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heche-psb / wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
https://wgdv2.readthedocs.io/en/latest/
GNU General Public License v3.0
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ERROR All families are singleton families, No Ks can be calculated - RBH #29

Closed dfmoralesb closed 2 months ago

dfmoralesb commented 2 months ago

Hello!

I've been using wgd dmd for whole paranome and then wgd ksd get the Ks distribution of single species and everything works great. But when trying to run dmd and ksd for RBHs, I got the same error below no mater what samples I use.

ERROR All families are singleton families, No Ks can be calculated

I used all defaults parameters as in the examples. I there any parameter that I'm missing? I'm using wgd v2.0.30

wgd dmd sequence1 sequence2 wgd ksd families sequence1 sequence2

Thanks for you help! Best, Diego

heche-psb commented 2 months ago

Hi, it seems that the gene families provided for wgd ksd has only singleton families. Is it the case?

dfmoralesb commented 2 months ago

Yes, that's the case. So, I don't understand why wgd dmd outputs only singleton families.

heche-psb commented 2 months ago

May you share me with your sequence file? It has something to do with the seq itself.

dfmoralesb commented 2 months ago

Here are the CDS files for two species. I tried with many others as well, but I got the same error. Thanks! CDS.zip

heche-psb commented 2 months ago

Hi, I spotted the issue, which is due to the missing of index (like GF00000001) in the RBH gene families file. I have fixed the issue and updated it in v2.0.31. May you install the latest version and try with this command for the wgd dmd step again? (note that the only difference is the addition of the flag -of)

$wgd dmd Cypripedium_macranthos_var_rebunense.cds.fa Vanilla_shenzhenica.cds.fa -of

dfmoralesb commented 2 months ago

It works now. Thanks for your help!!!