{"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 0 480 0 --:--:-- --:--:-- --:--:-- 480\n\r100 8231 100 8231 0 0 19270 0 --:--:-- --:--:-- --:--:-- 19270\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 \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_65e828da-f4d0-4f08-825d-33921c7c30cf4400432572163026590 []{}\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_96f8f7ce-59ad-4ac9-8ae2-72fa2667a00e17299850874475479347 []{}\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: BIOMD0000000001_url.sedml []{}\n INFO (SedmlJob:161) - 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:166) - Successful translation of SED-ML file : BIOMD0000000001_url.sedml []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}\n INFO (SedmlJob:186) - Creating Biomodel from pseudo SED-ML []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\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\n INFO (SBMLImporter:966) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (___TIME_SYMBOL___ > t2) []{}\nERROR (SEDMLImporter:187) - Task (id='task1)' is not compatible, no equivalent solver found in ontology for requested algorithm 'KISAO:0000694'; trying with deterministic default solver CombinedSundials []{}\ntaskToSimulationMap: 1\ntaskToListOfSubTasksMap: 1\ntaskToVariableMap: 1\ntopTaskToBaseTask: 1\n INFO (SolverHandler:430) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@1c98b4eb []{}\n INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}\n INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000001_url.sedml_BIOMD0000000001_url' Task 'task1'. []{}\n INFO (SolverHandler:489) - Running simulation task1_task1, 384 ms []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}\n INFO (SedmlJob:302) - Generating outputs... []{}\n INFO (SedmlJob:357) - Generating CSV file... []{}\n INFO (RunUtils:196) - Ignoring unsupported output `autogen_plot_for_task1` while CSV generation. []{}\n INFO (RunUtils:202) - Generating report `autogen_report_for_task1`. []{}\n INFO (RunUtils:381) - created csv file for report autogen_report_for_task1: /tmp/VCell_CLI_19387c91bdb13940040588083321565/BIOMD0000000001_url.sedml/autogen_report_for_task1.csv []{}\n INFO (RunUtils:202) - Generating report `__plot__autogen_plot_for_task1`. []{}\n INFO (RunUtils:381) - created csv file for report __plot__autogen_plot_for_task1: /tmp/VCell_CLI_19387c91bdb13940040588083321565/BIOMD0000000001_url.sedml/__plot__autogen_plot_for_task1.csv []{}\n INFO (SedmlJob:380) - Generating Plots... []{}\n INFO (SedmlJob:391) - Generating HDF5 file... []{}\n INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `autogen_plot_for_task1` while CSV generation. []{}\n INFO (SedmlJob:343) - Archiving result files []{}\n INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}\n INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}\n INFO (SedmlJob:350) - SED-ML : BIOMD0000000001_url.sedml successfully completed []{}\n INFO (ExecutionJob:144) - Processing of SedML succeeded.\n\t> 1 model\n\t> 1 simulation\n\t> 1 task\n\t> 2 outputs\n\t\t>> 1 report\n\t\t>> 1 2D plot\n\t\t>> 0 3D plots\n\t> Does not have Math Overrides\n\t> Does not have Parameter Scans []{}\n INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19387c91bdb13940040588083321565 []{}\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 (14s) []{}\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 6.2 KiB/6.2 KiB (77.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 5.1 KiB/5.1 KiB (64.