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error in running "STAARpipeline_Null_Model.r" #43
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I doubt if my GRM matrix is causing this problem,so i make a new one by tools:gcta(I think users who asked questions before did this),but i still get this error in Iteration 9 |
Xihao,and i have an another question,Can phenotypes be logical? |
Hi @Jerryliu0024, Thanks for reaching out. Let's address your questions one by one. Regarding your question on the null model, this post is most relevant. Can you check whether your GRM contains negative values? What are the minimum and maximum values of your generated GRM? Best, |
Hi Xihao,thanks for your reply!! the minimum values of your generated GRM is 0,and maximum one is 0.556215,my GRM doesn't contain negative values.However,when i set the |
Hi @Jerryliu0024, Yes, if your phenotype is dichotomous (0/1), then the Best, |
Hi Xihao,I think this is indeed feasible!However ,I have questions about some parameters. For example,what's the meaning of |
Hi @Jerryliu0024, Thanks for letting me know. It's great to hear you got the null model fitting step correctly. With your new questions, (1) The example scripts in the tutorial indicate that you would need to submit a list of array jobs to perform the association analysis (and here we use Harvard FAS RC cluster as an example, which is based on slurm workload manager). Specifically, for (2) I can confirm that this message is not an error, but rather indicates that the specific gene category is not a valid variant set (i.e. there is not enough variant annotated as Hope this helps. Best, |
Hi Xihao,a very impressive job!!but when I run the program to this point--“STAARpipeline_Null_Model.r”,I get this error
Iteration 20 : Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'chol2inv': error in evaluating the argument 'x' in selecting a method for function 't': leading principal minor of order 1 is not positive Calls: fit_nullmodel ... .Call -> .handleSimpleError -> h -> .handleSimpleError -> h In addition: Warning message: In .local(A, ...) : CHOLMOD warning 'not positive definite' at file '../Cholesky/t_cholmod_rowfac.c', line 430 Execution halted
When generating the GRM matrix, I input the bed file that I completed pruning on Plink myself, and then follow your process to get a sparse matrix,I don't know how to fix it
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