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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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ksd not finishing #39

Closed EmilyPhelps closed 1 month ago

EmilyPhelps commented 4 months ago

Hello,

I've been trying to use wgd V2 to calculate a Ks peak

I've taken a subset of my CDS (~3K sequences)

When I run 

 wgd dmd subset.fasta

I get: Screenshot 2024-06-25 at 11 23 09 But it finishes. So if I run:

wgd ksd wgd_dmd/subset.fasta.tsv subset.fasta

It will start off okay and just slow to a stop. I also get this error, for pretty much each gene family: Screenshot 2024-06-25 at 11 29 45

heche-psb commented 2 months ago

Hi, the percentage of collinear genes (i.e., anchor pairs) is small, based on which we could not decisively confirm the validity of the putative WGD event. But the whole paranome Ks distribution bears a WGD peak ~1.49 which agrees with the ~1.36 peak in anchor Ks distribution. Given that Ks 1.49 is already high, I think it's reasonable to assume that there is an ancient WGD event in the evolutionary past of your focal species whose remnants were highly diminished.

tomlewin commented 2 months ago

Hi @EmilyPhelps ! Did you ever solve this? Having the same problem and increasing memory allocation doesn't seem to help. Thanks!

Labella98 commented 1 month ago

Hi! I am encountering the same error, when using wgd ksd, it starts, but it crashes when parsing some specific families, when increasing nthreads, all families are parsed, but no output file is obtained. I have tried to increase the memory as proposed above, but I don't know why, it doesn't use more than 2Gb of memory.