How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid output format. Allowed values: 0,5,6,100,101,102)
1
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Entering edit mode
2.1 years ago
O.rka ▴ 540

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
alignment diamond • 2.0k views
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2
Entering edit mode
2.1 years ago

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'
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0
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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!

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

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