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DessimozLab / read2tree

a tool for inferring species tree from sequencing reads
MIT License
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OMA not generating the marker genes #64

Closed evo-eco-gen closed 4 months ago

evo-eco-gen commented 4 months ago

Hello,

I have not been able to produce a set of marker genes with OMA since about the end of June. It just gets stuck on a job: this is surprising, I only ask for a set of 5 rodent species. I am rather in need of a small marker set, with the mammalia markers you provided my job would take 10 CPU-months.

  1. Is OMA OK? Example failing jobs: https://omabrowser.org/oma/markers/a1c5517d1f98b966010291688f9ed597/? https://omabrowser.org/oma/markers/2cba11139be9c3e79fe38fce1642b7b3/?

  2. Is there a way to choose reference species when running read2tree? Thanks, KK

alpae commented 4 months ago

Dear @evo-eco-gen

thanks for reaching out. indeed, the maker export functionality somehow got stuck. I've reactivated the workers now and your dataset is now already ready. exporting markers should be normally really quick - it shouldn't take more than a few minutes even for relatively big datasets.

Your second question I don't really understand.

Best Adrian

evo-eco-gen commented 4 months ago

Thank you Adrian! As for my 2nd question: read2tree has a few options like "--ignore_species", I was wondering if that's a way to control which reference species are included in the analysis.

alpae commented 4 months ago

ok, I see. those options were mostly implemented during the development phase. The --ignore_species option for example was used to use a subset of the markers from an OMA standalone run. We rather recommend to build a tailored set of reference groups - that's also why we implemented a direct export from the OMA Browser website.

I hope this answers your question. Cheers Adrian

evo-eco-gen commented 4 months ago

Thank you, you did answer all my questions!