simple	20-Dec-2017 15:33:38	Build Clowder - extractors-msc - bugfix-BD-1903-fix-mscp01-server - Default Job #1 (CATS-MSC3-JOB1-1) started building on agent buildserver-3.os.ncsa.edu
simple	20-Dec-2017 15:33:38	Remote agent on host buildserver-3.os.ncsa.edu
simple	20-Dec-2017 15:33:39	Build working directory is /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1
simple	20-Dec-2017 15:33:39	Executing build Clowder - extractors-msc - bugfix-BD-1903-fix-mscp01-server - Default Job #1 (CATS-MSC3-JOB1-1)
simple	20-Dec-2017 15:33:39	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	20-Dec-2017 15:33:39	Updating source code to revision: 6aaab3692bc88bb1c0016521723c45399615c5f2
simple	20-Dec-2017 15:34:13	Creating local git repository in '/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1/.git'.
simple	20-Dec-2017 15:34:14	Initialized empty Git repository in /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1/.git/
simple	20-Dec-2017 15:34:14	Fetching 'refs/heads/bugfix/BD-1903-fix-mscp01-server' from 'ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git'. Will try to do a shallow fetch.
simple	20-Dec-2017 15:34:14	Warning: Permanently added '[127.0.0.1]:36347' (RSA) to the list of known hosts.
simple	20-Dec-2017 15:34:16	From ssh://127.0.0.1:36347/cats/extractors-msc
simple	20-Dec-2017 15:34:16	 * [new branch]      bugfix/BD-1903-fix-mscp01-server -> bugfix/BD-1903-fix-mscp01-server
simple	20-Dec-2017 15:34:16	 * [new tag]         browndog_v0.2.0 -> browndog_v0.2.0
simple	20-Dec-2017 15:34:16	Checking out revision 6aaab3692bc88bb1c0016521723c45399615c5f2.
simple	20-Dec-2017 15:34:16	Switched to branch 'bugfix/BD-1903-fix-mscp01-server'
simple	20-Dec-2017 15:34:16	Updated source code to revision: 6aaab3692bc88bb1c0016521723c45399615c5f2
simple	20-Dec-2017 15:34:16	Finished task 'Checkout Default Repository' with result: Success
simple	20-Dec-2017 15:34:16	Running pre-build action: VCS Version Collector
simple	20-Dec-2017 15:34:16	Starting task 'docker build' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	20-Dec-2017 15:34:16	Beginning to execute external process for build 'Clowder - extractors-msc - bugfix-BD-1903-fix-mscp01-server - Default Job #1 (CATS-MSC3-JOB1-1)'\n ... running command line: \n/bin/sh docker.sh\n ... in: /home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bugfix/BD-1903-fix-mscp01-server\nbamboo_capability_system_builder_node_Node_js_v6_9_1=/home/bamboo/node-v6.9.1/bin/node\nbamboo_capability_system_builder_command_npm_6=/home/bamboo/node-v6.9.1/bin/npm\nbamboo_capability_system_builder_command_buckminster_4_3=/home/bamboo/buckminster-4.3/buckminster\nbamboo_capability_system_builder_command_buckminster_4_2=/home/bamboo/buckminster-4.2/buckminster\nbamboo_planRepository_1_branchDisplayName=bugfix/BD-1903-fix-mscp01-server\nbamboo_repository_revision_number=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_resultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC3-JOB1-1\nbamboo_capability_system_builder_command_sphinx=/usr/bin/sphinx-build\nbamboo_planRepository_1_name=extractors-msc\nbamboo_build_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1\nbamboo_buildKey=CATS-MSC3-JOB1\nbamboo_capability_system_os=linux\nbamboo_shortPlanName=bugfix-BD-1903-fix-mscp01-server\nbamboo_repository_154271765_git_username=\nbamboo_planRepository_name=extractors-msc\nbamboo_repository_154271765_branch_name=bugfix/BD-1903-fix-mscp01-server\nbamboo_buildNumber=1\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://opensource.ncsa.illinois.edu/bamboo/browse/CATS-MSC3-JOB1-1\nbamboo_planRepository_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_repository_154271765_git_branch=bugfix/BD-1903-fix-mscp01-server\nbamboo_agentId=143032321\nbamboo_planName=Clowder - extractors-msc - bugfix-BD-1903-fix-mscp01-server\nbamboo_shortPlanKey=MSC3\nbamboo_capability_system_builder_command_sbt_0_13=/home/bamboo/sbt-0.13.2/bin/sbt\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_builder_node_Node_js_v0_10_28=/home/bamboo/node-v0.10.28/bin/node\nbamboo_planRepository_revision=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_buildTimeStamp=2017-12-20T15:33:34.646-06:00\nbamboo_capability_system_builder_command_npm=/home/bamboo/node-v0.10.28/bin/npm\nbamboo_capability_system_builder_mvn2_Maven_2=/home/bamboo/apache-maven-2.2.1\nbamboo_buildResultKey=CATS-MSC3-JOB1-1\nbamboo_repository_git_branch=bugfix/BD-1903-fix-mscp01-server\nbamboo_repository_branch_name=bugfix/BD-1903-fix-mscp01-server\nbamboo_buildPlanName=Clowder - extractors-msc - bugfix-BD-1903-fix-mscp01-server - Default Job\nbamboo_planRepository_1_revision=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_capability_system_builder_command_python3=/usr/bin/python3\nbamboo_repository_name=extractors-msc\nbamboo_repository_154271765_revision_number=6aaab3692bc88bb1c0016521723c45399615c5f2\nbamboo_buildFailed=false\nbamboo_repository_154271765_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_capability_system_docker_executable=/usr/bin/docker\nbamboo_capability_system_builder_command_grunt=/home/bamboo/node-v0.10.28/bin/grunt\nbamboo_planRepository_branch=bugfix/BD-1903-fix-mscp01-server\nbamboo_agentWorkingDirectory=/home/bamboo/bamboo-agent-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/usr/bin/git\nbamboo_repository_git_username=\nbamboo_capability_system_builder_sbt_SBT_0_13_13=/home/bamboo/sbt-0.13.13\nbamboo_planRepository_branchDisplayName=bugfix/BD-1903-fix-mscp01-server\nbamboo_capability_system_builder_command_phantomjs=/home/bamboo/phantomjs-1.9.8/bin/phantomjs\nbamboo_planRepository_1_type=bbserver\nbamboo_planRepository_branchName=bugfix/BD-1903-fix-mscp01-server\nbamboo_capability_system_builder_command_python2_7=/usr/bin/python2.7\nbamboo_capability_system_hostname=buildserver-1\nbamboo_repository_154271765_name=extractors-msc\nbamboo_capability_system_jdk_JDK=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_software_mongo=/usr/bin/mongo\nbamboo_plan_storageTag=plan-154075177\nbamboo_capability_system_software_rabbitmq=/usr/sbin/rabbitmqctl\nbamboo_capability_system_builder_command_casperjs=/home/bamboo/node-v0.10.28/bin/casperjs\nbamboo_planRepository_type=bbserver\nbamboo_planRepository_1_username=\nbamboo_capability_system_jdk_JDK_1_8_0_66=/home/bamboo/jdk1.8.0_66\nbamboo_repository_git_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_capability_system_builder_node_Node_js=/home/bamboo/node-v0.10.28/bin/node\nbamboo_capability_system_builder_ant_Ant=/home/bamboo/apache-ant-1.9.4\nbamboo_capability_system_builder_mvn3_Maven_3=/home/bamboo/apache-maven-3.3.9\nbamboo_working_directory=/home/bamboo/bamboo-agent-home/xml-data/build-dir/CATS-MSC3-JOB1\nbamboo_planKey=CATS-MSC3\nbamboo_planRepository_1_repositoryUrl=ssh://git@opensource.ncsa.illinois.edu:7999/cats/extractors-msc.git\nbamboo_planRepository_username=\nbamboo_capability_system_jdk_JDK_1_8=/home/bamboo/jdk1.8.0_66\nbamboo_capability_system_jdk_JDK_1_6=/home/bamboo/jdk1.6.0_41\nbamboo_capability_system_builder_command_mkcrx=/home/bamboo/mkcrx/mkcrx.sh\nbamboo_capability_system_jdk_JDK_1_7=/home/bamboo/jdk1.7.0_60\nbamboo_planRepository_1_branchName=bugfix/BD-1903-fix-mscp01-server\n
build	20-Dec-2017 15:36:02	Sending build context to Docker daemon 2.284 MB
build	20-Dec-2017 15:36:02	
build	20-Dec-2017 15:36:02	Step 1/11 : FROM clowder/pyclowder:1
build	20-Dec-2017 15:36:03	1: Pulling from clowder/pyclowder
build	20-Dec-2017 15:36:03	9fb6c798fa41: Pulling fs layer
build	20-Dec-2017 15:36:03	3b61febd4aef: Pulling fs layer
build	20-Dec-2017 15:36:03	9d99b9777eb0: Pulling fs layer
build	20-Dec-2017 15:36:03	d010c8cf75d7: Pulling fs layer
build	20-Dec-2017 15:36:03	7fac07fb303e: Pulling fs layer
build	20-Dec-2017 15:36:03	7ed77dc4484e: Pulling fs layer
build	20-Dec-2017 15:36:03	8703bf9e3153: Pulling fs layer
build	20-Dec-2017 15:36:03	1797373d3c97: Pulling fs layer
build	20-Dec-2017 15:36:03	bc81e92cfe84: Pulling fs layer
build	20-Dec-2017 15:36:03	7ed77dc4484e: Waiting
build	20-Dec-2017 15:36:03	1797373d3c97: Waiting
build	20-Dec-2017 15:36:03	bc81e92cfe84: Waiting
build	20-Dec-2017 15:36:03	8703bf9e3153: Waiting
build	20-Dec-2017 15:36:03	3b61febd4aef: Verifying Checksum
build	20-Dec-2017 15:36:03	3b61febd4aef: Download complete
build	20-Dec-2017 15:36:03	9d99b9777eb0: Download complete
build	20-Dec-2017 15:36:03	7fac07fb303e: Verifying Checksum
build	20-Dec-2017 15:36:03	7fac07fb303e: Download complete
build	20-Dec-2017 15:36:03	d010c8cf75d7: Verifying Checksum
build	20-Dec-2017 15:36:03	d010c8cf75d7: Download complete
build	20-Dec-2017 15:36:03	8703bf9e3153: Download complete
build	20-Dec-2017 15:36:04	1797373d3c97: Verifying Checksum
build	20-Dec-2017 15:36:04	1797373d3c97: Download complete
build	20-Dec-2017 15:36:04	9fb6c798fa41: Verifying Checksum
build	20-Dec-2017 15:36:04	9fb6c798fa41: Download complete
build	20-Dec-2017 15:36:04	7ed77dc4484e: Verifying Checksum
build	20-Dec-2017 15:36:04	7ed77dc4484e: Download complete
build	20-Dec-2017 15:36:04	bc81e92cfe84: Download complete
build	20-Dec-2017 15:36:08	9fb6c798fa41: Pull complete
build	20-Dec-2017 15:36:08	3b61febd4aef: Pull complete
build	20-Dec-2017 15:36:08	9d99b9777eb0: Pull complete
build	20-Dec-2017 15:36:09	d010c8cf75d7: Pull complete
build	20-Dec-2017 15:36:09	7fac07fb303e: Pull complete
build	20-Dec-2017 15:36:11	7ed77dc4484e: Pull complete
build	20-Dec-2017 15:36:11	8703bf9e3153: Pull complete
build	20-Dec-2017 15:36:11	1797373d3c97: Pull complete
build	20-Dec-2017 15:36:11	bc81e92cfe84: Pull complete
build	20-Dec-2017 15:36:11	Digest: sha256:c54f3dbe5c8afe1aaadf070212c982dc7b46a6c070aaed30edf17e59e5698316
build	20-Dec-2017 15:36:11	Status: Downloaded newer image for clowder/pyclowder:1
build	20-Dec-2017 15:36:11	 ---> d1a9e970ed30
build	20-Dec-2017 15:36:11	Step 2/11 : MAINTAINER Rob Kooper <kooper@illinois.edu>
build	20-Dec-2017 15:36:11	 ---> Running in d1e572bee4f8
build	20-Dec-2017 15:36:11	 ---> 0c3d83c8dd5a
build	20-Dec-2017 15:36:11	Removing intermediate container d1e572bee4f8
build	20-Dec-2017 15:36:11	Step 3/11 : VOLUME /matlab
build	20-Dec-2017 15:36:12	 ---> Running in ef4bee8f7f9b
build	20-Dec-2017 15:36:12	 ---> ae5e911d68dd
build	20-Dec-2017 15:36:12	Removing intermediate container ef4bee8f7f9b
build	20-Dec-2017 15:36:12	Step 4/11 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.diagnosis" MATLAB_BINARY "/matlab/bin/matlab" MAIN_SCRIPT "diagnosis.py"
build	20-Dec-2017 15:36:15	 ---> Running in 26d9188d4213
build	20-Dec-2017 15:36:17	 ---> 84657bbf52c3
build	20-Dec-2017 15:36:17	Removing intermediate container 26d9188d4213
build	20-Dec-2017 15:36:17	Step 5/11 : USER root
build	20-Dec-2017 15:36:17	 ---> Running in 5bb581027c68
build	20-Dec-2017 15:36:17	 ---> 3078e2128f2a
build	20-Dec-2017 15:36:18	Removing intermediate container 5bb581027c68
build	20-Dec-2017 15:36:18	Step 6/11 : RUN pip install --upgrade pip
build	20-Dec-2017 15:36:18	 ---> Running in 4de8e4c50caf
build	20-Dec-2017 15:36:19	Collecting pip
build	20-Dec-2017 15:36:19	  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
build	20-Dec-2017 15:36:19	Installing collected packages: pip
build	20-Dec-2017 15:36:19	  Found existing installation: pip 8.1.1
build	20-Dec-2017 15:36:19	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	20-Dec-2017 15:36:20	Successfully installed pip-9.0.1
build	20-Dec-2017 15:36:20	 ---> d9c94ca0bec0
build	20-Dec-2017 15:36:20	Removing intermediate container 4de8e4c50caf
build	20-Dec-2017 15:36:20	Step 7/11 : RUN apt-get -qq -y update && apt-get -y install         libxext6         libxmu6         libxt6         wget     && mkdir -p /matlab     && rm -rf /var/lib/apt/lists/*
build	20-Dec-2017 15:36:21	 ---> Running in eb51b6240594
build	20-Dec-2017 15:36:25	Reading package lists...
