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gatech-genemark / ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes
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proteins_from_gtf.pl issue #49

Closed francesco-ricci closed 2 years ago

francesco-ricci commented 2 years ago

Hello,

I am trying to use the prothint pipeline and one of the commands used in it (proteins_from_gtf.pl) does not produce a .yaml file as reported in the example folder. I am not skilled in perl but I think there is a problem with the code and I was wondering if you guys could please fix it.

I am attaching a screenshot of my output gene_stat.yaml file. As you can see the contigs code and info are not piled up one after the other, but the produced file has first all the contigs dodes and then all the contigs info.

Thanks Francesco

Screen Shot 2022-09-21 at 15 05 27
tomasbruna commented 2 years ago

Hi Francesco,

the file you shared looks OK to me. The contigs seem very short, but that's another topic. Is ProtHint running into errors?

The input in the example has only one contig, so maybe that's why the yaml appears "piled up".

Best, Tomas

francesco-ricci commented 2 years ago

Thanks for your help Tomas.

When I run the ProtHint pipeline, I get the error message in the attached file. The command nuseq_for_selected_genes.pl uses the .yaml file (generated through the command proteins_from_gtf.pl) at line 52, as highlighted in the error. That's one of the reasons why I thought that's was the problem.

Cheers Francesco

Screen Shot 2022-09-08 at 12 59 31
tomasbruna commented 2 years ago

And when you test ProtHint on the example, do you get the same error?

francesco-ricci commented 2 years ago

yes, just tried same error.

Screen Shot 2022-09-22 at 10 44 32
tomasbruna commented 2 years ago

Ok, this means that something is wrong with the installation of the YAML package. Did you install it with the following command or similarly?

cpan YAML
francesco-ricci commented 2 years ago

just tried again and it looks fine

Screen Shot 2022-09-22 at 10 50 01
tomasbruna commented 2 years ago

That seems fine... Maybe try installing with conda (https://anaconda.org/bioconda/perl-yaml) and not as a super user.

francesco-ricci commented 2 years ago

Already tried, it doesn't work.

francesco-ricci commented 2 years ago

I actually get this error message when I try to install cpan without sudo.

Screen Shot 2022-09-22 at 11 05 10
tomasbruna commented 2 years ago

Those are probably related, but I'm no expert at installing Perl packages :/

francesco-ricci commented 2 years ago

thanks for your help Tomas!

francesco-ricci commented 2 years ago

Fixed it!

I created another environment and reinstalled all the dependencies from scratches and now it works.