{"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    427      0 --:--:-- --:--:-- --:--:--   427\n\r100  301k  100  301k    0     0   681k      0 --:--:-- --:--:-- --:--:--  681k\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 (23.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (52.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000647.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000647.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 54%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 48.0 KiB/48.0 KiB (573.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/outputs/reports.h5\nCompleted 33.0 KiB/55.6 KiB (426.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/output.zip\nCompleted 33.0 KiB/55.6 KiB (426.9 KiB/s) with 3 file(s) remaining\rCompleted 44.8 KiB/55.6 KiB (411.1 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000647.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/outputs/BIOMD0000000647.sedml/plot_1_task1.pdf\nCompleted 44.8 KiB/55.6 KiB (411.1 KiB/s) with 2 file(s) remaining\rCompleted 53.0 KiB/55.6 KiB (425.5 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/outputs/plots.zip\nCompleted 53.0 KiB/55.6 KiB (425.5 KiB/s) with 1 file(s) remaining\rCompleted 55.6 KiB/55.6 KiB (441.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000647-biopax2.owl  \n  inflating: contents/BIOMD0000000647-biopax3.owl  \n  inflating: contents/BIOMD0000000647-matlab.m  \n  inflating: contents/BIOMD0000000647-octave.m  \n  inflating: contents/BIOMD0000000647.cps  \n  inflating: contents/BIOMD0000000647.m  \n  inflating: contents/BIOMD0000000647.ode  \n  inflating: contents/BIOMD0000000647.pdf  \n  inflating: contents/BIOMD0000000647.png  \n  inflating: contents/BIOMD0000000647.sci  \n  inflating: contents/BIOMD0000000647.sedml  \n  inflating: contents/BIOMD0000000647.svg  \n  inflating: contents/BIOMD0000000647.vcml  \n  inflating: contents/BIOMD0000000647_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 44.5 KiB/~623.3 KiB (575.4 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000647-biopax3.owl to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647-biopax3.owl\nCompleted 44.5 KiB/~623.3 KiB (575.4 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 52.8 KiB/662.6 KiB (471.3 KiB/s) with 17 file(s) remaining                   \rupload: contents/BIOMD0000000647-matlab.m to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647-matlab.m\nCompleted 52.8 KiB/662.6 KiB (471.3 KiB/s) with 16 file(s) remaining\rCompleted 61.2 KiB/662.6 KiB (533.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000647-octave.m to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647-octave.m\nCompleted 61.2 KiB/662.6 KiB (533.7 KiB/s) with 15 file(s) remaining\rCompleted 87.5 KiB/662.6 KiB (747.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000647-biopax2.owl to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647-biopax2.owl\nCompleted 87.5 KiB/662.6 KiB (747.4 KiB/s) with 14 file(s) remaining\rCompleted 141.5 KiB/662.6 KiB (992.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000647_url.xml to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647_url.xml\nCompleted 141.5 KiB/662.6 KiB (992.4 KiB/s) with 13 file(s) remaining\rCompleted 145.3 KiB/662.6 KiB (993.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000647.sci to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.sci\nCompleted 145.3 KiB/662.6 KiB (993.0 KiB/s) with 12 file(s) remaining\rCompleted 167.0 KiB/662.6 KiB (1.0 MiB/s) with 12 file(s) remaining  \rCompleted 247.9 KiB/662.6 KiB (1.5 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000647.png to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.png\nCompleted 247.9 KiB/662.6 KiB (1.5 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000647.sedml to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.sedml\nCompleted 247.9 KiB/662.6 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 248.0 KiB/662.6 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/curation_notes.txt\nCompleted 248.0 KiB/662.6 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 281.5 KiB/662.6 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000647.svg to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.svg\nCompleted 281.5 KiB/662.6 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 283.6 KiB/662.6 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/manifest.xml\nCompleted 283.6 KiB/662.6 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 287.7 KiB/662.6 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/metadata.rdf\nCompleted 287.7 KiB/662.6 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 372.4 KiB/662.6 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000647.vcml to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.vcml\nCompleted 372.4 KiB/662.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 377.2 KiB/662.6 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000647.ode to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.ode\nCompleted 377.2 KiB/662.6 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 410.3 KiB/662.6 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/curation_image.jpeg\nCompleted 410.3 KiB/662.6 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 418.7 KiB/662.6 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000647.m to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.m\nCompleted 418.7 KiB/662.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 588.7 KiB/662.6 KiB (2.5 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000647.pdf to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.pdf\nCompleted 588.7 KiB/662.6 KiB (2.5 MiB/s) with 1 file(s) remaining\rCompleted 662.6 KiB/662.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000647.cps to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/contents/BIOMD0000000647.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (139.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711bb049c0d898ffdf1642/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000647.sedml\ncreating dataset /BIOMD0000000647.sedml/autogen_report_for_task1, shape: (35, 101), type: float64\ndataset created, uuid: d-5b476b05-0bdadc67-f2e3-c9c2b9-9e14ab, chunk_size: (35, 101)\ncreating dataset /BIOMD0000000647.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-5b476b05-0bdadc67-7432-e589f2-a3e1cd, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /BIOMD0000000647.sedml\ncreating attribute uri in /BIOMD0000000647.sedml\ncreating attribute _type in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000647.sedml/autogen_report_for_task1\ncreating attribute _type in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlId in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute sedmlName in /BIOMD0000000647.sedml/plot_1_task1\ncreating attribute uri in /BIOMD0000000647.sedml/plot_1_task1\ncreate_links: /\ngot link: BIOMD0000000647.sedml\ncreate_links: /BIOMD0000000647.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /BIOMD0000000647.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000647.sedml/autogen_report_for_task1, shape: (35, 101), type: float64\niterating over chunks for /BIOMD0000000647.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 101, 1))\ndone with dataload for /BIOMD0000000647.sedml/autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000647.sedml/plot_1_task1 to tgt: /BIOMD0000000647.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /BIOMD0000000647.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /BIOMD0000000647.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711bb049c0d898ffdf1642\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.\nRetrieve 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 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":1.231123,"sedDocuments":[{"location":"BIOMD0000000647.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  BIOMD0000000647.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000647.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":0.759196,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.14847,"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":0.368656,"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":0.092501,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RKIP","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_ERKPP","status":"SUCCEEDED"},{"id":"autogen_task1_ERK","status":"SUCCEEDED"},{"id":"autogen_task1_RKIPP","status":"SUCCEEDED"},{"id":"autogen_task1_MEKPP","status":"SUCCEEDED"},{"id":"autogen_task1_MEKPP_ERK","status":"SUCCEEDED"},{"id":"autogen_task1_ERKPP","status":"SUCCEEDED"},{"id":"autogen_task1_RP","status":"SUCCEEDED"},{"id":"autogen_task1_RKIPP_RP","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_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_complex_disassembly","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_ERKPP_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_ERKPP_complex_disassembly__ERK_phosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_Raf1_RKIP_ERKPP_complex_disassembly__RKIP_phosphorylation","status":"SUCCEEDED"},{"id":"autogen_task1_MEKPP_ERK_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_MEKPP_ERK_complex_disassembly__ERK_unphosphorylated","status":"SUCCEEDED"},{"id":"autogen_task1_MEKPP_ERK_complex_disassembly__ERK_phosphorylated","status":"SUCCEEDED"},{"id":"autogen_task1_RKIPP_RP_comlex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_RKIPP_RP_complex_disassembly__phosphorylated_RKIP","status":"SUCCEEDED"},{"id":"autogen_task1_RKIPP_RP_complex_disassembly__unphosphorylated_RKIP","status":"SUCCEEDED"}]}]}]}