getAnnoFasta.pl fails to create output from .gff

[Jdbeck66]

After running

augustus --species=arabidopsis --strand=both --singlestrand=false --genemodel=partial --codingseq=on --protein=on --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=2  --exonnames=on ptg000034.fasta > augustus_ptg000034.gff

I attempted to run

perl getAnnoFasta.pl augustus_ptg000034l.gff

It produced no output. I was expecting a .aa and a .codingseq output file.

I also tried using --gff3=off thinking a similar problem as here existed.

I used the docker container built from per the instructions here

[Jdbeck66]

When I add print statements to the perl script's while loop - it seems as if the file is being read, but the parsing is not being satisfied.

[KatharinaHoff]

As an alternative, you can try to run getAnnoFastaFromJoingenes.py with the gtf file generated from AUGUSTUS output.

Best,

Katharina

On Sun, Nov 3, 2024 at 8:45 PM Jim Beck @.***> wrote:

When I add print statements to the perl script's while loop - it seems as if the file is being read, but the parsing is not being satisfied.

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[Jdbeck66]

Thanks Katharina for your quick response,

We are currently redirecting output to a .gff. Is there an option to produce the .gtf? When I run the above augustus script, it looks like it just defaults to print the gff file contents to the screen unless I redirect. I can't locate how produce the gtf to standard output. Or is gtf just gff version 2?

Jim