{"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    463      0 --:--:-- --:--:-- --:--:--   464\n\r100  164k  100  164k    0     0   396k      0 --:--:-- --:--:-- --:--:--  396k\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/647108909a62a8be53f762fc/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (75.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000124_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000124_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 236.0 KiB/236.0 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/outputs/reports.h5\nCompleted 209.5 KiB/224.6 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/output.zip\nCompleted 209.5 KiB/224.6 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 214.4 KiB/224.6 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/outputs/plots.zip\nCompleted 214.4 KiB/224.6 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 221.9 KiB/224.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000124_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/outputs/BIOMD0000000124_url.sedml/autogen_plot_for_task1.pdf\nCompleted 221.9 KiB/224.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 224.6 KiB/224.6 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000124-biopax2.owl  \n  inflating: contents/BIOMD0000000124-biopax3.owl  \n  inflating: contents/BIOMD0000000124-matlab.m  \n  inflating: contents/BIOMD0000000124-octave.m  \n  inflating: contents/BIOMD0000000124.m  \n  inflating: contents/BIOMD0000000124.ode  \n  inflating: contents/BIOMD0000000124.pdf  \n  inflating: contents/BIOMD0000000124.png  \n  inflating: contents/BIOMD0000000124.svg  \n  inflating: contents/BIOMD0000000124_url.sedml  \n  inflating: contents/BIOMD0000000124_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 8.5 KiB/314.3 KiB (118.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000124-biopax3.owl to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124-biopax3.owl\nCompleted 8.5 KiB/314.3 KiB (118.9 KiB/s) with 14 file(s) remaining\rCompleted 17.5 KiB/314.3 KiB (167.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000124-matlab.m to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124-matlab.m\nCompleted 17.5 KiB/314.3 KiB (167.1 KiB/s) with 13 file(s) remaining\rCompleted 26.6 KiB/314.3 KiB (217.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000124-octave.m to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124-octave.m\nCompleted 26.6 KiB/314.3 KiB (217.2 KiB/s) with 12 file(s) remaining\rCompleted 30.7 KiB/314.3 KiB (242.0 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/metadata.rdf\nCompleted 30.7 KiB/314.3 KiB (242.0 KiB/s) with 11 file(s) remaining\rCompleted 37.9 KiB/314.3 KiB (294.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000124-biopax2.owl to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124-biopax2.owl\nCompleted 37.9 KiB/314.3 KiB (294.9 KiB/s) with 10 file(s) remaining\rCompleted 41.8 KiB/314.3 KiB (311.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000124.svg to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124.svg\nCompleted 41.8 KiB/314.3 KiB (311.0 KiB/s) with 9 file(s) remaining\rCompleted 73.6 KiB/314.3 KiB (539.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000124_url.sedml to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124_url.sedml\nCompleted 73.6 KiB/314.3 KiB (539.0 KiB/s) with 8 file(s) remaining\rCompleted 108.4 KiB/314.3 KiB (681.5 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000124_url.xml to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124_url.xml\nCompleted 108.4 KiB/314.3 KiB (681.5 KiB/s) with 7 file(s) remaining\rCompleted 108.5 KiB/314.3 KiB (672.7 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/curation_notes.txt\nCompleted 108.5 KiB/314.3 KiB (672.7 KiB/s) with 6 file(s) remaining\rCompleted 120.2 KiB/314.3 KiB (678.1 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/curation_image.png\nCompleted 120.2 KiB/314.3 KiB (678.1 KiB/s) with 5 file(s) remaining\rCompleted 127.1 KiB/314.3 KiB (690.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000124.ode to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124.ode\nCompleted 127.1 KiB/314.3 KiB (690.0 KiB/s) with 4 file(s) remaining\rCompleted 136.2 KiB/314.3 KiB (728.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000124.m to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124.m\nCompleted 136.2 KiB/314.3 KiB (728.0 KiB/s) with 3 file(s) remaining\rCompleted 137.9 KiB/314.3 KiB (726.4 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/manifest.xml\nCompleted 137.9 KiB/314.3 KiB (726.4 KiB/s) with 2 file(s) remaining\rCompleted 301.4 KiB/314.3 KiB (1.5 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000124.pdf to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124.pdf\nCompleted 301.4 KiB/314.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 314.3 KiB/314.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000124.png to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/contents/BIOMD0000000124.