I have this line in a while read line loop:
lineage=$(esearch -query "$line" -db taxonomy | efetch -format xml | xtract -element Lineage)
The problem is that it returns lineage only for the first line and then kills the parent process. It's really killing me because like 1-2 months back I figured out how to circumvent this problem, but now I seem unable to find a solution. Perhaps some Biostar might help me with this? Nothing wrong with the input file or any other part of the script..