{"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    434      0 --:--:-- --:--:-- --:--:--   435\n\r100  176k  100  176k    0     0   411k      0 --:--:-- --:--:-- --:--:--  411k\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 (26.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (63.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/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/Fassoni2019 - 5A.sedml/ (stored 0%)\n  adding: outputs/Fassoni2019 - 5A.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 185.9 KiB/185.9 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/outputs/reports.h5\nCompleted 168.9 KiB/194.5 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/output.zip\nCompleted 168.9 KiB/194.5 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 178.0 KiB/194.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/outputs/plots.zip\nCompleted 178.0 KiB/194.5 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 191.9 KiB/194.5 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: outputs/Fassoni2019 - 5A.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/outputs/Fassoni2019 - 5A.sedml/plot_1_task1.pdf\nCompleted 191.9 KiB/194.5 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 194.5 KiB/194.5 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fassoni2019 - 5A.sedml  \n  inflating: contents/Fassoni2019 - Oncogenesis encompassing mutations and genetic instability.cps  \n  inflating: contents/Figure 5.png   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/model-biopax2.owl  \n  inflating: contents/model-biopax3.owl  \n  inflating: contents/model-matlab.m  \n  inflating: contents/model-octave.m  \n  inflating: contents/model.ode      \n  inflating: contents/model.xml      \n  inflating: contents/manifest.xml   \nCompleted 29.1 KiB/507.7 KiB (372.8 KiB/s) with 13 file(s) remaining\rupload: contents/Fassoni2019 - 5A.sedml to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/Fassoni2019 - 5A.sedml\nCompleted 29.1 KiB/507.7 KiB (372.8 KiB/s) with 12 file(s) remaining\rCompleted 56.0 KiB/507.7 KiB (426.4 KiB/s) with 12 file(s) remaining\rupload: contents/model-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model-biopax3.owl\nCompleted 56.0 KiB/507.7 KiB (426.4 KiB/s) with 11 file(s) remaining\rCompleted 73.4 KiB/507.7 KiB (550.9 KiB/s) with 11 file(s) remaining\rupload: contents/model-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model-biopax2.owl\nCompleted 73.4 KiB/507.7 KiB (550.9 KiB/s) with 10 file(s) remaining\rCompleted 74.6 KiB/507.7 KiB (552.5 KiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/curation_notes.txt\nCompleted 74.6 KiB/507.7 KiB (552.5 KiB/s) with 9 file(s) remaining\rCompleted 186.7 KiB/507.7 KiB (1.3 MiB/s) with 9 file(s) remaining \rupload: contents/Fassoni2019 - Oncogenesis encompassing mutations and genetic instability.cps to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/Fassoni2019 - Oncogenesis encompassing mutations and genetic instability.cps\nCompleted 186.7 KiB/507.7 KiB (1.3 MiB/s) with 8 file(s) remaining\rCompleted 188.2 KiB/507.7 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/manifest.xml\nCompleted 188.2 KiB/507.7 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 198.1 KiB/507.7 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/model-matlab.m to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model-matlab.m\nCompleted 198.1 KiB/507.7 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 208.1 KiB/507.7 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/model-octave.m to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model-octave.m\nCompleted 208.1 KiB/507.7 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 215.9 KiB/507.7 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/model.ode to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model.ode\nCompleted 215.9 KiB/507.7 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 219.3 KiB/507.7 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/metadata.rdf\nCompleted 219.3 KiB/507.7 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 316.3 KiB/507.7 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/model.xml to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/model.xml\nCompleted 316.3 KiB/507.7 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 412.0 KiB/507.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 507.7 KiB/507.7 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/Figure 5.png to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/Figure 5.png\nCompleted 507.7 KiB/507.7 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.8 KiB/7.8 KiB (116.