I am aware of two major issues affecting the workbench at the moment, one being that miRCat cannot currently use the pipeline mode. For now please use the adapter removal and filter tools by themselves and use your output data directly within miRCat through the history browser or standard file browser. Please email me or leave a comment if you require further instructions on this.
The second issue is related to the recent release of miRBase 19 and changes to their file structure and internal file information causing our auto update procedure to fail. If you have miRBase 18 installed from previous use of the workbench then do not update your miRBase files and the tool will work fine. If you have tried to update please remove any files related to miRBase 19 from your install directory (data/miRBase) and continue for now with miRBase 18. I can also supply miRBase files for anyone who did not manage to download that version.
The only tool that relies on miRBase to function is miRProf, miRCat will still work without this data. I am working on a fix to the miRBase issue and will release a new version of the software as soon as it is available and add a post to the feed to inform all of our users. This issue will not affect any other tools in the workbench