{"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    462      0 --:--:-- --:--:-- --:--:--   463\n\r100  474k  100  474k    0     0  1108k      0 --:--:-- --:--:-- --:--:-- 1108k\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 (21.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/rawLog.txt\nCompleted 5.8 KiB/5.8 KiB (62.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/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/BIOMD0000000061_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000061_url.sedml/autogen_plot_for_task1.pdf (deflated 15%)\n  adding: outputs/reports.h5 (deflated 5%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/498.4 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 498.4 KiB/498.4 KiB (4.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/outputs/reports.h5\nCompleted 256.0 KiB/546.8 KiB (5.6 MiB/s) with 4 file(s) remaining\rCompleted 497.4 KiB/546.8 KiB (4.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/output.zip\nCompleted 497.4 KiB/546.8 KiB (4.1 MiB/s) with 3 file(s) remaining\rCompleted 522.8 KiB/546.8 KiB (4.1 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000061_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/outputs/BIOMD0000000061_url.sedml/autogen_plot_for_task1.pdf\nCompleted 522.8 KiB/546.8 KiB (4.1 MiB/s) with 2 file(s) remaining\rCompleted 525.5 KiB/546.8 KiB (3.9 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/rawLog.txt\nCompleted 525.5 KiB/546.8 KiB (3.9 MiB/s) with 1 file(s) remaining\rCompleted 546.8 KiB/546.8 KiB (3.7 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000061-biopax2.owl  \n  inflating: contents/BIOMD0000000061-biopax3.owl  \n  inflating: contents/BIOMD0000000061-matlab.m  \n  inflating: contents/BIOMD0000000061-octave.m  \n  inflating: contents/BIOMD0000000061.m  \n  inflating: contents/BIOMD0000000061.ode  \n  inflating: contents/BIOMD0000000061.pdf  \n  inflating: contents/BIOMD0000000061.png  \n  inflating: contents/BIOMD0000000061.svg  \n  inflating: contents/BIOMD0000000061.vcml  \n  inflating: contents/BIOMD0000000061_url.sedml  \n  inflating: contents/BIOMD0000000061_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 17.8 KiB/1.0 MiB (169.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000061-matlab.m to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061-matlab.m\nCompleted 17.8 KiB/1.0 MiB (169.3 KiB/s) with 15 file(s) remaining\rCompleted 79.8 KiB/1.0 MiB (748.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000061-biopax2.owl to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061-biopax2.owl\nCompleted 79.8 KiB/1.0 MiB (748.1 KiB/s) with 14 file(s) remaining\rCompleted 97.6 KiB/1.0 MiB (869.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000061-octave.m to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061-octave.m\nCompleted 97.6 KiB/1.0 MiB (869.3 KiB/s) with 13 file(s) remaining\rCompleted 312.6 KiB/1.0 MiB (2.2 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000061.png to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.png\nCompleted 312.6 KiB/1.0 MiB (2.2 MiB/s) with 12 file(s) remaining\rCompleted 568.6 KiB/1.0 MiB (3.9 MiB/s) with 12 file(s) remaining\rCompleted 598.8 KiB/1.0 MiB (3.9 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000061_url.sedml to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061_url.sedml\nCompleted 598.8 KiB/1.0 MiB (3.9 MiB/s) with 11 file(s) remaining\rCompleted 650.0 KiB/1.0 MiB (4.2 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000061.svg to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.svg\nCompleted 650.0 KiB/1.0 MiB (4.2 MiB/s) with 10 file(s) remaining\rCompleted 654.3 KiB/1.0 MiB (3.8 MiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/metadata.rdf\nCompleted 654.3 KiB/1.0 MiB (3.8 MiB/s) with 9 file(s) remaining\rCompleted 740.9 KiB/1.0 MiB (4.0 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000061_url.xml to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061_url.xml\nCompleted 740.9 KiB/1.0 MiB (4.0 MiB/s) with 8 file(s) remaining\rCompleted 838.1 KiB/1.0 MiB (4.4 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000061.vcml to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.vcml\nCompleted 838.1 KiB/1.0 MiB (4.4 MiB/s) with 7 file(s) remaining\rCompleted 897.4 KiB/1.0 MiB (4.6 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/curation_image.png\nCompleted 897.4 KiB/1.0 MiB (4.6 MiB/s) with 6 file(s) remaining\rCompleted 917.4 KiB/1.0 MiB (4.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000061.pdf to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.pdf\nCompleted 917.4 KiB/1.0 MiB (4.6 MiB/s) with 5 file(s) remaining\rCompleted 917.5 KiB/1.0 MiB (4.6 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/curation_notes.txt\nCompleted 917.5 KiB/1.0 MiB (4.6 MiB/s) with 4 file(s) remaining\rCompleted 929.3 KiB/1.0 MiB (4.5 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000061.ode to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.ode\nCompleted 929.3 KiB/1.0 MiB (4.5 MiB/s) with 3 file(s) remaining\rCompleted 1017.6 KiB/1.0 MiB (4.