{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    365      0 --:--:-- --:--:-- --:--:--   365\n\r100 46637  100 46637    0     0  89699      0 --:--:-- --:--:-- --:--:-- 89699\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\ndocker: Command recieved::<-i /root/archive.omex -o /root/outputs>\n<-i>\nDefault case selected\nVCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>\n INFO (CLIStandalone:38) - Starting Vcell... []{}\n INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}\n INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{}\n INFO (BiosimulationsCommand:98) - Beginning execution []{}\n INFO (CLIPythonManager:116) - Initializing Python... []{}\n INFO (CLIPythonManager:136) - Python initialization success! []{}\n INFO (ExecuteImpl:100) - Preparing output directory... []{}\nERROR (RunUtils:507) - java.lang.Exception: File '/root/outputs' could not be deleted! []{}\n INFO (ExecutionJob:86) - Executing OMEX archive /root/archive.omex []{}\n-----------------------------------------------------------------------------------------------------\n INFO (NativeLib:29) - Loading combinej []{}\n INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c9fb41b9-99c7-4202-a7ce-95f8792c4e205109688810741472832 []{}\n INFO (SedmlJob:104) - Initializing SED-ML document... []{}\n WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}\n INFO (SedmlJob:117) - Processing SED-ML: VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml []{}\n INFO (SedmlJob:153) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)\n []{}\n INFO (SedmlJob:158) - Successful translation of SED-ML file : VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{}\n INFO (SedmlJob:174) - Creating Biomodel from pseudo SED-ML []{}\n INFO (SedmlJob:235) - Building solvers and starting simulation of all tasks...  []{}\n WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}\nERROR (SBMLImporter:1364) - unexpected assignment rule target 'SpeciesContext@50b1f030(id=null, name='Ca_c', species='Ca_c', structure='c', sbmlName='Ca_c')', adding as assignment rule - minimal support provided []{}\nERROR (SBMLImporter:1365) - need to create a VCLogger event []{}\n INFO (SBMLImporter:967) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (0.01 + (0.02 * ___TIME_SYMBOL___)) []{}\n INFO (SimulationContext:3205) - mathMapping: message = transforming the Rate Rules... []{}\n INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}\n INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}\n INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}\n WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}\n WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}\n WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}\n INFO (SEDMLImporter:182) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}\ntaskToSimulationMap: 1\ntaskToListOfSubTasksMap: 1\ntaskToVariableMap: 1\ntopTaskToBaseTask: 1\n INFO (SolverHandler:422) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@68dd39d2 []{}\n INFO (SolverHandler:423) - Status: Finished: SOLVER_FINISHED:completed []{}\n INFO (SolverHandler:469) - Succesful execution: Model 'archive_VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml_PC12_clearance' Task 'Simulation42'. []{}\n INFO (SolverHandler:481) - Running simulation Simulation42, 329 ms []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SolverHandler:594) - Ran 1 simulation jobs for 1 biomodels. []{}\n INFO (SedmlJob:268) - Generating outputs...  []{}\n INFO (SedmlJob:322) - Generating CSV file...  []{}\n INFO (RunUtils:194) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}\n INFO (RunUtils:200) - Generating report `report_Simulation42`. []{}\n INFO (RunUtils:380) - created csv file for report report_Simulation42: /root/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42.csv []{}\n INFO (RunUtils:200) - Generating report `__plot__plot2d_Simulation42`. []{}\n INFO (RunUtils:380) - created csv file for report __plot__plot2d_Simulation42: /root/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/__plot__plot2d_Simulation42.csv []{}\n INFO (SedmlJob:344) - Generating Plots...  []{}\n WARN (CLIPythonManager:78) - Using old style python invocation! []{}\n WARN (CLIPythonManager:250) - Temp out file didn't delete properly []{}\n WARN (CLIPythonManager:251) - Temp error file didn't delete properly []{}\n INFO (SedmlJob:356) - Generating HDF5 file...  []{}\n INFO (NonspatialResultsConverter:202) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}\n INFO (SpatialResultsConverter:155) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}\n WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}\n INFO (SedmlJob:308) - Archiving result files []{}\n INFO (RunUtils:449) - Archiving resultant PDF files to `plots.zip`. []{}\n INFO (RunUtils:449) - Archiving resultant CSV files to `reports.zip`. []{}\n INFO (SedmlJob:315) - SED-ML : VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml successfully completed []{}\n INFO (ExecutionJob:142) - Processing of SedML succeeded.