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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Is it possible to add new sequences to an existing "compare" result? #904

Open vladimirg opened 1 year ago

vladimirg commented 1 year ago

Hello,

I'm running a "funannotate compare" with 38 sequences. It's taking quite a while, due to ProteinOrtho - it's been 5 days already, and it's still going, even parallelized on 32 cores. I've realized that I'll need to add 3 more sequences to the analysis. Re-running the whole thing will take quite a while. My understanding is that ProteinOrtho compares all sequences in a pair-wise fashion, and probably each comparison is independent? If yes, is it possible to add the new sequences to its output, without rerunning the whole thing, which will mostly comprise of comparisons already performed?

Thank you!

nextgenusfs commented 1 year ago

funannotate compare was written solely for my own purposes of doing comparative genomics for about 7 genomes. I don't know if it will generate useful results when you feed it a whole bunch of genomes. The short answer would be that no I don't think you can add species, however, if the temp files still exist than perhaps ProteinOrtho will re-use existing files. Depending on what your question/goals are with compare, there are probably other/better tools out there to answer your specific question. funannotate compare will be deprecated in funannotate2.