{"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    430      0 --:--:-- --:--:-- --:--:--   431\n\r100 49992  100 49992    0     0   112k      0 --:--:-- --:--:-- --:--:--  112k\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 (13.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/rawLog.txt\nCompleted 7.6 KiB/7.6 KiB (58.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/Bachmann2011.sedml/ (stored 0%)\n  adding: outputs/Bachmann2011.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/491.7 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 491.7 KiB/491.7 KiB (3.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/outputs/reports.h5\nCompleted 256.0 KiB/483.0 KiB (4.1 MiB/s) with 4 file(s) remaining\rCompleted 464.4 KiB/483.0 KiB (3.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/output.zip\nCompleted 464.4 KiB/483.0 KiB (3.1 MiB/s) with 3 file(s) remaining\rCompleted 474.0 KiB/483.0 KiB (3.2 MiB/s) with 3 file(s) remaining\rupload: outputs/Bachmann2011.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/outputs/Bachmann2011.sedml/plot_1_task1.pdf\nCompleted 474.0 KiB/483.0 KiB (3.2 MiB/s) with 2 file(s) remaining\rCompleted 480.3 KiB/483.0 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/outputs/plots.zip\nCompleted 480.3 KiB/483.0 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 483.0 KiB/483.0 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Bachmann2011-biopax2.owl  \n  inflating: contents/Bachmann2011-biopax3.owl  \n  inflating: contents/Bachmann2011-matlab.m  \n  inflating: contents/Bachmann2011.cps  \n  inflating: contents/Bachmann2011.ode  \n  inflating: contents/Bachmann2011.sedml  \n  inflating: contents/Bachmann2011.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 73.5 KiB/594.5 KiB (562.0 KiB/s) with 11 file(s) remaining\rupload: contents/Bachmann2011-biopax3.owl to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011-biopax3.owl\nCompleted 73.5 KiB/594.5 KiB (562.0 KiB/s) with 10 file(s) remaining\rCompleted 73.6 KiB/594.5 KiB (369.6 KiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/curation_notes.txt\nCompleted 73.6 KiB/594.5 KiB (369.6 KiB/s) with 9 file(s) remaining\rCompleted 74.9 KiB/594.5 KiB (371.6 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/manifest.xml\nCompleted 74.9 KiB/594.5 KiB (371.6 KiB/s) with 8 file(s) remaining\rCompleted 76.9 KiB/594.5 KiB (375.8 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/metadata.rdf\nCompleted 76.9 KiB/594.5 KiB (375.8 KiB/s) with 7 file(s) remaining\rCompleted 300.0 KiB/594.5 KiB (1.4 MiB/s) with 7 file(s) remaining \rupload: contents/Bachmann2011.cps to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011.cps\nCompleted 300.0 KiB/594.5 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 318.9 KiB/594.5 KiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/Bachmann2011-matlab.m to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011-matlab.m\nCompleted 318.9 KiB/594.5 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 370.5 KiB/594.5 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/Bachmann2011.sedml to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011.sedml\nCompleted 370.5 KiB/594.5 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 386.5 KiB/594.5 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/Bachmann2011.ode to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011.ode\nCompleted 386.5 KiB/594.5 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 396.4 KiB/594.5 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/curation_image.png\nCompleted 396.4 KiB/594.5 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 442.0 KiB/594.5 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/Bachmann2011-biopax2.owl to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011-biopax2.owl\nCompleted 442.0 KiB/594.5 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 594.5 KiB/594.5 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/Bachmann2011.xml to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/contents/Bachmann2011.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.2 KiB/7.2 KiB (55.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5c9a0fb37cdb9ae75558/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Bachmann2011.sedml\ncreating dataset /Bachmann2011.sedml/autogen_report_for_task1, shape: (97, 1001), type: float64\ndataset created, uuid: d-58fabf67-2553a595-1905-dab6a1-42cdcd, chunk_size: (97, 1001)\ncreating dataset /Bachmann2011.sedml/plot_1_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-58fabf67-2553a595-3802-476142-a0527b, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /Bachmann2011.sedml\ncreating attribute uri in /Bachmann2011.sedml\ncreating attribute _type in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute uri in /Bachmann2011.sedml/autogen_report_for_task1\ncreating attribute _type in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlId in /Bachmann2011.sedml/plot_1_task1\ncreating attribute sedmlName in /Bachmann2011.sedml/plot_1_task1\ncreating attribute uri in /Bachmann2011.sedml/plot_1_task1\ncreate_links: /\ngot link: Bachmann2011.sedml\ncreate_links: /Bachmann2011.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Bachmann2011.sedml/autogen_report_for_task1 to tgt: /Bachmann2011.sedml/autogen_report_for_task1, shape: (97, 1001), type: float64\niterating over chunks for /Bachmann2011.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 97, 1), slice(0, 1001, 1))\ndone with dataload for /Bachmann2011.sedml/autogen_report_for_task1\nwrite_dataset src: /Bachmann2011.sedml/plot_1_task1 to tgt: /Bachmann2011.sedml/plot_1_task1, shape: (2, 1001), type: float64\niterating over chunks for /Bachmann2011.