{"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    293      0 --:--:-- --:--:-- --:--:--   293\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  3952  100  3952    0     0   5968      0 --:--:-- --:--:-- --:--:-- 32393\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n_XSERVTransmkdir: ERROR: euid != 0,directory /tmp/.X11-unix will not be created.\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\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 (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.7 KiB/1.7 KiB (13.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (68.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 70%)\n  adding: outputs/reports.h5 (deflated 27%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 72.8 KiB/72.8 KiB (534.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 57.5 KiB/60.4 KiB (380.6 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/output.zip\nCompleted 57.5 KiB/60.4 KiB (380.6 KiB/s) with 1 file(s) remaining\rCompleted 60.4 KiB/60.4 KiB (329.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/model.txt      \n  inflating: contents/simulation.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 484 Bytes/17.3 KiB (3.6 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/contents/manifest.xml\nCompleted 484 Bytes/17.3 KiB (3.6 KiB/s) with 3 file(s) remaining\rCompleted 3.8 KiB/17.3 KiB (23.1 KiB/s) with 3 file(s) remaining \rCompleted 14.1 KiB/17.3 KiB (85.3 KiB/s) with 3 file(s) remaining\rupload: contents/simulation.sedml to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/contents/simulation.sedml\nCompleted 14.1 KiB/17.3 KiB (85.3 KiB/s) with 2 file(s) remaining\rCompleted 17.3 KiB/17.3 KiB (103.2 KiB/s) with 2 file(s) remaining\rupload: contents/model.txt to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/contents/model.txt\nCompleted 17.3 KiB/17.3 KiB (103.2 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 4.8 KiB/4.8 KiB (38.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/65c65c54767b75b8f4bb61ba/rawLog.txt\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":13.143452,"sedDocuments":[{"location":"simulation.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n  simulation.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 13 data sets\r\n\r\nExecuting SED-ML file 1: simulation.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","duration":12.795795,"tasks":[{"id":"task","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"--------------------------------------------------------------\r\nRunning Smoldyn 2.72\r\n\r\nCONFIGURATION FILE\r\n Path: '/tmp/'\r\n Name: 'tmp1ko2yg8i.txt'\r\n Reading file: '/tmp/tmp1ko2yg8i.txt'\r\n Loaded file successfully\r\n setting up molecules\r\n setting up virtual boxes\r\n setting up compartments\r\n setting up reactions\r\n setting up surfaces\r\n setting up graphics\r\n\r\nSIMULATION PARAMETERS\r\n file: /tmp/tmp1ko2yg8i.txt\r\n starting clock time: Fri Feb  9 12:09:49 2024\r\n 3 dimensions\r\n Accuracy level: 5\r\n Random number seed: 1\r\n Time from 0 to 10 step 0.002\r\n\r\nGRAPHICS PARAMETERS\r\n No graphical output\r\n\r\nWALL PARAMETERS\r\n wall 0: dimension x, at -2\r\n wall 1: dimension x, at 2\r\n wall 2: dimension y, at -0.5\r\n wall 3: dimension y, at 0.5\r\n wall 4: dimension z, at -0.5\r\n wall 5: dimension z, at 0.5\r\n