When running checkReplicaSet in replsettest.js, we run collMod on all the collections to wait for any index builds before running awaitReplication. However, if there is a background thread running a command, it could potentially drop a collection after listCollections but before collMod, causing a "NamespaceNotFound" error.

To fix this, check the output of runCommand to see if there was a "NamespaceNotFound" error and if so, ignore it.