Error in a custom Perl script for detecting recombination

Question

[jigarnt]

Hi All,

I am trying to run this custom perl script available on GIThub for detecting recombination through Four-gamete test. As this is my first hands on Perl, I am not able to figure out where I am going wrong. Although I know the basic do's and dont's of a running scripts on command prompt/terminal. I am pasting the error below. Any comments/suggestions/inputs are appreciated:

C:\Users\Jigar>cd C:\Perl64\bin
C:\Perl64\bin>perl rmincutter.pl -i example.fasta
Bareword found where operator expected at rmincutter.pl line 6, near ""en" class"
        (Missing operator before class?)
Bareword found where operator expected at rmincutter.pl line 26, near "<title>rmin_cut"
        (Missing operator before rmin_cut?)
Can't modify numeric lt (<) in scalar assignment at rmincutter.pl line 6, near ""en" class"
syntax error at rmincutter.pl line 6, near ""en" class"
Unrecognized character \xC2; marked by <-- HERE after at master <-- HERE near column 45 at rmincutter.pl line 26.
C:\Perl64\bin> "perl rmincutter.pl -i example.fasta"
'"perl rmincutter.pl -i example.fasta"' is not recognized as an internal or external command,
operable program or batch file.
C:\Perl64\bin> "perl rmincutter.pl -i example.fasta
'"perl rmincutter.pl -i example.fasta' is not recognized as an internal or external command,
operable program or batch file.

[venu]

Seems you are using windows. Which perl you are using strawberry perl, active perl? and can you provide the link for GitHub repo?

[jigarnt]

Hi Venu,

Thanks for your response. I also ran this script in linux but I am getting the same error. I suspect there is an issue with the script. Whats your take?

[Jean-Karim Heriche]

I got this script from GitHub and it runs just fine on my Ubuntu installation (assuming this is the script you're talking about). In this version, line 6 is an empty commented line so your script seems different from the one I got on GitHub. I suggest you download the script again and try again. As the bareword error seems to come from the comments at the top of the script, it could be that you accidentally uncommented a line or maybe added some characters somewhere at the top.