{"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 0 450 0 --:--:-- --:--:-- --:--:-- 451\n\r100 2096k 100 2096k 0 0 4429k 0 --:--:-- --:--:-- --:--:-- 4429k\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 (20.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/rawLog.txt\nCompleted 112.5 KiB/112.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n adding: outputs/ (stored 0%)\n adding: outputs/log.yml (deflated 94%)\n adding: outputs/BIOMD0000000255_url.sedml/ (stored 0%)\n adding: outputs/BIOMD0000000255_url.sedml/autogen_plot_for_task1.pdf (deflated 22%)\n adding: outputs/reports.h5 (deflated 13%)\n adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/3.4 MiB (4.5 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/3.4 MiB (8.0 MiB/s) with 1 file(s) remaining\rCompleted 768.0 KiB/3.4 MiB (11.2 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/3.4 MiB (14.5 MiB/s) with 1 file(s) remaining \rCompleted 1.2 MiB/3.4 MiB (16.9 MiB/s) with 1 file(s) remaining \rCompleted 1.5 MiB/3.4 MiB (19.7 MiB/s) with 1 file(s) remaining \rCompleted 1.8 MiB/3.4 MiB (21.5 MiB/s) with 1 file(s) remaining \rCompleted 2.0 MiB/3.4 MiB (23.9 MiB/s) with 1 file(s) remaining \rCompleted 2.2 MiB/3.4 MiB (26.3 MiB/s) with 1 file(s) remaining \rCompleted 2.5 MiB/3.4 MiB (28.1 MiB/s) with 1 file(s) remaining \rCompleted 2.8 MiB/3.4 MiB (30.3 MiB/s) with 1 file(s) remaining \rCompleted 3.0 MiB/3.4 MiB (32.5 MiB/s) with 1 file(s) remaining \rCompleted 3.2 MiB/3.4 MiB (34.6 MiB/s) with 1 file(s) remaining \rCompleted 3.4 MiB/3.4 MiB (17.7 MiB/s) with 1 file(s) remaining \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/outputs/reports.h5\nCompleted 256.0 KiB/3.0 MiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 512.0 KiB/3.0 MiB (5.2 MiB/s) with 4 file(s) remaining\rCompleted 768.0 KiB/3.0 MiB (7.7 MiB/s) with 4 file(s) remaining\rCompleted 1.0 MiB/3.0 MiB (9.7 MiB/s) with 4 file(s) remaining \rCompleted 1.0 MiB/3.0 MiB (9.5 MiB/s) with 4 file(s) remaining \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/outputs/plots.zip\nCompleted 1.0 MiB/3.0 MiB (9.5 MiB/s) with 3 file(s) remaining\rCompleted 1.3 MiB/3.0 MiB (11.5 MiB/s) with 3 file(s) remaining\rCompleted 1.5 MiB/3.0 MiB (13.4 MiB/s) with 3 file(s) remaining\rCompleted 1.8 MiB/3.0 MiB (15.3 MiB/s) with 3 file(s) remaining\rCompleted 2.0 MiB/3.0 MiB (17.2 MiB/s) with 3 file(s) remaining\rCompleted 2.3 MiB/3.0 MiB (19.1 MiB/s) with 3 file(s) remaining\rCompleted 2.5 MiB/3.0 MiB (20.9 MiB/s) with 3 file(s) remaining\rCompleted 2.8 MiB/3.0 MiB (22.8 MiB/s) with 3 file(s) remaining\rCompleted 2.8 MiB/3.0 MiB (20.8 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/rawLog.txt\nCompleted 2.8 MiB/3.0 MiB (20.8 MiB/s) with 2 file(s) remaining\rCompleted 2.8 MiB/3.0 MiB (19.5 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000255_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/outputs/BIOMD0000000255_url.sedml/autogen_plot_for_task1.pdf\nCompleted 2.8 MiB/3.0 MiB (19.5 MiB/s) with 1 file(s) remaining\rCompleted 3.0 MiB/3.0 MiB (13.4 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive: archive.omex\n inflating: contents/BIOMD0000000255-biopax2.owl \n inflating: contents/BIOMD0000000255-biopax3.owl \n inflating: contents/BIOMD0000000255-matlab.m \n inflating: contents/BIOMD0000000255.m \n inflating: contents/BIOMD0000000255.ode \n inflating: contents/BIOMD0000000255.pdf \n inflating: contents/BIOMD0000000255.png \n inflating: contents/BIOMD0000000255.svg \n inflating: contents/BIOMD0000000255_url.sedml \n inflating: contents/BIOMD0000000255_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 256.0 KiB/~9.4 MiB (5.0 MiB/s) with ~11 file(s) remaining (calculating...)\rCompleted 512.0 KiB/~9.4 MiB (8.9 MiB/s) with ~12 file(s) remaining (calculating...)