Question: How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)
0
gravatar for O.rka
11 months ago by
O.rka240
O.rka240 wrote:

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
diamond alignment • 709 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum134k • written 11 months ago by O.rka240
2
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

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'
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum134k

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!

ADD REPLYlink written 11 months ago by O.rka240

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

ADD REPLYlink modified 11 months ago • written 11 months ago by GenoMax96k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1944 users visited in the last hour
_