{"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    454      0 --:--:-- --:--:-- --:--:--   455\n\r100  5669  100  5669    0     0  13304      0 --:--:-- --:--:-- --:--:-- 13304\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>\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\n INFO (CLIStandalone:36) - Starting Vcell... []{}\n INFO (BiosimulationsCommand:94) - Beginning execution []{}\n INFO (CLIPythonManager:125) - Initializing Python... []{}\n INFO (CLIPythonManager:150) - Python initialization success! []{}\n INFO (ExecuteImpl:134) - Preparing output directory... []{}\n INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}\n INFO (ExecutionJob:84) - Archive location: /root/archive.omex []{}\n-----------------------------------------------------------------------------------------------------\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_58681d7b-2c31-44bd-8840-6e21b22d7caa2297673737221594831 []{}\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_21d88899-cac5-4573-a8ca-e615dd4bb9d113738425661303297199 []{}\n INFO (SedmlJob:110) - Initializing SED-ML document... []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\n INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000138_url.sedml []{}\n INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  3 plot2D(s), and 0 plot3D(s)\n []{}\n INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000138_url.sedml []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}\nERROR (SedmlJob:465) - Failed to create plot file /tmp/VCell_CLI_19387ccc21712435001108078438454/temp/simulation_BIOMD0000000138_url.sedml []{}\njava.lang.RuntimeException: Failed to create plot file /tmp/VCell_CLI_19387ccc21712435001108078438454/temp/simulation_BIOMD0000000138_url.sedml\n\tat org.vcell.cli.run.SedmlJob.preProcessDoc(SedmlJob.java:180) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:98) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\nERROR (ExecutionJob:135) - Statistics of failed SedML:\norg.vcell.cli.run.SedmlStatistics@4482469c []{}\n INFO (SedmlJob:261) - Building solvers and starting simulation of all tasks...  []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\nERROR (SedmlJob:277) - Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"this.sedml\" is null []{}\njava.lang.NullPointerException: Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"this.sedml\" is null\n\tat org.vcell.sedml.SEDMLImporter.initialize(SEDMLImporter.java:108) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.sedml.SEDMLImporter.<init>(SEDMLImporter.java:95) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:263) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:234) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:98) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n INFO (SedmlJob:302) - Generating outputs...  []{}\n INFO (SedmlJob:391) - Generating HDF5 file...  []{}\nERROR (SedmlJob:465) - Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"sedml\" is null []{}\njava.lang.NullPointerException: Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"sedml\" is null\n\tat org.vcell.cli.run.hdf5.Hdf5DataExtractor.<init>(Hdf5DataExtractor.java:40) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.generateHDF5(SedmlJob.java:393) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:309) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:98) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n WARN (SedmlJob:242) - Outputs could not be processed. []{}\norg.vcell.cli.exceptions.ExecutionException: error while processing outputs: Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"sedml\" is null\n\tat org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:321) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:98) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\nCaused by: java.lang.NullPointerException: Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"sedml\" is null\n\tat org.vcell.cli.run.hdf5.Hdf5DataExtractor.<init>(Hdf5DataExtractor.java:40) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.generateHDF5(SedmlJob.java:393) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:309) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\t... 16 more\nERROR (SedmlJob:465) - Failure executing the sed document.  []{}\njava.lang.RuntimeException: Failure executing the sed document. \n\tat org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:327) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:248) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:98) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:21) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n WARN (SedmlJob:336) - Cannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"this.sedml\" is nullCannot invoke \"org.jlibsedml.SedML.getPathForURI()\" because \"sedml\" is nullFailure executing the sed document.  []{}\nERROR (ExecutionJob:146) - Processing of SedML has failed.\norg.vcell.cli.run.SedmlStatistics@4482469c []{}\n INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19387ccc21712435001108078438454 []{}\n WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}\n INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}\n INFO (ExecutionJob:174) - Omex archive.omex processing completed (3s) []{}\nERROR (BiosimulationsCommand:102) - Errors occurred during execution []{}\n | Root(root) | OMEX_EXECUTE(archive.omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: archive,BIOMD0000000138_url.sedml,Failed to create plot file /tmp/VCell_CLI_19387ccc21712435001108078438454/temp/simulation_BIOMD0000000138_url.sedml\n | Root(root) | OMEX_EXECUTE(archive.omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /tmp/vcell_temp_58681d7b-2c31-44bd-8840-6e21b22d7caa2297673737221594831/BIOMD0000000138_url.sedml failed with error: \n | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: \n | Root(root) | OMEX_EXECUTE(archive.omex) | PROCESSING_SIMULATION_OUTPUTS(processOutputs) | **** Error: Error processing outputs\nsrun: error: xanadu-73: task 0: Exited with exit code 1\nsrun: Terminating job step 8658195.