\rCompleted 768.0 KiB/~9.4 MiB (12.6 MiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 1.0 MiB/~9.4 MiB (16.3 MiB/s) with ~13 file(s) remaining (calculating...) \rCompleted 1.2 MiB/~9.4 MiB (18.8 MiB/s) with ~13 file(s) remaining (calculating...) \rCompleted 1.5 MiB/~9.4 MiB (22.4 MiB/s) with ~13 file(s) remaining (calculating...) \rCompleted 1.8 MiB/~9.4 MiB (24.4 MiB/s) with ~13 file(s) remaining (calculating...) \rCompleted 2.0 MiB/9.4 MiB (24.1 MiB/s) with 14 file(s) remaining \rCompleted 2.2 MiB/9.4 MiB (24.1 MiB/s) with 14 file(s) remaining \rCompleted 2.5 MiB/9.4 MiB (26.0 MiB/s) with 14 file(s) remaining \rCompleted 2.8 MiB/9.4 MiB (26.9 MiB/s) with 14 file(s) remaining \rCompleted 3.0 MiB/9.4 MiB (27.9 MiB/s) with 14 file(s) remaining \rCompleted 3.2 MiB/9.4 MiB (26.2 MiB/s) with 14 file(s) remaining \rCompleted 3.3 MiB/9.4 MiB (25.5 MiB/s) with 14 file(s) remaining \rupload: contents/BIOMD0000000255.svg to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255.svg\nCompleted 3.3 MiB/9.4 MiB (25.5 MiB/s) with 13 file(s) remaining\rCompleted 3.5 MiB/9.4 MiB (26.9 MiB/s) with 13 file(s) remaining\rCompleted 3.8 MiB/9.4 MiB (28.6 MiB/s) with 13 file(s) remaining\rCompleted 3.8 MiB/9.4 MiB (27.7 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000255-matlab.m to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255-matlab.m\nCompleted 3.8 MiB/9.4 MiB (27.7 MiB/s) with 12 file(s) remaining\rCompleted 4.0 MiB/9.4 MiB (29.3 MiB/s) with 12 file(s) remaining\rCompleted 4.3 MiB/9.4 MiB (30.9 MiB/s) with 12 file(s) remaining\rCompleted 4.5 MiB/9.4 MiB (31.4 MiB/s) with 12 file(s) remaining\rCompleted 4.8 MiB/9.4 MiB (33.0 MiB/s) with 12 file(s) remaining\rCompleted 5.0 MiB/9.4 MiB (34.0 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000255-biopax3.owl to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255-biopax3.owl\nCompleted 5.0 MiB/9.4 MiB (34.0 MiB/s) with 11 file(s) remaining\rCompleted 5.2 MiB/9.4 MiB (33.4 MiB/s) with 11 file(s) remaining\rCompleted 5.2 MiB/9.4 MiB (31.1 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000255-biopax2.owl to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255-biopax2.owl\nCompleted 5.2 MiB/9.4 MiB (31.1 MiB/s) with 10 file(s) remaining\rCompleted 5.3 MiB/9.4 MiB (29.8 MiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/curation_image.png\nCompleted 5.3 MiB/9.4 MiB (29.8 MiB/s) with 9 file(s) remaining\rCompleted 5.3 MiB/9.4 MiB (28.4 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/manifest.xml\nCompleted 5.3 MiB/9.4 MiB (28.4 MiB/s) with 8 file(s) remaining\rCompleted 5.3 MiB/9.4 MiB (28.1 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000255.png to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255.png\nCompleted 5.3 MiB/9.4 MiB (28.1 MiB/s) with 7 file(s) remaining\rCompleted 5.3 MiB/9.4 MiB (28.1 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000255_url.sedml to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255_url.sedml\nCompleted 5.3 MiB/9.4 MiB (28.1 MiB/s) with 6 file(s) remaining\rCompleted 5.3 MiB/9.4 MiB (27.7 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/curation_notes.txt\nCompleted 5.3 MiB/9.4 MiB (27.7 MiB/s) with 5 file(s) remaining\rCompleted 5.6 MiB/9.4 MiB (28.1 MiB/s) with 5 file(s) remaining\rCompleted 5.8 MiB/9.4 MiB (29.3 MiB/s) with 5 file(s) remaining\rCompleted 6.1 MiB/9.4 MiB (30.4 MiB/s) with 5 file(s) remaining\rCompleted 6.3 MiB/9.4 MiB (30.8 MiB/s) with 5 file(s) remaining\rCompleted 6.4 MiB/9.4 MiB (30.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000255.m to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255.m\nCompleted 6.4 MiB/9.4 MiB (30.8 MiB/s) with 4 file(s) remaining\rCompleted 6.6 MiB/9.4 MiB (31.9 MiB/s) with 4 file(s) remaining\rCompleted 6.7 MiB/9.4 MiB (32.