{"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    372      0 --:--:-- --:--:-- --:--:--   373\n\r100  110k  100  110k    0     0   223k      0 --:--:-- --:--:-- --:--:--  223k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n10:45:17 [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_73ade664-50b8-4883-8312-371a941355c05535249475297990719\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_95676312.sedml\n-----------------------------------------------------------------------------------------------------\nname:  biomodel_95676312\nsedml_name:  biomodel_95676312\ncontent.location:  ./biomodel_95676312.sedml\ncontent_filename:  /root/outputs/temp/./biomodel_95676312.sedml\nStarting simulate all tasks... \nModel [id=ode, name=ode, language=urn:sedml:language:sbml, src=biomodel_95676312_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]\nDataGenerator [math=org.jmathml.ASTRootNode@4b6e2263, name=dataGen_tsk_0_0_s0, getId()=dataGen_tsk_0_0_s0]\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], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_s0, logX=false, logY=false, name=dataGen_tsk_0_0_s0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_s0]], 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\nSuccesful model import: SBML file /tmp/temp1054764690439584488.xml\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique\n/root/outputs/biomodel_95676312.sedml\nfalse\ncbit.vcell.solver.ode.CVodeSolverStandalone@3b4d50b\nFinished: SOLVER_FINISHED:completed\nSuccesful execution: Model 'archive__ode' Task 'Simulation0'.\nRunning simulation tsk_0_0_Simulation0, 332 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_95676312.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 6.4 KiB/6.4 KiB (42.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/rawLog.txt\nCompleted 1.7 KiB/1.7 KiB (8.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/reports.zip (stored 0%)\n  adding: outputs/log.json (deflated 85%)\n  adding: outputs/fullSuccessLog.txt (stored 0%)\n  adding: outputs/biomodel_95676312.sedml/ (stored 0%)\n  adding: outputs/biomodel_95676312.sedml/idNamePlotsMap.txt (deflated 67%)\n  adding: outputs/biomodel_95676312.sedml/plot2d_Simulation0.pdf (deflated 29%)\n  adding: outputs/biomodel_95676312.sedml/report_Simulation0.csv (deflated 59%)\n  adding: outputs/biomodel_95676312.sedml/plot2d_Simulation0.csv (deflated 59%)\n  adding: outputs/reports.h5 (deflated 32%)\n  adding: outputs/detailedResultLog.txt (deflated 9%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 73.6 KiB/73.6 KiB (629.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/reports.h5\nCompleted 182.0 KiB/422.4 KiB (1.4 MiB/s) with 13 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/output.zip\nCompleted 182.0 KiB/422.4 KiB (1.4 MiB/s) with 12 file(s) remaining\rCompleted 182.2 KiB/422.4 KiB (1.2 MiB/s) with 12 file(s) remaining\rupload: outputs/biomodel_95676312.sedml/idNamePlotsMap.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/biomodel_95676312.sedml/idNamePlotsMap.txt\nCompleted 182.2 KiB/422.4 KiB (1.2 MiB/s) with 11 file(s) remaining\rCompleted 252.1 KiB/422.4 KiB (1.5 MiB/s) with 11 file(s) remaining\rupload: outputs/biomodel_95676312.sedml/plot2d_Simulation0.csv to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/biomodel_95676312.sedml/plot2d_Simulation0.csv\nCompleted 252.1 KiB/422.4 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 263.3 KiB/422.4 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/plots.zip\nCompleted 263.3 KiB/422.4 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 263.6 KiB/422.4 KiB (1.4 MiB/s) with 9 file(s) remaining\rupload: ./stdOut.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/stdOut.txt\nCompleted 263.6 KiB/422.4 KiB (1.4 MiB/s) with 8 file(s) remaining\rCompleted 267.6 KiB/422.4 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: ./temp16548075178469308861804289383.tmp to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/temp16548075178469308861804289383.tmp\nCompleted 267.6 KiB/422.4 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 271.0 KiB/422.4 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/log.json\nCompleted 271.0 KiB/422.4 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 328.9 KiB/422.4 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/reports.zip\nCompleted 328.9 KiB/422.4 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 328.9 KiB/422.4 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: outputs/detailedResultLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/detailedResultLog.txt\nCompleted 328.9 KiB/422.4 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 336.8 KiB/422.4 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/rawLog.txt\nCompleted 336.8 KiB/422.4 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 336.8 KiB/422.4 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/fullSuccessLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/fullSuccessLog.txt\nCompleted 336.8 KiB/422.4 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 352.3 KiB/422.4 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/biomodel_95676312.sedml/plot2d_Simulation0.pdf to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/biomodel_95676312.sedml/plot2d_Simulation0.pdf\nCompleted 352.3 KiB/422.4 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 422.4 KiB/422.