system volume: 4\r\n system corners: (-2,-0.5,-0.5) and (2,0.5,0.5)\r\n\r\nMOLECULE PARAMETERS\r\n 6 molecule lists:\r\n  list1, list2, list3, list4, list5, unassignedlist\r\n 4 species defined:\r\n MinD_ATP:\r\n  solution: difc=2.5, rms step=0.1, list=list1, number=0\r\n  front: difc=0.01, rms step=0.00632456, list=list2, number=4000\r\n  solution: color= 0,0,0.6, display size= 2\r\n  front: color= 0,0.6,0, display size= 4\r\n MinD_ADP:\r\n  solution: difc=2.5, rms step=0.1, list=list3, number=0\r\n  solution: color= 0.4,0.6,1, display size= 2\r\n MinE:\r\n  solution: difc=2.5, rms step=0.1, list=list4, number=1400\r\n  solution: color= 1,0,0, display size= 2\r\n MinDMinE:\r\n  front: difc=0.01, rms step=0.00632456, list=list5, number=0\r\n  front: color= 0.2,1,0.2, display size= 4\r\n Overall spatial resolution: 0.1\r\n\r\nSURFACE PARAMETERS\r\n Surface epsilon, margin, and neighbor distances: 2.22045e-14 2.22045e-14 2.22045e-15\r\n Molecule lists checked after diffusion: list1 list2 list3 list4 list5\r\n Molecule lists checked after reactions: list2 list5\r\n Molecule lists checked for surface-bound molecules: list2 list3 list4 list5 unassignedlist\r\n Surfaces defined: 1\r\n\r\n Surface: membrane\r\n  actions for molecules:\r\n   MinD_ATP(front) at front: transmit\r\n   MinD_ATP(solution) at back: reflect\r\n   MinD_ATP(front) at back: transmit\r\n   MinD_ADP(solution) at front: reflect\r\n   MinD_ADP(solution) at back: reflect\r\n   MinE(solution) at front: reflect\r\n   MinE(solution) at back: reflect\r\n   MinDMinE(front) at front: transmit\r\n   MinDMinE(front) at back: transmit\r\n  rates for molecules:\r\n    MinD_ATP(solution) solution -> front, requested rate=0.025, actual rate=0.0249991, prob=0.0012519\r\n  surface-bound molecules do not hop between neighboring panels upon collision\r\n  front color: 0 0 0 1\r\n  back color: 0 0 0 1\r\n  edge points: 1, polygon modes: edge edge\r\n  cylinder panels allocated: 1, defined: 1\r\n   cyl0: (-1.5,0,0) to (1.5,0,0), R=0.5, facing: in, draw: 20 10, area: 9.42478\r\n  hemisphere panels allocated: 3, defined: 2\r\n   hemi0: (-1.5,0,0), R=0.5, facing: in, opening: (1,0,0), draw: 20 5, area: 1.5708\r\n   hemi1: (1.5,0,0), R=0.5, facing: in, opening: (-1,0,0), draw: 20 5, area: 1.5708\r\n\r\nRUNTIME COMMAND INTERPRETER\r\n Output file root: '/tmp/'\r\n Output file paths and names:\r\n  modelout.txt (file closed): /tmp/modelout.txt\r\n No output data tables\r\n Commands:\r\n  i from: 0 to: 10 step: 2 'executiontime modelout.txt' (observe)\r\n  i from: 0 to: 10 step: 2 'listmols modelout.txt' (observe)\r\n\r\nVIRTUAL BOX PARAMETERS\r\n 1372 boxes\r\n Number of boxes on each side: 28 7 7\r\n Requested molecules per box: 4\r\n Box dimensions:  0.142857 0.142857 0.142857\r\n Box volumes: 0.00291545\r\n Molecules per box= 3.93586\r\n\r\nORDER 0 REACTION PARAMETERS\r\n No reactions of order 0\r\n\r\nORDER 1 REACTION PARAMETERS\r\n 2 reactions defined\r\n Reactive molecule lists: list3 list5\r\n Reactants, sorted by molecule species:\r\n  MinD_ADP : rxn4\r\n  MinDMinE : rxn3\r\n Reaction details:\r\n  Reaction rxn3: MinDMinE (front) -> MinD_ADP + MinE\r\n   requested and actual rate constants: 0.7, 0.7\r\n   characteristic time: 1.42857\r\n   conditional reaction probability per time step: 0.00139902\r\n   unbinding radius: 0\r\n  Reaction