3.4 years ago by
It could be that if when data was uploaded to the server it was truncated. So, double check the size versus that locally before upload. Reload using FTP and review the upload status reported by the FTP client. This is always a good first check, although I wouldn't expect this exact error message for this reason.
Next, if the SAM file is missing headers, these can be replaced with tools in the Picard tool group. Do that as needed or as a test.
Finally, SAM datasets do not need to be sorted before using this particular tool, but running the sort sam tool could provide more clues (another test on the dataset to confirm that it is complete and intact, although really any simple tool that executes with a sam input dataset would work for this purpose).
If working on the public Main Galaxy server, and none of these resolve the issue, a bug report can be sent in and we can also take a look. If working on another server, you could also see if the issue can be replicated on Main, to determine if the problem is server specific, plus this would allow you to submit a bug report. Note what you have tried from the above and include a link to this post.
Hopefully this helps to troubleshoot, but let us know. If you send in a bug report, we'll respond either there or here, but by all means will keep the private details in direct communications.
Best, Jen, Galaxy team