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funannotate update ERROR #1033

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ChuanzhengWei opened this issue Apr 22, 2024 · 0 comments
Open

funannotate update ERROR #1033

ChuanzhengWei opened this issue Apr 22, 2024 · 0 comments

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@ChuanzhengWei
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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

What command did you issue?

singularity exec funannotate.sif funannotate update \
  -f pilon.fasta.masked -g tmp2.gff3 --species "Sbicolor" \
  --trinity transcript.fa -o braker_utr.gff

Logfiles
funannotate-update.log

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