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corbinq / apex

Toolkit for QTL mapping and meta-analysis.
https://corbinq.github.io/apex/
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Error when running apex factor #4

Open azodichr opened 3 years ago

azodichr commented 3 years ago

Hello,

I am running into an error with the apex factor function. Below is my command and the output. These .bed and cov files can be successfully used to run apex lmm and cis, so I am confident in their formatting. The same error occurs if I don't provide the PC covariates and if I try to run it in PCA mode (--iter 0). Thanks for any advice you can provide!

./apex factor --bed sim_smartseq87.bed.gz --cov sim_smartseq87_PCA_covariates.tsv --prefix test --iter 3
Using 1 threads.
2 present in file.
Found 86 samples in covariate file ...
Found 86 samples in expression bed file ...
Processed data for 20 covariates across 85 samples.
Processed expression for 1255 genes across 86 samples.
Scaling expression traits ...
Estimating latent factors ...
terminate called after throwing an instance of 'std::invalid_argument'
  what():  nev must satisfy 1 <= nev <= n - 1, n is the size of matrix

Killed.
dfermin commented 2 years ago

I'm having the same issue. Were you able to fix it?

jean997 commented 2 years ago

I believe you need to specify --factors as some number less than sample size