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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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agat_sp_fix_longest_ORF.pl fails to produce gff #360

Closed r-mashoodh closed 3 months ago

r-mashoodh commented 1 year ago

AGAT has been working great for me so far, so thanks. I'm trying to determine if the ORFs of my GTF are properly defined. Trying to work out if the start/stop codons are missing from the CDS.

I've run into a bit of an issue. I'm using singularity to run AGAT. I have the original reference GTF (GCF_001412225.1, converted to and a modified GTF where I extracted CDS only). The error occurs in both -- though the full GTF has a lot more warnings.

agat_sp_fix_longest_ORF.pl -gff cds_all.gtf --fasta genome.fa -o cds

There error is as follows ...

Can't modify non-lvalue subroutine call of &Bio::SeqFeature::Generic::end at /usr/local/bin/agat_sp_fix_longest_ORF.pl line 484.

I've attached the std out here: agat_error.txt

Is this an issue with my gtf? My bioperl is up-to-date as far as I can tell ...

thanks in advance

Juke34 commented 1 year ago

Coud you share or point me to the files that I can try by myself and see if it is a bug?

What AGAT version are you using?

kdm9 commented 4 months ago

@Juke34 Was this bug identified and fixed, or was this issue just closed for inactivity? I ask as I'm hitting the same bug myself, and want to know if I should bother debugging it or just try installing from the latest git revision.

Juke34 commented 4 months ago

I closed it for inactivity

Juke34 commented 3 months ago

I have tried AGAT version 1.4.0 and I do not have any issue like this one. If you still hit the issue please re-open the issue and add more information. otherwise I would not be able to check/fix it.

123jjhy commented 2 weeks ago

hi， I have the same problem and need your help GFF3 file parsed Fasta file parsed Can't modify non-lvalue subroutine call of &Bio::SeqFeature::Generic::end at ./agat_sp_fix_longest_ORF.pl line 487.

123jjhy commented 2 weeks ago

It should be a problem of the GTF file, could be about SuspiciousFrame

Juke34 commented 2 weeks ago

Again I cannot help without sample to investigate myself. Please provide a piece of annotation file with the command you run to be able to reproduce the issue.