{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    442      0 --:--:-- --:--:-- --:--:--   442\n\r100 47012  100 47012    0     0   109k      0 --:--:-- --:--:-- --:--:--  109k\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 (27.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (47.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/MODEL1708250002_treatment_start10.sedml/ (stored 0%)\n  adding: outputs/MODEL1708250002_treatment_start10.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 30%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 68.3 KiB/68.3 KiB (706.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/outputs/reports.h5\nCompleted 59.0 KiB/82.1 KiB (715.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/output.zip\nCompleted 59.0 KiB/82.1 KiB (715.5 KiB/s) with 3 file(s) remaining\rCompleted 61.7 KiB/82.1 KiB (578.6 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/rawLog.txt\nCompleted 61.7 KiB/82.1 KiB (578.6 KiB/s) with 2 file(s) remaining\rCompleted 70.2 KiB/82.1 KiB (633.0 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/outputs/plots.zip\nCompleted 70.2 KiB/82.1 KiB (633.0 KiB/s) with 1 file(s) remaining\rCompleted 82.1 KiB/82.1 KiB (573.9 KiB/s) with 1 file(s) remaining\rupload: outputs/MODEL1708250002_treatment_start10.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/outputs/MODEL1708250002_treatment_start10.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000650-biopax2.owl  \n  inflating: contents/BIOMD0000000650-biopax3.owl  \n  inflating: contents/BIOMD0000000650-matlab.m  \n  inflating: contents/BIOMD0000000650-octave.m  \n  inflating: contents/BIOMD0000000650.m  \n  inflating: contents/BIOMD0000000650.ode  \n  inflating: contents/BIOMD0000000650.png  \n  inflating: contents/BIOMD0000000650.svg  \n  inflating: contents/BIOMD0000000650_url.xml  \n  inflating: contents/MODEL1708250002.cps  \n  inflating: contents/MODEL1708250002_treatment_start10.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 3.5 KiB/~138.6 KiB (53.6 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000650-biopax2.owl to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650-biopax2.owl\nCompleted 3.5 KiB/~138.6 KiB (53.6 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 7.7 KiB/143.1 KiB (63.3 KiB/s) with 14 file(s) remaining                   \rupload: contents/BIOMD0000000650-octave.m to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650-octave.m\nCompleted 7.7 KiB/143.1 KiB (63.3 KiB/s) with 13 file(s) remaining\rCompleted 11.9 KiB/143.1 KiB (93.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000650-matlab.m to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650-matlab.m\nCompleted 11.9 KiB/143.1 KiB (93.6 KiB/s) with 12 file(s) remaining\rCompleted 12.7 KiB/143.1 KiB (98.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000650.svg to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650.svg\nCompleted 12.7 KiB/143.1 KiB (98.7 KiB/s) with 11 file(s) remaining\rCompleted 13.1 KiB/143.1 KiB (100.8 KiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/curation_notes.txt\nCompleted 13.1 KiB/143.1 KiB (100.8 KiB/s) with 10 file(s) remaining\rCompleted 40.1 KiB/143.1 KiB (281.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000650_url.xml to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650_url.xml\nCompleted 40.1 KiB/143.1 KiB (281.2 KiB/s) with 9 file(s) remaining\rCompleted 50.8 KiB/143.1 KiB (330.8 KiB/s) with 9 file(s) remaining\rupload: contents/MODEL1708250002_treatment_start10.sedml to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/MODEL1708250002_treatment_start10.sedml\nCompleted 50.8 KiB/143.1 KiB (330.8 KiB/s) with 8 file(s) remaining\rCompleted 94.8 KiB/143.1 KiB (606.3 KiB/s) with 8 file(s) remaining\rupload: contents/MODEL1708250002.cps to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/MODEL1708250002.cps\nCompleted 94.8 KiB/143.1 KiB (606.3 KiB/s) with 7 file(s) remaining\rCompleted 96.6 KiB/143.1 KiB (557.4 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/manifest.xml\nCompleted 96.6 KiB/143.1 KiB (557.4 KiB/s) with 6 file(s) remaining\rCompleted 100.8 KiB/143.1 KiB (555.4 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000650.png to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650.png\nCompleted 100.8 KiB/143.1 KiB (555.4 KiB/s) with 5 file(s) remaining\rCompleted 104.7 KiB/143.1 KiB (567.4 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000650-biopax3.owl to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650-biopax3.owl\nCompleted 104.7 KiB/143.1 KiB (567.4 KiB/s) with 4 file(s) remaining\rCompleted 106.8 KiB/143.1 KiB (569.8 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000650.ode to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650.ode\nCompleted 106.8 KiB/143.1 KiB (569.8 KiB/s) with 3 file(s) remaining\rCompleted 134.5 KiB/143.1 KiB (706.3 KiB/s) with 3 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/curation_image.jpeg\nCompleted 134.5 KiB/143.1 KiB (706.3 KiB/s) with 2 file(s) remaining\rCompleted 138.9 KiB/143.1 KiB (721.2 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/metadata.rdf\nCompleted 138.9 KiB/143.1 KiB (721.2 KiB/s) with 1 file(s) remaining\rCompleted 143.1 KiB/143.1 KiB (725.3 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000650.m to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/contents/BIOMD0000000650.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (125.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb79a62a8be53f8c1e9/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1708250002_treatment_start10.sedml\ncreating dataset /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-8e6c6334-0065c31b-8d44-5d3eb5-454c3b, chunk_size: (18, 1001)\ncreating dataset /MODEL1708250002_treatment_start10.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-8e6c6334-0065c31b-18de-29fbae-8bf077, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /MODEL1708250002_treatment_start10.sedml\ncreating attribute uri in /MODEL1708250002_treatment_start10.sedml\ncreating attribute _type in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreating attribute uri in /MODEL1708250002_treatment_start10.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1708250002_treatment_start10.sedml\ncreate_links: /MODEL1708250002_treatment_start10.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1 to tgt: /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1708250002_treatment_start10.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1708250002_treatment_start10.sedml/plot_1_task1 to tgt: /MODEL1708250002_treatment_start10.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /MODEL1708250002_treatment_start10.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1708250002_treatment_start10.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711bb79a62a8be53f8c1e9\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 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.\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":1.545179,"sedDocuments":[{"location":"MODEL1708250002_treatment_start10.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  MODEL1708250002_treatment_start10.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 18 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: MODEL1708250002_treatment_start10.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":1.034999,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.246625,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.459822,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.189474,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_l","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_K_l","status":"SUCCEEDED"},{"id":"autogen_task1_delta_l","status":"SUCCEEDED"},{"id":"autogen_task1_K_m","status":"SUCCEEDED"},{"id":"autogen_task1_sigma","status":"SUCCEEDED"},{"id":"autogen_task1_xi","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_F","status":"SUCCEEDED"},{"id":"autogen_task1_treatment_start","status":"SUCCEEDED"},{"id":"autogen_task1_treatment_end","status":"SUCCEEDED"},{"id":"autogen_task1_sink","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]}]}]}