build	20-Dec-2017 15:36:26	Building dependency tree...
build	20-Dec-2017 15:36:26	Reading state information...
build	20-Dec-2017 15:36:26	The following additional packages will be installed:
build	20-Dec-2017 15:36:26	  libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
build	20-Dec-2017 15:36:26	  x11-common
build	20-Dec-2017 15:36:26	The following NEW packages will be installed:
build	20-Dec-2017 15:36:26	  libice6 libidn11 libsm6 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
build	20-Dec-2017 15:36:26	  libxext6 libxmu6 libxt6 wget x11-common
build	20-Dec-2017 15:36:26	0 upgraded, 13 newly installed, 0 to remove and 16 not upgraded.
build	20-Dec-2017 15:36:26	Need to get 1402 kB of archives.
build	20-Dec-2017 15:36:26	After this operation, 5596 kB of additional disk space will be used.
build	20-Dec-2017 15:36:26	Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B]
build	20-Dec-2017 15:36:26	Get:2 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxdmcp6 amd64 1:1.1.2-1.1 [11.0 kB]
build	20-Dec-2017 15:36:26	Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxcb1 amd64 1.11.1-1ubuntu1 [40.0 kB]
build	20-Dec-2017 15:36:26	Get:4 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-data all 2:1.6.3-1ubuntu2 [113 kB]
build	20-Dec-2017 15:36:26	Get:5 http://archive.ubuntu.com/ubuntu xenial/main amd64 libx11-6 amd64 2:1.6.3-1ubuntu2 [571 kB]
build	20-Dec-2017 15:36:27	Get:6 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB]
build	20-Dec-2017 15:36:27	Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 x11-common all 1:7.7+13ubuntu3 [22.4 kB]
build	20-Dec-2017 15:36:27	Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libice6 amd64 2:1.0.9-1 [39.2 kB]
build	20-Dec-2017 15:36:27	Get:9 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB]
build	20-Dec-2017 15:36:27	Get:10 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.2 [46.5 kB]
build	20-Dec-2017 15:36:27	Get:11 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 wget amd64 1.17.1-1ubuntu1.3 [299 kB]
build	20-Dec-2017 15:36:27	Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxt6 amd64 1:1.1.5-0ubuntu1 [160 kB]
build	20-Dec-2017 15:36:27	Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB]
build	20-Dec-2017 15:36:27	debconf: delaying package configuration, since apt-utils is not installed
build	20-Dec-2017 15:36:27	Fetched 1402 kB in 0s (1621 kB/s)
build	20-Dec-2017 15:36:27	Selecting previously unselected package libxau6:amd64.
build	20-Dec-2017 15:36:27	(Reading database ... 
build	20-Dec-2017 15:36:27	(Reading database ... 5%
build	20-Dec-2017 15:36:27	(Reading database ... 10%
build	20-Dec-2017 15:36:27	(Reading database ... 15%
build	20-Dec-2017 15:36:27	(Reading database ... 20%
build	20-Dec-2017 15:36:27	(Reading database ... 25%
build	20-Dec-2017 15:36:27	(Reading database ... 30%
build	20-Dec-2017 15:36:27	(Reading database ... 35%
build	20-Dec-2017 15:36:27	(Reading database ... 40%
build	20-Dec-2017 15:36:27	(Reading database ... 45%
build	20-Dec-2017 15:36:27	(Reading database ... 50%
build	20-Dec-2017 15:36:27	(Reading database ... 55%
build	20-Dec-2017 15:36:27	(Reading database ... 60%
build	20-Dec-2017 15:36:27	(Reading database ... 65%
build	20-Dec-2017 15:36:27	(Reading database ... 70%
build	20-Dec-2017 15:36:27	(Reading database ... 75%
build	20-Dec-2017 15:36:27	(Reading database ... 80%
build	20-Dec-2017 15:36:27	(Reading database ... 85%
build	20-Dec-2017 15:36:27	(Reading database ... 90%
build	20-Dec-2017 15:36:27	(Reading database ... 95%
build	20-Dec-2017 15:36:27	(Reading database ... 100%
build	20-Dec-2017 15:36:27	(Reading database ... 6101 files and directories currently installed.)
build	20-Dec-2017 15:36:27	Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ...
build	20-Dec-2017 15:36:27	Unpacking libxau6:amd64 (1:1.0.8-1) ...
build	20-Dec-2017 15:36:27	Selecting previously unselected package libxdmcp6:amd64.
build	20-Dec-2017 15:36:27	Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_amd64.deb ...
build	20-Dec-2017 15:36:27	Unpacking libxdmcp6:amd64 (1:1.1.2-1.1) ...
build	20-Dec-2017 15:36:27	Selecting previously unselected package libxcb1:amd64.
build	20-Dec-2017 15:36:27	Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_amd64.deb ...
build	20-Dec-2017 15:36:27	Unpacking libxcb1:amd64 (1.11.1-1ubuntu1) ...
build	20-Dec-2017 15:36:27	Selecting previously unselected package libx11-data.
build	20-Dec-2017 15:36:27	Preparing to unpack .../libx11-data_2%3a1.6.3-1ubuntu2_all.deb ...
build	20-Dec-2017 15:36:27	Unpacking libx11-data (2:1.6.3-1ubuntu2) ...
build	20-Dec-2017 15:36:28	Selecting previously unselected package libx11-6:amd64.
build	20-Dec-2017 15:36:28	Preparing to unpack .../libx11-6_2%3a1.6.3-1ubuntu2_amd64.deb ...
build	20-Dec-2017 15:36:28	Unpacking libx11-6:amd64 (2:1.6.3-1ubuntu2) ...
build	20-Dec-2017 15:36:28	Selecting previously unselected package libxext6:amd64.
build	20-Dec-2017 15:36:28	Preparing to unpack .../libxext6_2%3a1.3.3-1_amd64.deb ...
build	20-Dec-2017 15:36:28	Unpacking libxext6:amd64 (2:1.3.3-1) ...
build	20-Dec-2017 15:36:29	Selecting previously unselected package x11-common.
build	20-Dec-2017 15:36:29	Preparing to unpack .../x11-common_1%3a7.7+13ubuntu3_all.deb ...
build	20-Dec-2017 15:36:29	Unpacking x11-common (1:7.7+13ubuntu3) ...
build	20-Dec-2017 15:36:29	Selecting previously unselected package libice6:amd64.
build	20-Dec-2017 15:36:29	Preparing to unpack .../libice6_2%3a1.0.9-1_amd64.deb ...
build	20-Dec-2017 15:36:29	Unpacking libice6:amd64 (2:1.0.9-1) ...
