gtf2gff error

[tiramisutes]

Dear,
I have downloading the latest version of BRAKER2 and runing wiht --gff3 flag. But I get follows stderr in gtf output file convert to gff3 format.

ERROR in file /home/software/BRAKER/scripts/braker.pl at line 9415
Failed to execute: cat /home/results/BRAKER/augustus.hints.gtf | perl -ne 'if(m/\tAUGUSTUS\t/) {print $_;}' | perl /home/software/Augustus/scripts/gtf2gff.pl --gff3 --out=/home/results/BRAKER/augustus.hints.gff3 >> /home/results/BRAKER/gtf2gff3.log 2>> /home/results/BRAKER/errors/gtf2gff3.err

and gtf2gff3.err file show

transcript jg1.t1 has conflicting gene parents: and jg1. Remember: In GTF txids need to be overall unique. at /home/software/Augustus/scripts/gtf2gff.pl line 119, <STDIN> line 590303.

Any help is much appreciated.
Thanks.

[francicco]

Same error...

[KatharinaHoff]

This will be solved when the Augustus issue Gaius-Augustus/Augustus#31 is fixed.

[ayala-usma]

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.

[HSKim3824]

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.

[peterthorpe5]

same error. @KatharinaHoff do you now if there is a fix for the gtf2gff.pl script?

[KatharinaHoff]

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.

[peterthorpe5]

Excellent thank you … I will get this testing. Thanks again. Pete From: Katharina Hoff <notifications@github.com> Sent: 17 January 2019 16:10 To: Gaius-Augustus/BRAKER <BRAKER@noreply.github.com> Cc: Peter Thorpe <pjt6@st-andrews.ac.uk>; Comment <comment@noreply.github.com> Subject: {Disarmed} Re: [Gaius-Augustus/BRAKER] gtf2gff error (#9) A solution for running gtf2gff.pl, manually, has been posted at Gaius-Augustus/Augustus#31<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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#9 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AJhCqGU4soNvrBznVhYPfrg8Yrp4yR8aks5vEKA-gaJpZM4YDWKq>. {"api_version":"1.0","publisher":{"api_key":"05dde50f1d1a384dd78767c55493e4bb","name":"GitHub"},"entity":{"external_key":"github/Gaius-Augustus/BRAKER","title":"Gaius-Augustus/BRAKER","subtitle":"GitHub repository","main_image_url":"https://github.githubassets.com/images/email/message_cards/header.png","avatar_image_url":"https://github.githubassets.com/images/email/message_cards/avatar.png","action":{"name":"Open in GitHub","url":"https://github.com/Gaius-Augustus/BRAKER"}},"updates":{"snippets":[{"icon":"PERSON","message":"@KatharinaHoff in #9: 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. "}],"action":{"name":"View Issue","url":"#9 (comment)"}}} [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#9 (comment)", "url": "#9 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]