Error Running blastn job because of custom makeblastdb database

Question

[amber.e.bauer]

I'm trying to submit a job through linux terminal using bsub command and keep getting this message about my code. Is this a problem with the makeblastdb command or with my job submission?

Makeblastdb: makeblastdb -dbtype nucl -in /netscr/ambamb/abyss_assemblies/nivei.fasta -parse_seqids -out dbnivei

Job sumission: bsub -q week blastn \ -db ~/netscr/ambamb/db_nivei -show_gis -out niv_mit.txt -query /netscr/ambamb/mitoshell.fasta

Error message Exited with exit code 1 Error: Too many positional arguments (1), the offending value: -db Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: -db

[Pierre Lindenbaum]

what is that '\' after blastn ?

[st.ph.n]

your out name from makeblastdb is 'dbnivei'. the db name you're providing the blastn is 'db_nivei', where you should have 'dbnivei'