perl path in mirdeep

Question

[Sam]

Hi, could you help me about this error with mirdeep2 ?

Error: problem with DNA.fa /usr/bin/env: ‘perl -W’: No such file or directory

[GenoMax]

I assume the problem is with DNA.fa. Is that file present in the the directory you are trying to run this from? It would be odd if your system does not have perl available (but there is always a first time for everything).

Answer 1

[lieven.sterck]

the problem might be with the -W and/or the way you call perl. If you use the /bin/env approach you can't add 'flags' after perl .

Would it be possible to post the first (shebang line) of that perl script?

[Sam]

The problem was env after bin, so already I solved it. Thanks All

Answer 2

[h.mon]

As lieven.sterck said, you can't use flags with #!/usr/bin/env perl.

In addition, I don't understand why you need -W, as mirDeep2.pl already use warnings;.