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n adding: outputs/ (stored 0%)\n adding: outputs/log.yml (deflated 88%)\n adding: outputs/reports.zip (stored 0%)\n adding: outputs/BIOMD0000000001_url.sedml/ (stored 0%)\n adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.csv (deflated 59%)\n adding: outputs/BIOMD0000000001_url.sedml/autogen_report_for_task1.csv (deflated 70%)\n adding: outputs/log.json (deflated 95%)\n adding: outputs/reports.h5 (deflated 50%)\n adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/623.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/623.4 KiB (937.7 KiB/s) with 1 file(s) remaining\rCompleted 623.4 KiB/623.4 KiB (877.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/2.5 MiB (3.5 MiB/s) with 8 file(s) remaining\rCompleted 512.0 KiB/2.5 MiB (6.4 MiB/s) with 8 file(s) remaining\rCompleted 523.1 KiB/2.5 MiB (6.4 MiB/s) with 8 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf\nCompleted 523.1 KiB/2.5 MiB (6.4 MiB/s) with 7 file(s) remaining\rCompleted 779.1 KiB/2.5 MiB (9.4 MiB/s) with 7 file(s) remaining\rCompleted 1.0 MiB/2.5 MiB (12.4 MiB/s) with 7 file(s) remaining \rCompleted 1.3 MiB/2.5 MiB (9.1 MiB/s) with 7 file(s) remaining \rCompleted 1.5 MiB/2.5 MiB (10.1 MiB/s) with 7 file(s) remaining \rCompleted 1.5 MiB/2.5 MiB (9.8 MiB/s) with 7 file(s) remaining \rupload: outputs/log.json to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/log.json\nCompleted 1.5 MiB/2.5 MiB (9.8 MiB/s) with 6 file(s) remaining\rCompleted 1.6 MiB/2.5 MiB (9.7 MiB/s) with 6 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/output.zip\nCompleted 1.6 MiB/2.5 MiB (9.7 MiB/s) with 5 file(s) remaining\rCompleted 1.6 MiB/2.5 MiB (9.5 MiB/s) with 5 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/plots.zip\nCompleted 1.6 MiB/2.5 MiB (9.5 MiB/s) with 4 file(s) remaining\rCompleted 1.8 MiB/2.5 MiB (9.2 MiB/s) with 4 file(s) remaining\rCompleted 1.8 MiB/2.5 MiB (9.2 MiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/rawLog.txt\nCompleted 1.8 MiB/2.5 MiB (9.2 MiB/s) with 3 file(s) remaining\rCompleted 1.8 MiB/2.5 MiB (8.7 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.csv to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.csv\nCompleted 1.8 MiB/2.5 MiB (8.7 MiB/s) with 2 file(s) remaining\rCompleted 2.1 MiB/2.5 MiB (8.8 MiB/s) with 2 file(s) remaining\rCompleted 2.2 MiB/2.5 MiB (6.7 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_report_for_task1.csv to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/BIOMD0000000001_url.sedml/autogen_report_for_task1.csv\nCompleted 2.2 MiB/2.5 MiB (6.7 MiB/s) with 1 file(s) remaining\rCompleted 2.4 MiB/2.5 MiB (5.3 MiB/s) with 1 file(s) remaining\rCompleted 2.5 MiB/2.5 MiB (3.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/outputs/reports.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive: archive.omex\n inflating: contents/manifest.xml \n inflating: contents/BIOMD0000000001_url.sedml \n inflating: contents/BIOMD0000000001_url.xml \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 660 Bytes/85.3 KiB (5.7 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/contents/manifest.xml\nCompleted 660 Bytes/85.3 KiB (5.7 KiB/s) with 2 file(s) remaining\rCompleted 49.9 KiB/85.3 KiB (411.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000001_url.xml to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/contents/BIOMD0000000001_url.xml\nCompleted 49.9 KiB/85.3 KiB (411.7 KiB/s) with 1 file(s) remaining\rCompleted 85.3 KiB/85.3 KiB (249.2 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000001_url.sedml to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/contents/BIOMD0000000001_url.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 11.8 KiB/11.8 KiB (143.