I'm trying to retrieve some taxonomy information using esearch from NCBI, I have a list of tax IDs (one per line) in a file called ids.txt
I'm running this code and it keeps failing, I've checked all previous resolved posts about this issue and I followed the same syntax. Any ideas what's going on here?
cat ids.txt | while read line; do echo $line; esearch -db taxonomy -query “$line[taxID]" done
and the error message:
> sed: RE error: illegal byte sequence > ERROR: Missing -query argument
I tried removing the "taxID" part from the query to see if that was the problem, but then I get another error:
cat ids.txt | while read line; > do > echo $line; > esearch -db taxonomy -query $line > done WARNING: FAILURE ( Fri 7 May 2021 15:46:57 EDT ) nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db taxonomy -term $'743375\r' -tool edirect -edirect 15.0 -edirect_os Darwin -email <ERROR>Empty term and query_key - nothing todo</ERROR>