Significant SNP not counted in log file

[Sabi333]

Hi I am conducting a GWAS on several phenotypes and in the log file it says "GWAS yield minP: 0; MOST: 0". But if I check the *.most_orig.sumstats file and filter for all SNPs with a p-value < 5e-8, I get one significant SNP with p-value 1e-8. I also checked MAF and this is at 0.011, so your internal filter of 0.005 should not ignore this SNP. I also had a look at your code but could not figure out why this SNP should be ignored. Are there any other criteria for not counting SNPs in the log file?
Thanks in advance!