{"status":"SUCCEEDED","exception":null,"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    432      0 --:--:-- --:--:-- --:--:--   433\n\r100  108k  100  108k    0     0   249k      0 --:--:-- --:--:-- --:--:--  249k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n10:43:12 [main] WARN  cbit.vcell.resource.PropertyLoader - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory\nServerID=7.3.0.16, SoftwareVersion=unknown\nVCell CLI input archive /root/archive.omex\n-----------------------------------------------------------------------------------------------------\nTempPath Created: /tmp/vcell_temp_d6ecfeee-c74c-4721-9856-22f100daeccb4511942781277761659\nPython 3.8.10\nutilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils\ncliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils\ncliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py\nstatusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py\nFound 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)\n\nSuccessful translation of SED-ML file : biomodel_95675441.sedml\n-----------------------------------------------------------------------------------------------------\nname:  biomodel_95675441\nsedml_name:  biomodel_95675441\ncontent.location:  ./biomodel_95675441.sedml\ncontent_filename:  /root/outputs/temp/./biomodel_95675441.sedml\nStarting simulate all tasks... \nModel [id=ode, name=ode, language=urn:sedml:language:sbml, src=biomodel_95675441_ode.xml]\nThere are 0 changes.\nUniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Simulation0]\nTask [modelReference=ode, name=Simulation0, simulationReference=Simulation0, getId()=tsk_0_0]\nDataGenerator [math=org.jmathml.ASTRootNode@34f22f9d, name=time_tsk_0_0, getId()=time_tsk_0_0]\nDataGenerator [math=org.jmathml.ASTRootNode@3d1848cc, name=dataGen_tsk_0_0_PDE_cAMP, getId()=dataGen_tsk_0_0_PDE_cAMP]\nDataGenerator [math=org.jmathml.ASTRootNode@7dda48d9, name=dataGen_tsk_0_0_PDE_Cyto, getId()=dataGen_tsk_0_0_PDE_Cyto]\nDataGenerator [math=org.jmathml.ASTRootNode@6e4566f1, name=dataGen_tsk_0_0_cAMP_best, getId()=dataGen_tsk_0_0_cAMP_best]\nPlot2D [listOfCurves=[Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_cAMP, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_cAMP, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_cAMP], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_Cyto, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_Cyto, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_Cyto], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_cAMP_best, logX=false, logY=false, name=dataGen_tsk_0_0_cAMP_best, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_cAMP_best]], name=ode_Simulation0_plot]\norg.jlibsedml.Report@958bc87d\norg.jlibsedml.Report@5ce30dfd\nTask (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE\nnew symbol is uM,   old symbol is umol.l-1\nSBML Import: no assignment rules.\nSBML Import: no assignment rules.\nSuccesful model import: SBML file /tmp/temp8528562853315194767.xml\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:43:20 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n/root/outputs/biomodel_95675441.sedml\nfalse\ncbit.vcell.solver.ode.CVodeSolverStandalone@59942b48\nFinished: SOLVER_FINISHED:completed\nSuccesful execution: Model 'archive__ode' Task 'Simulation0'.\nRunning simulation tsk_0_0_Simulation0, 324 ms\n-----------------------------------------------------------------------------------------------------\nRan 1 simulations for 1 biomodels.\nIgnoring unsupported output `plot2d_Simulation0` while CSV generation.\nGenerating report `report_Simulation0`.\nGenerating report `__plot__plot2d_Simulation0`.\nIgnoring unsupported output `plot2d_Simulation0` while generating idNamePlotsMap.\n{'report_Simulation0': 'ode_Simulation0_plot', '__plot__plot2d_Simulation0': 'ode_Simulation0_plot', 'plot2d_Simulation0': 'ode_Simulation0_plot'}\n__plot__plot2d_Simulation0\nreport   :  /root/outputs/./biomodel_95675441.sedml/report_Simulation0.csv\nreport_Simulation0\nHDF conversion successful\nArchiving resultant PDF files to `plots.zip`.\nArchiving resultant CSV files to `reports.zip`.\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 6.2 KiB/6.2 KiB (50.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/rawLog.txt\nCompleted 1.5 KiB/1.5 KiB (13.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/reports.zip (stored 0%)\n  adding: outputs/log.json (deflated 84%)\n  adding: outputs/fullSuccessLog.txt (stored 0%)\n  adding: outputs/reports.h5 (deflated 32%)\n  adding: outputs/biomodel_95675441.sedml/ (stored 0%)\n  adding: outputs/biomodel_95675441.sedml/idNamePlotsMap.txt (deflated 67%)\n  adding: outputs/biomodel_95675441.sedml/plot2d_Simulation0.pdf (deflated 30%)\n  adding: outputs/biomodel_95675441.sedml/report_Simulation0.csv (deflated 56%)\n  adding: outputs/biomodel_95675441.sedml/plot2d_Simulation0.csv (deflated 56%)\n  adding: outputs/detailedResultLog.txt (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 73.4 KiB/73.4 KiB (458.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/reports.h5\nCompleted 128 Bytes/413.0 KiB (869 Bytes/s) with 13 file(s) remaining\rupload: outputs/biomodel_95675441.sedml/idNamePlotsMap.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/biomodel_95675441.sedml/idNamePlotsMap.txt\nCompleted 128 Bytes/413.0 KiB (869 Bytes/s) with 12 file(s) remaining\rCompleted 181.4 KiB/413.0 KiB (1.2 MiB/s) with 12 file(s) remaining  \rupload: ./output.zip to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/output.zip\nCompleted 181.4 KiB/413.0 KiB (1.2 MiB/s) with 11 file(s) remaining\rCompleted 192.5 KiB/413.0 KiB (1.2 MiB/s) with 11 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/plots.zip\nCompleted 192.5 KiB/413.0 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 200.1 KiB/413.0 KiB (1.1 MiB/s) with 10 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/rawLog.txt\nCompleted 200.1 KiB/413.0 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 200.5 KiB/413.0 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: ./stdOut.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/stdOut.txt\nCompleted 200.5 KiB/413.0 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 266.5 KiB/413.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: outputs/biomodel_95675441.sedml/plot2d_Simulation0.csv to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/biomodel_95675441.sedml/plot2d_Simulation0.csv\nCompleted 266.5 KiB/413.