build	20-Dec-2017 15:36:29	Selecting previously unselected package libsm6:amd64.
build	20-Dec-2017 15:36:29	Preparing to unpack .../libsm6_2%3a1.2.2-1_amd64.deb ...
build	20-Dec-2017 15:36:29	Unpacking libsm6:amd64 (2:1.2.2-1) ...
build	20-Dec-2017 15:36:29	Selecting previously unselected package libidn11:amd64.
build	20-Dec-2017 15:36:29	Preparing to unpack .../libidn11_1.32-3ubuntu1.2_amd64.deb ...
build	20-Dec-2017 15:36:29	Unpacking libidn11:amd64 (1.32-3ubuntu1.2) ...
build	20-Dec-2017 15:36:29	Selecting previously unselected package wget.
build	20-Dec-2017 15:36:29	Preparing to unpack .../wget_1.17.1-1ubuntu1.3_amd64.deb ...
build	20-Dec-2017 15:36:29	Unpacking wget (1.17.1-1ubuntu1.3) ...
build	20-Dec-2017 15:36:30	Selecting previously unselected package libxt6:amd64.
build	20-Dec-2017 15:36:30	Preparing to unpack .../libxt6_1%3a1.1.5-0ubuntu1_amd64.deb ...
build	20-Dec-2017 15:36:30	Unpacking libxt6:amd64 (1:1.1.5-0ubuntu1) ...
build	20-Dec-2017 15:36:30	Selecting previously unselected package libxmu6:amd64.
build	20-Dec-2017 15:36:30	Preparing to unpack .../libxmu6_2%3a1.1.2-2_amd64.deb ...
build	20-Dec-2017 15:36:30	Unpacking libxmu6:amd64 (2:1.1.2-2) ...
build	20-Dec-2017 15:36:30	Processing triggers for libc-bin (2.23-0ubuntu9) ...
build	20-Dec-2017 15:36:30	Processing triggers for systemd (229-4ubuntu19) ...
build	20-Dec-2017 15:36:30	Setting up libxau6:amd64 (1:1.0.8-1) ...
build	20-Dec-2017 15:36:30	Setting up libxdmcp6:amd64 (1:1.1.2-1.1) ...
build	20-Dec-2017 15:36:30	Setting up libxcb1:amd64 (1.11.1-1ubuntu1) ...
build	20-Dec-2017 15:36:31	Setting up libx11-data (2:1.6.3-1ubuntu2) ...
build	20-Dec-2017 15:36:31	Setting up libx11-6:amd64 (2:1.6.3-1ubuntu2) ...
build	20-Dec-2017 15:36:31	Setting up libxext6:amd64 (2:1.3.3-1) ...
build	20-Dec-2017 15:36:38	Setting up x11-common (1:7.7+13ubuntu3) ...
build	20-Dec-2017 15:36:39	debconf: unable to initialize frontend: Dialog
build	20-Dec-2017 15:36:39	debconf: (TERM is not set, so the dialog frontend is not usable.)
build	20-Dec-2017 15:36:39	debconf: falling back to frontend: Readline
build	20-Dec-2017 15:36:39	debconf: unable to initialize frontend: Readline
build	20-Dec-2017 15:36:39	debconf: (Can't locate Term/ReadLine.pm in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/perl5/Debconf/FrontEnd/Readline.pm line 7.)
build	20-Dec-2017 15:36:39	debconf: falling back to frontend: Teletype
build	20-Dec-2017 15:36:39	update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
build	20-Dec-2017 15:36:39	invoke-rc.d: could not determine current runlevel
build	20-Dec-2017 15:36:39	invoke-rc.d: policy-rc.d denied execution of start.
build	20-Dec-2017 15:36:39	Setting up libice6:amd64 (2:1.0.9-1) ...
build	20-Dec-2017 15:36:39	Setting up libsm6:amd64 (2:1.2.2-1) ...
build	20-Dec-2017 15:36:39	Setting up libidn11:amd64 (1.32-3ubuntu1.2) ...
build	20-Dec-2017 15:36:39	Setting up wget (1.17.1-1ubuntu1.3) ...
build	20-Dec-2017 15:36:40	Setting up libxt6:amd64 (1:1.1.5-0ubuntu1) ...
build	20-Dec-2017 15:36:40	Setting up libxmu6:amd64 (2:1.1.2-2) ...
build	20-Dec-2017 15:36:40	Processing triggers for libc-bin (2.23-0ubuntu9) ...
build	20-Dec-2017 15:36:40	Processing triggers for systemd (229-4ubuntu19) ...
build	20-Dec-2017 15:36:50	 ---> e906f8bc1eab
build	20-Dec-2017 15:36:50	Removing intermediate container eb51b6240594
build	20-Dec-2017 15:36:50	Step 8/11 : USER clowder
build	20-Dec-2017 15:36:50	 ---> Running in d7ff8fac5fa6
build	20-Dec-2017 15:36:51	 ---> 34223bdd36a4
build	20-Dec-2017 15:36:51	Removing intermediate container d7ff8fac5fa6
build	20-Dec-2017 15:36:51	Step 9/11 : COPY entrypoint.sh *.py *.m data/*.mat *.json /home/clowder/
build	20-Dec-2017 15:36:52	 ---> 90b911ebc015
build	20-Dec-2017 15:36:52	Removing intermediate container a117b7795746
build	20-Dec-2017 15:36:52	Step 10/11 : ENTRYPOINT /home/clowder/entrypoint.sh
build	20-Dec-2017 15:36:52	 ---> Running in 00a640ab43f5
build	20-Dec-2017 15:36:52	 ---> 3cf0b44bf0b1
build	20-Dec-2017 15:36:52	Removing intermediate container 00a640ab43f5
build	20-Dec-2017 15:36:52	Step 11/11 : CMD extractor
build	20-Dec-2017 15:36:53	 ---> Running in f55e68ae2acb
build	20-Dec-2017 15:36:53	 ---> 6a7c89ad04be
build	20-Dec-2017 15:36:53	Removing intermediate container f55e68ae2acb
build	20-Dec-2017 15:36:53	Successfully built 6a7c89ad04be
build	20-Dec-2017 15:36:53	Untagged: 6916:latest
build	20-Dec-2017 15:36:53	Sending build context to Docker daemon 67.07 kB
build	20-Dec-2017 15:36:53	
build	20-Dec-2017 15:36:53	Step 1/11 : FROM clowder/pyclowder:1
build	20-Dec-2017 15:36:53	 ---> d1a9e970ed30
build	20-Dec-2017 15:36:53	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	20-Dec-2017 15:36:53	 ---> Running in ec77661ea167
build	20-Dec-2017 15:36:53	 ---> 88bf4e1272c0
build	20-Dec-2017 15:36:53	Removing intermediate container ec77661ea167
build	20-Dec-2017 15:36:53	Step 3/11 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.IsletExtractor" MONGO_URI "" DB_USERNAME "" DB_PASSWORD "" MAIN_SCRIPT "extractor-Islet.py"
build	20-Dec-2017 15:36:53	 ---> Running in 2ab145a74f0f
build	20-Dec-2017 15:36:54	 ---> 1a7058c9602c
build	20-Dec-2017 15:36:54	Removing intermediate container 2ab145a74f0f
build	20-Dec-2017 15:36:54	Step 4/11 : USER root
build	20-Dec-2017 15:36:54	 ---> Running in ebc5073e2999
build	20-Dec-2017 15:36:56	 ---> b2ad44a0541c
build	20-Dec-2017 15:36:56	Removing intermediate container ebc5073e2999
build	20-Dec-2017 15:36:56	Step 5/11 : COPY requirements.txt /home/clowder/
build	20-Dec-2017 15:36:56	 ---> 739a2f87bcf6
build	20-Dec-2017 15:36:56	Removing intermediate container cebf630273f3
build	20-Dec-2017 15:36:56	Step 6/11 : RUN pip install --upgrade pip
