{"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    431      0 --:--:-- --:--:-- --:--:--   433\n\r100  226k  100  226k    0     0   509k      0 --:--:-- --:--:-- --:--:--  509k\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 (25.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/rawLog.txt\nCompleted 4.7 KiB/4.7 KiB (76.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000145_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000145_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/262.1 KiB (4.5 MiB/s) with 1 file(s) remaining\rCompleted 262.1 KiB/262.1 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/outputs/reports.h5\nCompleted 246.0 KiB/269.7 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/output.zip\nCompleted 246.0 KiB/269.7 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 254.5 KiB/269.7 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/outputs/plots.zip\nCompleted 254.5 KiB/269.7 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 267.1 KiB/269.7 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000145_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/outputs/BIOMD0000000145_url.sedml/autogen_plot_for_task1.pdf\nCompleted 267.1 KiB/269.7 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 269.7 KiB/269.7 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000145-biopax2.owl  \n  inflating: contents/BIOMD0000000145-biopax3.owl  \n  inflating: contents/BIOMD0000000145-matlab.m  \n  inflating: contents/BIOMD0000000145-octave.m  \n  inflating: contents/BIOMD0000000145.m  \n  inflating: contents/BIOMD0000000145.ode  \n  inflating: contents/BIOMD0000000145.pdf  \n  inflating: contents/BIOMD0000000145.png  \n  inflating: contents/BIOMD0000000145.svg  \n  inflating: contents/BIOMD0000000145_url.sedml  \n  inflating: contents/BIOMD0000000145_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 23.7 KiB/407.0 KiB (323.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000145-biopax3.owl to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145-biopax3.owl\nCompleted 23.7 KiB/407.0 KiB (323.1 KiB/s) with 14 file(s) remaining\rCompleted 66.4 KiB/407.0 KiB (506.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000145.png to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145.png\nCompleted 66.4 KiB/407.0 KiB (506.7 KiB/s) with 13 file(s) remaining\rCompleted 85.6 KiB/407.0 KiB (606.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000145.svg to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145.svg\nCompleted 85.6 KiB/407.0 KiB (606.1 KiB/s) with 12 file(s) remaining\rCompleted 103.1 KiB/407.0 KiB (719.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000145-biopax2.owl to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145-biopax2.owl\nCompleted 103.1 KiB/407.0 KiB (719.2 KiB/s) with 11 file(s) remaining\rCompleted 109.9 KiB/407.0 KiB (753.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000145-matlab.m to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145-matlab.m\nCompleted 109.9 KiB/407.0 KiB (753.1 KiB/s) with 10 file(s) remaining\rCompleted 114.5 KiB/407.0 KiB (773.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000145.ode to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145.ode\nCompleted 114.5 KiB/407.0 KiB (773.6 KiB/s) with 9 file(s) remaining\rCompleted 121.2 KiB/407.0 KiB (760.3 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000145-octave.m to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145-octave.m\nCompleted 121.2 KiB/407.0 KiB (760.3 KiB/s) with 8 file(s) remaining\rCompleted 123.0 KiB/407.0 KiB (766.0 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/manifest.xml\nCompleted 123.0 KiB/407.0 KiB (766.0 KiB/s) with 7 file(s) remaining\rCompleted 299.6 KiB/407.0 KiB (1.6 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000145.pdf to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145.pdf\nCompleted 299.6 KiB/407.0 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 306.3 KiB/407.0 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000145.m to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145.m\nCompleted 306.3 KiB/407.0 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 335.6 KiB/407.0 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000145_url.xml to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145_url.xml\nCompleted 335.6 KiB/407.0 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 340.6 KiB/407.0 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/metadata.rdf\nCompleted 340.6 KiB/407.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 367.9 KiB/407.0 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000145_url.sedml to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/BIOMD0000000145_url.sedml\nCompleted 367.9 KiB/407.0 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 368.1 KiB/407.0 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/curation_notes.txt\nCompleted 368.1 KiB/407.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 407.0 KiB/407.0 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (124.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108cd0dcacb55678b69e7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000145_url.sedml\ncreating dataset /BIOMD0000000145_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-827005ca-597b7c7c-e5eb-047b69-13a30d, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000145_url.sedml/autogen_report_for_task1, shape: (53, 1001), type: float64\ndataset created, uuid: d-827005ca-597b7c7c-a77e-d55006-052b8b, chunk_size: (53, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000145_url.sedml\ncreating attribute uri in /BIOMD0000000145_url.sedml\ncreating attribute _type in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000145_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000145_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000145_url.sedml\ncreate_links: /BIOMD0000000145_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000145_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000145_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000145_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000145_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000145_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000145_url.sedml/autogen_report_for_task1, shape: (53, 1001), type: float64\niterating over chunks for /BIOMD0000000145_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 53, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000145_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108cd0dcacb55678b69e7\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 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.\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.\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":1.728354,"sedDocuments":[{"location":"BIOMD0000000145_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  BIOMD0000000145_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 53 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000145_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":1.28615,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.18849,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.446215,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Galpha_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_APLC","status":"SUCCEEDED"},{"id":"autogen_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_Cyt","status":"SUCCEEDED"},{"id":"autogen_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_task1_DG","status":"SUCCEEDED"},{"id":"autogen_task1_Raplc","status":"SUCCEEDED"},{"id":"autogen_task1_Kp","status":"SUCCEEDED"},{"id":"autogen_task1_Rpkc","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_Kr","status":"SUCCEEDED"},{"id":"autogen_task1_Rgalpha_gtp","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_Kg","status":"SUCCEEDED"},{"id":"autogen_task1_Rdg","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_Rip3","status":"SUCCEEDED"},{"id":"autogen_task1_Ks","status":"SUCCEEDED"},{"id":"autogen_task1_Rcyt1","status":"SUCCEEDED"},{"id":"autogen_task1_Kc1","status":"SUCCEEDED"},{"id":"autogen_task1_Rcyt2","status":"SUCCEEDED"},{"id":"autogen_task1_Kc2","status":"SUCCEEDED"},{"id":"autogen_task1_Rer","status":"SUCCEEDED"},{"id":"autogen_task1_w","status":"SUCCEEDED"},{"id":"autogen_task1_Ker","status":"SUCCEEDED"},{"id":"autogen_task1_Cplc_total","status":"SUCCEEDED"},{"id":"autogen_task1_k0","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_Cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_ER","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.48885,"curves":[{"id":"autogen_curve_task1_Galpha_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APLC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_Cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DG","status":"SUCCEEDED"}]}]}]}