Comments (7)
Same error...
from braker.
This will be solved when the Augustus issue Gaius-Augustus/Augustus#31 is fixed.
from braker.
I am having the same error. And when I look at the gtf2gff3.err file in errors folder, the output is:
transcript jg1.t1 has conflicting gene parents: and jg1. Remember: In GTF txids need to be overall unique. at /path/to/Augustus/scripts/gtf2gff.pl line 120, <STDIN> line 137778.
from braker.
I also have same problem.
perl /BiO/Access/hskim3824/bioapps/Augustus/scripts/gtf2gff.pl <augustus.hints.gtf --out test.gff3
transcript jg1.t1 has conflicting gene parents: and jg1. Remember: In GTF txids need to be overall unique. at /BiO/Access/hskim3824/bioapps/Augustus/scripts/gtf2gff.pl line 120, line 612516.
so... I could not get gff3 output.
from braker.
same error. @KatharinaHoff do you now if there is a fix for the gtf2gff.pl script?
from braker.
A solution for running gtf2gff.pl, manually, has been posted at Gaius-Augustus/Augustus#31 . You'll have to update your Augustus from github in order to obtain the fix_joingenes_gtf.pl script. The "fix" has not been incorporated into the braker.pl pipeline, yet.
from braker.
from braker.
Related Issues (20)
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from braker.