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000061-biopax3.owl to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061-biopax3.owl\nCompleted 1017.6 KiB/1.0 MiB (4.7 MiB/s) with 2 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (4.4 MiB/s) with 2 file(s) remaining   \rupload: contents/BIOMD0000000061.m to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/BIOMD0000000061.m\nCompleted 1.0 MiB/1.0 MiB (4.4 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (4.3 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (93.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107bd49c0d898ffdda1f3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000061_url.sedml\ncreating dataset /BIOMD0000000061_url.sedml/autogen_plot_for_task1, shape: (26, 1001), type: float64\ndataset created, uuid: d-75249a56-67548d3f-e6cf-8a440e-82d62d, chunk_size: (26, 1001)\ncreating dataset /BIOMD0000000061_url.sedml/autogen_report_for_task1, shape: (52, 1001), type: float64\ndataset created, uuid: d-75249a56-67548d3f-d8ec-3a8834-16f111, chunk_size: (52, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000061_url.sedml\ncreating attribute uri in /BIOMD0000000061_url.sedml\ncreating attribute _type in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000061_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000061_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000061_url.sedml\ncreate_links: /BIOMD0000000061_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000061_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000061_url.sedml/autogen_plot_for_task1, shape: (26, 1001), type: float64\niterating over chunks for /BIOMD0000000061_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 26, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000061_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000061_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000061_url.sedml/autogen_report_for_task1, shape: (52, 1001), type: float64\niterating over chunks for /BIOMD0000000061_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 52, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000061_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107bd49c0d898ffdda1f3\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\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":27.579053,"sedDocuments":[{"location":"BIOMD0000000061_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  BIOMD0000000061_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 52 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 25 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000061_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":27.144036,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":25.838262,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.432918,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_GlcX","status":"SUCCEEDED"},{"id":"autogen_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_BPG","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_task1_ACA","status":"SUCCEEDED"},{"id":"autogen_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_task1_EtOHX","status":"SUCCEEDED"},{"id":"autogen_task1_Glyc","status":"SUCCEEDED"},{"id":"autogen_task1_GlycX","status":"SUCCEEDED"},{"id":"autogen_task1_ACAX","status":"SUCCEEDED"},{"id":"autogen_task1_CNX","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_CNX0","status":"SUCCEEDED"},{"id":"autogen_task1_GlcX0","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_vinGlc","status":"SUCCEEDED"},{"id":"autogen_task1_vGlcTrans","status":"SUCCEEDED"},{"id":"autogen_task1_vHK","status":"SUCCEEDED"},{"id":"autogen_task1_vPGI","status":"SUCCEEDED"},{"id":"autogen_task1_vPFK","status":"SUCCEEDED"},{"id":"autogen_task1_vALD","status":"SUCCEEDED"},{"id":"autogen_task1_vTIM","status":"SUCCEEDED"},{"id":"autogen_task1_vGAPDH","status":"SUCCEEDED"},{"id":"autogen_task1_vlpPEP","status":"SUCCEEDED"},{"id":"autogen_task1_vPK","status":"SUCCEEDED"},{"id":"autogen_task1_vPDC","status":"SUCCEEDED"},{"id":"autogen_task1_vADH","status":"SUCCEEDED"},{"id":"autogen_task1_vdifEtOH","status":"SUCCEEDED"},{"id":"autogen_task1_voutEtOH","status":"SUCCEEDED"},{"id":"autogen_task1_vlpGlyc","status":"SUCCEEDED"},{"id":"autogen_task1_vdifGlyc","status":"SUCCEEDED"},{"id":"autogen_task1_voutGlyc","status":"SUCCEEDED"},{"id":"autogen_task1_vdifACA","status":"SUCCEEDED"},{"id":"autogen_task1_voutACA","status":"SUCCEEDED"},{"id":"autogen_task1_vlacto","status":"SUCCEEDED"},{"id":"autogen_task1_vinCN","status":"SUCCEEDED"},{"id":"autogen_task1_vstorage","status":"SUCCEEDED"},{"id":"autogen_task1_vconsum","status":"SUCCEEDED"},{"id":"autogen_task1_vAK","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.671531,"curves":[{"id":"autogen_curve_task1_GlcX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BPG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ACA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_EtOHX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glyc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GlycX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ACAX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CNX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CNX0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GlcX0","status":"SUCCEEDED"}]}]}]}