Post by giopan on Nov 11, 2023 12:31:21 GMT
Hi everyone,
I've been trying to run SBayesRC and I keep getting an "Error: Zero SNP effect in the model for 100 cycles of sampling" for essentially every genomic block (I'm running block-wise with the 7M imputed SNPs).
After consulting the FAQ recommendations, I tried running with flags for inclusion p threshold and for removal of highly correlated SNPs: "--p-value 0.5 --rsq 0.99". Doing this, I get segmentation fault errors.
I should mention that:
1) My file of annotations is very minimal, just an Intercept column of ones, plus another annotation (with SNPs scattered across the genome) and
2) I have successfully run SBayesR on the same dataset.
Any suggestions as to what might be causing the algorithm to fail?
Thank you for any suggestions!
Best,
Gio
I've been trying to run SBayesRC and I keep getting an "Error: Zero SNP effect in the model for 100 cycles of sampling" for essentially every genomic block (I'm running block-wise with the 7M imputed SNPs).
After consulting the FAQ recommendations, I tried running with flags for inclusion p threshold and for removal of highly correlated SNPs: "--p-value 0.5 --rsq 0.99". Doing this, I get segmentation fault errors.
I should mention that:
1) My file of annotations is very minimal, just an Intercept column of ones, plus another annotation (with SNPs scattered across the genome) and
2) I have successfully run SBayesR on the same dataset.
Any suggestions as to what might be causing the algorithm to fail?
Thank you for any suggestions!
Best,
Gio