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (116.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108909a62a8be53f762fc/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000124_url.sedml\ncreating dataset /BIOMD0000000124_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-b0b49fa9-938eff5d-7a26-8c1338-14cd33, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000124_url.sedml/autogen_report_for_task1, shape: (63, 1001), type: float64\ndataset created, uuid: d-b0b49fa9-938eff5d-a32f-8596a9-ae67ef, chunk_size: (63, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000124_url.sedml\ncreating attribute uri in /BIOMD0000000124_url.sedml\ncreating attribute _type in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000124_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000124_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000124_url.sedml\ncreate_links: /BIOMD0000000124_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000124_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000124_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000124_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000124_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000124_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000124_url.sedml/autogen_report_for_task1, shape: (63, 1001), type: float64\niterating over chunks for /BIOMD0000000124_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 63, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000124_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108909a62a8be53f762fc\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.46584,"sedDocuments":[{"location":"BIOMD0000000124_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  BIOMD0000000124_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 63 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000124_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":1.071349,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.160622,"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":0.436157,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_cer","status":"SUCCEEDED"},{"id":"autogen_task1_gca","status":"SUCCEEDED"},{"id":"autogen_task1_gkca","status":"SUCCEEDED"},{"id":"autogen_task1_gk","status":"SUCCEEDED"},{"id":"autogen_task1_gir","status":"SUCCEEDED"},{"id":"autogen_task1_vca","status":"SUCCEEDED"},{"id":"autogen_task1_vk","status":"SUCCEEDED"},{"id":"autogen_task1_vir","status":"SUCCEEDED"},{"id":"autogen_task1_cm","status":"SUCCEEDED"},{"id":"autogen_task1_taun","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_fcyt","status":"SUCCEEDED"},{"id":"autogen_task1_kpmca","status":"SUCCEEDED"},{"id":"autogen_task1_kd","status":"SUCCEEDED"},{"id":"autogen_task1_vn","status":"SUCCEEDED"},{"id":"autogen_task1_vm","status":"SUCCEEDED"},{"id":"autogen_task1_sn","status":"SUCCEEDED"},{"id":"autogen_task1_sm","status":"SUCCEEDED"},{"id":"autogen_task1_kserca","status":"SUCCEEDED"},{"id":"autogen_task1_dact","status":"SUCCEEDED"},{"id":"autogen_task1_dinact","status":"SUCCEEDED"},{"id":"autogen_task1_fer","status":"SUCCEEDED"},{"id":"autogen_task1_pleak","status":"SUCCEEDED"},{"id":"autogen_task1_dip3","status":"SUCCEEDED"},{"id":"autogen_task1_vcytver","status":"SUCCEEDED"},{"id":"autogen_task1_ip3","status":"SUCCEEDED"},{"id":"autogen_task1_sa","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_taua","status":"SUCCEEDED"},{"id":"autogen_task1_gkatp","status":"SUCCEEDED"},{"id":"autogen_task1_alphaIRn","status":"SUCCEEDED"},{"id":"autogen_task1_betaIRn","status":"SUCCEEDED"},{"id":"autogen_task1_nIRinf","status":"SUCCEEDED"},{"id":"autogen_task1_tauIRn","status":"SUCCEEDED"},{"id":"autogen_task1_alphaIRr","status":"SUCCEEDED"},{"id":"autogen_task1_betaIRr","status":"SUCCEEDED"},{"id":"autogen_task1_rIRinf","status":"SUCCEEDED"},{"id":"autogen_task1_tauIRr","status":"SUCCEEDED"},{"id":"autogen_task1_ica","status":"SUCCEEDED"},{"id":"autogen_task1_ik","status":"SUCCEEDED"},{"id":"autogen_task1_ikca","status":"SUCCEEDED"},{"id":"autogen_task1_ikatp","status":"SUCCEEDED"},{"id":"autogen_task1_iir","status":"SUCCEEDED"},{"id":"autogen_task1_minf","status":"SUCCEEDED"},{"id":"autogen_task1_ninf","status":"SUCCEEDED"},{"id":"autogen_task1_ainf","status":"SUCCEEDED"},{"id":"autogen_task1_w","status":"SUCCEEDED"},{"id":"autogen_task1_jmem","status":"SUCCEEDED"},{"id":"autogen_task1_jserca","status":"SUCCEEDED"},{"id":"autogen_task1_jleak","status":"SUCCEEDED"},{"id":"autogen_task1_jip3","status":"SUCCEEDED"},{"id":"autogen_task1_oinf","status":"SUCCEEDED"},{"id":"autogen_task1_jer","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_nIR","status":"SUCCEEDED"},{"id":"autogen_task1_rIR","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000005","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000006","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.317333,"curves":[{"id":"autogen_curve_task1_c","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cer","status":"SUCCEEDED"}]}]}]}