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Old 09-02-2019, 01:41 AM   #4
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

OK. That is the latest release, good.

How did you install BLAST 2.9.0 on Windows 64? Was it using ncbi-blast-2.9.0+-win64.exe or ncbi-blast-2.9.0+-x64-win64.tar.gz (which one) from the NCBI FTP site?

If so, I suggest you email the BLAST help team with your reproducible example.

In the meantime, do you have access to a Mac or Linux machine to try the same example there? Or, if not any you are in a hurry, you could try an older BLAST release (in case this is a recent problem - this would also help in identifying the underlying problem for the NCBI to fix it).
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