GeneMark-ES, can't locate YAML.pm module

[tzaquin]

Hi,

I hope it is just me being slow, but I can't figure out why when I try to run the ProtHint example I encounter a missing module error:

[Thu Nov 24 09:34:37 2022] Pre-processing protein input
[Thu Nov 24 09:34:37 2022] Running GeneMark-ES.
Can't locate YAML.pm in @INC (you may need to install the YAML module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.32.1 /usr/local/share/perl/5.32.1 /usr/lib/x86_64-linux-gnu/perl5/5.32 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.32 /usr/share/perl/5.32 /usr/local/lib/site_perl) at /home/tzaquin/programs/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl line 87.
BEGIN failed--compilation aborted at /home/tzaquin/programs/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl line 87.
[Thu Nov 24 09:34:37 2022] error: ProtHint exited due to an error in command: /home/tzaquin/programs/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl --verbose --cores 8 --ES --seq /home/tzaquin/programs/ProtHint/example/input/genome.fasta --soft auto

However, when I run GeneMark-ES check_install.bash by itself, I get no errors:

Checking GeneMark-ES installation
Checking Perl setup
All required Perl modules were found
Checking GeneMark.hmm setup
GeneMark.hmm was found
GeneMark.hmm is set
GeneMark.hmm is executable
Performing GeneMark.hmm test run
All required components for GeneMark-ES were found

I'm using a conda environment and installed all dependencies using conda, for example: conda install -c bioconda perl-yaml

But I also tried a fresh environment and install all modules using cpan, still with no success.

I'm using a Debian system without root privilege.

Thank you!

[tzaquin]

So, I was slow. had to modify the shebang to the location of the perl in my conda environment (i.e., RTFM)