{"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    178      0 --:--:-- --:--:-- --:--:--   178\n\r100 50858  100 50858    0     0  58424      0 --:--:-- --:--:-- --:--:-- 58424\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 (27.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/rawLog.txt\nCompleted 6.6 KiB/6.6 KiB (90.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/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/Schokker2013.sedml/ (stored 0%)\n  adding: outputs/Schokker2013.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/307.6 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 307.6 KiB/307.6 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/outputs/reports.h5\nCompleted 256.0 KiB/299.2 KiB (6.7 MiB/s) with 4 file(s) remaining\rCompleted 280.8 KiB/299.2 KiB (2.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/output.zip\nCompleted 280.8 KiB/299.2 KiB (2.8 MiB/s) with 3 file(s) remaining\rCompleted 287.1 KiB/299.2 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/outputs/plots.zip\nCompleted 287.1 KiB/299.2 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 289.8 KiB/299.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/rawLog.txt\nCompleted 289.8 KiB/299.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 299.2 KiB/299.2 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/Schokker2013.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/outputs/Schokker2013.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Schokker2013-biopax2.owl  \n  inflating: contents/Schokker2013-biopax3.owl  \n  inflating: contents/Schokker2013-matlab.m  \n  inflating: contents/Schokker2013-octave.m  \n  inflating: contents/Schokker2013.cps  \n  inflating: contents/Schokker2013.ode  \n  inflating: contents/Schokker2013.sedml  \n  inflating: contents/Schokker2013.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 50.0 KiB/471.2 KiB (611.0 KiB/s) with 12 file(s) remaining\rupload: contents/Schokker2013-biopax3.owl to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013-biopax3.owl\nCompleted 50.0 KiB/471.2 KiB (611.0 KiB/s) with 11 file(s) remaining\rCompleted 63.6 KiB/471.2 KiB (494.1 KiB/s) with 11 file(s) remaining\rupload: contents/Schokker2013-matlab.m to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013-matlab.m\nCompleted 63.6 KiB/471.2 KiB (494.1 KiB/s) with 10 file(s) remaining\rCompleted 65.0 KiB/471.2 KiB (495.0 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/manifest.xml\nCompleted 65.0 KiB/471.2 KiB (495.0 KiB/s) with 9 file(s) remaining\rCompleted 97.7 KiB/471.2 KiB (715.7 KiB/s) with 9 file(s) remaining\rupload: contents/Schokker2013-biopax2.owl to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013-biopax2.owl\nCompleted 97.7 KiB/471.2 KiB (715.7 KiB/s) with 8 file(s) remaining\rCompleted 97.8 KiB/471.2 KiB (707.3 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/curation_notes.txt\nCompleted 97.8 KiB/471.2 KiB (707.3 KiB/s) with 7 file(s) remaining\rCompleted 111.3 KiB/471.2 KiB (795.7 KiB/s) with 7 file(s) remaining\rupload: contents/Schokker2013-octave.m to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013-octave.m\nCompleted 111.3 KiB/471.2 KiB (795.7 KiB/s) with 6 file(s) remaining\rCompleted 123.1 KiB/471.2 KiB (864.9 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/curation_image.png\nCompleted 123.1 KiB/471.2 KiB (864.9 KiB/s) with 5 file(s) remaining\rCompleted 169.4 KiB/471.2 KiB (1.1 MiB/s) with 5 file(s) remaining  \rupload: contents/Schokker2013.sedml to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013.sedml\nCompleted 169.4 KiB/471.2 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 348.1 KiB/471.2 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/Schokker2013.cps to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013.cps\nCompleted 348.1 KiB/471.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 359.2 KiB/471.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/Schokker2013.ode to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013.ode\nCompleted 359.2 KiB/471.2 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 361.1 KiB/471.2 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/metadata.rdf\nCompleted 361.1 KiB/471.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 471.2 KiB/471.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/Schokker2013.xml to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/contents/Schokker2013.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (124.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17f6262268786a362f7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Schokker2013.sedml\ncreating dataset /Schokker2013.sedml/autogen_report_for_task1, shape: (89, 1001), type: float64\ndataset created, uuid: d-6727de6d-e1868012-4630-5681af-d2a071, chunk_size: (89, 1001)\ncreating dataset /Schokker2013.sedml/plot_1_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-6727de6d-e1868012-66b9-542f65-6736c8, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /Schokker2013.sedml\ncreating attribute uri in /Schokker2013.sedml\ncreating attribute _type in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute uri in /Schokker2013.sedml/autogen_report_for_task1\ncreating attribute _type in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlId in /Schokker2013.sedml/plot_1_task1\ncreating attribute sedmlName in /Schokker2013.sedml/plot_1_task1\ncreating attribute uri in /Schokker2013.sedml/plot_1_task1\ncreate_links: /\ngot link: Schokker2013.sedml\ncreate_links: /Schokker2013.