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rajanil / fastStructure

A variational framework for inferring population structure from SNP genotype data.
MIT License
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Type error when running test data #42

Open hrivera28 opened 6 years ago

hrivera28 commented 6 years ago

Hello, I'm trying to run the test dataset on a cluster and am getting the following error:

Traceback (most recent call last): File "/vortexfs1/apps/bio/faststructure-1.0/structure.py", line 178, in params['prior'], params['cv']) File "fastStructure.pyx", line 101, in fastStructure.infer_variational_parameters E = mlhood.marginal_likelihood(G, psi, pi) TypeError: Argument 'psi' has incorrect type (expected admixprop.AdmixProp, got admixprop.AdmixProp)

I'm just running the code as suggested in the readme with the test data set: python structure.py -K 3 --input=test/testdata --output=testoutput_simple --full --seed=100

with the corresponding paths for my machine of course.

Any ideas what's happening? I haven't been able to find a mention of a similar error elsewhere. Thank you!

saurav-baral commented 6 years ago

same issue, any fix. I am thinking of shifting to admixture.

hrivera28 commented 6 years ago

Hey, no I didn't figure it out. Ended up running Structure on an HPC instead.

saurav-baral commented 6 years ago

me either. So I shifted to admixture. Do you know of any advantages of using structure over admixture or any disadvantage of admixture?

potant commented 6 years ago

Any progress with the TypeError: Argument 'psi' has incorrect type (expected admixprop.AdmixProp, got admixprop.AdmixProp)?????

I am facing the same issue..

potant commented 6 years ago

It seems that the problem comes from Cython package. I uninstalled Cython 0.29, installed 0.22, rebuild again and then the test runnings worked

qjy543 commented 6 years ago

me too