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Bachmann2011.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5c9a0fb37cdb9ae75558\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 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 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.\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":2.375811,"sedDocuments":[{"location":"Bachmann2011.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  Bachmann2011.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 97 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Bachmann2011.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":1.759824,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.394775,"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":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.416766,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.709622,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_npSTAT5","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_p1EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_p2EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_p12EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRJAK2_CIS","status":"SUCCEEDED"},{"id":"autogen_task1_SHP1","status":"SUCCEEDED"},{"id":"autogen_task1_SHP1Act","status":"SUCCEEDED"},{"id":"autogen_task1_STAT5","status":"SUCCEEDED"},{"id":"autogen_task1_pSTAT5","status":"SUCCEEDED"},{"id":"autogen_task1_CISnRNA1","status":"SUCCEEDED"},{"id":"autogen_task1_CISnRNA2","status":"SUCCEEDED"},{"id":"autogen_task1_CISnRNA3","status":"SUCCEEDED"},{"id":"autogen_task1_CISnRNA4","status":"SUCCEEDED"},{"id":"autogen_task1_CISnRNA5","status":"SUCCEEDED"},{"id":"autogen_task1_CISRNA","status":"SUCCEEDED"},{"id":"autogen_task1_CIS","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3nRNA1","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3nRNA2","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3nRNA3","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3nRNA4","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3nRNA5","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3RNA","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3","status":"SUCCEEDED"},{"id":"autogen_task1_Epo","status":"SUCCEEDED"},{"id":"autogen_task1_ActD","status":"SUCCEEDED"},{"id":"autogen_task1_CISEqc","status":"SUCCEEDED"},{"id":"autogen_task1_CISEqcOE","status":"SUCCEEDED"},{"id":"autogen_task1_CISInh","status":"SUCCEEDED"},{"id":"autogen_task1_CISRNADelay","status":"SUCCEEDED"},{"id":"autogen_task1_CISRNAEqc","status":"SUCCEEDED"},{"id":"autogen_task1_CISRNATurn","status":"SUCCEEDED"},{"id":"autogen_task1_CISTurn","status":"SUCCEEDED"},{"id":"autogen_task1_CISoe","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRActJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRCISInh","status":"SUCCEEDED"},{"id":"autogen_task1_EpoRCISRemove","status":"SUCCEEDED"},{"id":"autogen_task1_JAK2ActEpo","status":"SUCCEEDED"},{"id":"autogen_task1_JAK2EpoRDeaSHP1","status":"SUCCEEDED"},{"id":"autogen_task1_SHP1ActEpoR","status":"SUCCEEDED"},{"id":"autogen_task1_SHP1Dea","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3Eqc","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3EqcOE","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3Inh","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3RNADelay","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3RNAEqc","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3RNATurn","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3Turn","status":"SUCCEEDED"},{"id":"autogen_task1_SOCS3oe","status":"SUCCEEDED"},{"id":"autogen_task1_STAT5ActEpoR","status":"SUCCEEDED"},{"id":"autogen_task1_STAT5ActJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_STAT5Exp","status":"SUCCEEDED"},{"id":"autogen_task1_STAT5Imp","status":"SUCCEEDED"},{"id":"autogen_task1_epo_level","status":"SUCCEEDED"},{"id":"autogen_task1_init_EpoRJAK2","status":"SUCCEEDED"},{"id":"autogen_task1_init_SHP1","status":"SUCCEEDED"},{"id":"autogen_task1_init_STAT5","status":"SUCCEEDED"},{"id":"autogen_task1_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_12","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_13","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_14","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_15","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_16","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_17","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_18","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_19","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_20","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_21","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_22","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_23","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_24","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_25","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_26","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_27","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_28","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_29","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_30","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_31","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_32","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_33","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_34","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_35","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_36","status":"SUCCEEDED"}]}]}]}