build	20-Dec-2017 15:36:56	 ---> Running in 921e44f7bb7b
build	20-Dec-2017 15:36:57	Collecting pip
build	20-Dec-2017 15:36:57	  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
build	20-Dec-2017 15:36:58	Installing collected packages: pip
build	20-Dec-2017 15:36:58	  Found existing installation: pip 8.1.1
build	20-Dec-2017 15:36:58	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	20-Dec-2017 15:36:58	Successfully installed pip-9.0.1
build	20-Dec-2017 15:36:59	 ---> a766d33c47ad
build	20-Dec-2017 15:36:59	Removing intermediate container 921e44f7bb7b
build	20-Dec-2017 15:36:59	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	20-Dec-2017 15:36:59	 ---> Running in 4902eb7eb964
build	20-Dec-2017 15:37:00	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1))
build	20-Dec-2017 15:37:00	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	20-Dec-2017 15:37:00	  Downloading openpyxl-1.6.2.tar.gz (199kB)
build	20-Dec-2017 15:37:00	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	20-Dec-2017 15:37:00	  Downloading pika-0.9.14.tar.gz (72kB)
build	20-Dec-2017 15:37:01	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	20-Dec-2017 15:37:01	  Downloading pymongo-3.2.1.tar.gz (647kB)
build	20-Dec-2017 15:37:02	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	20-Dec-2017 15:37:02	  Downloading pytz-2014.3.zip (482kB)
build	20-Dec-2017 15:37:02	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	20-Dec-2017 15:37:02	  Downloading requests-2.2.1-py2.py3-none-any.whl (625kB)
build	20-Dec-2017 15:37:02	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7))
build	20-Dec-2017 15:37:02	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	20-Dec-2017 15:37:02	  Downloading xlrd-0.9.3.tar.gz (178kB)
build	20-Dec-2017 15:37:03	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	20-Dec-2017 15:37:03	  Running setup.py install for openpyxl: started
build	20-Dec-2017 15:37:03	    Running setup.py install for openpyxl: finished with status 'done'
build	20-Dec-2017 15:37:03	  Found existing installation: pika 0.11.0
build	20-Dec-2017 15:37:03	    Uninstalling pika-0.11.0:
build	20-Dec-2017 15:37:04	      Successfully uninstalled pika-0.11.0
build	20-Dec-2017 15:37:04	  Running setup.py install for pika: started
build	20-Dec-2017 15:37:04	    Running setup.py install for pika: finished with status 'done'
build	20-Dec-2017 15:37:04	  Running setup.py install for pymongo: started
build	20-Dec-2017 15:37:04	    Running setup.py install for pymongo: finished with status 'done'
build	20-Dec-2017 15:37:04	  Running setup.py install for pytz: started
build	20-Dec-2017 15:37:05	    Running setup.py install for pytz: finished with status 'done'
build	20-Dec-2017 15:37:05	  Found existing installation: requests 2.18.4
build	20-Dec-2017 15:37:05	    Uninstalling requests-2.18.4:
build	20-Dec-2017 15:37:06	      Successfully uninstalled requests-2.18.4
build	20-Dec-2017 15:37:06	  Running setup.py install for xlrd: started
build	20-Dec-2017 15:37:07	    Running setup.py install for xlrd: finished with status 'done'
build	20-Dec-2017 15:37:07	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	20-Dec-2017 15:37:07	 ---> b7fbce97d030
build	20-Dec-2017 15:37:08	Removing intermediate container 4902eb7eb964
build	20-Dec-2017 15:37:08	Step 8/11 : USER clowder
build	20-Dec-2017 15:37:08	 ---> Running in 7c0dce08225f
build	20-Dec-2017 15:37:08	 ---> 83cc95fd9157
build	20-Dec-2017 15:37:08	Removing intermediate container 7c0dce08225f
build	20-Dec-2017 15:37:08	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	20-Dec-2017 15:37:09	 ---> fe20e818307f
build	20-Dec-2017 15:37:09	Removing intermediate container a3fdf398d27e
build	20-Dec-2017 15:37:09	Step 10/11 : ENTRYPOINT /home/clowder/entrypoint.sh
build	20-Dec-2017 15:37:09	 ---> Running in 81cca27fa5b8
build	20-Dec-2017 15:37:09	 ---> fda20b6311fa
build	20-Dec-2017 15:37:09	Removing intermediate container 81cca27fa5b8
build	20-Dec-2017 15:37:09	Step 11/11 : CMD extractor
build	20-Dec-2017 15:37:09	 ---> Running in 18c9a19e2aba
build	20-Dec-2017 15:37:09	 ---> 5507b6e8844a
build	20-Dec-2017 15:37:09	Removing intermediate container 18c9a19e2aba
build	20-Dec-2017 15:37:09	Successfully built 5507b6e8844a
build	20-Dec-2017 15:37:09	Untagged: 6916:latest
build	20-Dec-2017 15:37:09	Sending build context to Docker daemon 66.05 kB
build	20-Dec-2017 15:37:09	
build	20-Dec-2017 15:37:10	Step 1/11 : FROM clowder/pyclowder:1
build	20-Dec-2017 15:37:10	 ---> d1a9e970ed30
build	20-Dec-2017 15:37:10	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	20-Dec-2017 15:37:10	 ---> Using cache
build	20-Dec-2017 15:37:10	 ---> 88bf4e1272c0
build	20-Dec-2017 15:37:10	Step 3/11 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.ChemCBCExtractor" MONGO_URI "" DB_USERNAME "" DB_PASSWORD "" MAIN_SCRIPT "extractor-Chem.py"
build	20-Dec-2017 15:37:10	 ---> Running in 09bcbd7d1e86
build	20-Dec-2017 15:37:10	 ---> 469947031c62
build	20-Dec-2017 15:37:10	Removing intermediate container 09bcbd7d1e86
build	20-Dec-2017 15:37:10	Step 4/11 : USER root
build	20-Dec-2017 15:37:10	 ---> Running in 074f0dca5721
build	20-Dec-2017 15:37:10	 ---> f4e27e086d55
build	20-Dec-2017 15:37:10	Removing intermediate container 074f0dca5721
build	20-Dec-2017 15:37:10	Step 5/11 : COPY requirements.txt /home/clowder/
build	20-Dec-2017 15:37:11	 ---> a8a33d6886a0
build	20-Dec-2017 15:37:11	Removing intermediate container 2f3c51860f18
build	20-Dec-2017 15:37:11	Step 6/11 : RUN pip install --upgrade pip
build	20-Dec-2017 15:37:11	 ---> Running in d638773e306b
build	20-Dec-2017 15:37:12	Collecting pip
build	20-Dec-2017 15:37:12	  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
build	20-Dec-2017 15:37:12	Installing collected packages: pip
