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.
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