funannotate update with mysql

[Nitin123-4]

Hi Team,

I did the required settings for funannotate to use mysql i.e. https://github.com/PASApipeline/PASApipeline/wiki/setting-up-pasa-mysql.

It is running fine with 12 cpus.

funannotate update -i Genome_funannotate_train/ --cpus 12 --pasa_db mysql

Any idea how long will it take to complete?

Previous annotation consists of: 28,846 protein coding gene models and 683 non-coding gene models.

[Nitin123-4]

Hi Team, Any idea about this ?

[nextgenusfs]

I guess it depends on how many transcripts you had in the initial round. It should be faster than when it ran train. I'm assuming that you ran train with the same mysql setup. The update step runs PASA genome comparison, so it takes your gene models from predict and looks at the alignments in the PASA database -- it can predict some new genes and/or alter some coding sequences. It runs this step two times iteratively. If it is still running after 7 days then I'd think something is wrong. I would guess several hours would be more typical.

[Nitin123-4]

Hi Thanks for your reply. I ran funannotate train with sqlite. I am running update with mysql.

[nextgenusfs]

That won't work.

[Nitin123-4]

Oh Okay. So funannotate train should also be with mysql and update also then it should be faster?

[nextgenusfs]

Yeah it tries to reuse the database. You could just run a fresh update but need to pass all the reads, etc and direct to new output folder. Update is capable of running the data from scratch as well.