{"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    453      0 --:--:-- --:--:-- --:--:--   452\n\r100  101k  100  101k    0     0   240k      0 --:--:-- --:--:-- --:--:--  240k\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 (16.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/rawLog.txt\nCompleted 5.5 KiB/5.5 KiB (61.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/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/BIOMD0000000327_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000327_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 230.7 KiB/230.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/outputs/reports.h5\nsrun: Job 6663953 step creation temporarily disabled, retrying\nsrun: Step created for job 6663953\nCompleted 204.9 KiB/221.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/output.zip\nCompleted 204.9 KiB/221.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 213.4 KiB/221.9 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000327_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/outputs/BIOMD0000000327_url.sedml/autogen_plot_for_task1.pdf\nCompleted 213.4 KiB/221.9 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 216.2 KiB/221.9 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/rawLog.txt\nCompleted 216.2 KiB/221.9 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 221.9 KiB/221.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000327-biopax2.owl  \n  inflating: contents/BIOMD0000000327-biopax3.owl  \n  inflating: contents/BIOMD0000000327-matlab.m  \n  inflating: contents/BIOMD0000000327-octave.m  \n  inflating: contents/BIOMD0000000327.m  \n  inflating: contents/BIOMD0000000327.ode  \n  inflating: contents/BIOMD0000000327.png  \n  inflating: contents/BIOMD0000000327.svg  \n  inflating: contents/BIOMD0000000327_url.sedml  \n  inflating: contents/BIOMD0000000327_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 15.7 KiB/256.9 KiB (136.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000327-biopax2.owl to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327-biopax2.owl\nCompleted 15.7 KiB/256.9 KiB (136.4 KiB/s) with 13 file(s) remaining\rCompleted 50.1 KiB/256.9 KiB (380.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000327_url.sedml to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327_url.sedml\nCompleted 50.1 KiB/256.9 KiB (380.1 KiB/s) with 12 file(s) remaining\rCompleted 71.2 KiB/256.9 KiB (491.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000327.svg to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327.svg\nCompleted 71.2 KiB/256.9 KiB (491.0 KiB/s) with 11 file(s) remaining\rCompleted 80.2 KiB/256.9 KiB (540.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000327-matlab.m to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327-matlab.m\nCompleted 80.2 KiB/256.9 KiB (540.4 KiB/s) with 10 file(s) remaining\rCompleted 89.3 KiB/256.9 KiB (578.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000327-octave.m to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327-octave.m\nCompleted 89.3 KiB/256.9 KiB (578.3 KiB/s) with 9 file(s) remaining\rCompleted 115.6 KiB/256.9 KiB (718.2 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/curation_image.png\nCompleted 115.6 KiB/256.9 KiB (718.2 KiB/s) with 8 file(s) remaining\rCompleted 156.6 KiB/256.9 KiB (890.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000327_url.xml to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327_url.xml\nCompleted 156.6 KiB/256.9 KiB (890.8 KiB/s) with 7 file(s) remaining\rCompleted 158.2 KiB/256.9 KiB (835.1 KiB/s) with 7 file(s) remaining\rCompleted 211.8 KiB/256.9 KiB (1.1 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000327.png to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327.png\nCompleted 211.8 KiB/256.9 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 236.8 KiB/256.9 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/manifest.xml\nCompleted 236.8 KiB/256.9 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000327-biopax3.owl to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327-biopax3.owl\nCompleted 236.8 KiB/256.9 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 241.2 KiB/256.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/metadata.rdf\nCompleted 241.2 KiB/256.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 241.4 KiB/256.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/curation_notes.txt\nCompleted 241.4 KiB/256.9 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 250.4 KiB/256.9 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000327.m to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327.m\nCompleted 250.4 KiB/256.9 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 256.9 KiB/256.9 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000327.ode to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/contents/BIOMD0000000327.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.3 KiB/8.3 KiB (127.