Bioseq must have Seq-data or delta containing only literals

[anikng]

Hi Members,

While trying to set up NCBI localblast db, I found an error saying that "Bioseq must have Seq-data or delta containing only literals". But I couldn't find a solution (eventhough some others asked same doubt in other forums). Pleas help me if you know the error.

Am using blast verson 2.2.29+ and working in Windows.

Please see the attached screenshot.

[maubp]

It sounds like your FASTA file is invalid in some way. Can you show use the exact command you ran, and a sample of your FASTA file?

[anikng]

Hi maubp,

As u suggested, it was an error with input fasta sequence. My fasta file had many 'N' and when i use a sequence without N, BLAST run correctly.
But still i would like to know how to run a sequence with 'N'. If u have any idea about handle N's in a DB (as well as query) sequence, kindly let me know. Also i attach the command used to run the Blast and sample DB sequence.

blastn -query db/JAPONICA.txt -db db/INDICA -out db/aligned.txt -outfmt 7 -max_target_seqs 3


Thanks,
anikng