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healthdisparities / rye

:herb: :bread: Large scale ancestry inference from PCA data
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error in rye.R --eigenval=1240k279popsadmixture_pca.eigenval --eigenvec=1240k279popsadmixture_pca.eigenvec --pop2group=pop_group --threads=10 --output=1240k279popsadmixturerye_output #6

Closed GuanglinHe1 closed 1 year ago

GuanglinHe1 commented 2 years ago

Dear Lavanya, i prepared the all files and run it and following errors occurred. Would you give me some advice.

Error in params[[bestError]] : attempt to select less than one element in get1index Calls: rye -> rye.optimize

AaronRuben commented 1 year ago

I got the same error. Make sure your pop2group.txt has the two columns Pop and Group. The capitalization is important. That solved it for me.

Taghrid-M commented 4 months ago

I'm facing the same issue, and I've double-checked my pop2group.txt file – the columns 'Pop' and 'Group' are indeed capitalized. Could you possibly help me figure this out?

[ Mar 09 2024 - 10:38:43 PM ] Parsing user supplied arguments... [ Mar 09 2024 - 10:38:44 PM ] Arguments passed validation [ Mar 09 2024 - 10:38:44 PM ] Running core rye with 2 threads [ Mar 09 2024 - 10:38:44 PM ] Reading in Eigenvector file [ Mar 09 2024 - 10:38:44 PM ] Reading in Eigenvalue file [ Mar 09 2024 - 10:38:44 PM ] Reading in pop2group file [ Mar 09 2024 - 10:38:44 PM ] Creating individual mapping [ Mar 09 2024 - 10:38:44 PM ] Scaling PCs [ Mar 09 2024 - 10:38:44 PM ] Weighting PCs [ Mar 09 2024 - 10:38:44 PM ] Aggregating individuals to population groups [ Mar 09 2024 - 10:38:44 PM ] Optimizing estimates using NNLS Round 1/5 Mean error: NA, Best error: Error in params[[bestError]] : attempt to select less than one element in get1index Calls: rye -> rye.optimize In addition: Warning messages: 1: In mclapply(seq(attempts), function(i) rye.gibbs(X = referenceX, : all scheduled cores encountered errors in user code 2: In which.min(errors) : NAs introduced by coercion 3: In mean.default(errors) : argument is not numeric or logical: returning NA Execution halted

Many thanks, Taghrid