simple 01-Nov-2018 10:05:50 Build Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job #208 (JB-JDB1-JOB1-208) started building on agent Default Agent simple 01-Nov-2018 10:05:50 simple 01-Nov-2018 10:05:50 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1 simple 01-Nov-2018 10:05:50 Executing build Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job #208 (JB-JDB1-JOB1-208) simple 01-Nov-2018 10:05:50 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 01-Nov-2018 10:05:50 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1 simple 01-Nov-2018 10:05:50 Updating source code to revision: f20ff42eac30f33cb69635ba3217a6224dbeb555 simple 01-Nov-2018 10:05:50 Fetching 'refs/heads/Jalview-BH/JAL-3026' from 'http://source.jalview.org/git/jalview.git'. simple 01-Nov-2018 10:05:51 Checking out revision f20ff42eac30f33cb69635ba3217a6224dbeb555. simple 01-Nov-2018 10:05:51 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 01-Nov-2018 10:05:51 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 01-Nov-2018 10:05:51 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 01-Nov-2018 10:05:51 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 01-Nov-2018 10:05:52 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 01-Nov-2018 10:05:52 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 01-Nov-2018 10:05:52 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 01-Nov-2018 10:05:52 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 01-Nov-2018 10:05:52 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 01-Nov-2018 10:05:52 7434a5c..f20ff42 Jalview-BH/JAL-3026 -> origin/Jalview-BH/JAL-3026 simple 01-Nov-2018 10:05:53 95d4b32..c42181e feature/JAL-3141_Create_a_backup_when_saving_projects_and_other_files -> origin/feature/JAL-3141_Create_a_backup_when_saving_projects_and_other_files simple 01-Nov-2018 10:05:53 a11ce31..181cd66 feature/JAL-3144noJTree -> origin/feature/JAL-3144noJTree simple 01-Nov-2018 10:05:53 error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! simple 01-Nov-2018 10:05:53 error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! simple 01-Nov-2018 10:05:53 Already on 'Jalview-BH/JAL-3026' simple 01-Nov-2018 10:05:53 Your branch is behind 'origin/Jalview-BH/JAL-3026' by 1 commit, and can be fast-forwarded. simple 01-Nov-2018 10:05:53 (use "git pull" to update your local branch) simple 01-Nov-2018 10:05:53 HEAD is now at f20ff42 JAL-3048 JAL-3056 reinstate save/load project, colour scheme dialogs in simple 01-Nov-2018 10:05:53 Updated source code to revision: f20ff42eac30f33cb69635ba3217a6224dbeb555 simple 01-Nov-2018 10:05:53 Finished task 'Checkout Default Repository' with result: Success simple 01-Nov-2018 10:05:53 Running pre-build action: VCS Version Collector simple 01-Nov-2018 10:05:53 Starting task 'Clover TestNG Suite' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant' command 01-Nov-2018 10:05:53 Beginning to execute external process for build 'Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job #208 (JB-JDB1-JOB1-208)'\n ... running command line: \n/home/bamboo/buildtools/x11-ant/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDB1-JOB1 -f build.xml -Dclover.jar=/home/bamboo/buildtools/clover/lib/clover.jar clean with.clover testng clover.report\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=Jalview-BH/JAL-3026\nbamboo_planRepository_1_branchDisplayName=Jalview-BH/JAL-3026\nbamboo_repository_revision_number=f20ff42eac30f33cb69635ba3217a6224dbeb555\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-208\nbamboo_repository_2228226_revision_number=f20ff42eac30f33cb69635ba3217a6224dbeb555\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-JDB1-JOB1\nbamboo_capability_system_jdk_JDK_1_8_0_171=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_shortPlanName=Jalview-BH-JAL-3026\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_2228226_git_username=\nbamboo_buildNumber=208\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-JDB1-JOB1-208\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - jalview develop build - Jalview-BH-JAL-3026\nbamboo_shortPlanKey=JDB1\nbamboo_repository_2228226_branch_name=Jalview-BH/JAL-3026\nbamboo_shortJobKey=JOB1\nbamboo_planRepository_revision=f20ff42eac30f33cb69635ba3217a6224dbeb555\nbamboo_buildTimeStamp=2018-11-01T10:04:19.982Z\nbamboo_repository_previous_revision_number=7434a5c8bf464bf806a6e88a17bae3f217a5ec68\nbamboo_planRepository_previousRevision=7434a5c8bf464bf806a6e88a17bae3f217a5ec68\nbamboo_repository_git_branch=Jalview-BH/JAL-3026\nbamboo_buildResultKey=JB-JDB1-JOB1-208\nbamboo_repository_branch_name=Jalview-BH/JAL-3026\nbamboo_buildPlanName=Jalview Builds - jalview develop build - Jalview-BH-JAL-3026 - Default Job\nbamboo_planRepository_1_revision=f20ff42eac30f33cb69635ba3217a6224dbeb555\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_2228226_git_branch=Jalview-BH/JAL-3026\nbamboo_repository_name=Jalview Git\nbamboo_repository_2228226_previous_revision_number=7434a5c8bf464bf806a6e88a17bae3f217a5ec68\nbamboo_repository_2228226_name=Jalview