build	20-Dec-2017 15:37:12	  Found existing installation: pip 8.1.1
build	20-Dec-2017 15:37:12	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	20-Dec-2017 15:37:13	Successfully installed pip-9.0.1
build	20-Dec-2017 15:37:14	 ---> 8db0cd85544e
build	20-Dec-2017 15:37:14	Removing intermediate container d638773e306b
build	20-Dec-2017 15:37:14	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	20-Dec-2017 15:37:14	 ---> Running in 923a42f17fe2
build	20-Dec-2017 15:37:14	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1))
build	20-Dec-2017 15:37:14	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	20-Dec-2017 15:37:14	  Downloading openpyxl-1.6.2.tar.gz (199kB)
build	20-Dec-2017 15:37:15	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	20-Dec-2017 15:37:15	  Downloading pika-0.9.14.tar.gz (72kB)
build	20-Dec-2017 15:37:15	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	20-Dec-2017 15:37:15	  Downloading pymongo-3.2.1.tar.gz (647kB)
build	20-Dec-2017 15:37:16	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	20-Dec-2017 15:37:16	  Downloading pytz-2014.3.zip (482kB)
build	20-Dec-2017 15:37:16	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	20-Dec-2017 15:37:16	  Downloading requests-2.2.1-py2.py3-none-any.whl (625kB)
build	20-Dec-2017 15:37:16	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7))
build	20-Dec-2017 15:37:17	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	20-Dec-2017 15:37:17	  Downloading xlrd-0.9.3.tar.gz (178kB)
build	20-Dec-2017 15:37:17	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	20-Dec-2017 15:37:17	  Running setup.py install for openpyxl: started
build	20-Dec-2017 15:37:17	    Running setup.py install for openpyxl: finished with status 'done'
build	20-Dec-2017 15:37:17	  Found existing installation: pika 0.11.0
build	20-Dec-2017 15:37:17	    Uninstalling pika-0.11.0:
build	20-Dec-2017 15:37:18	      Successfully uninstalled pika-0.11.0
build	20-Dec-2017 15:37:18	  Running setup.py install for pika: started
build	20-Dec-2017 15:37:18	    Running setup.py install for pika: finished with status 'done'
build	20-Dec-2017 15:37:18	  Running setup.py install for pymongo: started
build	20-Dec-2017 15:37:18	    Running setup.py install for pymongo: finished with status 'done'
build	20-Dec-2017 15:37:18	  Running setup.py install for pytz: started
build	20-Dec-2017 15:37:19	    Running setup.py install for pytz: finished with status 'done'
build	20-Dec-2017 15:37:19	  Found existing installation: requests 2.18.4
build	20-Dec-2017 15:37:19	    Uninstalling requests-2.18.4:
build	20-Dec-2017 15:37:19	      Successfully uninstalled requests-2.18.4
build	20-Dec-2017 15:37:19	  Running setup.py install for xlrd: started
build	20-Dec-2017 15:37:20	    Running setup.py install for xlrd: finished with status 'done'
build	20-Dec-2017 15:37:20	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	20-Dec-2017 15:37:21	 ---> baedcb234d46
build	20-Dec-2017 15:37:21	Removing intermediate container 923a42f17fe2
build	20-Dec-2017 15:37:21	Step 8/11 : USER clowder
build	20-Dec-2017 15:37:21	 ---> Running in 4c59021cf0eb
build	20-Dec-2017 15:37:21	 ---> d1e3a94a30bb
build	20-Dec-2017 15:37:21	Removing intermediate container 4c59021cf0eb
build	20-Dec-2017 15:37:21	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	20-Dec-2017 15:37:22	 ---> 814b964d93e7
build	20-Dec-2017 15:37:22	Removing intermediate container 1bba0ad1dfff
build	20-Dec-2017 15:37:22	Step 10/11 : ENTRYPOINT /home/clowder/entrypoint.sh
build	20-Dec-2017 15:37:22	 ---> Running in 9768433ce396
build	20-Dec-2017 15:37:22	 ---> a49f28def0f8
build	20-Dec-2017 15:37:22	Removing intermediate container 9768433ce396
build	20-Dec-2017 15:37:22	Step 11/11 : CMD extractor
build	20-Dec-2017 15:37:22	 ---> Running in 72362dbb767b
build	20-Dec-2017 15:37:22	 ---> efe2258fd926
build	20-Dec-2017 15:37:22	Removing intermediate container 72362dbb767b
build	20-Dec-2017 15:37:22	Successfully built efe2258fd926
build	20-Dec-2017 15:37:22	Untagged: 6916:latest
build	20-Dec-2017 15:37:22	Sending build context to Docker daemon 198.1 kB
build	20-Dec-2017 15:37:22	
build	20-Dec-2017 15:37:22	Step 1/11 : FROM clowder/pyclowder:1
build	20-Dec-2017 15:37:22	 ---> d1a9e970ed30
build	20-Dec-2017 15:37:22	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	20-Dec-2017 15:37:22	 ---> Using cache
build	20-Dec-2017 15:37:22	 ---> 88bf4e1272c0
build	20-Dec-2017 15:37:22	Step 3/11 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.MonitorExtractor" MONGO_URI "" DB_USERNAME "" DB_PASSWORD "" MAIN_SCRIPT "extractor-Monitor.py"
build	20-Dec-2017 15:37:22	 ---> Running in 75d5af31d62b
build	20-Dec-2017 15:37:23	 ---> 59c05db485d7
build	20-Dec-2017 15:37:23	Removing intermediate container 75d5af31d62b
build	20-Dec-2017 15:37:23	Step 4/11 : USER root
build	20-Dec-2017 15:37:23	 ---> Running in b0b3f6ba5384
build	20-Dec-2017 15:37:23	 ---> 7552d75a6504
build	20-Dec-2017 15:37:23	Removing intermediate container b0b3f6ba5384
build	20-Dec-2017 15:37:23	Step 5/11 : COPY requirements.txt /home/clowder/
build	20-Dec-2017 15:37:23	 ---> 1960fd834489
build	20-Dec-2017 15:37:23	Removing intermediate container 30bc77570e7c
build	20-Dec-2017 15:37:23	Step 6/11 : RUN pip install --upgrade pip
build	20-Dec-2017 15:37:23	 ---> Running in ccc06d3709cd
build	20-Dec-2017 15:37:24	Collecting pip
build	20-Dec-2017 15:37:24	  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
build	20-Dec-2017 15:37:24	Installing collected packages: pip
build	20-Dec-2017 15:37:24	  Found existing installation: pip 8.1.1
build	20-Dec-2017 15:37:24	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	20-Dec-2017 15:37:25	Successfully installed pip-9.0.1
