Hello,
This is likely an issue with the webserver not realizing that X!Tandem has finished running.
Can you see if there are any "tandem.exe" processes running by opening the Task Manager?
- If you do not see any and if you can see .tandem output files, it means that the job is done, but the connection to the interface timed out. You can (in most cases) safely move on to converting this .tandem file to pepXML and then continue your analysis.
- If Tandem is still running, then check the parameters (are there too many variable modifications, for example), or try using a more powerful machine.
Furthermore, to tell the interface to consider the job as finished, click on the Jobs link in Petunia, find the "Running" job and click on "View" under the Output column. Then, in that page click on the following link:
If your commands have actually completed, or the queue did not work, click here.
Another situation in which this may happen is if the computer shuts down or goes into sleep mode before the job is finished, so make sure that is not the case. If so, you will need to re-start the search.
Hope this helps,
--Luis