simple	29-Jan-2020 15:08:31	Build Clowder - extractors-core - cert-pyclowder-install - Default Job #1 (CATS-EXCORE13-JOB1-1) started building on agent buildserver-3.os.ncsa.edu
simple	29-Jan-2020 15:08:31	Remote agent on host buildserver-3.os.ncsa.edu
simple	29-Jan-2020 15:08:31	Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1
simple	29-Jan-2020 15:08:31	Executing build Clowder - extractors-core - cert-pyclowder-install - Default Job #1 (CATS-EXCORE13-JOB1-1)
simple	29-Jan-2020 15:08:31	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	29-Jan-2020 15:08:31	Checking out into /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1
simple	29-Jan-2020 15:08:31	Updating source code to revision: 7e6a415e09e2919ede79c05c285de803340648eb
simple	29-Jan-2020 15:08:31	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git'.
simple	29-Jan-2020 15:08:31	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git/
simple	29-Jan-2020 15:08:31	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'. Will try to do a shallow fetch.
simple	29-Jan-2020 15:08:31	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:32	From ssh://127.0.0.1:38885/cats/extractors-core
simple	29-Jan-2020 15:08:32	 * [new branch]      cert-pyclowder-install -> cert-pyclowder-install
simple	29-Jan-2020 15:08:32	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:32	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:32	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
simple	29-Jan-2020 15:08:32	Warning: failed to checkout source code to directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1', trying to recover...
simple	29-Jan-2020 15:08:32	Cleaned source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1'...
simple	29-Jan-2020 15:08:32	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git'.
simple	29-Jan-2020 15:08:32	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git/
simple	29-Jan-2020 15:08:32	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'.
simple	29-Jan-2020 15:08:32	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:32	From ssh://127.0.0.1:38885/cats/extractors-core
simple	29-Jan-2020 15:08:32	 * [new branch]      cert-pyclowder-install -> cert-pyclowder-install
simple	29-Jan-2020 15:08:32	 * [new tag]         SEAD_2.0   -> SEAD_2.0
simple	29-Jan-2020 15:08:32	 * [new tag]         browndog_v0.2.0 -> browndog_v0.2.0
simple	29-Jan-2020 15:08:32	 * [new tag]         browndog_v0.3.0 -> browndog_v0.3.0
simple	29-Jan-2020 15:08:32	 * [new tag]         v0.9.4     -> v0.9.4
simple	29-Jan-2020 15:08:32	 * [new tag]         v1.0.0     -> v1.0.0
simple	29-Jan-2020 15:08:32	 * [new tag]         v2.0.0     -> v2.0.0
simple	29-Jan-2020 15:08:32	Fetching to source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1' completed, proceeding with checkout...
simple	29-Jan-2020 15:08:32	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:32	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:32	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
simple	29-Jan-2020 15:08:32	Updating source code to revision: 7e6a415e09e2919ede79c05c285de803340648eb
simple	29-Jan-2020 15:08:32	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'. Will try to do a shallow fetch.
simple	29-Jan-2020 15:08:32	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:32	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:32	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:32	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
simple	29-Jan-2020 15:08:32	Warning: failed to checkout source code to directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1', trying to recover...
simple	29-Jan-2020 15:08:32	Cleaned source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1'...
simple	29-Jan-2020 15:08:32	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git'.
simple	29-Jan-2020 15:08:32	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git/
simple	29-Jan-2020 15:08:32	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'.
simple	29-Jan-2020 15:08:32	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:33	From ssh://127.0.0.1:38885/cats/extractors-core
simple	29-Jan-2020 15:08:33	 * [new branch]      cert-pyclowder-install -> cert-pyclowder-install
simple	29-Jan-2020 15:08:33	 * [new tag]         SEAD_2.0   -> SEAD_2.0
simple	29-Jan-2020 15:08:33	 * [new tag]         browndog_v0.2.0 -> browndog_v0.2.0
simple	29-Jan-2020 15:08:33	 * [new tag]         browndog_v0.3.0 -> browndog_v0.3.0
simple	29-Jan-2020 15:08:33	 * [new tag]         v0.9.4     -> v0.9.4
simple	29-Jan-2020 15:08:33	 * [new tag]         v1.0.0     -> v1.0.0
simple	29-Jan-2020 15:08:33	 * [new tag]         v2.0.0     -> v2.0.0
simple	29-Jan-2020 15:08:33	Fetching to source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1' completed, proceeding with checkout...
