{"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    446      0 --:--:-- --:--:-- --:--:--   446\n\r100  219k  100  219k    0     0   518k      0 --:--:-- --:--:-- --:--:--  518k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (24.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (57.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000167_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000167_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 31%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 67.7 KiB/67.7 KiB (840.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/outputs/reports.h5\nCompleted 56.9 KiB/78.9 KiB (691.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/output.zip\nCompleted 56.9 KiB/78.9 KiB (691.8 KiB/s) with 3 file(s) remaining\rCompleted 64.6 KiB/78.9 KiB (617.2 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/outputs/plots.zip\nCompleted 64.6 KiB/78.9 KiB (617.2 KiB/s) with 2 file(s) remaining\rCompleted 76.3 KiB/78.9 KiB (708.0 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000167_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/outputs/BIOMD0000000167_url.sedml/autogen_plot_for_task1.pdf\nCompleted 76.3 KiB/78.9 KiB (708.0 KiB/s) with 1 file(s) remaining\rCompleted 78.9 KiB/78.9 KiB (699.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000167-biopax2.owl  \n  inflating: contents/BIOMD0000000167-biopax3.owl  \n  inflating: contents/BIOMD0000000167-matlab.m  \n  inflating: contents/BIOMD0000000167.m  \n  inflating: contents/BIOMD0000000167.ode  \n  inflating: contents/BIOMD0000000167.pdf  \n  inflating: contents/BIOMD0000000167.png  \n  inflating: contents/BIOMD0000000167.svg  \n  inflating: contents/BIOMD0000000167_url.sedml  \n  inflating: contents/BIOMD0000000167_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.2 KiB/392.5 KiB (213.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000167-biopax2.owl to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167-biopax2.owl\nCompleted 16.2 KiB/392.5 KiB (213.4 KiB/s) with 13 file(s) remaining\rCompleted 20.8 KiB/392.5 KiB (184.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000167.ode to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167.ode\nCompleted 20.8 KiB/392.5 KiB (184.7 KiB/s) with 12 file(s) remaining\rCompleted 44.4 KiB/392.5 KiB (381.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000167-biopax3.owl to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167-biopax3.owl\nCompleted 44.4 KiB/392.5 KiB (381.1 KiB/s) with 11 file(s) remaining\rCompleted 57.8 KiB/392.5 KiB (469.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000167_url.sedml to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167_url.sedml\nCompleted 57.8 KiB/392.5 KiB (469.7 KiB/s) with 10 file(s) remaining\rCompleted 80.1 KiB/392.5 KiB (586.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000167.svg to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167.svg\nCompleted 80.1 KiB/392.5 KiB (586.7 KiB/s) with 9 file(s) remaining\rCompleted 135.7 KiB/392.5 KiB (922.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000167.png to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167.png\nCompleted 135.7 KiB/392.5 KiB (922.0 KiB/s) with 8 file(s) remaining\rCompleted 162.3 KiB/392.5 KiB (1.0 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000167_url.xml to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167_url.xml\nCompleted 162.3 KiB/392.5 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 194.4 KiB/392.5 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/curation_image.jpeg\nCompleted 194.4 KiB/392.5 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 194.5 KiB/392.5 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/curation_notes.txt\nCompleted 194.5 KiB/392.5 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 201.6 KiB/392.5 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000167.m to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167.m\nCompleted 201.6 KiB/392.5 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 203.2 KiB/392.5 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/manifest.xml\nCompleted 203.2 KiB/392.5 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 210.4 KiB/392.5 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000167-matlab.m to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167-matlab.m\nCompleted 210.4 KiB/392.5 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 214.0 KiB/392.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/metadata.rdf\nCompleted 214.0 KiB/392.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 392.5 KiB/392.5 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000167.pdf to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/contents/BIOMD0000000167.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (130.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109170dcacb55678b7008/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000167_url.sedml\ncreating dataset /BIOMD0000000167_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-0be9ec6d-80654a5c-4abf-65fcce-c410d4, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000167_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-0be9ec6d-80654a5c-a279-2df855-9dfe83, chunk_size: (20, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000167_url.sedml\ncreating attribute uri in /BIOMD0000000167_url.sedml\ncreating attribute _type in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000167_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000167_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000167_url.sedml\ncreate_links: /BIOMD0000000167_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000167_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000167_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000167_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000167_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000167_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000167_url.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000167_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000167_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109170dcacb55678b7008\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.530513,"sedDocuments":[{"location":"BIOMD0000000167_url.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  BIOMD0000000167_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000167_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":1.088018,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.218874,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.200783,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_stat_sol","status":"SUCCEEDED"},{"id":"autogen_task1_Pstat_sol","status":"SUCCEEDED"},{"id":"autogen_task1_statKinase_sol","status":"SUCCEEDED"},{"id":"autogen_task1_PstatDimer_sol","status":"SUCCEEDED"},{"id":"autogen_task1_PstatDimer_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_stat_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_Pstat_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_statPhosphatase_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_species_test","status":"SUCCEEDED"},{"id":"autogen_task1_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_sol","status":"SUCCEEDED"},{"id":"autogen_task1_nm","status":"SUCCEEDED"},{"id":"autogen_task1_PstatDimerisation","status":"SUCCEEDED"},{"id":"autogen_task1_statDephosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_statPhosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_PstatDimerisationNuc","status":"SUCCEEDED"},{"id":"autogen_task1_PstatDimer__import","status":"SUCCEEDED"},{"id":"autogen_task1_stat_export","status":"SUCCEEDED"},{"id":"autogen_task1_stat_import","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.534499,"curves":[{"id":"autogen_curve_task1_stat_sol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pstat_sol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_statKinase_sol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PstatDimer_sol","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PstatDimer_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_stat_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pstat_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_statPhosphatase_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_test","status":"SUCCEEDED"}]}]}]}