\norg.vcell.cli.run.SedmlStatistics@5cf8676a []{}\n INFO (NativeLib:29) - Loading jhdf5 []{}\n INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/root/outputs []{}\n INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}\n INFO (ExecutionJob:171) - Omex archive.omex processing completed (14s) []{}\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 10.6 KiB/10.6 KiB (86.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (22.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/reports.zip (stored 0%)\n  adding: outputs/log.json (deflated 91%)\n  adding: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/ (stored 0%)\n  adding: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42.csv (deflated 94%)\n  adding: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.pdf (deflated 31%)\n  adding: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.csv (deflated 94%)\n  adding: outputs/reports.h5 (deflated 96%)\n  adding: rawLog.txt (deflated 77%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/257.3 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 257.3 KiB/257.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/reports.h5\nCompleted 48.7 KiB/306.8 KiB (398.7 KiB/s) with 10 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/output.zip\nCompleted 48.7 KiB/306.8 KiB (398.7 KiB/s) with 9 file(s) remaining\rCompleted 63.7 KiB/306.8 KiB (404.2 KiB/s) with 9 file(s) remaining\rupload: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.pdf to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.pdf\nCompleted 63.7 KiB/306.8 KiB (404.2 KiB/s) with 8 file(s) remaining\rCompleted 64.1 KiB/306.8 KiB (378.0 KiB/s) with 8 file(s) remaining\rupload: ./stdOut.txt to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/stdOut.txt\nCompleted 64.1 KiB/306.8 KiB (378.0 KiB/s) with 7 file(s) remaining\rCompleted 69.8 KiB/306.8 KiB (387.9 KiB/s) with 7 file(s) remaining\rupload: ./temp16879171158469308861804289383.tmp to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/temp16879171158469308861804289383.tmp\nCompleted 69.8 KiB/306.8 KiB (387.9 KiB/s) with 6 file(s) remaining\rCompleted 81.9 KiB/306.8 KiB (449.6 KiB/s) with 6 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/rawLog.txt\nCompleted 81.9 KiB/306.8 KiB (449.6 KiB/s) with 5 file(s) remaining\rCompleted 179.3 KiB/306.8 KiB (967.2 KiB/s) with 5 file(s) remaining\rupload: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.csv to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42.csv\nCompleted 179.3 KiB/306.8 KiB (967.2 KiB/s) with 4 file(s) remaining\rCompleted 190.7 KiB/306.8 KiB (993.5 KiB/s) with 4 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/reports.zip\nCompleted 190.7 KiB/306.8 KiB (993.5 KiB/s) with 3 file(s) remaining\rCompleted 198.3 KiB/306.8 KiB (992.7 KiB/s) with 3 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/log.json\nCompleted 198.3 KiB/306.8 KiB (992.7 KiB/s) with 2 file(s) remaining\rCompleted 296.2 KiB/306.8 KiB (1.3 MiB/s) with 2 file(s) remaining  \rupload: outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42.csv to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42.csv\nCompleted 296.2 KiB/306.8 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 306.8 KiB/306.8 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml  \n  inflating: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853_PC12_clearance.xml  \n  inflating: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.vcml  \n  inflating: contents/diagram.png    \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 43.2 KiB/128.0 KiB (335.1 KiB/s) with 6 file(s) remaining\rupload: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.vcml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.vcml\nCompleted 43.2 KiB/128.0 KiB (335.1 KiB/s) with 5 file(s) remaining\rCompleted 72.6 KiB/128.0 KiB (521.4 KiB/s) with 5 file(s) remaining\rupload: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853_PC12_clearance.xml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853_PC12_clearance.xml\nCompleted 72.6 KiB/128.0 KiB (521.4 KiB/s) with 4 file(s) remaining\rCompleted 107.9 KiB/128.0 KiB (665.6 KiB/s) with 4 file(s) remaining\rupload: contents/diagram.png to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/diagram.png\nCompleted 107.9 KiB/128.0 KiB (665.6 KiB/s) with 3 file(s) remaining\rCompleted 108.7 KiB/128.0 KiB (650.9 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/manifest.xml\nCompleted 108.7 KiB/128.0 KiB (650.9 KiB/s) with 2 file(s) remaining\rCompleted 114.4 KiB/128.0 KiB (647.7 KiB/s) with 2 file(s) remaining\rCompleted 128.0 KiB/128.0 KiB (715.8 KiB/s) with 2 file(s) remaining\rupload: contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\nCompleted 128.0 KiB/128.0 KiB (715.8 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 17.3 KiB/17.3 KiB (155.