Are you using the latest release?
YES, my version is 1.8.17
Describe the bug
I used BRAKER to obtain predicted gene models (without UTRs), and I want to update my GTF file using funannotate. After converting it to a GFF file, I used the following command and it did not indicate any issues with the GFF file. I am not sure if funannotate supports updating GTF files from BRAKER, or if there is an error in my script.
[Apr 22 08:12 PM]: OS: Debian GNU/Linux 10, 52 cores, ~ 197 GB RAM. Python: 3.8.12
[Apr 22 08:12 PM]: Running 1.8.17
[Apr 22 08:12 PM]: No NCBI SBT file given, will use default, for NCBI submissions pass one here '--sbt'
[Apr 22 08:14 PM]: Previous annotation consists of: 44,376 protein coding gene models and 0 non-coding gene models
[Apr 22 08:14 PM]: Existing annotation: locustag=g genenumber=79313
[Apr 22 08:14 PM]: Trimmomatic will be skipped
[Apr 22 08:14 PM]: Read normalization will be skipped
[Apr 22 08:14 PM]: No reads to generate transcriptome assemblies, exiting
Are you using the latest release? YES, my version is 1.8.17
Describe the bug I used BRAKER to obtain predicted gene models (without UTRs), and I want to update my GTF file using funannotate. After converting it to a GFF file, I used the following command and it did not indicate any issues with the GFF file. I am not sure if funannotate supports updating GTF files from BRAKER, or if there is an error in my script.
What command did you issue?
Logfiles funannotate-update.log