Git\nJAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_buildFailed=false\nANT_HOME=/home/bamboo/buildtools/x11-ant\nbamboo_planRepository_branch=Jalview-BH/JAL-3026\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_1_previousRevision=7434a5c8bf464bf806a6e88a17bae3f217a5ec68\nbamboo_planRepository_branchDisplayName=Jalview-BH/JAL-3026\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=Jalview-BH/JAL-3026\nbamboo_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_plan_storageTag=plan-2031619\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_2228226_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1\nbamboo_planKey=JB-JDB1\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64\nbamboo_planRepository_1_branchName=Jalview-BH/JAL-3026\nPATH=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 01-Nov-2018 10:05:57 Buildfile: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml build 01-Nov-2018 10:05:58 [clover-env] Loading clover.xml: jar:file:/home/bamboo/buildtools/clover/lib/clover.jar!/clover.xml build 01-Nov-2018 10:05:58 build 01-Nov-2018 10:05:58 init: build 01-Nov-2018 10:05:58 build 01-Nov-2018 10:05:58 clean: build 01-Nov-2018 10:05:59 build 01-Nov-2018 10:05:59 with.clover: build 01-Nov-2018 10:05:59 [clover-setup] OpenClover Version 4.2.1, built on November 21 2017 (build-1004) build 01-Nov-2018 10:05:59 [clover-setup] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar build 01-Nov-2018 10:05:59 [clover-setup] Clover free edition. build 01-Nov-2018 10:05:59 [clover-setup] Clover is enabled with initstring '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db' build 01-Nov-2018 10:05:59 build 01-Nov-2018 10:05:59 init: build 01-Nov-2018 10:05:59 build 01-Nov-2018 10:05:59 prepare: build 01-Nov-2018 10:05:59 [copy] Copying 286 files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses build 01-Nov-2018 10:06:01 build 01-Nov-2018 10:06:01 build: build 01-Nov-2018 10:06:01 [javac] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/build.xml:279: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds build 01-Nov-2018 10:06:01 [javac] Compiling 970 source files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses build 01-Nov-2018 10:06:01 [clover] OpenClover Version 4.2.1, built on November 21 2017 (build-1004) build 01-Nov-2018 10:06:01 [clover] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar build 01-Nov-2018 10:06:01 [clover] Clover free edition. build 01-Nov-2018 10:06:01 [clover] Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'. build 01-Nov-2018 10:06:01 [clover] Processing files at 1.8 source level. build 01-Nov-2018 10:06:14 [clover] Clover all over. Instrumented 970 files (102 packages). build 01-Nov-2018 10:06:14 [clover] Elapsed time = 12.744 secs. (76.114 files/sec, 28,006.827 srclines/sec) build 01-Nov-2018 10:06:26 [javac] /tmp/clover5180571753586823193.tmp/org/xml/sax/helpers/NewInstance.java:63: warning: non-varargs call of varargs method with inexact argument type for last parameter; build 01-Nov-2018 10:06:26 [javac] __CLR4_2_1nyenyejnyfd32n.R.inc(31057);m = Thread.class.getMethod("getContextClassLoader", null); build 01-Nov-2018 10:06:26 [javac] ^ build 01-Nov-2018 10:06:26 [javac] cast to Class for a varargs call build 01-Nov-2018 10:06:26 [javac] cast to Class[] for a non-varargs call and to suppress this warning build 01-Nov-2018 10:06:26 [javac] /tmp/clover5180571753586823193.tmp/org/xml/sax/helpers/NewInstance.java:70: warning: non-varargs call of varargs method with inexact argument type for last parameter; build 01-Nov-2018 10:06:26 [javac] __CLR4_2_1nyenyejnyfd32n.R.inc(31060);return (ClassLoader) m.invoke(Thread.currentThread(), null); build 01-Nov-2018 10:06:26 [javac] ^ build 01-Nov-2018 10:06:26 [javac] cast to Object for a varargs call build 01-Nov-2018 10:06:26 [javac] cast to Object[] for a non-varargs call and to suppress this warning build 01-Nov-2018 10:06:29 [javac] Note: Some input files use or override a deprecated API. build 01-Nov-2018 10:06:29 [javac] Note: Recompile with -Xlint:deprecation for details. build 01-Nov-2018 10:06:29 [javac] Note: Some input files use unchecked or unsafe operations. build 01-Nov-2018 10:06:29 [javac] Note: Recompile with -Xlint:unchecked for details. build 01-Nov-2018 10:06:29 [javac] 2 warnings build 01-Nov-2018 10:06:29 build 01-Nov-2018 10:06:29 buildindices: build 01-Nov-2018 10:06:31 build 01-Nov-2018 10:06:31 testclean: build 01-Nov-2018 10:06:31 build 01-Nov-2018 10:06:31 prepareTests: build 01-Nov-2018 10:06:31 build 01-Nov-2018 10:06:31 buildTests: build 01-Nov-2018 10:06:31 [javac] Compiling 252 source files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/tests build 01-Nov-2018 10:06:31 [clover] OpenClover Version 4.2.1, built on November 21 2017 (build-1004) build 01-Nov-2018 10:06:31 [clover] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar build 01-Nov-2018 10:06:31 [clover] Clover free edition. build 01-Nov-2018 10:06:31 [clover] Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/.clover/clover4_2_1.db'. build 01-Nov-2018 10:06:31 [clover] Processing files at 1.8 source level. build 01-Nov-2018 10:06:34 [clover] Clover all over. Instrumented 252 files (47 packages). build 01-Nov-2018 10:06:34 [clover] 1293 test methods