I'm trying to find those of a subset of species without a certain protein.
For this, I tried to use blast-2.2.31+ (newest version) remote feature with an entrez queries limiting it to those species, e.g.:
blastp -query sequence.fa -db nr -remote -entrez_query "txid387662 [ORGN]" -evalue 10E-3 -outfmt "7 sseqid pident positive evalue staxids"
And sometimes it works, sometimes it doesn't terminate within an hour (usually doesn't take a minute), sometimes it only returns
# BLAST processed 1 queries
and I don't know why... I'm guessing the remote feature isn't that stable...
Any help is appreciated :)