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 269.5 KiB/413.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/log.json\nCompleted 269.5 KiB/413.0 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 269.6 KiB/413.0 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 273.6 KiB/413.0 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: ./temp16548073938469308861804289383.tmp to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/temp16548073938469308861804289383.tmp\nCompleted 273.6 KiB/413.0 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: outputs/detailedResultLog.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/detailedResultLog.txt\nCompleted 273.6 KiB/413.0 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 331.4 KiB/413.0 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/reports.zip\nCompleted 331.4 KiB/413.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 346.9 KiB/413.0 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/biomodel_95675441.sedml/plot2d_Simulation0.pdf to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/biomodel_95675441.sedml/plot2d_Simulation0.pdf\nCompleted 346.9 KiB/413.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/fullSuccessLog.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/fullSuccessLog.txt\nCompleted 346.9 KiB/413.0 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 413.0 KiB/413.0 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/biomodel_95675441.sedml/report_Simulation0.csv to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/outputs/biomodel_95675441.sedml/report_Simulation0.csv\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/diagram.png    \n  inflating: contents/metadata.rdf   \n  inflating: contents/biomodel_95675441_ode.xml  \n  inflating: contents/biomodel_95675441.sedml  \n  inflating: contents/biomodel_95675441.vcml  \n  inflating: contents/manifest.xml   \nCompleted 256.0 KiB/292.7 KiB (2.7 MiB/s) with 6 file(s) remaining\rCompleted 260.8 KiB/292.7 KiB (2.4 MiB/s) with 6 file(s) remaining\rupload: contents/biomodel_95675441.sedml to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/biomodel_95675441.sedml\nCompleted 260.8 KiB/292.7 KiB (2.4 MiB/s) with 5 file(s) remaining\rCompleted 271.0 KiB/292.7 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/biomodel_95675441_ode.xml to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/biomodel_95675441_ode.xml\nCompleted 271.0 KiB/292.7 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 275.0 KiB/292.7 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/metadata.rdf\nCompleted 275.0 KiB/292.7 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 275.7 KiB/292.7 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/manifest.xml\nCompleted 275.7 KiB/292.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 285.7 KiB/292.7 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/biomodel_95675441.vcml to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/biomodel_95675441.vcml\nCompleted 285.7 KiB/292.7 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 292.7 KiB/292.7 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/diagram.png to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/contents/diagram.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 13.1 KiB/13.1 KiB (123.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a2150c4ffe186f420c4588/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /biomodel_95675441.sedml\ncreating dataset /biomodel_95675441.sedml/plot2d_Simulation0, shape: (4, 1001), type: float64\ndataset created, uuid: d-4903ea0d-f9a3d804-6cd0-55439c-872419, chunk_size: (4, 1001)\ncreating dataset /biomodel_95675441.sedml/report_Simulation0, shape: (4, 1001), type: float64\ndataset created, uuid: d-4903ea0d-f9a3d804-f591-c40fdd-071526, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /biomodel_95675441.sedml\ncreating attribute uri in /biomodel_95675441.sedml\ncreating attribute _type in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlId in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute sedmlName in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute uri in /biomodel_95675441.sedml/plot2d_Simulation0\ncreating attribute _type in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlId in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute sedmlName in /biomodel_95675441.sedml/report_Simulation0\ncreating attribute uri in /biomodel_95675441.sedml/report_Simulation0\ncreate_links: /\ngot link: biomodel_95675441.sedml\ncreate_links: /biomodel_95675441.sedml\ngot link: plot2d_Simulation0\ngot link: report_Simulation0\nwrite_dataset src: /biomodel_95675441.sedml/plot2d_Simulation0 to tgt: /biomodel_95675441.sedml/plot2d_Simulation0, shape: (4, 1001), type: float64\niterating over chunks for /biomodel_95675441.sedml/plot2d_Simulation0\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95675441.sedml/plot2d_Simulation0\nwrite_dataset src: /biomodel_95675441.sedml/report_Simulation0 to tgt: /biomodel_95675441.sedml/report_Simulation0, shape: (4, 1001), type: float64\niterating over chunks for /biomodel_95675441.sedml/report_Simulation0\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95675441.sedml/report_Simulation0\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/62a2150c4ffe186f420c4588\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19,"sedDocuments":[{"location":"biomodel_95675441.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... Generating outputs... Done. Generating HDF5 file... Done. ","duration":null,"tasks":[{"id":"tsk_0_0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing simulation... done. Starting simulation... done. ","duration":1,"algorithm":"KISAO_0000019","simulatorDetails":null}],"outputs":[{"id":"plot2d_Simulation0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_cAMP","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_Cyto","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation0_dataGen_tsk_0_0_cAMP_best","status":"SUCCEEDED"}]},{"id":"report_Simulation0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"__data_set__plot2d_Simulation0time_tsk_0_0","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_PDE_cAMP","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_PDE_Cyto","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_cAMP_best","status":"SUCCEEDED"}]}]}]}