detected. build 01-Nov-2018 10:06:34 [clover] Elapsed time = 3.044 secs. (82.786 files/sec, 23,242.444 srclines/sec) build 01-Nov-2018 10:06:37 [javac] Note: Some input files use or override a deprecated API. build 01-Nov-2018 10:06:37 [javac] Note: Recompile with -Xlint:deprecation for details. build 01-Nov-2018 10:06:37 [javac] Note: Some input files use unchecked or unsafe operations. build 01-Nov-2018 10:06:37 [javac] Note: Recompile with -Xlint:unchecked for details. build 01-Nov-2018 10:06:37 build 01-Nov-2018 10:06:37 testng: build 01-Nov-2018 10:06:39 [testng] - Getting messages for lang: en_GB build 01-Nov-2018 10:06:39 [testng] >SEQ1/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ2/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNYGMYPALTLE-NVWN build 01-Nov-2018 10:06:39 [testng] >SEQ3/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPATTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ4/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGDYPALTLN-EVWI build 01-Nov-2018 10:06:39 [testng] >SEQ5/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYLALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ6/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ7/1-20 build 01-Nov-2018 10:06:39 [testng] WMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ8/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPARTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ9/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNDGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ10/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLNYE-WN build 01-Nov-2018 10:06:39 [testng] >SEQ11/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLE-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ12/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNPGMYPAYTLN-EVWL build 01-Nov-2018 10:06:39 [testng] >SEQ13/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLV-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ14/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLL-EVWF build 01-Nov-2018 10:06:39 [testng] >SEQ15/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EKWN build 01-Nov-2018 10:06:39 [testng] >SEQ16/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-LVWN build 01-Nov-2018 10:06:39 [testng] >SEQ17/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ18/1-20 build 01-Nov-2018 10:06:39 [testng] FMWINNQGMYDALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ19/1-20 build 01-Nov-2018 10:06:39 [testng] FENINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ20/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPAGTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ21/1-20 build 01-Nov-2018 10:06:39 [testng] VMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ22/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGKYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ23/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ24/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ25/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNHGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ26/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ27/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ28/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGNYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ29/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALTLN-EVWN build 01-Nov-2018 10:06:39 [testng] >SEQ30/1-20 build 01-Nov-2018 10:06:39 [testng] FMNINNQGMYPALFLN-TVWN build 01-Nov-2018 10:06:39 [testng] build 01-Nov-2018 10:06:39 [testng] >SEQ1/1-7 build 01-Nov-2018 10:06:39 [testng] CFCVVEV build 01-Nov-2018 10:06:39 [testng] >SEQ2/1-7 build 01-Nov-2018 10:06:39 [testng] CFCVVEV build 01-Nov-2018 10:06:39 [testng] build 01-Nov-2018 10:06:39 [testng] Method public boolean jalview.ws.jws2.ParameterUtilsTest.isForTesting(jalview.ws.jws2.jabaws2.Jws2Instance) has a @Test annotation but also a return value: ignoring it. Use to fix this build 01-Nov-2018 10:06:40 [testng] [TestNG] Running: build 01-Nov-2018 10:06:40 [testng] Ant suite build 01-Nov-2018 10:06:40 [testng] build 01-Nov-2018 10:06:40 [testng] CMD [-open examples/uniref50.fa -noquestionnaire -nousagestats] build 01-Nov-2018 10:06:49 [testng] INFO - Getting messages for lang: en_GB build 01-Nov-2018 10:06:49 [testng] CMD [-nousagestats] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-noquestionnaire] executed successfully! build 01-Nov-2018 10:06:49 [testng] javax.net.ssl.SSLKeyException: RSA premaster secret error build 01-Nov-2018 10:06:49 [testng] at sun.security.ssl.RSAClientKeyExchange.