{"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    431      0 --:--:-- --:--:-- --:--:--   431\r100   139  100   139    0     0    426      0 --:--:-- --:--:-- --:--:--   426\n\r100  244k  100  244k    0     0   555k      0 --:--:-- --:--:-- --:--:--  555k\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 (23.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/rawLog.txt\nCompleted 5.7 KiB/5.7 KiB (70.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: outputs/BIOMD0000000204_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000204_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 163.4 KiB/163.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/outputs/reports.h5\nCompleted 147.1 KiB/173.7 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/output.zip\nCompleted 147.1 KiB/173.7 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 161.2 KiB/173.7 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000204_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/outputs/BIOMD0000000204_url.sedml/autogen_plot_for_task1.pdf\nCompleted 161.2 KiB/173.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 163.9 KiB/173.7 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/rawLog.txt\nCompleted 163.9 KiB/173.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 173.7 KiB/173.7 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000204-biopax2.owl  \n  inflating: contents/BIOMD0000000204-biopax3.owl  \n  inflating: contents/BIOMD0000000204-matlab.m  \n  inflating: contents/BIOMD0000000204-octave.m  \n  inflating: contents/BIOMD0000000204.m  \n  inflating: contents/BIOMD0000000204.ode  \n  inflating: contents/BIOMD0000000204.pdf  \n  inflating: contents/BIOMD0000000204.png  \n  inflating: contents/BIOMD0000000204.svg  \n  inflating: contents/BIOMD0000000204_url.sedml  \n  inflating: contents/BIOMD0000000204_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 28.0 KiB/457.9 KiB (400.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000204-biopax3.owl to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204-biopax3.owl\nCompleted 28.0 KiB/457.9 KiB (400.2 KiB/s) with 14 file(s) remaining\rCompleted 35.4 KiB/457.9 KiB (335.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000204-matlab.m to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204-matlab.m\nCompleted 35.4 KiB/457.9 KiB (335.5 KiB/s) with 13 file(s) remaining\rCompleted 54.1 KiB/457.9 KiB (441.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000204-biopax2.owl to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204-biopax2.owl\nCompleted 54.1 KiB/457.9 KiB (441.9 KiB/s) with 12 file(s) remaining\rCompleted 59.4 KiB/457.9 KiB (456.4 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/metadata.rdf\nCompleted 59.4 KiB/457.9 KiB (456.4 KiB/s) with 11 file(s) remaining\rCompleted 89.3 KiB/457.9 KiB (656.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000204_url.sedml to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204_url.sedml\nCompleted 89.3 KiB/457.9 KiB (656.3 KiB/s) with 10 file(s) remaining\rCompleted 96.7 KiB/457.9 KiB (700.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000204-octave.m to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204-octave.m\nCompleted 96.7 KiB/457.9 KiB (700.4 KiB/s) with 9 file(s) remaining\rCompleted 129.0 KiB/457.9 KiB (920.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000204_url.xml to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204_url.xml\nCompleted 129.0 KiB/457.9 KiB (920.9 KiB/s) with 8 file(s) remaining\rCompleted 156.2 KiB/457.9 KiB (1.1 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000204.svg to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204.svg\nCompleted 156.2 KiB/457.9 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 156.4 KiB/457.9 KiB (992.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/curation_notes.txt\nCompleted 156.4 KiB/457.9 KiB (992.2 KiB/s) with 6 file(s) remaining\rCompleted 167.3 KiB/457.9 KiB (1004.3 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/curation_image.png\nCompleted 167.3 KiB/457.9 KiB (1004.3 KiB/s) with 5 file(s) remaining\rCompleted 169.0 KiB/457.9 KiB (996.6 KiB/s) with 5 file(s) remaining \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/manifest.xml\nCompleted 169.0 KiB/457.9 KiB (996.6 KiB/s) with 4 file(s) remaining\rCompleted 351.0 KiB/457.9 KiB (1.9 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000204.pdf to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204.pdf\nCompleted 351.0 KiB/457.9 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 445.2 KiB/457.9 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000204.png to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204.png\nCompleted 445.2 KiB/457.9 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 452.5 KiB/457.9 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000204.m to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204.m\nCompleted 452.5 KiB/457.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 457.9 KiB/457.9 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000204.ode to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/contents/BIOMD0000000204.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (141.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471099149c0d898ffdddae3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000204_url.sedml\ncreating dataset /BIOMD0000000204_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-2c3ed6de-8463367f-027c-bac464-51908c, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000204_url.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\ndataset created, uuid: d-2c3ed6de-8463367f-687d-3cfeac-13d8d4, chunk_size: (56, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000204_url.sedml\ncreating attribute uri in /BIOMD0000000204_url.sedml\ncreating attribute _type in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000204_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000204_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000204_url.sedml\ncreate_links: /BIOMD0000000204_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000204_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000204_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000204_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000204_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000204_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000204_url.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\niterating over chunks for /BIOMD0000000204_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 56, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000204_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471099149c0d898ffdddae3\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.712816,"sedDocuments":[{"location":"BIOMD0000000204_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  BIOMD0000000204_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 56 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000204_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":1.275551,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.226318,"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":0.368505,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_NANOG_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_SOX2_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_targetGene","status":"SUCCEEDED"},{"id":"autogen_task1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_p53","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4","status":"SUCCEEDED"},{"id":"autogen_task1_SOX2","status":"SUCCEEDED"},{"id":"autogen_task1_NANOG","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4_SOX2","status":"SUCCEEDED"},{"id":"autogen_task1_Protein","status":"SUCCEEDED"},{"id":"autogen_task1_eta1","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_a3","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_b3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma1","status":"SUCCEEDED"},{"id":"autogen_task1_eta5","status":"SUCCEEDED"},{"id":"autogen_task1_e1","status":"SUCCEEDED"},{"id":"autogen_task1_e2","status":"SUCCEEDED"},{"id":"autogen_task1_f2","status":"SUCCEEDED"},{"id":"autogen_task1_f1","status":"SUCCEEDED"},{"id":"autogen_task1_f3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma2","status":"SUCCEEDED"},{"id":"autogen_task1_k1c","status":"SUCCEEDED"},{"id":"autogen_task1_k2c","status":"SUCCEEDED"},{"id":"autogen_task1_k3c","status":"SUCCEEDED"},{"id":"autogen_task1_eta3","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_c3","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_d3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma3","status":"SUCCEEDED"},{"id":"autogen_task1_g1","status":"SUCCEEDED"},{"id":"autogen_task1_eta7","status":"SUCCEEDED"},{"id":"autogen_task1_h1","status":"SUCCEEDED"},{"id":"autogen_task1_h2","status":"SUCCEEDED"},{"id":"autogen_task1_gamma4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_J0","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_J5","status":"SUCCEEDED"},{"id":"autogen_task1_J6","status":"SUCCEEDED"},{"id":"autogen_task1_J7","status":"SUCCEEDED"},{"id":"autogen_task1_J8","status":"SUCCEEDED"},{"id":"autogen_task1_J9","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.515399,"curves":[{"id":"autogen_curve_task1_OCT4_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NANOG_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SOX2_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_targetGene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_degradation","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p53","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OCT4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SOX2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NANOG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OCT4_SOX2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Protein","status":"SUCCEEDED"}]}]}]}