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?