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000255_url.xml to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255_url.xml\nCompleted 6.7 MiB/9.4 MiB (32.0 MiB/s) with 3 file(s) remaining\rCompleted 6.9 MiB/9.4 MiB (33.1 MiB/s) with 3 file(s) remaining\rCompleted 7.2 MiB/9.4 MiB (34.1 MiB/s) with 3 file(s) remaining\rCompleted 7.4 MiB/9.4 MiB (35.1 MiB/s) with 3 file(s) remaining\rCompleted 7.7 MiB/9.4 MiB (35.9 MiB/s) with 3 file(s) remaining\rCompleted 7.9 MiB/9.4 MiB (36.9 MiB/s) with 3 file(s) remaining\rCompleted 8.2 MiB/9.4 MiB (37.9 MiB/s) with 3 file(s) remaining\rCompleted 8.4 MiB/9.4 MiB (38.9 MiB/s) with 3 file(s) remaining\rCompleted 8.7 MiB/9.4 MiB (39.9 MiB/s) with 3 file(s) remaining\rCompleted 8.9 MiB/9.4 MiB (40.9 MiB/s) with 3 file(s) remaining\rCompleted 8.9 MiB/9.4 MiB (40.7 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/metadata.rdf\nCompleted 8.9 MiB/9.4 MiB (40.7 MiB/s) with 2 file(s) remaining\rCompleted 9.2 MiB/9.4 MiB (41.7 MiB/s) with 2 file(s) remaining\rCompleted 9.4 MiB/9.4 MiB (40.5 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000255.ode to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255.ode\nCompleted 9.4 MiB/9.4 MiB (40.5 MiB/s) with 1 file(s) remaining\rCompleted 9.4 MiB/9.4 MiB (25.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000255.pdf to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/contents/BIOMD0000000255.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 12.1 KiB/12.1 KiB (177.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f1326262268786a35f07/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000255_url.sedml\ncreating dataset /BIOMD0000000255_url.sedml/autogen_plot_for_task1, shape: (505, 1001), type: float64\ndataset created, uuid: d-84748f64-62277360-45a6-0da082-d7b4b6, chunk_size: (256, 1001)\ncreating dataset /BIOMD0000000255_url.sedml/autogen_report_for_task1, shape: (1576, 1001), type: float64\ndataset created, uuid: d-84748f64-62277360-c01d-7cade9-7df565, chunk_size: (396, 504)\ncreating attribute combineArchiveLocation in /BIOMD0000000255_url.sedml\ncreating attribute uri in /BIOMD0000000255_url.sedml\ncreating attribute _type in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000255_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000255_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000255_url.sedml\ncreate_links: /BIOMD0000000255_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000255_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000255_url.sedml/autogen_plot_for_task1, shape: (505, 1001), type: float64\niterating over chunks for /BIOMD0000000255_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 256, 1), slice(0, 1001, 1))\nwriting dataset data for slice: (slice(256, 505, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000255_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000255_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000255_url.sedml/autogen_report_for_task1, shape: (1576, 1001), type: float64\niterating over chunks for /BIOMD0000000255_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 396, 1), slice(0, 504, 1))\nwriting dataset data for slice: (slice(0, 396, 1), slice(504, 1001, 1))\nwriting dataset data for slice: (slice(396, 792, 1), slice(0, 504, 1))\nwriting dataset data for slice: (slice(396, 792, 1), slice(504, 1001, 1))\nwriting dataset data for slice: (slice(792, 1188, 1), slice(0, 504, 1))\nwriting dataset data for slice: (slice(792, 1188, 1), slice(504, 1001, 1))\nwriting dataset data for slice: (slice(1188, 1576, 1), slice(0, 504, 1))\nwriting dataset data for slice: (slice(1188, 1576, 1), slice(504, 1001, 1))\ndone with dataload for /BIOMD0000000255_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f1326262268786a35f07\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 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.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":30.166554,"sedDocuments":[{"location":"BIOMD0000000255_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 BIOMD0000000255_url.sedml:\r\n Tasks (1):\r\n task1\r\n Reports (1):\r\n autogen_report_for_task1: 1576 data sets\r\n Plots (1):\r\n autogen_plot_for_task1: 504 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000255_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` 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