Question: Admixture cv error
gravatar for s.bourne
5.0 years ago by
s.bourne0 wrote:

Hi all,

When doing Admixture and outputting cv error rate for a range of k values, one of the k values keeps on outputting "nan" as the error rate. It works for the other k values, but not for this one. Has this happened to anyone else?

Cheers, Steve

ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 5.0 years ago by s.bourne0

Same here. Here's some sample output from the bottom of the file. I'm not so worried about the numbers as I am about the fact that the job isn't finishing. It's been running for four hours and all the other versions are done, including ones with higher K values.

586 (QN/Block)  Elapsed: 70.414 Loglikelihood: -nan     (delta): -nan
587 (QN/Block)  Elapsed: 70.526 Loglikelihood: -nan     (delta): -nan
588 (QN/Block)  Elapsed: 70.537 Loglikelihood: -nan     (delta): -nan
589 (QN/Block)  Elapsed: 70.47  Loglikelihood: -nan     (delta): -nan
ADD REPLYlink written 4.3 years ago by jenn.drummond80
gravatar for jcolella.jc
4.9 years ago by
jcolella.jc0 wrote:

Hi Steve, did you ever figure this out?? I get the same issue every time I run K=3 on my data.

Open to suggestions!

ADD COMMENTlink written 4.9 years ago by jcolella.jc0
gravatar for chengcw
4.2 years ago by
United Kingdom
chengcw0 wrote:

You may want to run with admixture32 instead. Hope it helps.

ADD COMMENTlink written 4.2 years ago by chengcw0
gravatar for blair.chr
4.0 years ago by
blair.chr0 wrote:

I'm running into the same issue. I am receiving 'nan' for Loglikelihood and delta for K=6 only. K=1-5 works fine as does K=7. This is quite odd. Any thoughts?


ADD COMMENTlink written 4.0 years ago by blair.chr0
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