2.6 years ago by
United States
Hello,
Either could be the case.
If a data input problem, the error message reported by GATK will in most cases describe exactly what the problem is, just the same as if executed on the line-command. Click on the bug report to review this. But, you do not need to submit this - just review the issue and fix it - as GATK is no longer supported at Galaxy Main. The exception is if the error should be due to a cluster problem (this is also reported in the error message) - in that case, just re-run the job (again, no need to submit a bug report). The server is undergoing major changes right now, a few jobs have been failing, and a re-run is the path to a successful job.
That said, the GATK tools on http://usegalaxy.org have been deprecated and some are known to not work for certain use cases and there are almost certainly more use cases coming up that are yet unknown but that are still problematic. These won't be corrected.
If you want to use GATK, then set up a local or cloud Galaxy and install the tools from the tool shed. This would require setting up the data as well - somewhat tricky as these tools are not well supported anywhere due to licensing. I state tricky, but this is possible - meaning that there are no Data Managers to do this automatically for all data types and unix skills will be needed. This is how to get started on that if you wish to try: https://wiki.galaxyproject.org/BigPicture/Choices
Best, Jen, Galaxy team
