{"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    413      0 --:--:-- --:--:-- --:--:--   414\n\r  0  223k    0   581    0     0   1350      0  0:02:49 --:--:--  0:02:49  1350\r100  223k  100  223k    0     0   492k      0 --:--:-- --:--:-- --:--:-- 9698k\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 (14.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/rawLog.txt\nCompleted 4.8 KiB/4.8 KiB (50.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000069_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000069_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 245.6 KiB/245.6 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/outputs/reports.h5\nCompleted 230.8 KiB/256.5 KiB (2.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/output.zip\nCompleted 230.8 KiB/256.5 KiB (2.5 MiB/s) with 3 file(s) remaining\rCompleted 240.2 KiB/256.5 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/outputs/plots.zip\nCompleted 240.2 KiB/256.5 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 253.8 KiB/256.5 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000069_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/outputs/BIOMD0000000069_url.sedml/autogen_plot_for_task1.pdf\nCompleted 253.8 KiB/256.5 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 256.5 KiB/256.5 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000069-biopax2.owl  \n  inflating: contents/BIOMD0000000069-biopax3.owl  \n  inflating: contents/BIOMD0000000069-matlab.m  \n  inflating: contents/BIOMD0000000069-octave.m  \n  inflating: contents/BIOMD0000000069.m  \n  inflating: contents/BIOMD0000000069.ode  \n  inflating: contents/BIOMD0000000069.pdf  \n  inflating: contents/BIOMD0000000069.png  \n  inflating: contents/BIOMD0000000069.sci  \n  inflating: contents/BIOMD0000000069.svg  \n  inflating: contents/BIOMD0000000069.vcml  \n  inflating: contents/BIOMD0000000069_url.sedml  \n  inflating: contents/BIOMD0000000069_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 22.5 KiB/416.9 KiB (322.5 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000069-biopax3.owl to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069-biopax3.owl\nCompleted 22.5 KiB/416.9 KiB (322.5 KiB/s) with 16 file(s) remaining\rCompleted 28.6 KiB/416.9 KiB (276.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000069-matlab.m to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069-matlab.m\nCompleted 28.6 KiB/416.9 KiB (276.5 KiB/s) with 15 file(s) remaining\rCompleted 32.7 KiB/416.9 KiB (263.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000069.sci to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.sci\nCompleted 32.7 KiB/416.9 KiB (263.6 KiB/s) with 14 file(s) remaining\rCompleted 38.8 KiB/416.9 KiB (309.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000069-octave.m to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069-octave.m\nCompleted 38.8 KiB/416.9 KiB (309.4 KiB/s) with 13 file(s) remaining\rCompleted 54.4 KiB/416.9 KiB (419.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000069-biopax2.owl to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069-biopax2.owl\nCompleted 54.4 KiB/416.9 KiB (419.1 KiB/s) with 12 file(s) remaining\rCompleted 96.7 KiB/416.9 KiB (603.1 KiB/s) with 12 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/curation_image.png\nCompleted 96.7 KiB/416.9 KiB (603.1 KiB/s) with 11 file(s) remaining\rCompleted 118.8 KiB/416.9 KiB (696.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000069_url.sedml to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069_url.sedml\nCompleted 118.8 KiB/416.9 KiB (696.8 KiB/s) with 10 file(s) remaining\rCompleted 120.3 KiB/416.9 KiB (662.2 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/metadata.rdf\nCompleted 120.3 KiB/416.9 KiB (662.2 KiB/s) with 9 file(s) remaining\rCompleted 141.9 KiB/416.9 KiB (754.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000069.svg to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.svg\nCompleted 141.9 KiB/416.9 KiB (754.9 KiB/s) with 8 file(s) remaining\rCompleted 142.1 KiB/416.9 KiB (735.6 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/curation_notes.txt\nCompleted 142.1 KiB/416.9 KiB (735.6 KiB/s) with 7 file(s) remaining\rCompleted 144.0 KiB/416.9 KiB (732.8 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/manifest.xml\nCompleted 144.0 KiB/416.9 KiB (732.8 KiB/s) with 6 file(s) remaining\rCompleted 305.7 KiB/416.9 KiB (1.5 MiB/s) with 6 file(s) remaining  \rupload: contents/BIOMD0000000069.pdf to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.pdf\nCompleted 305.7 KiB/416.9 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 338.2 KiB/416.9 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000069.vcml to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.vcml\nCompleted 338.2 KiB/416.9 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 386.0 KiB/416.