{"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    433      0 --:--:-- --:--:-- --:--:--   434\n\r100  331k  100  331k    0     0   760k      0 --:--:-- --:--:-- --:--:--  760k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (51.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/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/BIOMD0000000242_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000242_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 212.0 KiB/212.0 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/outputs/reports.h5\nCompleted 2.6 KiB/214.0 KiB (23.8 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/rawLog.txt\nCompleted 2.6 KiB/214.0 KiB (23.8 KiB/s) with 3 file(s) remaining\rCompleted 13.5 KiB/214.0 KiB (119.3 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000242_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/outputs/BIOMD0000000242_url.sedml/autogen_plot_for_task1.pdf\nCompleted 13.5 KiB/214.0 KiB (119.3 KiB/s) with 2 file(s) remaining\rCompleted 206.6 KiB/214.0 KiB (1.7 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/output.zip\nCompleted 206.6 KiB/214.0 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 214.0 KiB/214.0 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000242-biopax2.owl  \n  inflating: contents/BIOMD0000000242-biopax3.owl  \n  inflating: contents/BIOMD0000000242-matlab.m  \n  inflating: contents/BIOMD0000000242-octave.m  \n  inflating: contents/BIOMD0000000242.m  \n  inflating: contents/BIOMD0000000242.ode  \n  inflating: contents/BIOMD0000000242.pdf  \n  inflating: contents/BIOMD0000000242.png  \n  inflating: contents/BIOMD0000000242.svg  \n  inflating: contents/BIOMD0000000242.vcml  \n  inflating: contents/BIOMD0000000242_url.sedml  \n  inflating: contents/BIOMD0000000242_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 26.9 KiB/580.6 KiB (275.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000242-biopax3.owl to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242-biopax3.owl\nCompleted 26.9 KiB/580.6 KiB (275.5 KiB/s) with 15 file(s) remaining\rCompleted 33.9 KiB/580.6 KiB (261.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000242-octave.m to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242-octave.m\nCompleted 33.9 KiB/580.6 KiB (261.2 KiB/s) with 14 file(s) remaining\rCompleted 68.3 KiB/580.6 KiB (510.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000242.svg to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.svg\nCompleted 68.3 KiB/580.6 KiB (510.2 KiB/s) with 13 file(s) remaining\rCompleted 87.2 KiB/580.6 KiB (642.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000242-biopax2.owl to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242-biopax2.owl\nCompleted 87.2 KiB/580.6 KiB (642.9 KiB/s) with 12 file(s) remaining\rCompleted 94.2 KiB/580.6 KiB (681.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000242-matlab.m to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242-matlab.m\nCompleted 94.2 KiB/580.6 KiB (681.1 KiB/s) with 11 file(s) remaining\rCompleted 132.1 KiB/580.6 KiB (845.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000242.vcml to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.vcml\nCompleted 132.1 KiB/580.6 KiB (845.7 KiB/s) with 10 file(s) remaining\rCompleted 133.9 KiB/580.6 KiB (846.6 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/manifest.xml\nCompleted 133.9 KiB/580.6 KiB (846.6 KiB/s) with 9 file(s) remaining\rCompleted 166.0 KiB/580.6 KiB (942.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000242_url.xml to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242_url.xml\nCompleted 166.0 KiB/580.6 KiB (942.5 KiB/s) with 8 file(s) remaining\rCompleted 191.2 KiB/580.6 KiB (1.0 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000242_url.sedml to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242_url.sedml\nCompleted 191.2 KiB/580.6 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 191.3 KiB/580.6 KiB (1023.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/curation_notes.txt\nCompleted 191.3 KiB/580.6 KiB (1023.4 KiB/s) with 6 file(s) remaining\rCompleted 252.0 KiB/580.6 KiB (1.3 MiB/s) with 6 file(s) remaining   \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/curation_image.png\nCompleted 252.0 KiB/580.6 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 256.0 KiB/580.6 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/metadata.rdf\nCompleted 256.0 KiB/580.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 263.0 KiB/580.6 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000242.m to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.m\nCompleted 263.0 KiB/580.6 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 267.6 KiB/580.6 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000242.ode to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.ode\nCompleted 267.6 KiB/580.6 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 461.3 KiB/580.6 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000242.pdf to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.pdf\nCompleted 461.3 KiB/580.6 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 580.6 KiB/580.6 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000242.png to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/contents/BIOMD0000000242.