{"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    180      0 --:--:-- --:--:-- --:--:--   180\n\r100 51850  100 51850    0     0  58787      0 --:--:-- --:--:-- --:--:-- 58787\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 3 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 3\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 (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (28.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (50.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/Evans2004.sedml/ (stored 0%)\n  adding: outputs/Evans2004.sedml/plot_2_task1.pdf (deflated 34%)\n  adding: outputs/Evans2004.sedml/plot_1_task1.pdf (deflated 37%)\n  adding: outputs/reports.h5 (deflated 32%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 108.5 KiB/108.5 KiB (1009.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/outputs/reports.h5\nCompleted 88.5 KiB/122.2 KiB (933.0 KiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/output.zip\nCompleted 88.5 KiB/122.2 KiB (933.0 KiB/s) with 4 file(s) remaining\rCompleted 98.5 KiB/122.2 KiB (804.1 KiB/s) with 4 file(s) remaining\rupload: outputs/Evans2004.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/outputs/Evans2004.sedml/plot_2_task1.pdf\nCompleted 98.5 KiB/122.2 KiB (804.1 KiB/s) with 3 file(s) remaining\rCompleted 110.4 KiB/122.2 KiB (838.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/outputs/plots.zip\nCompleted 110.4 KiB/122.2 KiB (838.5 KiB/s) with 2 file(s) remaining\rCompleted 113.1 KiB/122.2 KiB (812.1 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/rawLog.txt\nCompleted 113.1 KiB/122.2 KiB (812.1 KiB/s) with 1 file(s) remaining\rCompleted 122.2 KiB/122.2 KiB (761.1 KiB/s) with 1 file(s) remaining\rupload: outputs/Evans2004.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/outputs/Evans2004.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Evans2004-biopax2.owl  \n  inflating: contents/Evans2004-biopax3.owl  \n  inflating: contents/Evans2004-matlab.m  \n  inflating: contents/Evans2004-octave.m  \n  inflating: contents/Evans2004.cps  \n  inflating: contents/Evans2004.ode  \n  inflating: contents/Evans2004.sedml  \n  inflating: contents/Evans2004.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/fig4_left_extracellular.png  \n  inflating: contents/fig4_right_intracellular.png  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 9.8 KiB/165.0 KiB (125.0 KiB/s) with 14 file(s) remaining\rupload: contents/Evans2004-biopax3.owl to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004-biopax3.owl\nCompleted 9.8 KiB/165.0 KiB (125.0 KiB/s) with 13 file(s) remaining\rCompleted 14.2 KiB/165.0 KiB (120.2 KiB/s) with 13 file(s) remaining\rupload: contents/Evans2004-matlab.m to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004-matlab.m\nCompleted 14.2 KiB/165.0 KiB (120.2 KiB/s) with 12 file(s) remaining\rCompleted 14.4 KiB/165.0 KiB (117.6 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/curation_notes.txt\nCompleted 14.4 KiB/165.0 KiB (117.6 KiB/s) with 11 file(s) remaining\rCompleted 25.6 KiB/165.0 KiB (204.0 KiB/s) with 11 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/curation_image.png\nCompleted 25.6 KiB/165.0 KiB (204.0 KiB/s) with 10 file(s) remaining\rCompleted 34.8 KiB/165.0 KiB (271.9 KiB/s) with 10 file(s) remaining\rupload: contents/Evans2004-biopax2.owl to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004-biopax2.owl\nCompleted 34.8 KiB/165.0 KiB (271.9 KiB/s) with 9 file(s) remaining\rCompleted 39.3 KiB/165.0 KiB (291.0 KiB/s) with 9 file(s) remaining\rupload: contents/Evans2004-octave.m to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004-octave.m\nCompleted 39.3 KiB/165.0 KiB (291.0 KiB/s) with 8 file(s) remaining\rCompleted 50.4 KiB/165.0 KiB (370.1 KiB/s) with 8 file(s) remaining\rupload: contents/fig4_left_extracellular.png to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/fig4_left_extracellular.png\nCompleted 50.4 KiB/165.0 KiB (370.1 KiB/s) with 7 file(s) remaining\rCompleted 63.3 KiB/165.0 KiB (460.3 KiB/s) with 7 file(s) remaining\rupload: contents/Evans2004.sedml to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004.sedml\nCompleted 63.3 KiB/165.0 KiB (460.3 KiB/s) with 6 file(s) remaining\rCompleted 65.6 KiB/165.0 KiB (418.2 KiB/s) with 6 file(s) remaining\rupload: contents/Evans2004.ode to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004.ode\nCompleted 65.6 KiB/165.0 KiB (418.2 KiB/s) with 5 file(s) remaining\rCompleted 99.6 KiB/165.0 KiB (619.0 KiB/s) with 5 file(s) remaining\rupload: contents/Evans2004.xml to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004.xml\nCompleted 99.6 KiB/165.0 KiB (619.0 KiB/s) with 4 file(s) remaining\rCompleted 149.0 KiB/165.0 KiB (833.8 KiB/s) with 4 file(s) remaining\rupload: contents/Evans2004.cps to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/Evans2004.cps\nCompleted 149.0 KiB/165.0 KiB (833.8 KiB/s) with 3 file(s) remaining\rCompleted 150.6 KiB/165.0 KiB (796.0 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/metadata.rdf\nCompleted 150.6 KiB/165.0 KiB (796.0 KiB/s) with 2 file(s) remaining\rCompleted 152.1 KiB/165.0 KiB (769.1 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/manifest.xml\nCompleted 152.1 KiB/165.0 KiB (769.1 KiB/s) with 1 file(s) remaining\rCompleted 165.0 KiB/165.0 KiB (802.6 KiB/s) with 1 file(s) remaining\rupload: contents/fig4_right_intracellular.png to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/contents/fig4_right_intracellular.