Hi there I've got a workflow that uses BioPerl's bp_genbank2gff3 to convert Genbank to GFF3, then hands the GFF3 to Extract features to filter to only genes, before moving on. The workflow JSON is at http://pastebin.com/zHWsC6YT. Step 4 - the Genbank2GFF runs fine, and if I view the output in the history I can see the resulting GFF, but step 8 - the Extract features, fails with a LateValidationError, as follows: Traceback (most recent call last): File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 144, in queue_job job_wrapper.prepare() File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/jobs/__init__.py", line 130, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1872, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1890, in handle_unvalidated_param_values_helper self.handle_unvalidated_param_values_helper( input.cases[current].inputs, values, app, context, prefix ) File "/net/datasrv3.sanbi.ac.za/datastore/cip0/software/galaxy-dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1912, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError This Galaxy is Postgres and SGE, with galaxy-dist as of last night. Another strange thing is that while I select that the output of step 4 should be visible, it is, in fact, hidden in the new history. How to debug this? How can I see which input is not validating? Thanks, Peter