How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)

Question

[O.rka]

I'm trying to get taxonomy identifiers when using diamond but it's not working.

I made the database so I can pull taxonomy info in addition to blast hit information. In particular:

'6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames stitle' 

I'm getting an error when I try to pull taxonomy info.

My command to make the database with taxonomy info:

diamond makedb --in nr.gz --db nr.dmnd --taxonmap ../ncbi_taxonomy/prot.accession2taxid.gz --taxonnodes ../ncbi_taxonomy/nodes.dmp --taxonnames ../ncbi_taxonomy/names.dmp

My command to run diamond:

diamond blastp --db $DB --query ./orfs/caries.orfs.1652968.faa --threads $N_JOBS -o ./diamond_output/caries.orfs.1652968.faa.nr.blast6 -f '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames stitle' --evalue 1.0

My error message:

diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org

#CPU threads: 32
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: ./diamond_output
Opening the database...  [0.134s]
Error: Invalid output format. Allowed values: 0,5,6,100,101,102

Answer 1

[Pierre Lindenbaum]

can you please try without the quote ?

-f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames stitle

instead of

-f '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames stitle'

[O.rka]

Wow, it's running now. Sorry, I should have tried that before posting. All of the examples with blast I saw required the quotes. Thank you!

[GenoMax]

But you did not check the manual. This is noted there :-)