{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r 41  317k   41  130k    0     0   304k      0  0:00:01 --:--:--  0:00:01  304k\r100  317k  100  317k    0     0   718k      0 --:--:-- --:--:-- --:--:-- 16.5M\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 (18.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/rawLog.txt\nCompleted 6.0 KiB/6.0 KiB (61.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/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/BIOMD0000000081_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000081_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 8%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/310.4 KiB (5.5 MiB/s) with 1 file(s) remaining\rCompleted 310.4 KiB/310.4 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/outputs/reports.h5\nCompleted 256.0 KiB/327.0 KiB (6.0 MiB/s) with 4 file(s) remaining\rCompleted 298.9 KiB/327.0 KiB (3.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/output.zip\nCompleted 298.9 KiB/327.0 KiB (3.0 MiB/s) with 3 file(s) remaining\rCompleted 314.0 KiB/327.0 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000081_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/outputs/BIOMD0000000081_url.sedml/autogen_plot_for_task1.pdf\nCompleted 314.0 KiB/327.0 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 324.2 KiB/327.0 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/outputs/plots.zip\nCompleted 324.2 KiB/327.0 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 327.0 KiB/327.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000081-biopax2.owl  \n  inflating: contents/BIOMD0000000081-biopax3.owl  \n  inflating: contents/BIOMD0000000081-matlab.m  \n  inflating: contents/BIOMD0000000081.m  \n  inflating: contents/BIOMD0000000081.ode  \n  inflating: contents/BIOMD0000000081.pdf  \n  inflating: contents/BIOMD0000000081.png  \n  inflating: contents/BIOMD0000000081.svg  \n  inflating: contents/BIOMD0000000081_url.sedml  \n  inflating: contents/BIOMD0000000081_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 41.2 KiB/700.1 KiB (501.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000081-biopax2.owl to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081-biopax2.owl\nCompleted 41.2 KiB/700.1 KiB (501.4 KiB/s) with 13 file(s) remaining\rCompleted 55.0 KiB/700.1 KiB (471.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000081-matlab.m to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081-matlab.m\nCompleted 55.0 KiB/700.1 KiB (471.5 KiB/s) with 12 file(s) remaining\rCompleted 66.8 KiB/700.1 KiB (563.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000081.m to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081.m\nCompleted 66.8 KiB/700.1 KiB (563.8 KiB/s) with 11 file(s) remaining\rCompleted 98.7 KiB/700.1 KiB (722.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000081_url.sedml to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081_url.sedml\nCompleted 98.7 KiB/700.1 KiB (722.7 KiB/s) with 10 file(s) remaining\rCompleted 109.3 KiB/700.1 KiB (787.6 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/curation_image.png\nCompleted 109.3 KiB/700.1 KiB (787.6 KiB/s) with 9 file(s) remaining\rCompleted 146.4 KiB/700.1 KiB (1006.1 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000081.svg to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081.svg\nCompleted 146.4 KiB/700.1 KiB (1006.1 KiB/s) with 8 file(s) remaining\rCompleted 266.3 KiB/700.1 KiB (1.7 MiB/s) with 8 file(s) remaining   \rupload: contents/BIOMD0000000081.png to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081.png\nCompleted 266.3 KiB/700.1 KiB (1.7 MiB/s) with 7 file(s) remaining\rCompleted 380.2 KiB/700.1 KiB (2.3 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000081_url.xml to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081_url.xml\nCompleted 380.2 KiB/700.1 KiB (2.3 MiB/s) with 6 file(s) remaining\rCompleted 380.3 KiB/700.1 KiB (2.1 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/curation_notes.txt\nCompleted 380.3 KiB/700.1 KiB (2.1 MiB/s) with 5 file(s) remaining\rCompleted 437.6 KiB/700.1 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000081-biopax3.owl to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081-biopax3.owl\nCompleted 437.6 KiB/700.1 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 449.0 KiB/700.1 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000081.ode to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081.ode\nCompleted 449.0 KiB/700.1 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 450.6 KiB/700.1 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/manifest.xml\nCompleted 450.6 KiB/700.1 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 454.4 KiB/700.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/metadata.rdf\nCompleted 454.4 KiB/700.1 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 700.1 KiB/700.1 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000081.pdf to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/contents/BIOMD0000000081.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (137.