Michał T. Lorenc

Thank you the error disappeared. Maybe, it would be a good idea to provide a warning to update diamond because otherwise it can't be used for bigger genomes.

P.S. Looking at the log files and it appears it still does not use frameshift [funannotate-p2g.log](https://github.com/nextgenusfs/funannotate/files/7566998/funannotate-p2g.log) [funannotate-predict.log](https://github.com/nextgenusfs/funannotate/files/7566999/funannotate-predict.log) However, it creates a new error: ``` $ funannotate predict -i NbLab330.genome.softmasked.fasta -o...

Ops, my fault. I updated and it used now frameshift. Unfortunately, I got again the same error: ``` $ funannotate predict -i NbLab330.genome.softmasked.fasta -o annotate --species LAB330 --protein_evidence NbenthamianaGenbankAA.clean.fasta -o...

Dear Katharina, I have started to use STAR, but how is it possible to include the second pass of STAR and Augustus? At the moment came so far: ``` #Index...

Thank you for your reply. After which step should I run hints for AUGUSTUS? Additionally, I found [here](https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq) a walkthrough of the STAR 2-pass alignment steps: ``` 1) STAR uses...

In our genome, we expect to see 50.000 to 70.000 genes. However, 3 out of 19 choromosomes appears to have too many genes: ``` > grep "NbV1Ch01" NbV1Ch01.gff3 | grep...

Hi Katharina, Is there a reason why it is turn off as default? Thank you in advance, Michal

Hi Katharina, Thank you, it worked. However, I noticed that I got double `five_prime_utr` and `three_prime_utr` in a gene. Is it normal and if not then how is it possible...

Thank you, `tty: true` removed the error, but now it stuck at: ``` $ docker-compose up Recreating portal_sequenceserver_1 ... done Attaching to portal_sequenceserver_1 sequenceserver_1 | [2022-04-21 00:53:38] INFO Reading configuration...

Hi Nathan, Our genome is at the moment, not public. We gave external users access to it. However, we would like to exclude a few tracks from the external uses...