Error: file not found

[kdarragh1994]

I am running ProtHint on a plant genome with a set of plant proteins. After a day with things running well until the step : " predict final gene set"

I get this error message:
error, file not found /global/scratch/users/kdarragh/prothint/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl: output/gmhmm/dna.fa_44151.out
[Wed Feb 1 17:13:01 2023] error: ProtHint exited due to an error in command: /global/scratch/users/kdarragh/prothint/ProtHint/bin/../dependencies/GeneMarkES/gmes_petap.pl --verbose --cores 1 --ES --seq /global/scratch/users/kdarragh/annotation/Gongorav1.fa.masked --soft auto

And it's true that when I check the folder dna.fa_44151.out isn't present but I'm not sure what could be causing this type of error.

Thanks in advance for the help with this!

[kdarragh1994]

I have tried running this again multiple times and have never received the same error. Instead I repeatedly get this new error:
"Can't locate object method "limit" via package "Thread::Queue" at /global/scratch/users/kdarragh/prothint/ProtHint/bin/run_spliced_alignment.pl line 64."

Any ideas what this might be caused by? Again it happens after running for around a day.

[tomasbruna]

Hi @kdarragh1994,

this is an annoying Perl module issue, as the readme mentions:

Core module Thread::Queue needs to be updated to a version 3.11 or higher.

You can use the small example which comes with ProtHint to test this installation https://github.com/gatech-genemark/ProtHint/tree/master/example

[kdarragh1994]

Thank you. I have Thread::Queue version 3.14. I just tried running the small example and I actually get a different error.
"IndexError: list index out of range"
I think this might be a python error? I have tried running with python 3.8.8 and python 3.9 and still get the same error.

[tomasbruna]

Do you get this error when running on the example?

[kdarragh1994]

Yes. I am running this:
/global/scratch/users/kdarragh/prothint/ProtHint/bin/prothint.py genome.fasta proteins.fasta --geneSeeds genemark.gtf

From the input folder where the example files are.

"[Tue Mar 21 15:19:44 2023] Translating gene seeds to proteins
Traceback (most recent call last):
File "/global/scratch/users/kdarragh/prothint/ProtHint/bin/print_longest_isoform.py", line 88, in
main()
File "/global/scratch/users/kdarragh/prothint/ProtHint/bin/print_longest_isoform.py", line 69, in main
transcriptLengths = computeLengths(args.input)
File "/global/scratch/users/kdarragh/prothint/ProtHint/bin/print_longest_isoform.py", line 29, in computeLengths
if (row[2] == 'CDS'):
IndexError: list index out of range
[Tue Mar 21 15:19:45 2023] error: ProtHint exited due to an error in command: /global/scratch/users/kdarragh/prothint/ProtHint/bin/print_longest_isoform.py /global/scratch/users/kdarragh/prothint/ProtHint/input/genemark.gtf > longest_seed_isoforms.gtf
"

[tomasbruna]

Hmm, the format of genemark.gtf might have changed (this is out of my control). Can you share the genemark.gtf file?