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 15.3 KiB/15.3 KiB (180.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 3.6 KiB/3.6 KiB (43.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000138_url.sedml/ (stored 0%)\n  adding: outputs/log.json (deflated 92%)\n  adding: outputs/reports.h5 (deflated 44%)\n  adding: rawLog.txt (deflated 84%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 196 Bytes/196 Bytes (2.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 4.9 KiB/31.0 KiB (54.3 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/output.zip\nCompleted 4.9 KiB/31.0 KiB (54.3 KiB/s) with 2 file(s) remaining\rCompleted 14.4 KiB/31.0 KiB (133.3 KiB/s) with 2 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/outputs/log.json\nCompleted 14.4 KiB/31.0 KiB (133.3 KiB/s) with 1 file(s) remaining\rCompleted 31.0 KiB/31.0 KiB (150.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/BIOMD0000000138_url.sedml  \n  inflating: contents/BIOMD0000000138_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 23.0 KiB/43.3 KiB (231.0 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000138_url.sedml to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/contents/BIOMD0000000138_url.sedml\nCompleted 23.0 KiB/43.3 KiB (231.0 KiB/s) with 2 file(s) remaining\rCompleted 42.7 KiB/43.3 KiB (335.3 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000138_url.xml to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/contents/BIOMD0000000138_url.xml\nCompleted 42.7 KiB/43.3 KiB (335.3 KiB/s) with 1 file(s) remaining\rCompleted 43.3 KiB/43.3 KiB (336.8 KiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 18.4 KiB/18.4 KiB (209.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc5ca10bb4455d618759a/rawLog.txt\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 and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... 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.\u001b[0m\n\u001b[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;31mPost the SED-ML file to the API ... failed due to: Failed to post SED-ML specs:\nThere was an error uploading the SED-ML specifications to the API.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":3,"sedDocuments":[{"location":"BIOMD0000000138_url.sedml","status":"FAILED","exception":{"type":"RuntimeException","message":"Cannot invoke 'org.jlibsedml.SedML.getPathForURI()' because 'this.sedml' is nullCannot invoke 'org.jlibsedml.SedML.getPathForURI()' because 'sedml' is nullFailure executing the sed document."},"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 HDF5 file...","duration":null,"tasks":[{"id":"task1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"autogen_plot1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"autogen_curve_task1_c","status":"QUEUED"}]},{"id":"autogen_plot2","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"autogen_curve_for_task1_V","status":"QUEUED"}]},{"id":"autogen_plot3","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[]},{"id":"autogen_report_for_task1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"autogen_time_for_task1","status":"QUEUED"},{"id":"autogen_task1_c","status":"QUEUED"},{"id":"autogen_task1_vca","status":"QUEUED"},{"id":"autogen_task1_vk","status":"QUEUED"},{"id":"autogen_task1_Cm","status":"QUEUED"},{"id":"autogen_task1_gk","status":"QUEUED"},{"id":"autogen_task1_gcal","status":"QUEUED"},{"id":"autogen_task1_gsk","status":"QUEUED"},{"id":"autogen_task1_ga","status":"QUEUED"},{"id":"autogen_task1_gf","status":"QUEUED"},{"id":"autogen_task1_vn","status":"QUEUED"},{"id":"autogen_task1_va","status":"QUEUED"},{"id":"autogen_task1_vm","status":"QUEUED"},{"id":"autogen_task1_vh","status":"QUEUED"},{"id":"autogen_task1_vf","status":"QUEUED"},{"id":"autogen_task1_sn","status":"QUEUED"},{"id":"autogen_task1_sa","status":"QUEUED"},{"id":"autogen_task1_sm","status":"QUEUED"},{"id":"autogen_task1_sh","status":"QUEUED"},{"id":"autogen_task1_sf","status":"QUEUED"},{"id":"autogen_task1_taun","status":"QUEUED"},{"id":"autogen_task1_tauh","status":"QUEUED"},{"id":"autogen_task1_lambda","status":"QUEUED"},{"id":"autogen_task1_kc","status":"QUEUED"},{"id":"autogen_task1_ks","status":"QUEUED"},{"id":"autogen_task1_ff","status":"QUEUED"},{"id":"autogen_task1_alpha","status":"QUEUED"},{"id":"autogen_task1_phik","status":"QUEUED"},{"id":"autogen_task1_phia","status":"QUEUED"},{"id":"autogen_task1_phih","status":"QUEUED"},{"id":"autogen_task1_phif","status":"QUEUED"},{"id":"autogen_task1_phical","status":"QUEUED"},{"id":"autogen_task1_cinf","status":"QUEUED"},{"id":"autogen_task1_ica","status":"QUEUED"},{"id":"autogen_task1_isk","status":"QUEUED"},{"id":"autogen_task1_ibk","status":"QUEUED"},{"id":"autogen_task1_ikdr","status":"QUEUED"},{"id":"autogen_task1_ia","status":"QUEUED"},{"id":"autogen_task1_ik","status":"QUEUED"},{"id":"autogen_task1_n","status":"QUEUED"},{"id":"autogen_task1_h","status":"QUEUED"},{"id":"autogen_task1_V","status":"QUEUED"},{"id":"autogen_task1_cell","status":"QUEUED"},{"id":"autogen_task1_reaction_0000004","status":"QUEUED"}]}]}]}