2.5 years ago by
Did you sort the input BAM file by coordinates first, using "SortSam". Right now that is requrired, even for output that may appear to be already coordinate sorted (Tophat is one example). Our team is investigating why. But this may get you going now. Just add the sort set to your workflow (and hide it, delete intermediate datasets, whatever works to manage disk space/quota).
For all - if errors come up with Picard or SAMtools - try a "SortSam" as a first pass solution. Upload BAM datasets are automatically sorted, but intermediate analysis datasets may not have the sorting exactly how SAM/Picard are expecting it. This has been manifesting as a range of errors and some messages can be cryptic (meaning, not obviously resolved by this additional processing step). We are working to make this more clear across the application.
If something else is going on, please let us know. I may ask for you to share a history (privately - there are specific instructions for that - no need to share with the entire forum). But, any resolution we can share in general terms.
Thanks, Jen, Galaxy team