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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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how can i get the sequence access number? #516

Open vagnerfonseca opened 2 years ago

vagnerfonseca commented 2 years ago

I'm generating my database using the command:

diamond makedb --in viral.1.protein.faa.gz -d all_virus --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp --taxonnames names.dmp --in: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.faa.gz --taxonmap: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz --taxonnodes: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip --taxonnames: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip

diamond blastx -d all_virus -q myfasta.fasta -a myFile -p 32 --sensitive -c 1 diamond view -d all_virus -a myFile -o myFile.m8

But the taxonomy numbers and even the accession numbers are not coming in the output tab file. Could you let me know what I'm doing wrong?

bbuchfink commented 2 years ago

Taxonomy features are not supported by the DAA format. You have to use the tabular format directly (option -f 6).