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Schokker2013.sedml/autogen_report_for_task1 to tgt: /Schokker2013.sedml/autogen_report_for_task1, shape: (89, 1001), type: float64\niterating over chunks for /Schokker2013.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 89, 1), slice(0, 1001, 1))\ndone with dataload for /Schokker2013.sedml/autogen_report_for_task1\nwrite_dataset src: /Schokker2013.sedml/plot_1_task1 to tgt: /Schokker2013.sedml/plot_1_task1, shape: (2, 1001), type: float64\niterating over chunks for /Schokker2013.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Schokker2013.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f17f6262268786a362f7\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.732447,"sedDocuments":[{"location":"Schokker2013.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  Schokker2013.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 89 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Schokker2013.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":1.282437,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.223296,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.283605,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.584855,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CD4","status":"SUCCEEDED"},{"id":"autogen_task1_CD8","status":"SUCCEEDED"},{"id":"autogen_task1_Mr","status":"SUCCEEDED"},{"id":"autogen_task1_Ma","status":"SUCCEEDED"},{"id":"autogen_task1_Mi","status":"SUCCEEDED"},{"id":"autogen_task1_Se","status":"SUCCEEDED"},{"id":"autogen_task1_Si","status":"SUCCEEDED"},{"id":"autogen_task1_CD4rec","status":"SUCCEEDED"},{"id":"autogen_task1_Mrrec","status":"SUCCEEDED"},{"id":"autogen_task1_sMr","status":"SUCCEEDED"},{"id":"autogen_task1_drMr","status":"SUCCEEDED"},{"id":"autogen_task1_aMr","status":"SUCCEEDED"},{"id":"autogen_task1_cSeMr","status":"SUCCEEDED"},{"id":"autogen_task1_iMr","status":"SUCCEEDED"},{"id":"autogen_task1_cSeMri","status":"SUCCEEDED"},{"id":"autogen_task1_kSeMr","status":"SUCCEEDED"},{"id":"autogen_task1_gbMr","status":"SUCCEEDED"},{"id":"autogen_task1_ccMr","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_vrecMr","status":"SUCCEEDED"},{"id":"autogen_task1_kmrecMr","status":"SUCCEEDED"},{"id":"autogen_task1_drMa","status":"SUCCEEDED"},{"id":"autogen_task1_kSeMa","status":"SUCCEEDED"},{"id":"autogen_task1_daMa","status":"SUCCEEDED"},{"id":"autogen_task1_cdaMa","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_bMi","status":"SUCCEEDED"},{"id":"autogen_task1_mMi","status":"SUCCEEDED"},{"id":"autogen_task1_lMi","status":"SUCCEEDED"},{"id":"autogen_task1_cCD4CD8","status":"SUCCEEDED"},{"id":"autogen_task1_apop","status":"SUCCEEDED"},{"id":"autogen_task1_drMi","status":"SUCCEEDED"},{"id":"autogen_task1_sCD4","status":"SUCCEEDED"},{"id":"autogen_task1_drCD4","status":"SUCCEEDED"},{"id":"autogen_task1_gbCD4","status":"SUCCEEDED"},{"id":"autogen_task1_cc1CD4","status":"SUCCEEDED"},{"id":"autogen_task1_ngbCD4","status":"SUCCEEDED"},{"id":"autogen_task1_k2CD4","status":"SUCCEEDED"},{"id":"autogen_task1_kmrecCD4","status":"SUCCEEDED"},{"id":"autogen_task1_vrecCD4","status":"SUCCEEDED"},{"id":"autogen_task1_CD4n","status":"SUCCEEDED"},{"id":"autogen_task1_ndCD4","status":"SUCCEEDED"},{"id":"autogen_task1_kSedCD4","status":"SUCCEEDED"},{"id":"autogen_task1_kSeCD4","status":"SUCCEEDED"},{"id":"autogen_task1_drCD8","status":"SUCCEEDED"},{"id":"autogen_task1_sCD8","status":"SUCCEEDED"},{"id":"autogen_task1_gbCD8","status":"SUCCEEDED"},{"id":"autogen_task1_cc1CD8","status":"SUCCEEDED"},{"id":"autogen_task1_k2CD8","status":"SUCCEEDED"},{"id":"autogen_task1_ncompCD4","status":"SUCCEEDED"},{"id":"autogen_task1_kcompCD4","status":"SUCCEEDED"},{"id":"autogen_task1_compCD8","status":"SUCCEEDED"},{"id":"autogen_task1_w1","status":"SUCCEEDED"},{"id":"autogen_task1_drSe","status":"SUCCEEDED"},{"id":"autogen_task1_pSe","status":"SUCCEEDED"},{"id":"autogen_task1_ccSe","status":"SUCCEEDED"},{"id":"autogen_task1_drSi","status":"SUCCEEDED"},{"id":"autogen_task1_pSi","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Source","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Growth_Boost","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Recruitment","status":"SUCCEEDED"},{"id":"autogen_task1_Ma_Deactivation","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Infection","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Activation","status":"SUCCEEDED"},{"id":"autogen_task1_Se_Killing_Mr","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Death","status":"SUCCEEDED"},{"id":"autogen_task1_CD4_Source","status":"SUCCEEDED"},{"id":"autogen_task1_CD4_Growth_Boost","status":"SUCCEEDED"},{"id":"autogen_task1_CD4_Recruitment","status":"SUCCEEDED"},{"id":"autogen_task1_Se_Killing_CD4","status":"SUCCEEDED"},{"id":"autogen_task1_CD4_Interaction_Naive_Se","status":"SUCCEEDED"},{"id":"autogen_task1_CD4_Death","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Source","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Growth_Boost","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Competition","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Ma_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Se_Killing_Ma","status":"SUCCEEDED"},{"id":"autogen_task1_Mi_Bursting","status":"SUCCEEDED"},{"id":"autogen_task1_Mi_Lysis","status":"SUCCEEDED"},{"id":"autogen_task1_Mi_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Se_Proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_Se_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Si_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Si_Proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_Mr_Infection_Si","status":"SUCCEEDED"},{"id":"autogen_task1_Mi_Lysis_Si","status":"SUCCEEDED"}]}]}]}