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (109.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ede49c0d898ffdf9c0c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Evans2004.sedml\ncreating dataset /Evans2004.sedml/autogen_report_for_task1, shape: (22, 1001), type: float64\ndataset created, uuid: d-8cf824d8-0e917f85-c285-008906-62576e, chunk_size: (22, 1001)\ncreating dataset /Evans2004.sedml/plot_1_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-8cf824d8-0e917f85-7bf4-22192d-778363, chunk_size: (3, 1001)\ncreating dataset /Evans2004.sedml/plot_2_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-8cf824d8-0e917f85-2911-9485fb-2930fa, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /Evans2004.sedml\ncreating attribute uri in /Evans2004.sedml\ncreating attribute _type in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute uri in /Evans2004.sedml/autogen_report_for_task1\ncreating attribute _type in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlId in /Evans2004.sedml/plot_1_task1\ncreating attribute sedmlName in /Evans2004.sedml/plot_1_task1\ncreating attribute uri in /Evans2004.sedml/plot_1_task1\ncreating attribute _type in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlId in /Evans2004.sedml/plot_2_task1\ncreating attribute sedmlName in /Evans2004.sedml/plot_2_task1\ncreating attribute uri in /Evans2004.sedml/plot_2_task1\ncreate_links: /\ngot link: Evans2004.sedml\ncreate_links: /Evans2004.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Evans2004.sedml/autogen_report_for_task1 to tgt: /Evans2004.sedml/autogen_report_for_task1, shape: (22, 1001), type: float64\niterating over chunks for /Evans2004.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 22, 1), slice(0, 1001, 1))\ndone with dataload for /Evans2004.sedml/autogen_report_for_task1\nwrite_dataset src: /Evans2004.sedml/plot_1_task1 to tgt: /Evans2004.sedml/plot_1_task1, shape: (3, 1001), type: float64\niterating over chunks for /Evans2004.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Evans2004.sedml/plot_1_task1\nwrite_dataset src: /Evans2004.sedml/plot_2_task1 to tgt: /Evans2004.sedml/plot_2_task1, shape: (3, 1001), type: float64\niterating over chunks for /Evans2004.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /Evans2004.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711ede49c0d898ffdf9c0c\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.322376,"sedDocuments":[{"location":"Evans2004.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  Evans2004.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 22 data sets\r\n    Plots (2):\r\n      plot_1_task1: 2 curves\r\n      plot_2_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Evans2004.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":0.932822,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.106767,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.309649,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.174873,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"},{"id":"p2_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.177346,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H_m","status":"SUCCEEDED"},{"id":"autogen_task1_L_m","status":"SUCCEEDED"},{"id":"autogen_task1_H_c","status":"SUCCEEDED"},{"id":"autogen_task1_L_c","status":"SUCCEEDED"},{"id":"autogen_task1_L_n","status":"SUCCEEDED"},{"id":"autogen_task1_k_0_m","status":"SUCCEEDED"},{"id":"autogen_task1_k_i","status":"SUCCEEDED"},{"id":"autogen_task1_k_e","status":"SUCCEEDED"},{"id":"autogen_task1_k_o_c","status":"SUCCEEDED"},{"id":"autogen_task1_k_c_c","status":"SUCCEEDED"},{"id":"autogen_task1_k_d","status":"SUCCEEDED"},{"id":"autogen_task1_k_c_m","status":"SUCCEEDED"},{"id":"autogen_task1_k_b","status":"SUCCEEDED"},{"id":"autogen_task1_B_T","status":"SUCCEEDED"},{"id":"autogen_task1_v_1","status":"SUCCEEDED"},{"id":"autogen_task1_v_2","status":"SUCCEEDED"},{"id":"autogen_task1_V_m","status":"SUCCEEDED"},{"id":"autogen_task1_V_c","status":"SUCCEEDED"},{"id":"autogen_task1_V_n","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_human_lymphoma_cells","status":"SUCCEEDED"}]}]}]}