{"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    462      0 --:--:-- --:--:-- --:--:--   461\n\r100  216k  100  216k    0     0   507k      0 --:--:-- --:--:-- --:--:--  507k\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 (16.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (42.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000275_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000275_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 161.3 KiB/161.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/outputs/reports.h5\nCompleted 10.5 KiB/164.5 KiB (90.6 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000275_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/outputs/BIOMD0000000275_url.sedml/autogen_plot_for_task1.pdf\nCompleted 10.5 KiB/164.5 KiB (90.6 KiB/s) with 3 file(s) remaining\rCompleted 154.4 KiB/164.5 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/output.zip\nCompleted 154.4 KiB/164.5 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 161.8 KiB/164.5 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/outputs/plots.zip\nCompleted 161.8 KiB/164.5 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 164.5 KiB/164.5 KiB (971.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000275-biopax2.owl  \n  inflating: contents/BIOMD0000000275-biopax3.owl  \n  inflating: contents/BIOMD0000000275-matlab.m  \n  inflating: contents/BIOMD0000000275-octave.m  \n  inflating: contents/BIOMD0000000275.m  \n  inflating: contents/BIOMD0000000275.ode  \n  inflating: contents/BIOMD0000000275.pdf  \n  inflating: contents/BIOMD0000000275.png  \n  inflating: contents/BIOMD0000000275.svg  \n  inflating: contents/BIOMD0000000275_url.sedml  \n  inflating: contents/BIOMD0000000275_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 17.4 KiB/379.8 KiB (166.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000275-biopax2.owl to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275-biopax2.owl\nCompleted 17.4 KiB/379.8 KiB (166.2 KiB/s) with 14 file(s) remaining\rCompleted 22.9 KiB/379.8 KiB (160.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000275-octave.m to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275-octave.m\nCompleted 22.9 KiB/379.8 KiB (160.0 KiB/s) with 13 file(s) remaining\rCompleted 28.4 KiB/379.8 KiB (183.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000275-matlab.m to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275-matlab.m\nCompleted 28.4 KiB/379.8 KiB (183.8 KiB/s) with 12 file(s) remaining\rCompleted 69.0 KiB/379.8 KiB (405.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000275.png to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275.png\nCompleted 69.0 KiB/379.8 KiB (405.6 KiB/s) with 11 file(s) remaining\rCompleted 87.7 KiB/379.8 KiB (504.6 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000275.svg to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275.svg\nCompleted 87.7 KiB/379.8 KiB (504.6 KiB/s) with 10 file(s) remaining\rCompleted 92.0 KiB/379.8 KiB (483.4 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/metadata.rdf\nCompleted 92.0 KiB/379.8 KiB (483.4 KiB/s) with 9 file(s) remaining\rCompleted 113.3 KiB/379.8 KiB (573.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000275_url.sedml to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275_url.sedml\nCompleted 113.3 KiB/379.8 KiB (573.4 KiB/s) with 8 file(s) remaining\rCompleted 138.8 KiB/379.8 KiB (693.9 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/curation_image.png\nCompleted 138.8 KiB/379.8 KiB (693.9 KiB/s) with 7 file(s) remaining\rCompleted 165.2 KiB/379.8 KiB (805.2 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000275_url.xml to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275_url.xml\nCompleted 165.2 KiB/379.8 KiB (805.2 KiB/s) with 6 file(s) remaining\rCompleted 165.5 KiB/379.8 KiB (802.6 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/curation_notes.txt\nCompleted 165.5 KiB/379.8 KiB (802.6 KiB/s) with 5 file(s) remaining\rCompleted 167.2 KiB/379.8 KiB (799.7 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/manifest.xml\nCompleted 167.2 KiB/379.8 KiB (799.7 KiB/s) with 4 file(s) remaining\rCompleted 349.0 KiB/379.8 KiB (1.4 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000275.pdf to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275.pdf\nCompleted 349.0 KiB/379.8 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 370.9 KiB/379.8 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000275-biopax3.owl to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275-biopax3.owl\nCompleted 370.9 KiB/379.8 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 374.3 KiB/379.8 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000275.ode to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275.ode\nCompleted 374.3 KiB/379.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 379.8 KiB/379.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000275.m to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/contents/BIOMD0000000275.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (73.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f134da4ff2037f59be5f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000275_url.sedml\ncreating dataset /BIOMD0000000275_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-9e57eada-813b6881-4584-1b35c0-f5652a, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000275_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\ndataset created, uuid: d-9e57eada-813b6881-0efe-36fca5-ee72a0, chunk_size: (40, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000275_url.sedml\ncreating attribute uri in /BIOMD0000000275_url.sedml\ncreating attribute _type in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000275_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000275_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000275_url.sedml\ncreate_links: /BIOMD0000000275_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000275_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000275_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000275_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000275_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000275_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000275_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\niterating over chunks for /BIOMD0000000275_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 40, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000275_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f134da4ff2037f59be5f\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.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.444299,"sedDocuments":[{"location":"BIOMD0000000275_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  BIOMD0000000275_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 40 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000275_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":1.006708,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.20007,"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":0.268366,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RA","status":"SUCCEEDED"},{"id":"autogen_task1_M_C","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_F","status":"SUCCEEDED"},{"id":"autogen_task1_M_F","status":"SUCCEEDED"},{"id":"autogen_task1_vs1","status":"SUCCEEDED"},{"id":"autogen_task1_kd5","status":"SUCCEEDED"},{"id":"autogen_task1_kd1","status":"SUCCEEDED"},{"id":"autogen_task1_V0","status":"SUCCEEDED"},{"id":"autogen_task1_Vsc","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_Ka","status":"SUCCEEDED"},{"id":"autogen_task1_kd3","status":"SUCCEEDED"},{"id":"autogen_task1_ks2","status":"SUCCEEDED"},{"id":"autogen_task1_kd2","status":"SUCCEEDED"},{"id":"autogen_task1_ks3","status":"SUCCEEDED"},{"id":"autogen_task1_Ki","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_kd4","status":"SUCCEEDED"},{"id":"autogen_task1_ks1","status":"SUCCEEDED"},{"id":"autogen_task1_RALDH2_0","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_M_0","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_Kr1","status":"SUCCEEDED"},{"id":"autogen_task1_Kr2","status":"SUCCEEDED"},{"id":"autogen_task1_PSM","status":"SUCCEEDED"},{"id":"autogen_task1_RA_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_RA_decay","status":"SUCCEEDED"},{"id":"autogen_task1_RA_deg_by_Cyp26","status":"SUCCEEDED"},{"id":"autogen_task1_M_C_transcription","status":"SUCCEEDED"},{"id":"autogen_task1_M_C_decay","status":"SUCCEEDED"},{"id":"autogen_task1_C_translation","status":"SUCCEEDED"},{"id":"autogen_task1_C_decay","status":"SUCCEEDED"},{"id":"autogen_task1_FGF_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_FGF_decay","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.39158,"curves":[{"id":"autogen_curve_task1_RA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M_F","status":"SUCCEEDED"}]}]}]}