I suspect you've hit a limit imposed by their database, the documentation suggest you download the database locally so that you're not hammering theirs.

"Another example is the ability to blast a sequence using the facilities as NCBI. Please be careful not to abuse the compute that NCBI provides and so use this only for individual searches. If you want to do a large number of BLAST searches, please download the blast package locally."

In reply to Re: more then 2000 file download from database error. by marto
in thread problem when more then 2000 file downloading from database by sarf13

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