Incomplete annotation by SnpEff eff

Dear Galaxy community,

I performed the SnpEff eff on my vcf in order to add variant effect prediction on the called variants.
I did get results for about half of the lines, but the other half did not get the prediction information.

I need to have these information so I can further filter my data to look for the variants of interests.
Are there any reasons why not all lines get the prediction info? I tried to select as many output INFO options as I can (so not those which says “Do not show…”).

Or are there other tool swhich I can use to add the snp effect (such as exonic, nonsense mutation, protein change…)?

Thanks a lot for your support in advance.