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/biomodel_95676312.sedml/report_Simulation0.csv to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/biomodel_95676312.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_95676312_ode.xml  \n  inflating: contents/biomodel_95676312.sedml  \n  inflating: contents/biomodel_95676312.vcml  \n  inflating: contents/manifest.xml   \nCompleted 256.0 KiB/307.9 KiB (2.8 MiB/s) with 6 file(s) remaining\rCompleted 261.5 KiB/307.9 KiB (2.3 MiB/s) with 6 file(s) remaining\rupload: contents/biomodel_95676312.sedml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/biomodel_95676312.sedml\nCompleted 261.5 KiB/307.9 KiB (2.3 MiB/s) with 5 file(s) remaining\rCompleted 265.5 KiB/307.9 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/metadata.rdf\nCompleted 265.5 KiB/307.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 277.6 KiB/307.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/biomodel_95676312_ode.xml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/biomodel_95676312_ode.xml\nCompleted 277.6 KiB/307.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 299.2 KiB/307.9 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/biomodel_95676312.vcml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/biomodel_95676312.vcml\nCompleted 299.2 KiB/307.9 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 307.1 KiB/307.9 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/diagram.png to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/diagram.png\nCompleted 307.1 KiB/307.9 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 307.9 KiB/307.9 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 13.3 KiB/13.3 KiB (89.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /biomodel_95676312.sedml\ncreating dataset /biomodel_95676312.sedml/plot2d_Simulation0, shape: (5, 1001), type: float64\ndataset created, uuid: d-debe96ba-604c1152-b47f-c5aa02-17e659, chunk_size: (5, 1001)\ncreating dataset /biomodel_95676312.sedml/report_Simulation0, shape: (5, 1001), type: float64\ndataset created, uuid: d-debe96ba-604c1152-fbf4-fc90ad-6c01ef, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /biomodel_95676312.sedml\ncreating attribute uri in /biomodel_95676312.sedml\ncreating attribute _type in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlId in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute sedmlName in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute uri in /biomodel_95676312.sedml/plot2d_Simulation0\ncreating attribute _type in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlDataSetDataTypes in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlDataSetIds in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlDataSetLabels in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlDataSetNames in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlDataSetShapes in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlId in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute sedmlName in /biomodel_95676312.sedml/report_Simulation0\ncreating attribute uri in /biomodel_95676312.sedml/report_Simulation0\ncreate_links: /\ngot link: biomodel_95676312.sedml\ncreate_links: /biomodel_95676312.sedml\ngot link: plot2d_Simulation0\ngot link: report_Simulation0\nwrite_dataset src: /biomodel_95676312.sedml/plot2d_Simulation0 to tgt: /biomodel_95676312.sedml/plot2d_Simulation0, shape: (5, 1001), type: float64\niterating over chunks for /biomodel_95676312.sedml/plot2d_Simulation0\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95676312.sedml/plot2d_Simulation0\nwrite_dataset src: /biomodel_95676312.sedml/report_Simulation0 to tgt: /biomodel_95676312.sedml/report_Simulation0, shape: (5, 1001), type: float64\niterating over chunks for /biomodel_95676312.sedml/report_Simulation0\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /biomodel_95676312.sedml/report_Simulation0\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/62a215894ffe186f420c45bb\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20,"sedDocuments":[{"location":"biomodel_95676312.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":"curve_plot2d_Simulation0_dataGen_tsk_0_0_s0","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"},{"id":"__data_set__plot2d_Simulation0dataGen_tsk_0_0_s0","status":"SUCCEEDED"}]}]}]}