build	20-Dec-2017 15:37:26	 ---> 725eae486d95
build	20-Dec-2017 15:37:26	Removing intermediate container ccc06d3709cd
build	20-Dec-2017 15:37:26	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	20-Dec-2017 15:37:26	 ---> Running in 2137931a495b
build	20-Dec-2017 15:37:27	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1))
build	20-Dec-2017 15:37:27	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	20-Dec-2017 15:37:27	  Downloading openpyxl-1.6.2.tar.gz (199kB)
build	20-Dec-2017 15:37:27	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	20-Dec-2017 15:37:27	  Downloading pika-0.9.14.tar.gz (72kB)
build	20-Dec-2017 15:37:28	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	20-Dec-2017 15:37:28	  Downloading pymongo-3.2.1.tar.gz (647kB)
build	20-Dec-2017 15:37:29	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	20-Dec-2017 15:37:29	  Downloading pytz-2014.3.zip (482kB)
build	20-Dec-2017 15:37:29	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	20-Dec-2017 15:37:29	  Downloading requests-2.2.1-py2.py3-none-any.whl (625kB)
build	20-Dec-2017 15:37:29	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7))
build	20-Dec-2017 15:37:29	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	20-Dec-2017 15:37:29	  Downloading xlrd-0.9.3.tar.gz (178kB)
build	20-Dec-2017 15:37:29	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	20-Dec-2017 15:37:29	  Running setup.py install for openpyxl: started
build	20-Dec-2017 15:37:30	    Running setup.py install for openpyxl: finished with status 'done'
build	20-Dec-2017 15:37:30	  Found existing installation: pika 0.11.0
build	20-Dec-2017 15:37:30	    Uninstalling pika-0.11.0:
build	20-Dec-2017 15:37:31	      Successfully uninstalled pika-0.11.0
build	20-Dec-2017 15:37:31	  Running setup.py install for pika: started
build	20-Dec-2017 15:37:31	    Running setup.py install for pika: finished with status 'done'
build	20-Dec-2017 15:37:31	  Running setup.py install for pymongo: started
build	20-Dec-2017 15:37:32	    Running setup.py install for pymongo: finished with status 'done'
build	20-Dec-2017 15:37:32	  Running setup.py install for pytz: started
build	20-Dec-2017 15:37:32	    Running setup.py install for pytz: finished with status 'done'
build	20-Dec-2017 15:37:32	  Found existing installation: requests 2.18.4
build	20-Dec-2017 15:37:32	    Uninstalling requests-2.18.4:
build	20-Dec-2017 15:37:33	      Successfully uninstalled requests-2.18.4
build	20-Dec-2017 15:37:33	  Running setup.py install for xlrd: started
build	20-Dec-2017 15:37:33	    Running setup.py install for xlrd: finished with status 'done'
build	20-Dec-2017 15:37:33	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	20-Dec-2017 15:37:34	 ---> c968cf4638cc
build	20-Dec-2017 15:37:34	Removing intermediate container 2137931a495b
build	20-Dec-2017 15:37:34	Step 8/11 : USER clowder
build	20-Dec-2017 15:37:34	 ---> Running in 18d38de78328
build	20-Dec-2017 15:37:34	 ---> 3c2c6d98ab5e
build	20-Dec-2017 15:37:34	Removing intermediate container 18d38de78328
build	20-Dec-2017 15:37:34	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	20-Dec-2017 15:37:35	 ---> 611434efdfbc
build	20-Dec-2017 15:37:35	Removing intermediate container 0c160c097f44
build	20-Dec-2017 15:37:35	Step 10/11 : ENTRYPOINT /home/clowder/entrypoint.sh
build	20-Dec-2017 15:37:36	 ---> Running in 44904bea16c4
build	20-Dec-2017 15:37:36	 ---> 0fa56bff72a6
build	20-Dec-2017 15:37:36	Removing intermediate container 44904bea16c4
build	20-Dec-2017 15:37:36	Step 11/11 : CMD extractor
build	20-Dec-2017 15:37:36	 ---> Running in d6e650cd13fe
build	20-Dec-2017 15:37:36	 ---> a8bebd73a260
build	20-Dec-2017 15:37:36	Removing intermediate container d6e650cd13fe
build	20-Dec-2017 15:37:36	Successfully built a8bebd73a260
build	20-Dec-2017 15:37:36	Untagged: 6916:latest
build	20-Dec-2017 15:37:37	Sending build context to Docker daemon  12.1 MB
build	20-Dec-2017 15:37:37	
build	20-Dec-2017 15:37:37	Step 1/11 : FROM clowder/pyclowder:1
build	20-Dec-2017 15:37:37	 ---> d1a9e970ed30
build	20-Dec-2017 15:37:37	Step 2/11 : MAINTAINER Yan Zhao <yanzhao3@illinois.edu>
build	20-Dec-2017 15:37:37	 ---> Using cache
build	20-Dec-2017 15:37:37	 ---> 88bf4e1272c0
build	20-Dec-2017 15:37:37	Step 3/11 : ENV RABBITMQ_URI "" RABBITMQ_EXCHANGE "clowder" RABBITMQ_VHOST "%2F" RABBITMQ_QUEUE "ncsa.msc.PhenotypeExtractor" MONGO_URI "" DB_USERNAME "" DB_PASSWORD "" MAIN_SCRIPT "extractor-Phenotype.py"
build	20-Dec-2017 15:37:37	 ---> Running in 6324d5c03839
build	20-Dec-2017 15:37:37	 ---> 9ae2b5c45643
build	20-Dec-2017 15:37:37	Removing intermediate container 6324d5c03839
build	20-Dec-2017 15:37:37	Step 4/11 : USER root
build	20-Dec-2017 15:37:37	 ---> Running in 174e76d0eb29
build	20-Dec-2017 15:37:37	 ---> 18e3e0f2f99b
build	20-Dec-2017 15:37:37	Removing intermediate container 174e76d0eb29
build	20-Dec-2017 15:37:37	Step 5/11 : COPY requirements.txt /home/clowder/
build	20-Dec-2017 15:37:38	 ---> 0f1dec8b0232
build	20-Dec-2017 15:37:38	Removing intermediate container 6cfa5900d175
build	20-Dec-2017 15:37:38	Step 6/11 : RUN pip install --upgrade pip
build	20-Dec-2017 15:37:38	 ---> Running in 1f862310a082
build	20-Dec-2017 15:37:39	Collecting pip
build	20-Dec-2017 15:37:39	  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
build	20-Dec-2017 15:37:39	Installing collected packages: pip
build	20-Dec-2017 15:37:39	  Found existing installation: pip 8.1.1
build	20-Dec-2017 15:37:39	    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
build	20-Dec-2017 15:37:40	Successfully installed pip-9.0.1
build	20-Dec-2017 15:37:41	 ---> d05b2e1fad22
build	20-Dec-2017 15:37:41	Removing intermediate container 1f862310a082
