bbuchfink
how can i get the sequence access number?
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?
Taxonomy features are not supported by the DAA format. You have to use the tabular format directly (option -f 6).
