Bug #121336 for NCBI: blastdbcmd (NCBI Blast 2.6.0) bug report:

Hello! Software: blastdbcmd, NCBI Blast 2.6.0 Operating system: Windows 8.1 Bug: blastdbcmd -entry "gnl|BL_ORD_ID|0" -out "retrievedsequence.txt" -db "Blast1L" returns Error: [blastdbcmd] CObject_id::GetId(): Invalid choice selection: NCBI-General::Object-id.str By contrast, blastdbcmd -entry "gnl|BL_ORD_ID|1" -out "retrievedsequence.txt" -db "Blast1L" outputs the second FASTA entry in the database to the indicated file. While sending this email, two minor inconveniences: Minor inconvenience 1: As far as I can tell, blastn can only return the title (as from blastdbcmd -outfmt %t), and cannot return the ID (as from blastdbcmd -outfmt %i) of a subject strand (in a database) that matches a query, while to retrieve that full subject strand from the database blastdbcmd will only accept the ID. (This is only a minor inconvenience because I realised I could use .fasta for the subject strands as well, thus leading to the next minor inconvenience.) Minor inconvenience 2: While blastn allows indication of multiple subject strand collections at once when databases are used (e.g. ' -db "Blast1R Blast1L" '), .fasta subject strand collections must be blasted one by one, e.g. Command line argument error: Argument "subject". File is not accessible: '1.fasta 2.fasta' Thank you for your time! Mark Cowlishaw