2018.09.13 15:58:28.160 PDT: [INFO] Planner invoked with following arguments -vvvvv --conf pegasus.properties --dax hic.dax --dir /home/georgepap/GitHub/papajim/HIC-HQ-Workflow/workflow/submit --sites condorpool --output-site local --cleanup leaf --force 2018.09.13 15:58:28.165 PDT: [DEBUG] All sites will be loaded from the site catalog 2018.09.13 15:58:28.173 PDT: [DEBUG] Retrieving Metadata from the file sites.xml 2018.09.13 15:58:28.285 PDT: [DEBUG] Site Catalog Schema Version as determined from catalog file 4.1 2018.09.13 15:58:28.286 PDT: [CONFIG] Site Catalog Parser Class to be loaded is SiteCatalogXMLParser4 2018.09.13 15:58:28.290 PDT: [DEBUG] event.pegasus.parse.site-catalog site-catalog.id sites.xml - STARTED 2018.09.13 15:58:28.291 PDT: [CONFIG] Picking schema /home/georgepap/pegasus-dist/pegasus-4.8.2dev/share/pegasus/schema/sc-4.2.xsd 2018.09.13 15:58:28.507 PDT: [TRACE] For element site found handle -> local 2018.09.13 15:58:28.507 PDT: [TRACE] For element site found arch -> x86_64 2018.09.13 15:58:28.508 PDT: [TRACE] For element site found os -> LINUX 2018.09.13 15:58:28.511 PDT: [TRACE] For element directory found type -> shared-scratch 2018.09.13 15:58:28.512 PDT: [TRACE] For element file-server found operation -> all 2018.09.13 15:58:28.514 PDT: [TRACE] For element file-server found url -> file:///home/georgepap/GitHub/papajim/HIC-HQ-Workflow/workflow/scratch 2018.09.13 15:58:28.514 PDT: [TRACE] at 9:117 2018.09.13 15:58:28.515 PDT: [TRACE] at 10:19 2018.09.13 15:58:28.515 PDT: [TRACE] For element directory found type -> shared-storage 2018.09.13 15:58:28.516 PDT: [TRACE] For element file-server found operation -> all 2018.09.13 15:58:28.516 PDT: [TRACE] For element file-server found url -> file:///home/georgepap/GitHub/papajim/HIC-HQ-Workflow/workflow/output 2018.09.13 15:58:28.516 PDT: [TRACE] at 13:116 2018.09.13 15:58:28.516 PDT: [TRACE] at 14:19 2018.09.13 15:58:28.516 PDT: [TRACE] at 15:11 2018.09.13 15:58:28.518 PDT: [DEBUG] Loading site in SiteStore local 2018.09.13 15:58:28.518 PDT: [TRACE] For element site found handle -> condorpool 2018.09.13 15:58:28.518 PDT: [TRACE] For element site found arch -> x86_64 2018.09.13 15:58:28.518 PDT: [TRACE] For element site found os -> LINUX 2018.09.13 15:58:28.520 PDT: [TRACE] For element profile found namespace -> pegasus 2018.09.13 15:58:28.520 PDT: [TRACE] For element profile found key -> style 2018.09.13 15:58:28.521 PDT: [TRACE] at 19:64 2018.09.13 15:58:28.521 PDT: [TRACE] Set Profile Value to condor 2018.09.13 15:58:28.522 PDT: [TRACE] For element profile found namespace -> pegasus 2018.09.13 15:58:28.523 PDT: [TRACE] For element profile found key -> data.configuration 2018.09.13 15:58:28.523 PDT: [TRACE] at 20:79 2018.09.13 15:58:28.523 PDT: [TRACE] Set Profile Value to condorio 2018.09.13 15:58:28.523 PDT: [TRACE] For element profile found namespace -> condor 2018.09.13 15:58:28.524 PDT: [TRACE] For element profile found key -> universe 2018.09.13 15:58:28.524 PDT: [TRACE] at 21:67 2018.09.13 15:58:28.524 PDT: [TRACE] Set Profile Value to vanilla 2018.09.13 15:58:28.524 PDT: [TRACE] at 24:11 2018.09.13 15:58:28.525 PDT: [DEBUG] Loading site in SiteStore condorpool 2018.09.13 15:58:28.525 PDT: [TRACE] at 25:15 2018.09.13 15:58:28.525 PDT: [DEBUG] End of last element reached 2018.09.13 15:58:28.529 PDT: [DEBUG] Object constructed is vanilla condorio condor 2018.09.13 15:58:28.532 PDT: [DEBUG] event.pegasus.parse.site-catalog site-catalog.id sites.xml (0.239 seconds) - FINISHED 2018.09.13 15:58:28.533 PDT: [DEBUG] Sites loaded are [condorpool, local] 2018.09.13 15:58:28.533 PDT: [DEBUG] Execution sites are [condorpool] 2018.09.13 15:58:28.687 PDT: [DEBUG] Style detected for site condorpool is class edu.isi.pegasus.planner.code.generator.condor.style.Condor 2018.09.13 15:58:28.687 PDT: [DEBUG] Style detected for site local is class edu.isi.pegasus.planner.code.generator.condor.style.Condor 2018.09.13 15:58:28.691 PDT: [CONFIG] Transformation Catalog Type used Multiline Textual TC 2018.09.13 15:58:28.691 PDT: [CONFIG] Transformation Catalog File used tc.txt 2018.09.13 15:58:28.701 PDT: [FATAL ERROR] [1]: Unable to instantiate Transformation Catalog at edu.isi.pegasus.planner.catalog.transformation.TransformationFactory.loadInstance(TransformationFactory.java:172) [2]: edu.isi.pegasus.planner.catalog.transformation.impl.Text caught edu.isi.pegasus.planner.parser.ScannerException line 8: at edu.isi.pegasus.planner.parser.TransformationCatalogTextParser.parse(TransformationCatalogTextParser.java:236) [3]: Unable to compute singularity extension from url url -> docker:///papajim/hic_hq:latest , protocol -> docker , host -> , path -> /papajim/hic_hq:latest , url-prefix -> docker:// at edu.isi.pegasus.planner.catalog.transformation.classes.Container.computeLFN(Container.java:184) ERROR while logging metrics The metrics file location is not yet initialized 2018.09.13 15:58:28.704 PDT: [DEBUG] Exiting with non-zero exit-code 2 2018.09.13 15:58:28.704 PDT: [INFO] event.pegasus.planner planner.version 4.8.2dev (0.557 seconds) - FINISHED