{"status":"QUEUED","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    487      0 --:--:-- --:--:-- --:--:--   487\n\r100  8231  100  8231    0     0  20667      0 --:--:-- --:--:-- --:--:-- 20667\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\ndocker: Command recieved::<-i /root/archive.omex -o /root/outputs>\n<-i>\nDefault case selected\nVCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\n INFO (CLIStandalone:36) - Starting Vcell... []{}\n INFO (BiosimulationsCommand:92) - Beginning execution []{}\n INFO (CLIPythonManager:116) - Initializing Python... []{}\n INFO (CLIPythonManager:136) - Python initialization success! []{}\n INFO (ExecuteImpl:133) - Preparing output directory... []{}\nERROR (RunUtils:508) - java.lang.Exception: File '/root/outputs' could not be deleted! []{}\n INFO (ExecutionJob:84) - Executing OMEX archive /root/archive.omex []{}\n-----------------------------------------------------------------------------------------------------\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ec84538d-4767-4bfc-a920-946dee234a8615842134608936751059 []{}\nERROR (ExecutionJob:101) - Error for archive /root/archive.omex []{}\n | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message\nERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}\njava.lang.RuntimeException: Error for archive /root/archive.omex\n\tat org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:252) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]\n\tat picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]\n\tat org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]\nCaused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: \n\tat org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\t... 14 more\nCaused by: java.nio.file.FileSystemException: /metadata.rdf: Read-only file system\n\tat java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source) ~[?:?]\n\tat java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[?:?]\n\tat java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[?:?]\n\tat java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(Unknown Source) ~[?:?]\n\tat java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(Unknown Source) ~[?:?]\n\tat java.base/java.nio.file.Files.newOutputStream(Unknown Source) ~[?:?]\n\tat java.base/java.nio.file.Files.write(Unknown Source) ~[?:?]\n\tat org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:88) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\tat org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]\n\t... 14 more\nsrun: error: xanadu-69: task 0: Exited with exit code 1\nsrun: Terminating job step 8581703.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 5.7 KiB/5.7 KiB (74.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 4.5 KiB/4.5 KiB (58.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 90%)\n  adding: rawLog.txt (deflated 74%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 2.5 KiB/9.1 KiB (33.5 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/output.zip\nCompleted 2.5 KiB/9.1 KiB (33.5 KiB/s) with 1 file(s) remaining\rCompleted 9.1 KiB/9.1 KiB (83.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/BIOMD0000000001_url.sedml  \n  inflating: contents/BIOMD0000000001_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 35.4 KiB/85.3 KiB (342.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000001_url.sedml to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/contents/BIOMD0000000001_url.sedml\nCompleted 35.4 KiB/85.3 KiB (342.1 KiB/s) with 2 file(s) remaining\rCompleted 36.0 KiB/85.3 KiB (322.2 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/contents/manifest.xml\nCompleted 36.0 KiB/85.3 KiB (322.2 KiB/s) with 1 file(s) remaining\rCompleted 85.3 KiB/85.3 KiB (693.9 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000001_url.xml to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/contents/BIOMD0000000001_url.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 8.3 KiB/8.3 KiB (103.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;31mPost the SED-ML file to the API ... failed due to: Failed to post SED-ML specs:\nThere was an error uploading the SED-ML specifications to the API.