Makeblastdb can spit out warning notices when a higher count of N ambiguous 
nucleotides occurs in the first row of fasta data, but goes ahead and completes 
the blast database.

"Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is 
about 45% ambiguous nucleotides (shouldn't be over 40%)"

At moment the NCBI Blast+ wrappers 
are saying "yup those are errors", but i think they should be downgraded to 
just Notices?  If the tool is part of a workflow it fails - on db's like RDP 
RNA this is quite a nuisance.

Anyone else run into the same thing?


Also see:

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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