I want to run diamond and also get taxon identifiers for each hit. Is the only way to do this by incorporating it during the makedb step? Is there any other option? The reason why I'm asking is because I would have to ask IT to recreate the databases but it would be cool if I could do it post hoc. I have my own scripts going from taxon id to species/genus/etc but I still need the taxonomy identifier.
Command
source activate diamond_env
diamond blastp -f 6 qseqid sseqid pident nident length mismatch gapopen qstart qend sstart send evalue bitscore staxids stitle -o cylindrotheca.diamond.nr.blast6 -p 16 -d /usr/local/db/diamond/nr.dmnd -e 0.001 -q ./assembly_cylindrotheca/assembly.orf.faa"
Output
diamond v0.9.29.130 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.
#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database... [0.040975s]
Error: Output format requires taxonomy mapping information built into the database (use --taxonmap parameter for the makedb command)
Can I use any of these files?
(diamond_env) -bash-4.1$ ls /usr/local/db/taxdb/taxdb_current/
taxdb.btd taxdb.bti
(diamond_env) -bash-4.1$ ls /usr/local/scratch/METAGENOMICS/jespinoz/db/ncbi_taxonomy/
citations.dmp delnodes.dmp division.dmp gc.prt gencode.dmp merged.dmp names.dmp nodes.dmp readme.txt taxdump.tar.gz
•
written
by
O.rka
1 answer
In order to incorporate the taxonomy information into the diamond database, you'd have to use the prot.accession2taxid with nodes.dmp when you build the diamond database.
More info: http://www.diamondsearch.org/index.php?pages/command_line_options/
This can be achieved by using the following command:
diamond makedb --in nr --db nr_diamond --taxonmap prot.accession2taxid --taxonnodes nodes.dmp --threads 20
The link above is out now. In case someone needs it, now the command line options can be found here: https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options
The taxon nodes.dmp and names.dmp file can be retrieve with:
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
Link has changed to https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
Log in to answer this question.
-
Problem in making database for metabarcoding using OBITools
written by saeedmn2005 •
-
blastdbcmd issue
written by Chvatil
Have you solved this problem？
No I gave up. Have you?