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":null,"sedDocuments":[{"location":"BIOMD0000000001_url.sedml","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"tasks":[{"id":"task1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"autogen_plot_for_task1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"curves":[{"id":"autogen_curve_task1_BLL","status":"QUEUED"},{"id":"autogen_curve_task1_IL","status":"QUEUED"},{"id":"autogen_curve_task1_AL","status":"QUEUED"},{"id":"autogen_curve_task1_A","status":"QUEUED"},{"id":"autogen_curve_task1_BL","status":"QUEUED"},{"id":"autogen_curve_task1_B","status":"QUEUED"},{"id":"autogen_curve_task1_DLL","status":"QUEUED"},{"id":"autogen_curve_task1_D","status":"QUEUED"},{"id":"autogen_curve_task1_ILL","status":"QUEUED"},{"id":"autogen_curve_task1_DL","status":"QUEUED"},{"id":"autogen_curve_task1_I","status":"QUEUED"},{"id":"autogen_curve_task1_ALL","status":"QUEUED"}]},{"id":"autogen_report_for_task1","status":"QUEUED","exception":null,"skipReason":null,"output":null,"duration":null,"dataSets":[{"id":"autogen_time_for_task1","status":"QUEUED"},{"id":"autogen_task1_BLL","status":"QUEUED"},{"id":"autogen_task1_IL","status":"QUEUED"},{"id":"autogen_task1_AL","status":"QUEUED"},{"id":"autogen_task1_A","status":"QUEUED"},{"id":"autogen_task1_BL","status":"QUEUED"},{"id":"autogen_task1_B","status":"QUEUED"},{"id":"autogen_task1_DLL","status":"QUEUED"},{"id":"autogen_task1_D","status":"QUEUED"},{"id":"autogen_task1_ILL","status":"QUEUED"},{"id":"autogen_task1_DL","status":"QUEUED"},{"id":"autogen_task1_I","status":"QUEUED"},{"id":"autogen_task1_ALL","status":"QUEUED"},{"id":"autogen_task1_kf_0","status":"QUEUED"},{"id":"autogen_task1_kr_0","status":"QUEUED"},{"id":"autogen_task1_kf_1","status":"QUEUED"},{"id":"autogen_task1_kr_1","status":"QUEUED"},{"id":"autogen_task1_kf_2","status":"QUEUED"},{"id":"autogen_task1_kr_2","status":"QUEUED"},{"id":"autogen_task1_kf_3","status":"QUEUED"},{"id":"autogen_task1_kr_3","status":"QUEUED"},{"id":"autogen_task1_kf_4","status":"QUEUED"},{"id":"autogen_task1_kr_4","status":"QUEUED"},{"id":"autogen_task1_kf_5","status":"QUEUED"},{"id":"autogen_task1_kr_5","status":"QUEUED"},{"id":"autogen_task1_kf_6","status":"QUEUED"},{"id":"autogen_task1_kr_6","status":"QUEUED"},{"id":"autogen_task1_kf_7","status":"QUEUED"},{"id":"autogen_task1_kr_7","status":"QUEUED"},{"id":"autogen_task1_kf_8","status":"QUEUED"},{"id":"autogen_task1_kr_8","status":"QUEUED"},{"id":"autogen_task1_kf_9","status":"QUEUED"},{"id":"autogen_task1_kr_9","status":"QUEUED"},{"id":"autogen_task1_kf_10","status":"QUEUED"},{"id":"autogen_task1_kr_10","status":"QUEUED"},{"id":"autogen_task1_kf_11","status":"QUEUED"},{"id":"autogen_task1_kr_11","status":"QUEUED"},{"id":"autogen_task1_kf_12","status":"QUEUED"},{"id":"autogen_task1_kr_12","status":"QUEUED"},{"id":"autogen_task1_kf_13","status":"QUEUED"},{"id":"autogen_task1_kr_13","status":"QUEUED"},{"id":"autogen_task1_kf_14","status":"QUEUED"},{"id":"autogen_task1_kr_14","status":"QUEUED"},{"id":"autogen_task1_kf_15","status":"QUEUED"},{"id":"autogen_task1_kr_15","status":"QUEUED"},{"id":"autogen_task1_kf_16","status":"QUEUED"},{"id":"autogen_task1_kr_16","status":"QUEUED"},{"id":"autogen_task1_t2","status":"QUEUED"},{"id":"autogen_task1_comp1","status":"QUEUED"},{"id":"autogen_task1_React0","status":"QUEUED"},{"id":"autogen_task1_React1","status":"QUEUED"},{"id":"autogen_task1_React2","status":"QUEUED"},{"id":"autogen_task1_React3","status":"QUEUED"},{"id":"autogen_task1_React4","status":"QUEUED"},{"id":"autogen_task1_React5","status":"QUEUED"},{"id":"autogen_task1_React6","status":"QUEUED"},{"id":"autogen_task1_React7","status":"QUEUED"},{"id":"autogen_task1_React8","status":"QUEUED"},{"id":"autogen_task1_React9","status":"QUEUED"},{"id":"autogen_task1_React10","status":"QUEUED"},{"id":"autogen_task1_React11","status":"QUEUED"},{"id":"autogen_task1_React12","status":"QUEUED"},{"id":"autogen_task1_React13","status":"QUEUED"},{"id":"autogen_task1_React14","status":"QUEUED"},{"id":"autogen_task1_React15","status":"QUEUED"},{"id":"autogen_task1_React16","status":"QUEUED"}]}]}]}