build	20-Dec-2017 15:37:41	Step 7/11 : RUN pip install -r /home/clowder/requirements.txt
build	20-Dec-2017 15:37:42	 ---> Running in 2a3e3b6f0916
build	20-Dec-2017 15:37:42	Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 1))
build	20-Dec-2017 15:37:42	Collecting openpyxl==1.6.2 (from -r /home/clowder/requirements.txt (line 2))
build	20-Dec-2017 15:37:42	  Downloading openpyxl-1.6.2.tar.gz (199kB)
build	20-Dec-2017 15:37:43	Collecting pika==0.9.14 (from -r /home/clowder/requirements.txt (line 3))
build	20-Dec-2017 15:37:43	  Downloading pika-0.9.14.tar.gz (72kB)
build	20-Dec-2017 15:37:43	Collecting pymongo==3.2.1 (from -r /home/clowder/requirements.txt (line 4))
build	20-Dec-2017 15:37:43	  Downloading pymongo-3.2.1.tar.gz (647kB)
build	20-Dec-2017 15:37:44	Collecting pytz==2014.3 (from -r /home/clowder/requirements.txt (line 5))
build	20-Dec-2017 15:37:44	  Downloading pytz-2014.3.zip (482kB)
build	20-Dec-2017 15:37:44	Collecting requests==2.2.1 (from -r /home/clowder/requirements.txt (line 6))
build	20-Dec-2017 15:37:44	  Downloading requests-2.2.1-py2.py3-none-any.whl (625kB)
build	20-Dec-2017 15:37:44	Requirement already satisfied: wsgiref==0.1.2 in /usr/lib/python2.7 (from -r /home/clowder/requirements.txt (line 7))
build	20-Dec-2017 15:37:44	Collecting xlrd==0.9.3 (from -r /home/clowder/requirements.txt (line 8))
build	20-Dec-2017 15:37:44	  Downloading xlrd-0.9.3.tar.gz (178kB)
build	20-Dec-2017 15:37:45	Installing collected packages: openpyxl, pika, pymongo, pytz, requests, xlrd
build	20-Dec-2017 15:37:45	  Running setup.py install for openpyxl: started
build	20-Dec-2017 15:37:45	    Running setup.py install for openpyxl: finished with status 'done'
build	20-Dec-2017 15:37:45	  Found existing installation: pika 0.11.0
build	20-Dec-2017 15:37:45	    Uninstalling pika-0.11.0:
build	20-Dec-2017 15:37:46	      Successfully uninstalled pika-0.11.0
build	20-Dec-2017 15:37:46	  Running setup.py install for pika: started
build	20-Dec-2017 15:37:47	    Running setup.py install for pika: finished with status 'done'
build	20-Dec-2017 15:37:47	  Running setup.py install for pymongo: started
build	20-Dec-2017 15:37:47	    Running setup.py install for pymongo: finished with status 'done'
build	20-Dec-2017 15:37:47	  Running setup.py install for pytz: started
build	20-Dec-2017 15:37:47	    Running setup.py install for pytz: finished with status 'done'
build	20-Dec-2017 15:37:47	  Found existing installation: requests 2.18.4
build	20-Dec-2017 15:37:47	    Uninstalling requests-2.18.4:
build	20-Dec-2017 15:37:48	      Successfully uninstalled requests-2.18.4
build	20-Dec-2017 15:37:48	  Running setup.py install for xlrd: started
build	20-Dec-2017 15:37:48	    Running setup.py install for xlrd: finished with status 'done'
build	20-Dec-2017 15:37:48	Successfully installed openpyxl-1.6.2 pika-0.9.14 pymongo-3.2.1 pytz-2014.3 requests-2.2.1 xlrd-0.9.3
build	20-Dec-2017 15:37:49	 ---> 460323f0aaf2
build	20-Dec-2017 15:37:49	Removing intermediate container 2a3e3b6f0916
build	20-Dec-2017 15:37:49	Step 8/11 : USER clowder
build	20-Dec-2017 15:37:49	 ---> Running in 4263b77e090d
build	20-Dec-2017 15:37:49	 ---> 41f2e271dcf3
build	20-Dec-2017 15:37:49	Removing intermediate container 4263b77e090d
build	20-Dec-2017 15:37:49	Step 9/11 : COPY entrypoint.sh *.py *.json /home/clowder/
build	20-Dec-2017 15:37:50	 ---> c6babd7641a7
build	20-Dec-2017 15:37:50	Removing intermediate container 355f8896d57e
build	20-Dec-2017 15:37:50	Step 10/11 : ENTRYPOINT /home/clowder/entrypoint.sh
build	20-Dec-2017 15:37:50	 ---> Running in f5a7e2748294
build	20-Dec-2017 15:37:50	 ---> 0dcf03a07511
build	20-Dec-2017 15:37:50	Removing intermediate container f5a7e2748294
build	20-Dec-2017 15:37:50	Step 11/11 : CMD extractor
build	20-Dec-2017 15:37:51	 ---> Running in 4865c6dcee24
build	20-Dec-2017 15:37:51	 ---> 654c463ea8f2
build	20-Dec-2017 15:37:51	Removing intermediate container 4865c6dcee24
build	20-Dec-2017 15:37:51	Successfully built 654c463ea8f2
build	20-Dec-2017 15:37:51	Untagged: 6916:latest
build	20-Dec-2017 15:37:51	Untagged: clowder/extractors-msc-kidney:latest
build	20-Dec-2017 15:37:51	Untagged: clowder/extractors-msc-islet:latest
build	20-Dec-2017 15:37:51	Untagged: clowder/extractors-msc-chemcbc:latest
build	20-Dec-2017 15:37:51	Untagged: clowder/extractors-msc-monitor:latest
build	20-Dec-2017 15:37:51	Untagged: clowder/extractors-msc-phenotype:latest
simple	20-Dec-2017 15:37:51	Finished task 'docker build' with result: Success
simple	20-Dec-2017 15:37:51	Running post build plugin 'Docker Container Cleanup'
simple	20-Dec-2017 15:37:51	Running post build plugin 'NCover Results Collector'
simple	20-Dec-2017 15:37:51	Running post build plugin 'Clover Results Collector'
simple	20-Dec-2017 15:37:51	Running post build plugin 'npm Cache Cleanup'
simple	20-Dec-2017 15:37:51	Running post build plugin 'Artifact Copier'
simple	20-Dec-2017 15:37:51	Finalising the build...
simple	20-Dec-2017 15:37:51	Stopping timer.
simple	20-Dec-2017 15:37:51	Build CATS-MSC3-JOB1-1 completed.
simple	20-Dec-2017 15:37:51	Running on server: post build plugin 'NCover Results Collector'
simple	20-Dec-2017 15:37:51	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	20-Dec-2017 15:37:51	Running on server: post build plugin 'Clover Delta Calculator'
simple	20-Dec-2017 15:37:51	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	20-Dec-2017 15:37:51	All post build plugins have finished
simple	20-Dec-2017 15:37:51	Generating build results summary...
simple	20-Dec-2017 15:37:51	Saving build results to disk...
simple	20-Dec-2017 15:37:51	Logging substituted variables...
simple	20-Dec-2017 15:37:51	Indexing build results...
simple	20-Dec-2017 15:37:51	Finished building CATS-MSC3-JOB1-1.