globus-url-copy -dbg -udt -pp -p 3 -r file:///staging/LowCov-JPT/NA18940/ gsiftp://xx.xx.xx.xx/tmp/NA18940/
try -cc 4 instead of -pp. -cc is the recommended 'lots of small files' optimization and -pp has shown some strange behavior in the past.
globus-url-copy -dbg -udt -pp -p 3 -r file:///staging/LowCov-JPT/NA18940/ gsiftp://xx.xx.xx.xx/tmp/NA18940/
try -cc 4 instead of -pp. -cc is the recommended 'lots of small files' optimization and -pp has shown some strange behavior in the past.