GapFiller standalone interpreter error

Question

[sharmisradha]

the image below is a screenshot of error that occured while running gapfiller tool to fill gaps in contigs. how am i supposed to rectify it?

https://ibb.co/hhnsUG

[lieven.sterck]

any luck resolving your issue?

L.

Answer 1

[lieven.sterck]

Looking at the accompanying image it looks to me you have an illegal character in the perl shebang line . more specifically the ' ^M ' . Did you copy-paste the shebang line ?

anyway, removing that char will most likely solve you issue.

[sharmisradha]

thank you for the information sir...but where shall I find that character and how am I supposed to fix it?

[lieven.sterck]

Well, I suppose it's gonna be at the very first line of this GapFiller.pl script. Just open that file in a text-editor (linux based) and remove. You might not see that char in the text editor though so just make sure you remove anything behind /usr/bin/perl to the end of that line .

Alternatively you can open that file in vi and activate the show all chars option ( :set list) , then it should appear and you can then remove it