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\ncreating dataset /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42, shape: (16, 1001), type: float64\ndataset created, uuid: d-b5d152e5-1f660ac2-72c0-9c17f7-d0a9ea, chunk_size: (16, 1001)\ncreating dataset /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42, shape: (16, 1001), type: float64\ndataset created, uuid: d-b5d152e5-1f660ac2-cd54-b915ec-aa756e, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\ncreating attribute uri in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\ncreating attribute _type in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute scanParameterNames in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlDataSetDataTypes in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlDataSetIds in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlDataSetLabels in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlDataSetNames in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlDataSetShapes in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlId in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute sedmlName in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute uri in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\ncreating attribute _type in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute scanParameterNames in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlDataSetDataTypes in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlDataSetIds in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlDataSetLabels in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlDataSetNames in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlDataSetShapes in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlId in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute sedmlName in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreating attribute uri in /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\ncreate_links: /\ngot link: VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\ncreate_links: /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml\ngot link: plot2d_Simulation42\ngot link: report_Simulation42\nwrite_dataset src: /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42 to tgt: /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42, shape: (16, 1001), type: float64\niterating over chunks for /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/plot2d_Simulation42\nwrite_dataset src: /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42 to tgt: /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42, shape: (16, 1001), type: float64\niterating over chunks for /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/649b4bde642531fcf940a42a\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":14,"sedDocuments":[{"location":"VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...","duration":null,"tasks":[{"id":"tsk_0_0","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing simulation job 0 ... done. Starting simulation... done.","duration":1,"algorithm":"KISAO_0000019","simulatorDetails":null}],"outputs":[{"id":"plot2d_Simulation42","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_junk_c","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_junk_ex","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Ca_er","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_H_c","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Ca_mi","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_PMCA_m","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_NCX_m","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_SERCA_erm","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_MtU_mim","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Na_ex","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Na_c","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_H_ex","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Channel_m","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Ca_ex","status":"SUCCEEDED"},{"id":"curve_plot2d_Simulation42_dataGen_tsk_0_0_Ca_c","status":"SUCCEEDED"}]},{"id":"report_Simulation42","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"__data_set__plot2d_Simulation42time_tsk_0_0","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_junk_c","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_junk_ex","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Ca_er","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_H_c","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Ca_mi","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_PMCA_m","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_NCX_m","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_SERCA_erm","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_MtU_mim","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Na_ex","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Na_c","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_H_ex","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Channel_m","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Ca_ex","status":"SUCCEEDED"},{"id":"__data_set__plot2d_Simulation42dataGen_tsk_0_0_Ca_c","status":"SUCCEEDED"}]}]}]}