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000069.png to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.png\nCompleted 386.0 KiB/416.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 406.8 KiB/416.9 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000069_url.xml to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069_url.xml\nCompleted 406.8 KiB/416.9 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 412.9 KiB/416.9 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000069.m to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.m\nCompleted 412.9 KiB/416.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 416.9 KiB/416.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000069.ode to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/contents/BIOMD0000000069.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (127.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107d60dcacb55678b4bda/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000069_url.sedml\ncreating dataset /BIOMD0000000069_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-7beba075-3f37c8b6-b39a-ae9ce0-781962, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000069_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\ndataset created, uuid: d-7beba075-3f37c8b6-6e1b-f325d3-c0d187, chunk_size: (39, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000069_url.sedml\ncreating attribute uri in /BIOMD0000000069_url.sedml\ncreating attribute _type in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000069_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000069_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000069_url.sedml\ncreate_links: /BIOMD0000000069_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000069_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000069_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000069_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000069_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000069_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000069_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\niterating over chunks for /BIOMD0000000069_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 39, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000069_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107d60dcacb55678b4bda\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 and upload the outputs of the simulation run ... 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.796615,"sedDocuments":[{"location":"BIOMD0000000069_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  BIOMD0000000069_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 39 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000069_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":1.291,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.242748,"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":0.314643,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_srci","status":"SUCCEEDED"},{"id":"autogen_task1_srco","status":"SUCCEEDED"},{"id":"autogen_task1_srca","status":"SUCCEEDED"},{"id":"autogen_task1_srcc","status":"SUCCEEDED"},{"id":"autogen_task1_Cbp_P_CSK","status":"SUCCEEDED"},{"id":"autogen_task1_CSK_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_PTP","status":"SUCCEEDED"},{"id":"autogen_task1_PTP_pY789","status":"SUCCEEDED"},{"id":"autogen_task1_Cbp","status":"SUCCEEDED"},{"id":"autogen_task1_Cbp_P","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_kPTP","status":"SUCCEEDED"},{"id":"autogen_task1_kCbp","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_p3","status":"SUCCEEDED"},{"id":"autogen_task1_src_background","status":"SUCCEEDED"},{"id":"autogen_task1_PTP_background","status":"SUCCEEDED"},{"id":"autogen_task1_kCSKon","status":"SUCCEEDED"},{"id":"autogen_task1_kCSKoff","status":"SUCCEEDED"},{"id":"autogen_task1_rho_srca","status":"SUCCEEDED"},{"id":"autogen_task1_rho_srco","status":"SUCCEEDED"},{"id":"autogen_task1_rho_srcc","status":"SUCCEEDED"},{"id":"autogen_task1_Kser","status":"SUCCEEDED"},{"id":"autogen_task1_acsk0","status":"SUCCEEDED"},{"id":"autogen_task1_ptp_activity","status":"SUCCEEDED"},{"id":"autogen_task1_src_activity","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_CSK_translocation","status":"SUCCEEDED"},{"id":"autogen_task1_PTP_phosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_Cbp_phosphorylation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.570798,"curves":[{"id":"autogen_curve_task1_srci","status":"SUCCEEDED"},{"id":"autogen_curve_task1_srco","status":"SUCCEEDED"},{"id":"autogen_curve_task1_srca","status":"SUCCEEDED"},{"id":"autogen_curve_task1_srcc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cbp_P_CSK","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CSK_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PTP_pY789","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cbp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cbp_P","status":"SUCCEEDED"}]}]}]}