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.
>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.
thank you in advance
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_