First, try at least one rerun. There were some server issues at Galaxy Main https://usegalaxy.org this morning. This may have impacted some jobs in odd/unpredictable ways.
If the job fails again now, then there is an input problem … Picard is very picky about input formats, including the
MergeSamFiles tool. Use “lenient” validation for all Picard tools unless there is a specific reason not to.
Some tools that can help to find formatting problems:
CleanSam perform SAM/BAM grooming
ValidateSamFile assess validity of SAM/BAM dataset (warning: can produce a LOT of output that can be confusing to act on, and some doesn’t need to be acted on – but still worth a try!)
Common reasons for problems:
Most of this help is deprecated when using BAM data, but could still apply for SAM data. Tool error? Try Sorting Your Inputs
Give those options a try and see if it resolves the problems. If not, let us know and we can troubleshoot more. Keep your tests in the history (don’t delete them) if you want more review/feedback.