Monday, December 16, 2013

KNIME: duplicate column issue

Sometimes if you try to read in multiple SDFs with the "SDF Reader" node and "extract all properties" at the same time (in order to extract all the associated tag data) the node can fail with:

"Execute failed: Duplicate column name "<colname>" at positions 1 and 2" - (the column names and reported positions depend on the format of the input data).

I tried to fix up the columns thinking this was a whitespace issue or some such but had no joy. For me the solution was to read the molecules without extracting the data and then use the "SDF Extractor" node to grab the data. This worked with no issues.