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (94.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a1849c0d898ffddec5b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000242_url.sedml\ncreating dataset /BIOMD0000000242_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-0e9f418d-89106f65-2e09-28ffe0-367df9, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000242_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\ndataset created, uuid: d-0e9f418d-89106f65-5b71-0c3667-fa79ec, chunk_size: (46, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000242_url.sedml\ncreating attribute uri in /BIOMD0000000242_url.sedml\ncreating attribute _type in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000242_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000242_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000242_url.sedml\ncreate_links: /BIOMD0000000242_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000242_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000242_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000242_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000242_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000242_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000242_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\niterating over chunks for /BIOMD0000000242_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 46, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000242_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a1849c0d898ffddec5b\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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.483909,"sedDocuments":[{"location":"BIOMD0000000242_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  BIOMD0000000242_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 46 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000242_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":20.115007,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.28358,"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":0.373098,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_D_1","status":"SUCCEEDED"},{"id":"autogen_task1_E_1","status":"SUCCEEDED"},{"id":"autogen_task1_R_1","status":"SUCCEEDED"},{"id":"autogen_task1_RS_1","status":"SUCCEEDED"},{"id":"autogen_task1_theta_1","status":"SUCCEEDED"},{"id":"autogen_task1_X_1","status":"SUCCEEDED"},{"id":"autogen_task1_GF_1","status":"SUCCEEDED"},{"id":"autogen_task1_k1_1","status":"SUCCEEDED"},{"id":"autogen_task1_dD_1","status":"SUCCEEDED"},{"id":"autogen_task1_aD_1","status":"SUCCEEDED"},{"id":"autogen_task1_aE_1","status":"SUCCEEDED"},{"id":"autogen_task1_k2_1","status":"SUCCEEDED"},{"id":"autogen_task1_aF_1","status":"SUCCEEDED"},{"id":"autogen_task1_pX_1","status":"SUCCEEDED"},{"id":"autogen_task1_RT_1","status":"SUCCEEDED"},{"id":"autogen_task1_qX_1","status":"SUCCEEDED"},{"id":"autogen_task1_pS_1","status":"SUCCEEDED"},{"id":"autogen_task1_pD_1","status":"SUCCEEDED"},{"id":"autogen_task1_qD_1","status":"SUCCEEDED"},{"id":"autogen_task1_pE_1","status":"SUCCEEDED"},{"id":"autogen_task1_qE_1","status":"SUCCEEDED"},{"id":"autogen_task1_atheta_1","status":"SUCCEEDED"},{"id":"autogen_task1_k3_1","status":"SUCCEEDED"},{"id":"autogen_task1_dtheta_1","status":"SUCCEEDED"},{"id":"autogen_task1_qtheta_1","status":"SUCCEEDED"},{"id":"autogen_task1_aX_1","status":"SUCCEEDED"},{"id":"autogen_task1_f_1","status":"SUCCEEDED"},{"id":"autogen_task1_g_1","status":"SUCCEEDED"},{"id":"autogen_task1_dX_1","status":"SUCCEEDED"},{"id":"autogen_task1_dE_1","status":"SUCCEEDED"},{"id":"autogen_task1_fC_1_1","status":"SUCCEEDED"},{"id":"autogen_task1_Rb_phos","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1__1","status":"SUCCEEDED"},{"id":"autogen_task1_cyclinD_1","status":"SUCCEEDED"},{"id":"autogen_task1_cyclinEsynthesis_1","status":"SUCCEEDED"},{"id":"autogen_task1_cyclinEdegradation_1","status":"SUCCEEDED"},{"id":"autogen_task1_pRBsynthesis_1","status":"SUCCEEDED"},{"id":"autogen_task1_pRBdeplation_1","status":"SUCCEEDED"},{"id":"autogen_task1__2","status":"SUCCEEDED"},{"id":"autogen_task1_null2_1","status":"SUCCEEDED"},{"id":"autogen_task1_null3_1","status":"SUCCEEDED"},{"id":"autogen_task1_E2Fdegradationviacellcycleprogression_1","status":"SUCCEEDED"},{"id":"autogen_task1_cellcycleprogression_1","status":"SUCCEEDED"},{"id":"autogen_task1_cellcycleprogressionslow_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.305267,"curves":[{"id":"autogen_curve_task1_D_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RS_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_theta_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X_1","status":"SUCCEEDED"}]}]}]}