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107ff9a62a8be53f750aa/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000081_url.sedml\ncreating dataset /BIOMD0000000081_url.sedml/autogen_plot_for_task1, shape: (24, 1001), type: float64\ndataset created, uuid: d-8d5374ed-d8132340-ba35-f700ba-086708, chunk_size: (24, 1001)\ncreating dataset /BIOMD0000000081_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\ndataset created, uuid: d-8d5374ed-d8132340-9a81-a7841c-6fa63b, chunk_size: (54, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000081_url.sedml\ncreating attribute uri in /BIOMD0000000081_url.sedml\ncreating attribute _type in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000081_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000081_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000081_url.sedml\ncreate_links: /BIOMD0000000081_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000081_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000081_url.sedml/autogen_plot_for_task1, shape: (24, 1001), type: float64\niterating over chunks for /BIOMD0000000081_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000081_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000081_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000081_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\niterating over chunks for /BIOMD0000000081_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 54, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000081_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107ff9a62a8be53f750aa\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.\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 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":23.405576,"sedDocuments":[{"location":"BIOMD0000000081_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  BIOMD0000000081_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 54 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 23 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000081_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":23.02965,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.816405,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.415086,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_GTPgS_C","status":"SUCCEEDED"},{"id":"autogen_task1_KCNQsites_M","status":"SUCCEEDED"},{"id":"autogen_task1_PIP2_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGDPbS_M","status":"SUCCEEDED"},{"id":"autogen_task1_Mg2_C","status":"SUCCEEDED"},{"id":"autogen_task1_ATP_C","status":"SUCCEEDED"},{"id":"autogen_task1_oxoM_EX","status":"SUCCEEDED"},{"id":"autogen_task1_GDPbS_C","status":"SUCCEEDED"},{"id":"autogen_task1_GGTPMg_M","status":"SUCCEEDED"},{"id":"autogen_task1_GDP_C","status":"SUCCEEDED"},{"id":"autogen_task1_GTP_C","status":"SUCCEEDED"},{"id":"autogen_task1_GGDPAlF4Mg_M","status":"SUCCEEDED"},{"id":"autogen_task1_ip3_C","status":"SUCCEEDED"},{"id":"autogen_task1_AlF4_C","status":"SUCCEEDED"},{"id":"autogen_task1_G_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGTP_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGDPAlF4_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGTPgS_M","status":"SUCCEEDED"},{"id":"autogen_task1_PI_M","status":"SUCCEEDED"},{"id":"autogen_task1_PIP_M","status":"SUCCEEDED"},{"id":"autogen_task1_PIP2xKCNQ_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGTPgSMg_M","status":"SUCCEEDED"},{"id":"autogen_task1_GGDP_M","status":"SUCCEEDED"},{"id":"autogen_task1_MgSat20","status":"SUCCEEDED"},{"id":"autogen_task1_ATPSat300","status":"SUCCEEDED"},{"id":"autogen_task1_MgSat10","status":"SUCCEEDED"},{"id":"autogen_task1_OxoSat","status":"SUCCEEDED"},{"id":"autogen_task1_Gactive","status":"SUCCEEDED"},{"id":"autogen_task1_ATPSat1000","status":"SUCCEEDED"},{"id":"autogen_task1_KMgGTPase","status":"SUCCEEDED"},{"id":"autogen_task1_Koxom","status":"SUCCEEDED"},{"id":"autogen_task1_I_KCNQ","status":"SUCCEEDED"},{"id":"autogen_task1_nHill","status":"SUCCEEDED"},{"id":"autogen_task1_fGactive","status":"SUCCEEDED"},{"id":"autogen_task1_NA_micro","status":"SUCCEEDED"},{"id":"autogen_task1_EX","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_PIP5kinase","status":"SUCCEEDED"},{"id":"autogen_task1_IP3Phosphatase","status":"SUCCEEDED"},{"id":"autogen_task1_PIP2binding","status":"SUCCEEDED"},{"id":"autogen_task1_MgonGGTPgS","status":"SUCCEEDED"},{"id":"autogen_task1_GGTPase","status":"SUCCEEDED"},{"id":"autogen_task1_GTPon","status":"SUCCEEDED"},{"id":"autogen_task1_GTPgSon","status":"SUCCEEDED"},{"id":"autogen_task1_GDPbSon","status":"SUCCEEDED"},{"id":"autogen_task1_MgGTPon","status":"SUCCEEDED"},{"id":"autogen_task1_GDPdissoc","status":"SUCCEEDED"},{"id":"autogen_task1_PIP2_5Pase","status":"SUCCEEDED"},{"id":"autogen_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_task1_AlF4on","status":"SUCCEEDED"},{"id":"autogen_task1_PI4Kinase","status":"SUCCEEDED"},{"id":"autogen_task1_MgonGDPAlF4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.599125,"curves":[{"id":"autogen_curve_task1_GTPgS_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_KCNQsites_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PIP2_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGDPbS_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mg2_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_oxoM_EX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GDPbS_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGTPMg_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GDP_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GTP_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGDPAlF4Mg_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ip3_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AlF4_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGTP_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGDPAlF4_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGTPgS_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PI_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PIP_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PIP2xKCNQ_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGTPgSMg_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GGDP_M","status":"SUCCEEDED"}]}]}]}