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c510bb4455d61874b6/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 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.\nProcess the SED-ML file in the COMBINE archive ... 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":14,"sedDocuments":[{"location":"BIOMD0000000001_url.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":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing simulation job 0 ... done. Starting simulation... done.","duration":1,"algorithm":"KISAO_0000019","simulatorDetails":null}],"outputs":[{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"autogen_curve_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_B","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ALL","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_task1_IL","status":"SUCCEEDED"},{"id":"autogen_task1_AL","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_BL","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_task1_DL","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_ALL","status":"SUCCEEDED"},{"id":"autogen_task1_kf_0","status":"SUCCEEDED"},{"id":"autogen_task1_kr_0","status":"SUCCEEDED"},{"id":"autogen_task1_kf_1","status":"SUCCEEDED"},{"id":"autogen_task1_kr_1","status":"SUCCEEDED"},{"id":"autogen_task1_kf_2","status":"SUCCEEDED"},{"id":"autogen_task1_kr_2","status":"SUCCEEDED"},{"id":"autogen_task1_kf_3","status":"SUCCEEDED"},{"id":"autogen_task1_kr_3","status":"SUCCEEDED"},{"id":"autogen_task1_kf_4","status":"SUCCEEDED"},{"id":"autogen_task1_kr_4","status":"SUCCEEDED"},{"id":"autogen_task1_kf_5","status":"SUCCEEDED"},{"id":"autogen_task1_kr_5","status":"SUCCEEDED"},{"id":"autogen_task1_kf_6","status":"SUCCEEDED"},{"id":"autogen_task1_kr_6","status":"SUCCEEDED"},{"id":"autogen_task1_kf_7","status":"SUCCEEDED"},{"id":"autogen_task1_kr_7","status":"SUCCEEDED"},{"id":"autogen_task1_kf_8","status":"SUCCEEDED"},{"id":"autogen_task1_kr_8","status":"SUCCEEDED"},{"id":"autogen_task1_kf_9","status":"SUCCEEDED"},{"id":"autogen_task1_kr_9","status":"SUCCEEDED"},{"id":"autogen_task1_kf_10","status":"SUCCEEDED"},{"id":"autogen_task1_kr_10","status":"SUCCEEDED"},{"id":"autogen_task1_kf_11","status":"SUCCEEDED"},{"id":"autogen_task1_kr_11","status":"SUCCEEDED"},{"id":"autogen_task1_kf_12","status":"SUCCEEDED"},{"id":"autogen_task1_kr_12","status":"SUCCEEDED"},{"id":"autogen_task1_kf_13","status":"SUCCEEDED"},{"id":"autogen_task1_kr_13","status":"SUCCEEDED"},{"id":"autogen_task1_kf_14","status":"SUCCEEDED"},{"id":"autogen_task1_kr_14","status":"SUCCEEDED"},{"id":"autogen_task1_kf_15","status":"SUCCEEDED"},{"id":"autogen_task1_kr_15","status":"SUCCEEDED"},{"id":"autogen_task1_kf_16","status":"SUCCEEDED"},{"id":"autogen_task1_kr_16","status":"SUCCEEDED"},{"id":"autogen_task1_t2","status":"SUCCEEDED"},{"id":"autogen_task1_comp1","status":"SUCCEEDED"},{"id":"autogen_task1_React0","status":"SUCCEEDED"},{"id":"autogen_task1_React1","status":"SUCCEEDED"},{"id":"autogen_task1_React2","status":"SUCCEEDED"},{"id":"autogen_task1_React3","status":"SUCCEEDED"},{"id":"autogen_task1_React4","status":"SUCCEEDED"},{"id":"autogen_task1_React5","status":"SUCCEEDED"},{"id":"autogen_task1_React6","status":"SUCCEEDED"},{"id":"autogen_task1_React7","status":"SUCCEEDED"},{"id":"autogen_task1_React8","status":"SUCCEEDED"},{"id":"autogen_task1_React9","status":"SUCCEEDED"},{"id":"autogen_task1_React10","status":"SUCCEEDED"},{"id":"autogen_task1_React11","status":"SUCCEEDED"},{"id":"autogen_task1_React12","status":"SUCCEEDED"},{"id":"autogen_task1_React13","status":"SUCCEEDED"},{"id":"autogen_task1_React14","status":"SUCCEEDED"},{"id":"autogen_task1_React15","status":"SUCCEEDED"},{"id":"autogen_task1_React16","status":"SUCCEEDED"}]}]}]}