Hi I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each. "Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py", line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion" I also found this in the handler.log file: "galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' " Do you know how could this be sorted? Thanks in advance, Nikos