{"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    455      0 --:--:-- --:--:-- --:--:--   457\n\r100  148k  100  148k    0     0   334k      0 --:--:-- --:--:-- --:--:--  334k\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 (27.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/rawLog.txt\nCompleted 5.5 KiB/5.5 KiB (75.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/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/BIOMD0000000119_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000119_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 210.3 KiB/210.3 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/outputs/reports.h5\nCompleted 188.0 KiB/209.4 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/output.zip\nCompleted 188.0 KiB/209.4 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 195.5 KiB/209.4 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/outputs/plots.zip\nCompleted 195.5 KiB/209.4 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 206.8 KiB/209.4 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000119_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/outputs/BIOMD0000000119_url.sedml/autogen_plot_for_task1.pdf\nCompleted 206.8 KiB/209.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 209.4 KiB/209.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000119-biopax2.owl  \n  inflating: contents/BIOMD0000000119-biopax3.owl  \n  inflating: contents/BIOMD0000000119-matlab.m  \n  inflating: contents/BIOMD0000000119-octave.m  \n  inflating: contents/BIOMD0000000119.m  \n  inflating: contents/BIOMD0000000119.ode  \n  inflating: contents/BIOMD0000000119.pdf  \n  inflating: contents/BIOMD0000000119.png  \n  inflating: contents/BIOMD0000000119.svg  \n  inflating: contents/BIOMD0000000119_url.sedml  \n  inflating: contents/BIOMD0000000119_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 6.1 KiB/281.3 KiB (86.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000119-biopax3.owl to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119-biopax3.owl\nCompleted 6.1 KiB/281.3 KiB (86.1 KiB/s) with 14 file(s) remaining\rCompleted 15.6 KiB/281.3 KiB (148.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000119-matlab.m to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119-matlab.m\nCompleted 15.6 KiB/281.3 KiB (148.2 KiB/s) with 13 file(s) remaining\rCompleted 21.1 KiB/281.3 KiB (172.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000119-biopax2.owl to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119-biopax2.owl\nCompleted 21.1 KiB/281.3 KiB (172.8 KiB/s) with 12 file(s) remaining\rCompleted 30.5 KiB/281.3 KiB (241.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000119-octave.m to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119-octave.m\nCompleted 30.5 KiB/281.3 KiB (241.9 KiB/s) with 11 file(s) remaining\rCompleted 67.1 KiB/281.3 KiB (472.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000119_url.sedml to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119_url.sedml\nCompleted 67.1 KiB/281.3 KiB (472.3 KiB/s) with 10 file(s) remaining\rCompleted 69.3 KiB/281.3 KiB (449.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000119.svg to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119.svg\nCompleted 69.3 KiB/281.3 KiB (449.8 KiB/s) with 9 file(s) remaining\rCompleted 72.3 KiB/281.3 KiB (463.7 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/metadata.rdf\nCompleted 72.3 KiB/281.3 KiB (463.7 KiB/s) with 8 file(s) remaining\rCompleted 72.4 KiB/281.3 KiB (455.1 KiB/s) with 8 file(s) remaining\rCompleted 74.9 KiB/281.3 KiB (465.4 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/curation_image.png\nCompleted 74.9 KiB/281.3 KiB (465.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/curation_notes.txt\nCompleted 74.9 KiB/281.3 KiB (465.4 KiB/s) with 6 file(s) remaining\rCompleted 99.2 KiB/281.3 KiB (581.8 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000119_url.xml to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119_url.xml\nCompleted 99.2 KiB/281.3 KiB (581.8 KiB/s) with 5 file(s) remaining\rCompleted 101.0 KiB/281.3 KiB (583.4 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/manifest.xml\nCompleted 101.0 KiB/281.3 KiB (583.4 KiB/s) with 4 file(s) remaining\rCompleted 110.4 KiB/281.3 KiB (605.4 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000119.m to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119.m\nCompleted 110.4 KiB/281.3 KiB (605.4 KiB/s) with 3 file(s) remaining\rCompleted 113.8 KiB/281.3 KiB (600.9 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000119.png to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119.png\nCompleted 113.8 KiB/281.3 KiB (600.9 KiB/s) with 2 file(s) remaining\rCompleted 274.4 KiB/281.3 KiB (1.4 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000119.pdf to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119.pdf\nCompleted 274.4 KiB/281.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 281.3 KiB/281.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000119.ode to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/contents/BIOMD0000000119.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (102.