Notice the multiple "Deletes" below. The result is that the final directory just has partial content.

2012-02-22 00:55:22,316:pegasus-plots:595: INFO: pegasus-plots : initializing...
2012-02-22 00:55:22,316:utils.py:147: WARNING: Deleting existing directory. Deleting... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:22,318:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:22,318:properties.py:240: INFO: processing properties file /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/pegasus.3371912325036655968.properties...
2012-02-22 00:55:22,381:nllog.py:165: INFO: ts=2012-02-22T00:55:22.381398Z event=netlogger.analysis.schema.schema_check.SchemaCheck.init level=Info
2012-02-22 00:55:22,381:nllog.py:165: INFO: ts=2012-02-22T00:55:22.381534Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema.start level=Info
2012-02-22 00:55:22,403:nllog.py:165: INFO: ts=2012-02-22T00:55:22.403526Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Current version set to: 3.2"
2012-02-22 00:55:22,403:nllog.py:165: INFO: ts=2012-02-22T00:55:22.403661Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Schema up to date"
2012-02-22 00:55:22,420:nllog.py:165: INFO: ts=2012-02-22T00:55:22.420557Z event=netlogger.analysis.schema.schema_check.SchemaCheck.init level=Info
2012-02-22 00:55:22,420:nllog.py:165: INFO: ts=2012-02-22T00:55:22.420676Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema.start level=Info
2012-02-22 00:55:22,422:nllog.py:165: INFO: ts=2012-02-22T00:55:22.422070Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Current version set to: 3.2"
2012-02-22 00:55:22,422:nllog.py:165: INFO: ts=2012-02-22T00:55:22.422203Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Schema up to date"
2012-02-22 00:55:22,426:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/gantt_chart
2012-02-22 00:55:22,427:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/gantt_chart/js
2012-02-22 00:55:22,427:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/gantt_chart/images/
2012-02-22 00:55:22,430:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/host_chart
2012-02-22 00:55:22,430:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/host_chart/js
2012-02-22 00:55:22,430:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/host_chart/images/
2012-02-22 00:55:22,434:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/breakdown_chart
2012-02-22 00:55:22,434:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/breakdown_chart/js
2012-02-22 00:55:22,434:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/breakdown_chart/images/
2012-02-22 00:55:22,453:nllog.py:165: INFO: ts=2012-02-22T00:55:22.452965Z event=netlogger.analysis.schema.schema_check.SchemaCheck.init level=Info
2012-02-22 00:55:22,453:nllog.py:165: INFO: ts=2012-02-22T00:55:22.453092Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema.start level=Info
2012-02-22 00:55:22,454:nllog.py:165: INFO: ts=2012-02-22T00:55:22.454642Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Current version set to: 3.2"
2012-02-22 00:55:22,454:nllog.py:165: INFO: ts=2012-02-22T00:55:22.454773Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Schema up to date"
2012-02-22 00:55:22,458:pegasus-plots:451: INFO: Generating graphs/charts for the workflow 1f9ac96b-5fff-486d-b713-b6bbcfcb6c8e (montage) ...
2012-02-22 00:55:27,629:nllog.py:165: INFO: ts=2012-02-22T00:55:27.629507Z event=netlogger.analysis.schema.schema_check.SchemaCheck.init level=Info
2012-02-22 00:55:27,629:nllog.py:165: INFO: ts=2012-02-22T00:55:27.629659Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema.start level=Info
2012-02-22 00:55:27,631:nllog.py:165: INFO: ts=2012-02-22T00:55:27.631042Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Current version set to: 3.2"
2012-02-22 00:55:27,631:nllog.py:165: INFO: ts=2012-02-22T00:55:27.631176Z event=netlogger.analysis.schema.schema_check.SchemaCheck.check_schema level=Info msg="Schema up to date"
2012-02-22 00:55:27,635:utils.py:147: WARNING: Deleting existing directory. Deleting... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:27,638:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:27,638:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/js
2012-02-22 00:55:27,638:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/images/
2012-02-22 00:55:27,642:utils.py:147: WARNING: Deleting existing directory. Deleting... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:27,642:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots
2012-02-22 00:55:27,642:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/js
2012-02-22 00:55:27,643:utils.py:154: INFO: Creating directory... /local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/images/

*********************************************SUMMARY**********************************************

Graphs and charts generated by pegasus-plots can be viewed by opening the generated html file in the web browser :
/local-scratch/rynge/montage-workflow/2012-02-21_195918/work/rynge/pegasus/montage/run0001/plots/index.html