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b660fb37cdb9ae736a1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Fassoni2019 - 5A.sedml\ncreating dataset /Fassoni2019 - 5A.sedml/autogen_report_for_task1, shape: (48, 1001), type: float64\ndataset created, uuid: d-8cb0300d-6c2f7f3d-684d-8e6547-3276ff, chunk_size: (48, 1001)\ncreating dataset /Fassoni2019 - 5A.sedml/plot_1_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-8cb0300d-6c2f7f3d-c6b2-1821cd-53df27, chunk_size: (12, 1001)\ncreating attribute combineArchiveLocation in /Fassoni2019 - 5A.sedml\ncreating attribute uri in /Fassoni2019 - 5A.sedml\ncreating attribute _type in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute uri in /Fassoni2019 - 5A.sedml/autogen_report_for_task1\ncreating attribute _type in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlId in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute sedmlName in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreating attribute uri in /Fassoni2019 - 5A.sedml/plot_1_task1\ncreate_links: /\ngot link: Fassoni2019 - 5A.sedml\ncreate_links: /Fassoni2019 - 5A.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Fassoni2019 - 5A.sedml/autogen_report_for_task1 to tgt: /Fassoni2019 - 5A.sedml/autogen_report_for_task1, shape: (48, 1001), type: float64\niterating over chunks for /Fassoni2019 - 5A.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 48, 1), slice(0, 1001, 1))\ndone with dataload for /Fassoni2019 - 5A.sedml/autogen_report_for_task1\nwrite_dataset src: /Fassoni2019 - 5A.sedml/plot_1_task1 to tgt: /Fassoni2019 - 5A.sedml/plot_1_task1, shape: (12, 1001), type: float64\niterating over chunks for /Fassoni2019 - 5A.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /Fassoni2019 - 5A.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b660fb37cdb9ae736a1\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 and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":22.716661,"sedDocuments":[{"location":"Fassoni2019 - 5A.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  Fassoni2019 - 5A.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 48 data sets\r\n    Plots (1):\r\n      plot_1_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: Fassoni2019 - 5A.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":22.307877,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.349381,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.402896,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"},{"id":"p1_curve_9_task1","status":"SUCCEEDED"},{"id":"p1_curve_10_task1","status":"SUCCEEDED"},{"id":"p1_curve_11_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.384374,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_normalized_normal_cell_n","status":"SUCCEEDED"},{"id":"autogen_task1_normalized_pre_cancer_cell_g","status":"SUCCEEDED"},{"id":"autogen_task1_normalized_cancer_cell_a","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_N0","status":"SUCCEEDED"},{"id":"autogen_task1_n0","status":"SUCCEEDED"},{"id":"autogen_task1_a0","status":"SUCCEEDED"},{"id":"autogen_task1_g0","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_r_N","status":"SUCCEEDED"},{"id":"autogen_task1_mu_N","status":"SUCCEEDED"},{"id":"autogen_task1_beta_1","status":"SUCCEEDED"},{"id":"autogen_task1_beta_4","status":"SUCCEEDED"},{"id":"autogen_task1_r_G","status":"SUCCEEDED"},{"id":"autogen_task1_mu_G","status":"SUCCEEDED"},{"id":"autogen_task1_xi_G","status":"SUCCEEDED"},{"id":"autogen_task1_beta_2","status":"SUCCEEDED"},{"id":"autogen_task1_beta_5","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_xi","status":"SUCCEEDED"},{"id":"autogen_task1_r_A","status":"SUCCEEDED"},{"id":"autogen_task1_K_A","status":"SUCCEEDED"},{"id":"autogen_task1_mu_A","status":"SUCCEEDED"},{"id":"autogen_task1_xi_A","status":"SUCCEEDED"},{"id":"autogen_task1_beta_3","status":"SUCCEEDED"},{"id":"autogen_task1_beta_6","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_G0","status":"SUCCEEDED"},{"id":"autogen_task1_A0","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_damage_A","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_damage_G","status":"SUCCEEDED"},{"id":"autogen_task1_pre_cancer_cell_logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_pre_cancer_cell_natural_death","status":"SUCCEEDED"},{"id":"autogen_task1_pre_cancer_cell_death_tissue_repair_system","status":"SUCCEEDED"},{"id":"autogen_task1_pre_cancer_cell_death_apoptosis","status":"SUCCEEDED"},{"id":"autogen_task1_negative_effect_on_G_A","status":"SUCCEEDED"},{"id":"autogen_task1_negative_effect_on_A_G","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_cell_natural_death","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_cell_logistic_growth","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_cell_death_tissue_repair_system","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_cell_death_apoptosis","status":"SUCCEEDED"},{"id":"autogen_task1_transition_to_cancer_cell","status":"SUCCEEDED"}]}]}]}