Info: This issue occurs while using non-sharedfs mode with containers and while having pegasus.dir.staging.mapper set to Hashed.
Using Hashed as the staging mapper, creates deeper directories (eg. /00/00) and the input and output files are getting created there.

Issue: Planner fails to set the correct source location in the stage out job and as a result the job fails. In the following example the source should have been file:///global/cscratch1/sd/papajim/georgpap/pegasus/namd_wf/run0001/00/00/production_250.dcd

{ "type": "transfer",
   "linkage": "output",
   "lfn": "production_250.dcd",
   "id": 2,
   "verify_checksum_remote": true,
   "src_urls": [
     { "site_label": "cori", "url": "file:///global/cscratch1/sd/papajim/georgpap/pegasus/namd_wf/run0001/production_250.dcd" }
   ],
   "dest_urls": [
     { "site_label": "cori", "url": "file:///global/project/projectdirs/m2187/papajim/sns-wf-test/production_250.dcd" }
   ] }

Temporary solution: use pegasus.dir.staging.mapper = Flat

I have attached an example.