Why Does Blastdbcmd Produce The Error: Oid Not Found

Question

[chevivien]

hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fasta

For the output i got fasta sequences which was my goal but my problem is that at the command line i get two error message"

: OID not found : OID not found

"Does it meet not all my sequences was extracted or?or wjat doe this message imply?

[5heikki]

It means that two ids listed in your 93hmmsearchacc.txt were not found from 9311

Answer 1

[biostar]

There could be redundant sequences in nr database itself (due to recent updates or corrections) and those ids could not be retrieved as they are removed from the database.

[chevivien]

Thanks for the response