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108820dcacb55678b5fbf/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000119_url.sedml\ncreating dataset /BIOMD0000000119_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-de681118-0ca1c1fb-3cf1-f2dbbe-e649e2, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000119_url.sedml/autogen_report_for_task1, shape: (73, 1001), type: float64\ndataset created, uuid: d-de681118-0ca1c1fb-7c9b-4cce43-bad037, chunk_size: (73, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000119_url.sedml\ncreating attribute uri in /BIOMD0000000119_url.sedml\ncreating attribute _type in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000119_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000119_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000119_url.sedml\ncreate_links: /BIOMD0000000119_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000119_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000119_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000119_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000119_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000119_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000119_url.sedml/autogen_report_for_task1, shape: (73, 1001), type: float64\niterating over chunks for /BIOMD0000000119_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 73, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000119_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108820dcacb55678b5fbf\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":22.153789,"sedDocuments":[{"location":"BIOMD0000000119_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  BIOMD0000000119_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 73 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000119_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":21.769729,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":20.866457,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.527834,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_Cm","status":"SUCCEEDED"},{"id":"autogen_task1_pms","status":"SUCCEEDED"},{"id":"autogen_task1_pns","status":"SUCCEEDED"},{"id":"autogen_task1_VNa","status":"SUCCEEDED"},{"id":"autogen_task1_t_tauh","status":"SUCCEEDED"},{"id":"autogen_task1_t_taun","status":"SUCCEEDED"},{"id":"autogen_task1_thetaa","status":"SUCCEEDED"},{"id":"autogen_task1_sigmaa","status":"SUCCEEDED"},{"id":"autogen_task1_thetab","status":"SUCCEEDED"},{"id":"autogen_task1_sigmab","status":"SUCCEEDED"},{"id":"autogen_task1_tauBs","status":"SUCCEEDED"},{"id":"autogen_task1_sigmam","status":"SUCCEEDED"},{"id":"autogen_task1_sigmah","status":"SUCCEEDED"},{"id":"autogen_task1_sigman","status":"SUCCEEDED"},{"id":"autogen_task1_sigmaz","status":"SUCCEEDED"},{"id":"autogen_task1_gNa","status":"SUCCEEDED"},{"id":"autogen_task1_gKdr","status":"SUCCEEDED"},{"id":"autogen_task1_gL","status":"SUCCEEDED"},{"id":"autogen_task1_Iapp","status":"SUCCEEDED"},{"id":"autogen_task1_gA","status":"SUCCEEDED"},{"id":"autogen_task1_gNaP","status":"SUCCEEDED"},{"id":"autogen_task1_gZ","status":"SUCCEEDED"},{"id":"autogen_task1_thetaz","status":"SUCCEEDED"},{"id":"autogen_task1_tauZs","status":"SUCCEEDED"},{"id":"autogen_task1_phi","status":"SUCCEEDED"},{"id":"autogen_task1_thetah","status":"SUCCEEDED"},{"id":"autogen_task1_thetam","status":"SUCCEEDED"},{"id":"autogen_task1_thetan","status":"SUCCEEDED"},{"id":"autogen_task1_thetap","status":"SUCCEEDED"},{"id":"autogen_task1_sigmap","status":"SUCCEEDED"},{"id":"autogen_task1_VK","status":"SUCCEEDED"},{"id":"autogen_task1_VL","status":"SUCCEEDED"},{"id":"autogen_task1_INa","status":"SUCCEEDED"},{"id":"autogen_task1_INaP","status":"SUCCEEDED"},{"id":"autogen_task1_IKdr","status":"SUCCEEDED"},{"id":"autogen_task1_IA","status":"SUCCEEDED"},{"id":"autogen_task1_Iz","status":"SUCCEEDED"},{"id":"autogen_task1_Minfs","status":"SUCCEEDED"},{"id":"autogen_task1_Pinfs","status":"SUCCEEDED"},{"id":"autogen_task1_Ainfs","status":"SUCCEEDED"},{"id":"autogen_task1_zzs","status":"SUCCEEDED"},{"id":"autogen_task1_bbs","status":"SUCCEEDED"},{"id":"autogen_task1_nns","status":"SUCCEEDED"},{"id":"autogen_task1_hhs","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_rrs","status":"SUCCEEDED"},{"id":"autogen_task1_ccs","status":"SUCCEEDED"},{"id":"autogen_task1_qqs","status":"SUCCEEDED"},{"id":"autogen_task1_thetar","status":"SUCCEEDED"},{"id":"autogen_task1_VCa","status":"SUCCEEDED"},{"id":"autogen_task1_sigmar","status":"SUCCEEDED"},{"id":"autogen_task1_sigmac","status":"SUCCEEDED"},{"id":"autogen_task1_thetac","status":"SUCCEEDED"},{"id":"autogen_task1_pwrc","status":"SUCCEEDED"},{"id":"autogen_task1_pwrq","status":"SUCCEEDED"},{"id":"autogen_task1_gCa","status":"SUCCEEDED"},{"id":"autogen_task1_gKCa","status":"SUCCEEDED"},{"id":"autogen_task1_gKAHP","status":"SUCCEEDED"},{"id":"autogen_task1_tauRs","status":"SUCCEEDED"},{"id":"autogen_task1_aq","status":"SUCCEEDED"},{"id":"autogen_task1_ac","status":"SUCCEEDED"},{"id":"autogen_task1_tauq","status":"SUCCEEDED"},{"id":"autogen_task1_tauCa","status":"SUCCEEDED"},{"id":"autogen_task1_uuCa","status":"SUCCEEDED"},{"id":"autogen_task1_tauKc","status":"SUCCEEDED"},{"id":"autogen_task1_mKCa","status":"SUCCEEDED"},{"id":"autogen_task1_ICa","status":"SUCCEEDED"},{"id":"autogen_task1_IAHP","status":"SUCCEEDED"},{"id":"autogen_task1_IKC","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000001","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.198267,"curves":[{"id":"autogen_curve_task1_Ca","status":"SUCCEEDED"}]}]}]}