Question: Why Does Blastdbcmd Produce The Error: Oid Not Found
gravatar for chevivien
5.3 years ago by
chevivien70 wrote:

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?

blast • 3.1k views
ADD COMMENTlink modified 5.3 years ago by biostar150 • written 5.3 years ago by chevivien70

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

ADD REPLYlink written 5.3 years ago by 5heikki8.4k
gravatar for biostar
5.3 years ago by
biostar150 wrote:

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.

ADD COMMENTlink written 5.3 years ago by biostar150

Thanks for the response

ADD REPLYlink written 5.2 years ago by chevivien70
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