written by GenoMax GenoMax

Getting the same error . legacy_blast.pl command not found

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written by venura venura

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?

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written by GenoMax GenoMax

No output. nothing at all:|

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written by venura venura

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.

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written by GenoMax GenoMax

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

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written by venura venura

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.

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written by GenoMax GenoMax

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

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written by venura venura

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