Troubleshooting ~2 minute runtime on Toronto Cis-BP servers

[ernstki]

@XiaotingChen, @mihai-albu please provide in follow-up comments:

• the command line you ran as a test, and any specifics about the resources you requested, e.g., on a cluster compute node
• the runtime; the Unix time command will be helpful here.
• the inputs (if they're small enough, kilobytes perhaps, to upload into an issue comment here)

I'll try to do a run on the Cincinnati Cis-BP server and then update the issue description.