These jobs are actually running out of memory during processing. The sample that did process correctly has under half the data, and slightly shorter reads.
We are reviewing whether the tools can be allocated more resources. This will not be immediate, but we might have some feedback later next week. We’ll follow up here.
For now, to get this data processed, you can try at the UseGalaxy.eu server since all of these tools have a bit more runtime processing memory allocated by default.
This guide explains how to move data between servers and how to manage the account quota resources at each. This error is unrelated to quota but if you are running batches of work, that probably matters to you for other reasons. 
Thanks! More followup next week! Please feel free to ping me for an update.