I'm trying to retrieve the genome from which a series of proteins are derived. there is more than one assembly for each protein, so I need to create a file where they are linked.
I use the following:
for id in `cat gi-list-file`; do
elink -target nuccore -db protein -id $id |
elink -target assembly |
esummary |
xtract -pattern AssemblyAccession -element AssemblyAccession
done
the first result I get is the assembly accession, but the second result is the following error message:
Retrying elink, step 2: callMLink: Error reading an UID blob, ,CNCHistory::ReadIdListBuf, result (false) error, blobid=empty
Any ideas on what the problem is?
what happens if you run that accession directly outside of the loop?
Can you also show us some examples of accessions which work, and some that don't?