simple	29-Jan-2020 15:08:33	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:33	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:33	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
simple	29-Jan-2020 15:08:34	Updating source code to revision: 7e6a415e09e2919ede79c05c285de803340648eb
simple	29-Jan-2020 15:08:34	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'. Will try to do a shallow fetch.
simple	29-Jan-2020 15:08:34	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:34	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:34	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:34	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
simple	29-Jan-2020 15:08:34	Warning: failed to checkout source code to directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1', trying to recover...
simple	29-Jan-2020 15:08:34	Cleaned source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1'...
simple	29-Jan-2020 15:08:34	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git'.
simple	29-Jan-2020 15:08:34	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1/.git/
simple	29-Jan-2020 15:08:34	Fetching 'refs/heads/cert-pyclowder-install' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-core.git'.
simple	29-Jan-2020 15:08:34	Warning: Permanently added '[127.0.0.1]:38885' (RSA) to the list of known hosts.
simple	29-Jan-2020 15:08:34	From ssh://127.0.0.1:38885/cats/extractors-core
simple	29-Jan-2020 15:08:34	 * [new branch]      cert-pyclowder-install -> cert-pyclowder-install
simple	29-Jan-2020 15:08:34	 * [new tag]         SEAD_2.0   -> SEAD_2.0
simple	29-Jan-2020 15:08:34	 * [new tag]         browndog_v0.2.0 -> browndog_v0.2.0
simple	29-Jan-2020 15:08:34	 * [new tag]         browndog_v0.3.0 -> browndog_v0.3.0
simple	29-Jan-2020 15:08:34	 * [new tag]         v0.9.4     -> v0.9.4
simple	29-Jan-2020 15:08:34	 * [new tag]         v1.0.0     -> v1.0.0
simple	29-Jan-2020 15:08:34	 * [new tag]         v2.0.0     -> v2.0.0
simple	29-Jan-2020 15:08:34	Fetching to source directory '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1' completed, proceeding with checkout...
simple	29-Jan-2020 15:08:34	Checking out revision 7e6a415e09e2919ede79c05c285de803340648eb.
simple	29-Jan-2020 15:08:34	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:34	Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.
error	29-Jan-2020 15:08:34	Error occurred while running Task 'Checkout Default Repository(1)' of type com.atlassian.bamboo.plugins.vcs:task.vcs.checkout.
error	29-Jan-2020 15:08:34	java.lang.RuntimeException: com.atlassian.bamboo.plugins.stash.repository.StashRepositoryException
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.executor.RetryingTaskExecutor.rerun(RetryingTaskExecutor.java:141)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.executor.RetryingTaskExecutor.runTask(RetryingTaskExecutor.java:99)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.executor.RetryingTaskExecutor.retry(RetryingTaskExecutor.java:207)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.executor.RetryingTaskExecutor.retry(RetryingTaskExecutor.java:188)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.execute(VcsCheckoutTask.java:123)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.task.TaskExecutorImpl.lambda$executeTasks$3(TaskExecutorImpl.java:319)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.task.TaskExecutorImpl.executeTaskWithPrePostActions(TaskExecutorImpl.java:252)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.task.TaskExecutorImpl.executeTasks(TaskExecutorImpl.java:319)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.task.TaskExecutorImpl.executePreparationTasks(TaskExecutorImpl.java:91)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.build.pipeline.tasks.PrepareBuildTask.call(PrepareBuildTask.java:81)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.v2.build.agent.DefaultBuildAgent.executeBuildPhase(DefaultBuildAgent.java:204)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.v2.build.agent.DefaultBuildAgent.build(DefaultBuildAgent.java:176)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.v2.build.agent.BuildAgentControllerImpl.lambda$waitAndPerformBuild$0(BuildAgentControllerImpl.java:131)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.variable.CustomVariableContextImpl.withVariableSubstitutor(CustomVariableContextImpl.java:185)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.v2.build.agent.BuildAgentControllerImpl.waitAndPerformBuild(BuildAgentControllerImpl.java:125)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.v2.build.agent.DefaultBuildAgent$1.run(DefaultBuildAgent.java:127)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.utils.BambooRunnables$1.run(BambooRunnables.java:48)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.security.ImpersonationHelper.runWith(ImpersonationHelper.java:26)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.security.ImpersonationHelper.runWithSystemAuthority(ImpersonationHelper.java:17)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.security.ImpersonationHelper$1.run(ImpersonationHelper.java:41)
error	29-Jan-2020 15:08:34		at java.lang.Thread.run(Thread.java:745)
error	29-Jan-2020 15:08:34	Caused by: com.atlassian.bamboo.plugins.stash.repository.StashRepositoryException
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.retrieveSourceCode(BitbucketServerWorkingCopyManager.java:100)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.fillWorkingDirFromVcs(VcsCheckoutTask.java:206)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask.access$000(VcsCheckoutTask.java:54)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask$1.call(VcsCheckoutTask.java:126)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.vcs.task.VcsCheckoutTask$1.call(VcsCheckoutTask.java:123)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.executor.RetryingTaskExecutor.rerun(RetryingTaskExecutor.java:112)
error	29-Jan-2020 15:08:34		... 20 more
error	29-Jan-2020 15:08:34	Caused by: com.atlassian.bamboo.repository.RepositoryException: Checkout to revision 7e6a415e09e2919ede79c05c285de803340648eb has failed.command [/usr/bin/git checkout -f 7e6a415e09e2919ede79c05c285de803340648eb] failed with code 128. Working directory was [/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1]., stderr:
error	29-Jan-2020 15:08:34	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:493)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.checkout(GitWorkingCopyManager.java:285)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.v2.GitWorkingCopyManager.retrieveSourceCode(GitWorkingCopyManager.java:102)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.stash.v2.BitbucketServerWorkingCopyManager.retrieveSourceCode(BitbucketServerWorkingCopyManager.java:90)
error	29-Jan-2020 15:08:34		... 25 more
error	29-Jan-2020 15:08:34	Caused by: com.atlassian.bamboo.plugins.git.GitCommandException: command [/usr/bin/git checkout -f 7e6a415e09e2919ede79c05c285de803340648eb] failed with code 128. Working directory was [/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-EXCORE13-JOB1]., stderr:
error	29-Jan-2020 15:08:34	fatal: reference is not a tree: 7e6a415e09e2919ede79c05c285de803340648eb
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:728)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:657)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCommand(GitCommandProcessor.java:648)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCheckoutCommandForBranchOrRevision(GitCommandProcessor.java:389)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.GitCommandProcessor.runCheckoutCommand(GitCommandProcessor.java:375)
error	29-Jan-2020 15:08:34		at com.atlassian.bamboo.plugins.git.NativeGitOperationHelper.checkout(NativeGitOperationHelper.java:472)
error	29-Jan-2020 15:08:34		... 28 more
error	29-Jan-2020 15:08:34	Failed to prepare the build 'Clowder - extractors-core - cert-pyclowder-install - Default Job #1 (CATS-EXCORE13-JOB1-1)'
simple	29-Jan-2020 15:08:34	Running on server: post build plugin 'NCover Results Collector'
simple	29-Jan-2020 15:08:34	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	29-Jan-2020 15:08:34	Running on server: post build plugin 'Clover Delta Calculator'
simple	29-Jan-2020 15:08:34	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	29-Jan-2020 15:08:34	All post build plugins have finished
simple	29-Jan-2020 15:08:34	Generating build results summary...
simple	29-Jan-2020 15:08:34	Saving build results to disk...
simple	29-Jan-2020 15:08:34	Logging substituted variables...
simple	29-Jan-2020 15:08:34	Indexing build results...
simple	29-Jan-2020 15:08:34	Finished building CATS-EXCORE13-JOB1-1.