{"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 --:--:-- --:--:-- --:--:--   431\n\r100  243k  100  243k    0     0   551k      0 --:--:-- --:--:-- --:--:--  551k\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 (26.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/rawLog.txt\nCompleted 5.2 KiB/5.2 KiB (76.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/BIOMD0000000203_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000203_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 160.6 KiB/160.6 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/outputs/reports.h5\nCompleted 143.9 KiB/170.4 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/output.zip\nCompleted 143.9 KiB/170.4 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 146.5 KiB/170.4 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/rawLog.txt\nCompleted 146.5 KiB/170.4 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 160.6 KiB/170.4 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000203_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/outputs/BIOMD0000000203_url.sedml/autogen_plot_for_task1.pdf\nCompleted 160.6 KiB/170.4 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 170.4 KiB/170.4 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000203-biopax2.owl  \n  inflating: contents/BIOMD0000000203-biopax3.owl  \n  inflating: contents/BIOMD0000000203-matlab.m  \n  inflating: contents/BIOMD0000000203-octave.m  \n  inflating: contents/BIOMD0000000203.m  \n  inflating: contents/BIOMD0000000203.ode  \n  inflating: contents/BIOMD0000000203.pdf  \n  inflating: contents/BIOMD0000000203.png  \n  inflating: contents/BIOMD0000000203.svg  \n  inflating: contents/BIOMD0000000203_url.sedml  \n  inflating: contents/BIOMD0000000203_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 19.1 KiB/~451.8 KiB (278.5 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000203-biopax2.owl to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203-biopax2.owl\nCompleted 19.1 KiB/~451.8 KiB (278.5 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 26.4 KiB/457.1 KiB (242.5 KiB/s) with 14 file(s) remaining                   \rupload: contents/BIOMD0000000203-matlab.m to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203-matlab.m\nCompleted 26.4 KiB/457.1 KiB (242.5 KiB/s) with 13 file(s) remaining\rCompleted 33.8 KiB/457.1 KiB (292.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000203-octave.m to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203-octave.m\nCompleted 33.8 KiB/457.1 KiB (292.5 KiB/s) with 12 file(s) remaining\rCompleted 35.5 KiB/457.1 KiB (267.8 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/manifest.xml\nCompleted 35.5 KiB/457.1 KiB (267.8 KiB/s) with 11 file(s) remaining\rCompleted 129.7 KiB/457.1 KiB (949.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000203.png to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203.png\nCompleted 129.7 KiB/457.1 KiB (949.8 KiB/s) with 10 file(s) remaining\rCompleted 156.9 KiB/457.1 KiB (1.1 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000203.svg to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203.svg\nCompleted 156.9 KiB/457.1 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 189.6 KiB/457.1 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000203_url.xml to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203_url.xml\nCompleted 189.6 KiB/457.1 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 200.5 KiB/457.1 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/curation_image.png\nCompleted 200.5 KiB/457.1 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 230.4 KiB/457.1 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000203_url.sedml to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203_url.sedml\nCompleted 230.4 KiB/457.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 258.7 KiB/457.1 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000203-biopax3.owl to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203-biopax3.owl\nCompleted 258.7 KiB/457.1 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 266.1 KiB/457.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000203.m to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203.m\nCompleted 266.1 KiB/457.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 446.2 KiB/457.1 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000203.pdf to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203.pdf\nCompleted 446.2 KiB/457.1 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 451.5 KiB/457.1 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000203.ode to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/BIOMD0000000203.ode\nCompleted 451.5 KiB/457.1 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 451.8 KiB/457.1 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/curation_notes.txt\nCompleted 451.8 KiB/457.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 457.1 KiB/457.1 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (128.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098e49c0d898ffddda8e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000203_url.sedml\ncreating dataset /BIOMD0000000203_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-2c64102a-c0346963-e4cd-759c1a-fcb2ce, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000203_url.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\ndataset created, uuid: d-2c64102a-c0346963-7647-ebc23e-a8ecbd, chunk_size: (56, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000203_url.sedml\ncreating attribute uri in /BIOMD0000000203_url.sedml\ncreating attribute _type in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000203_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000203_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000203_url.sedml\ncreate_links: /BIOMD0000000203_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000203_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000203_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000203_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000203_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000203_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000203_url.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\niterating over chunks for /BIOMD0000000203_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 56, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000203_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471098e49c0d898ffddda8e\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.\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.80454,"sedDocuments":[{"location":"BIOMD0000000203_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  BIOMD0000000203_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 56 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000203_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":1.356313,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.194414,"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":0.445084,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_NANOG_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_SOX2_Gene","status":"SUCCEEDED"},{"id":"autogen_task1_targetGene","status":"SUCCEEDED"},{"id":"autogen_task1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_p53","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4","status":"SUCCEEDED"},{"id":"autogen_task1_SOX2","status":"SUCCEEDED"},{"id":"autogen_task1_NANOG","status":"SUCCEEDED"},{"id":"autogen_task1_OCT4_SOX2","status":"SUCCEEDED"},{"id":"autogen_task1_Protein","status":"SUCCEEDED"},{"id":"autogen_task1_eta1","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_a3","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_b3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma1","status":"SUCCEEDED"},{"id":"autogen_task1_eta5","status":"SUCCEEDED"},{"id":"autogen_task1_e1","status":"SUCCEEDED"},{"id":"autogen_task1_e2","status":"SUCCEEDED"},{"id":"autogen_task1_f2","status":"SUCCEEDED"},{"id":"autogen_task1_f1","status":"SUCCEEDED"},{"id":"autogen_task1_f3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma2","status":"SUCCEEDED"},{"id":"autogen_task1_k1c","status":"SUCCEEDED"},{"id":"autogen_task1_k2c","status":"SUCCEEDED"},{"id":"autogen_task1_k3c","status":"SUCCEEDED"},{"id":"autogen_task1_eta3","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_c3","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_d3","status":"SUCCEEDED"},{"id":"autogen_task1_gamma3","status":"SUCCEEDED"},{"id":"autogen_task1_g1","status":"SUCCEEDED"},{"id":"autogen_task1_eta7","status":"SUCCEEDED"},{"id":"autogen_task1_h1","status":"SUCCEEDED"},{"id":"autogen_task1_h2","status":"SUCCEEDED"},{"id":"autogen_task1_gamma4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_J0","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_J5","status":"SUCCEEDED"},{"id":"autogen_task1_J6","status":"SUCCEEDED"},{"id":"autogen_task1_J7","status":"SUCCEEDED"},{"id":"autogen_task1_J8","status":"SUCCEEDED"},{"id":"autogen_task1_J9","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.563114,"curves":[{"id":"autogen_curve_task1_OCT4_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NANOG_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SOX2_Gene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_targetGene","status":"SUCCEEDED"},{"id":"autogen_curve_task1_degradation","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p53","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OCT4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SOX2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NANOG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OCT4_SOX2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Protein","status":"SUCCEEDED"}]}]}]}