Question: Strange "Error: OID not found" in NCBI's blastdbcmd
0
gravatar for juanma_lace
4.7 years ago by
juanma_lace20
Argentina
juanma_lace20 wrote:

I'm getting a OID not found when executin blastdbcmd. My file is as follows:

>cat data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted  | grep scaffold00001_37_1_21

>scaffold00001_37_1_21

And I run

>makeblastdb -dbtype 'nucl' -in data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted -out data/4D/blastdb-parseqid/4ds_splitted -parse_seqids

Building a new DB, current time: 12/18/2014 14:12:08
New DB name:   data/4D/blastdb-parseqid/4ds_splitted
New DB title:  data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted
Sequence type: Nucleotide
Deleted existing BLAST database with identical name.
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 307 sequences in 0.021672 seconds.

 

And then

>blastdbcmd -db data/4D/blastdb-parseqid/4ds_splitted -entry scaffold00001_37_1_21 -outfmt %f -out 1_scaffold00001_37_1_21.fsa

Error: scaffold00001_37_1_21: OID not found
BLAST query/options error: Entry not found in BLAST database
Please refer to the BLAST+ user manual.

Any ideas?

 

thank you in advance

EDIT:

if I take a look to the output of blastdbcmd with entry "all" I cannot find the  original sequence, why is it missing?

>blastdbcmd -db data/4D/blastdb-parseqid/4ds_splitted -entry all -outfmt %f -out 1_scaffold00001_37_1_21.fsa

>cat 1_scaffold00001_37_1_21.fsa | grep 0001_

nothing. 

 

 

ADD COMMENTlink modified 4.7 years ago by Siva1.6k • written 4.7 years ago by juanma_lace20

are you sure about "-parse_seqids" ?

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum122k
1
gravatar for juanma_lace
4.7 years ago by
juanma_lace20
Argentina
juanma_lace20 wrote:

Deleting previous generated databases with makeblastdb solve the issue. I was getting no error, but the database was not being generated again.

ADD COMMENTlink written 4.7 years ago by juanma_lace20
1
gravatar for Siva
4.7 years ago by
Siva1.6k
United States
Siva1.6k wrote:

If you want to create BLAST databases with an option to retrieve individual sequences using sequence ID, you need to have the sequence ID in a specific format that is described in the BLAST user manual.

ADD COMMENTlink written 4.7 years ago by Siva1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 860 users visited in the last hour