rxn4: MinD_ADP -> MinD_ATP\r\n   requested and actual rate constants: 1, 1\r\n   characteristic time: 1\r\n   conditional reaction probability per time step: 0.001998\r\n\r\nORDER 2 REACTION PARAMETERS\r\n 3 reactions defined\r\n Reactive molecule lists: list2+list1 list5+list1 list1+list2 list4+list2 list2+list4 list1+list5\r\n Reactants, sorted by molecule species:\r\n  MinD_ATP+MinD_ATP : rxn1b\r\n  MinD_ATP+MinE : rxn2\r\n  MinD_ATP+MinDMinE : rxn1c\r\n Reaction details:\r\n  Reaction rxn1b: MinD_ATP + MinD_ATP (front) -> MinD_ATP (front) + MinD_ATP (front)\r\n   requested and actual rate constants: 0.0015, 0.00150008\r\n   characteristic time: 1.33326\r\n   binding radius: 0.0142114\r\n   unbinding radius: 0.01\r\n   product placement method and parameter: unbindrad 0.01\r\n   product MinD_ATP displacement: 0.005 0 0\r\n   product MinD_ATP displacement: -0.005 0 0\r\n   probability of geminate reverse reaction 'rxn1b' is 0.640142\r\n  Reaction rxn1c: MinD_ATP + MinDMinE (front) -> MinD_ATP (front) + MinDMinE (front)\r\n   requested and actual rate constants: 0.0015, 0.00150008\r\n   characteristic time: inf\r\n   binding radius: 0.0112758\r\n   unbinding radius: 0.01\r\n   product placement method and parameter: unbindrad 0.01\r\n   product MinD_ATP displacement: 0.005 0 0\r\n   product MinDMinE displacement: -0.005 0 0\r\n   probability of geminate reverse reaction 'rxn1c' is 0.467451\r\n  Reaction rxn2: MinE + MinD_ATP (front) -> MinDMinE (front)\r\n   requested and actual rate constants: 0.093, 0.093003\r\n   characteristic time: 0.0414733\r\n   binding radius: 0.0455085\r\n\r\nRULES:\r\n none\r\n\r\nCOMPARTMENT PARAMETERS\r\n Compartments allocated: 5, compartments defined: 1\r\n Compartment: cell\r\n  1 bounding surfaces:\r\n   membrane\r\n  1 interior-defining points:\r\n   0: (0,0,0)\r\n  0 logically combined compartments\r\n  volume: 2.87778\r\n  1214 virtual boxes listed\r\n\r\nPARAMETER CHECK\r\n WARNING: reactive volume of MinE is 13.8177 % of total volume\r\n WARNING: total reactive volume is a large fraction of total volume\r\n No errors\r\n 2 total warnings\r\n\r\nSimulating\r\nLibsmoldyn notification from smolRunSim: Simulation complete\r\n","duration":12.125515,"algorithm":"KISAO_0000057","simulatorDetails":[{"key":"class","value":"smoldyn.Simulation"},{"key":"instanceAttributes"},{"key":"method","value":"run"},{"key":"methodArguments","value":{"dt":0.002,"start":0,"stop":10}}]}],"outputs":[{"id":"report","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.454111,"dataSets":[{"id":"time","status":"SUCCEEDED"},{"id":"count_species_MinD_ADP","status":"SUCCEEDED"},{"id":"count_species_MinD_ADP_compartment_cell","status":"SUCCEEDED"},{"id":"count_species_MinD_ADP_surface_membrane","status":"SUCCEEDED"},{"id":"count_species_MinD_ATP","status":"SUCCEEDED"},{"id":"count_species_MinD_ATP_compartment_cell","status":"SUCCEEDED"},{"id":"count_species_MinD_ATP_surface_membrane","status":"SUCCEEDED"},{"id":"count_species_MinDMinE","status":"SUCCEEDED"},{"id":"count_species_MinDMinE_compartment_cell","status":"SUCCEEDED"},{"id":"count_species_MinDMinE_surface_membrane","status":"SUCCEEDED"},{"id":"count_species_MinE","status":"SUCCEEDED"},{"id":"count_species_MinE_compartment_cell","status":"SUCCEEDED"},{"id":"count_species_MinE_surface_membrane","status":"SUCCEEDED"}]}]}]}