Started by upstream project "mango-prb" build number 983 originally caused by: GitHub pull request #559 of commit d2f718bd1bf977f83381bf228ce8757f2b812fcf automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/mango.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/mango.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/mango.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 1337fe88b5df666bf1d2582d52f417acfd03561f (origin/pr/559/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 1337fe88b5df666bf1d2582d52f417acfd03561f FATAL: Could not checkout 1337fe88b5df666bf1d2582d52f417acfd03561f hudson.plugins.git.GitException: Could not checkout 1337fe88b5df666bf1d2582d52f417acfd03561f at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$9.execute(CliGitAPIImpl.java:2185) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:153) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:146) at hudson.remoting.UserRequest.perform(UserRequest.java:120) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:326) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) at ......remote call to research-jenkins-worker-09(Native Method) at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416) at hudson.remoting.UserResponse.retrieve(UserRequest.java:220) at hudson.remoting.Channel.call(Channel.java:781) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler.execute(RemoteGitImpl.java:146) at sun.reflect.GeneratedMethodAccessor612.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler.invoke(RemoteGitImpl.java:132) at com.sun.proxy.$Proxy63.execute(Unknown Source) at hudson.plugins.git.GitSCM.checkout(GitSCM.java:1155) at hudson.scm.SCM.checkout(SCM.java:485) at hudson.model.AbstractProject.checkout(AbstractProject.java:1269) at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:607) at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86) at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:529) at hudson.model.Run.execute(Run.java:1738) at hudson.matrix.MatrixRun.run(MatrixRun.java:146) at hudson.model.ResourceController.execute(ResourceController.java:98) at hudson.model.Executor.run(Executor.java:410) Caused by: hudson.plugins.git.GitException: Command "git checkout -f 1337fe88b5df666bf1d2582d52f417acfd03561f" returned status code 128: stdout: stderr: fatal: reference is not a tree: 1337fe88b5df666bf1d2582d52f417acfd03561f at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:1877) at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.access$800(CliGitAPIImpl.java:71) at org.jenkinsci.plugins.gitclient.CliGitAPIImpl$9.execute(CliGitAPIImpl.java:2162) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:153) at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:146) at hudson.remoting.UserRequest.perform(UserRequest.java:120) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:326) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Finished: FAILURE