{"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    440      0 --:--:-- --:--:-- --:--:--   441\n\r100 47598  100 47598    0     0   111k      0 --:--:-- --:--:-- --:--:--  111k\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 (21.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (44.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/Alharbi2020 - Fig 5.sedml/ (stored 0%)\n  adding: outputs/Alharbi2020 - Fig 5.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 62%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 32.6 KiB/32.6 KiB (385.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/outputs/reports.h5\nCompleted 22.0 KiB/41.3 KiB (255.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/output.zip\nCompleted 22.0 KiB/41.3 KiB (255.9 KiB/s) with 3 file(s) remaining\rCompleted 28.9 KiB/41.3 KiB (269.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/outputs/plots.zip\nCompleted 28.9 KiB/41.3 KiB (269.7 KiB/s) with 2 file(s) remaining\rCompleted 38.7 KiB/41.3 KiB (327.0 KiB/s) with 2 file(s) remaining\rupload: outputs/Alharbi2020 - Fig 5.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/outputs/Alharbi2020 - Fig 5.sedml/plot_1_task1.pdf\nCompleted 38.7 KiB/41.3 KiB (327.0 KiB/s) with 1 file(s) remaining\rCompleted 41.3 KiB/41.3 KiB (239.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Alharbi2020 - Fig 5.png  \n  inflating: contents/Alharbi2020 - Fig 5.sedml  \n  inflating: contents/Alharbi2020-biopax2.owl  \n  inflating: contents/Alharbi2020-biopax3.owl  \n  inflating: contents/Alharbi2020-matlab.m  \n  inflating: contents/Alharbi2020-octave.m  \n  inflating: contents/Alharbi2020.cps  \n  inflating: contents/Alharbi2020.ode  \n  inflating: contents/Alharbi2020.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.3 KiB/205.4 KiB (202.8 KiB/s) with 13 file(s) remaining\rupload: contents/Alharbi2020 - Fig 5.sedml to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020 - Fig 5.sedml\nCompleted 16.3 KiB/205.4 KiB (202.8 KiB/s) with 12 file(s) remaining\rCompleted 27.8 KiB/205.4 KiB (228.4 KiB/s) with 12 file(s) remaining\rupload: contents/Alharbi2020 - Fig 5.png to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020 - Fig 5.png\nCompleted 27.8 KiB/205.4 KiB (228.4 KiB/s) with 11 file(s) remaining\rCompleted 68.6 KiB/205.4 KiB (505.7 KiB/s) with 11 file(s) remaining\rupload: contents/Alharbi2020.xml to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020.xml\nCompleted 68.6 KiB/205.4 KiB (505.7 KiB/s) with 10 file(s) remaining\rCompleted 80.6 KiB/205.4 KiB (569.7 KiB/s) with 10 file(s) remaining\rupload: contents/Alharbi2020-biopax2.owl to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020-biopax2.owl\nCompleted 80.6 KiB/205.4 KiB (569.7 KiB/s) with 9 file(s) remaining\rCompleted 82.1 KiB/205.4 KiB (530.0 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/manifest.xml\nCompleted 82.1 KiB/205.4 KiB (530.0 KiB/s) with 8 file(s) remaining\rCompleted 82.2 KiB/205.4 KiB (510.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/curation_notes.txt\nCompleted 82.2 KiB/205.4 KiB (510.4 KiB/s) with 7 file(s) remaining\rCompleted 159.5 KiB/205.4 KiB (961.4 KiB/s) with 7 file(s) remaining\rupload: contents/Alharbi2020.cps to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020.cps\nCompleted 159.5 KiB/205.4 KiB (961.4 KiB/s) with 6 file(s) remaining\rCompleted 171.0 KiB/205.4 KiB (1017.3 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/curation_image.png\nCompleted 171.0 KiB/205.4 KiB (1017.3 KiB/s) with 5 file(s) remaining\rCompleted 175.1 KiB/205.4 KiB (1.0 MiB/s) with 5 file(s) remaining   \rupload: contents/Alharbi2020.ode to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020.ode\nCompleted 175.1 KiB/205.4 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 180.8 KiB/205.4 KiB (966.8 KiB/s) with 4 file(s) remaining\rupload: contents/Alharbi2020-octave.m to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020-octave.m\nCompleted 180.8 KiB/205.4 KiB (966.8 KiB/s) with 3 file(s) remaining\rCompleted 184.2 KiB/205.4 KiB (863.6 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/metadata.rdf\nCompleted 184.2 KiB/205.4 KiB (863.6 KiB/s) with 2 file(s) remaining\rCompleted 189.9 KiB/205.4 KiB (835.8 KiB/s) with 2 file(s) remaining\rupload: contents/Alharbi2020-matlab.m to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020-matlab.m\nCompleted 189.9 KiB/205.4 KiB (835.8 KiB/s) with 1 file(s) remaining\rCompleted 205.4 KiB/205.4 KiB (837.8 KiB/s) with 1 file(s) remaining\rupload: contents/Alharbi2020-biopax3.owl to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/contents/Alharbi2020-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.8 KiB/7.8 KiB (87.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a619d0fb37cdb9ae76ea5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Alharbi2020 - Fig 5.sedml\ncreating dataset /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\ndataset created, uuid: d-cf2888ad-afb9ca2e-3481-2aaf15-95bc9f, chunk_size: (27, 101)\ncreating dataset /Alharbi2020 - Fig 5.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-cf2888ad-afb9ca2e-bf78-b7a434-82a53d, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Alharbi2020 - Fig 5.sedml\ncreating attribute uri in /Alharbi2020 - Fig 5.sedml\ncreating attribute _type in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute uri in /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\ncreating attribute _type in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlId in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute sedmlName in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreating attribute uri in /Alharbi2020 - Fig 5.sedml/plot_1_task1\ncreate_links: /\ngot link: Alharbi2020 - Fig 5.sedml\ncreate_links: /Alharbi2020 - Fig 5.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1 to tgt: /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\niterating over chunks for /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 101, 1))\ndone with dataload for /Alharbi2020 - Fig 5.sedml/autogen_report_for_task1\nwrite_dataset src: /Alharbi2020 - Fig 5.sedml/plot_1_task1 to tgt: /Alharbi2020 - Fig 5.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Alharbi2020 - Fig 5.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Alharbi2020 - Fig 5.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a619d0fb37cdb9ae76ea5\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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.20931,"sedDocuments":[{"location":"Alharbi2020 - Fig 5.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  Alharbi2020 - Fig 5.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Alharbi2020 - Fig 5.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":0.751564,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.219052,"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":0.339639,"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":0.073001,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Immune_cells","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_beta_1","status":"SUCCEEDED"},{"id":"autogen_task1_eta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task1_beta_2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_3","status":"SUCCEEDED"},{"id":"autogen_task1_sigma","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_mu_1","status":"SUCCEEDED"},{"id":"autogen_task1_rho_1","status":"SUCCEEDED"},{"id":"autogen_task1_m_1","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_death_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_death_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_Immune_cell_increase","status":"SUCCEEDED"},{"id":"autogen_task1_Immune_cell_decrease","status":"SUCCEEDED"}]}]}]}