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13e6262268786a35f2d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000327_url.sedml\ncreating dataset /BIOMD0000000327_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-176040cb-0f0df605-5b83-711224-76cbba, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000327_url.sedml/autogen_report_for_task1, shape: (67, 1001), type: float64\ndataset created, uuid: d-176040cb-0f0df605-d105-10c5f3-31e3f3, chunk_size: (67, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000327_url.sedml\ncreating attribute uri in /BIOMD0000000327_url.sedml\ncreating attribute _type in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000327_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000327_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000327_url.sedml\ncreate_links: /BIOMD0000000327_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000327_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000327_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000327_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000327_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000327_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000327_url.sedml/autogen_report_for_task1, shape: (67, 1001), type: float64\niterating over chunks for /BIOMD0000000327_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 67, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000327_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f13e6262268786a35f2d\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.\nRetrieve 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.921438,"sedDocuments":[{"location":"BIOMD0000000327_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  BIOMD0000000327_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 67 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000327_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":1.443145,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.251813,"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":0.520715,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_bb","status":"SUCCEEDED"},{"id":"autogen_task1_cb","status":"SUCCEEDED"},{"id":"autogen_task1_nb","status":"SUCCEEDED"},{"id":"autogen_task1_bi","status":"SUCCEEDED"},{"id":"autogen_task1_ci","status":"SUCCEEDED"},{"id":"autogen_task1_ni","status":"SUCCEEDED"},{"id":"autogen_task1_bl","status":"SUCCEEDED"},{"id":"autogen_task1_cl","status":"SUCCEEDED"},{"id":"autogen_task1_g_bi","status":"SUCCEEDED"},{"id":"autogen_task1_g_cl","status":"SUCCEEDED"},{"id":"autogen_task1_zeta","status":"SUCCEEDED"},{"id":"autogen_task1_kbi","status":"SUCCEEDED"},{"id":"autogen_task1_kcl","status":"SUCCEEDED"},{"id":"autogen_task1_gnbc","status":"SUCCEEDED"},{"id":"autogen_task1_gapl","status":"SUCCEEDED"},{"id":"autogen_task1_gapbl","status":"SUCCEEDED"},{"id":"autogen_task1_vr","status":"SUCCEEDED"},{"id":"autogen_task1_bi0","status":"SUCCEEDED"},{"id":"autogen_task1_buf","status":"SUCCEEDED"},{"id":"autogen_task1_gcftron","status":"SUCCEEDED"},{"id":"autogen_task1_gcftrbase","status":"SUCCEEDED"},{"id":"autogen_task1_ek","status":"SUCCEEDED"},{"id":"autogen_task1_gk","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_temp","status":"SUCCEEDED"},{"id":"autogen_task1_ionstr","status":"SUCCEEDED"},{"id":"autogen_task1_gnak","status":"SUCCEEDED"},{"id":"autogen_task1_np0","status":"SUCCEEDED"},{"id":"autogen_task1_epump","status":"SUCCEEDED"},{"id":"autogen_task1_gnaleak","status":"SUCCEEDED"},{"id":"autogen_task1_jac","status":"SUCCEEDED"},{"id":"autogen_task1_rat","status":"SUCCEEDED"},{"id":"autogen_task1_ton","status":"SUCCEEDED"},{"id":"autogen_task1_toff","status":"SUCCEEDED"},{"id":"autogen_task1_gcftr","status":"SUCCEEDED"},{"id":"autogen_task1_eb","status":"SUCCEEDED"},{"id":"autogen_task1_enbc","status":"SUCCEEDED"},{"id":"autogen_task1_ec","status":"SUCCEEDED"},{"id":"autogen_task1_ena","status":"SUCCEEDED"},{"id":"autogen_task1_kccf","status":"SUCCEEDED"},{"id":"autogen_task1_kbcf","status":"SUCCEEDED"},{"id":"autogen_task1_knbc","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_jnbc","status":"SUCCEEDED"},{"id":"autogen_task1_jbcftr","status":"SUCCEEDED"},{"id":"autogen_task1_jccftr","status":"SUCCEEDED"},{"id":"autogen_task1_japl","status":"SUCCEEDED"},{"id":"autogen_task1_japbl","status":"SUCCEEDED"},{"id":"autogen_task1_jlum","status":"SUCCEEDED"},{"id":"autogen_task1_jnak","status":"SUCCEEDED"},{"id":"autogen_task1_jnaleak","status":"SUCCEEDED"},{"id":"autogen_task1_plasma","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_lumen","status":"SUCCEEDED"},{"id":"autogen_task1_nbc","status":"SUCCEEDED"},{"id":"autogen_task1_bcftr","status":"SUCCEEDED"},{"id":"autogen_task1_ccftr","status":"SUCCEEDED"},{"id":"autogen_task1_apl","status":"SUCCEEDED"},{"id":"autogen_task1_apbl","status":"SUCCEEDED"},{"id":"autogen_task1_nak","status":"SUCCEEDED"},{"id":"autogen_task1_naleak","status":"SUCCEEDED"},{"id":"autogen_task1_buffering","status":"SUCCEEDED"},{"id":"autogen_task1_bac","status":"SUCCEEDED"},{"id":"autogen_task1_cac","status":"SUCCEEDED"},{"id":"autogen_task1_outflow","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.472356,"curves":[{"id":"autogen_curve_task1_bb","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cb","status":"SUCCEEDED"},{"id":"autogen_curve_task1_nb","status":"SUCCEEDED"},{"id":"autogen_curve_task1_bi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ci","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ni","status":"SUCCEEDED"},{"id":"autogen_curve_task1_bl","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cl","status":"SUCCEEDED"}]}]}]}