Has anyone had this problem with blastn (newest version)?

Trying 14mil reads to the ref_viruses_rep_genomes database. Has worked perfectly in the past but not with a new blast install and newest db.

If I do smaller number of reads or if I put the word_size at less than 11 I don't get this error:

Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options

Used to work fine - in less than 5 mins to run all 14mil reads. Help!