(RSAClientKeyExchange.java:87) build 01-Nov-2018 10:06:49 [testng] at sun.security.ssl.ClientHandshaker.serverHelloDone(ClientHandshaker.java:962) build 01-Nov-2018 10:06:49 [testng] CMD [nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo -jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com -features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree] build 01-Nov-2018 10:06:49 [testng] Java version: 1.8.0_171 build 01-Nov-2018 10:06:49 [testng] amd64 Linux 3.10.0-862.3.3.el7.x86_64 build 01-Nov-2018 10:06:49 [testng] Error reading properties file: java.io.FileNotFoundException: FILE (No such file or directory) build 01-Nov-2018 10:06:49 [testng] Error reading author details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes (Is a directory) build 01-Nov-2018 10:06:49 [testng] Error reading build details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/classes (Is a directory) build 01-Nov-2018 10:06:49 [testng] Jalview Version: Test build 01-Nov-2018 10:06:49 [testng] CMD [-props FILE] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-open examples/uniref50.fa] executed successfully! build 01-Nov-2018 10:06:49 [testng] File format identified as Fasta build 01-Nov-2018 10:06:49 [testng] CMD [-color zappo] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-features examples/testdata/plantfdx.features] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-sortbytree] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-nosortbytree] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-tree examples/testdata/uniref50_test_tree] executed successfully! build 01-Nov-2018 10:06:49 [testng] CMD [-dasserver nickname=www.test.com] executed successfully! build 01-Nov-2018 10:06:51 [testng] File format identified as Fasta build 01-Nov-2018 10:06:51 [testng] Error reading author details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:51 [testng] Error reading build details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:51 [testng] Jalview Version: Test build 01-Nov-2018 10:06:51 [testng] Error reading author details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:51 [testng] Error reading build details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:51 [testng] Jalview Version: Test build 01-Nov-2018 10:06:51 [testng] >>> SIFTS File already downloaded for 1A70 build 01-Nov-2018 10:06:52 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:52 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:52 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:52 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:52 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:52 [testng] os.name: Linux build 01-Nov-2018 10:06:52 [testng] Access: ALL build 01-Nov-2018 10:06:52 [testng] memory: 27.1/144.7 build 01-Nov-2018 10:06:52 [testng] processors available: 4 build 01-Nov-2018 10:06:52 [testng] useCommandThread: false build 01-Nov-2018 10:06:52 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:52 [testng] COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS build 01-Nov-2018 10:06:52 [testng] 1YCS build 01-Nov-2018 10:06:52 [testng] reading 10 atoms build 01-Nov-2018 10:06:52 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:52 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:52 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:52 [testng] 10 atoms created build 01-Nov-2018 10:06:52 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:52 [testng] Time for creating model: 20 ms build 01-Nov-2018 10:06:52 [testng] >>> SIFTS File already downloaded for 1YCS build 01-Nov-2018 10:06:52 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:52 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:52 [testng] Getting SIFTS mapping for 1YCS|A: seq 1YCS|A build 01-Nov-2018 10:06:52 [testng] Getting SIFTS mapping for 1YCS|B: seq 1YCS|B build 01-Nov-2018 10:06:52 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:52 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:52 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:52 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:52 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:52 [testng] os.name: Linux build 01-Nov-2018 10:06:52 [testng] Access: ALL build 01-Nov-2018 10:06:52 [testng] memory: 33.9/157.3 build 01-Nov-2018 10:06:52 [testng] processors available: 4 build 01-Nov-2018 10:06:52 [testng] useCommandThread: false build 01-Nov-2018 10:06:52 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:52 [testng] HYDROLASE 09-SEP-09 3A6S build 01-Nov-2018 10:06:52 [testng] 3A6S build 01-Nov-2018 10:06:52 [testng] reading 5 atoms build 01-Nov-2018 10:06:52 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:52 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:52 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:52 [testng] 5 atoms created build 01-Nov-2018 10:06:52 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:52 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] >>> SIFTS File already downloaded for 3A6S build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 3A6S|B: seq 3A6S build 01-Nov-2018 10:06:53 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:53 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:53 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:53 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:53 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:53 [testng] os.name: Linux build 01-Nov-2018 10:06:53 [testng] Access: ALL build 01-Nov-2018 10:06:53 [testng] memory: 31.0/156.8 build 01-Nov-2018 10:06:53 [testng] processors available: 4 build 01-Nov-2018 10:06:53 [testng] useCommandThread: false build 01-Nov-2018 10:06:53 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:53 [testng] STRUCTURAL GENOMICS 04-MAR-03 1OOT build 01-Nov-2018 10:06:53 [testng] 1OOT build 01-Nov-2018 10:06:53 [testng] reading 5 atoms build 01-Nov-2018 10:06:53 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:53 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:53 [testng] model 1.1 alternative locations: A build 01-Nov-2018 10:06:53 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:53 [testng] 5 atoms created build 01-Nov-2018 10:06:53 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:53 [testng] Time for creating model: 2 ms build 01-Nov-2018 10:06:53 [testng] >>> SIFTS File already downloaded for 1OOT build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 1OOT|A: seq 1OOT build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:53 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:53 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:53 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:53 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:53 [testng] os.name: Linux build 01-Nov-2018 10:06:53 [testng] Access: ALL build 01-Nov-2018 10:06:53 [testng] memory: 30.6/155.2 build 01-Nov-2018 10:06:53 [testng] processors available: 4 build 01-Nov-2018 10:06:53 [testng] useCommandThread: false build 01-Nov-2018 10:06:53 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:53 [testng] COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS build 01-Nov-2018 10:06:53 [testng] 1YCS build 01-Nov-2018 10:06:53 [testng] reading 10 atoms build 01-Nov-2018 10:06:53 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:53 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:53 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:53 [testng] 10 atoms created build 01-Nov-2018 10:06:53 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:53 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:53 [testng] >>> SIFTS File already downloaded for 1YCS build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 1YCS|A: seq 1YCS|A build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 1YCS|B: seq 1YCS|B build 01-Nov-2018 10:06:53 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:53 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:53 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:53 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:53 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:53 [testng] os.name: Linux build 01-Nov-2018 10:06:53 [testng] Access: ALL build 01-Nov-2018 10:06:53 [testng] memory: 33.2/146.3 build 01-Nov-2018 10:06:53 [testng] processors available: 4 build 01-Nov-2018 10:06:53 [testng] useCommandThread: false build 01-Nov-2018 10:06:53 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:53 [testng] HYDROLASE 09-SEP-09 3A6S build 01-Nov-2018 10:06:53 [testng] 3A6S build 01-Nov-2018 10:06:53 [testng] reading 5 atoms build 01-Nov-2018 10:06:53 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:53 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:53 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:53 [testng] 5 atoms created build 01-Nov-2018 10:06:53 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:53 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] >>> SIFTS File already downloaded for 3A6S build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 3A6S|B: seq 3A6S build 01-Nov-2018 10:06:53 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:53 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:53 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:53 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:53 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:53 [testng] os.name: Linux build 01-Nov-2018 10:06:53 [testng] Access: ALL build 01-Nov-2018 10:06:53 [testng] memory: 31.3/152.6 build 01-Nov-2018 10:06:53 [testng] processors available: 4 build 01-Nov-2018 10:06:53 [testng] useCommandThread: false build 01-Nov-2018 10:06:53 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:53 [testng] STRUCTURAL GENOMICS 04-MAR-03 1OOT build 01-Nov-2018 10:06:53 [testng] 1OOT build 01-Nov-2018 10:06:53 [testng] reading 5 atoms build 01-Nov-2018 10:06:53 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:53 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:53 [testng] model 1.1 alternative locations: A build 01-Nov-2018 10:06:53 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:53 [testng] 5 atoms created build 01-Nov-2018 10:06:53 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:53 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:53 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:53 [testng] >>> SIFTS File already downloaded for 1OOT build 01-Nov-2018 10:06:53 [testng] Getting SIFTS mapping for 1OOT|A: seq 1OOT build 01-Nov-2018 10:06:53 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:53 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:53 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:53 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:53 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:53 [testng] os.name: Linux build 01-Nov-2018 10:06:53 [testng] Access: ALL build 01-Nov-2018 10:06:53 [testng] memory: 29.9/146.3 build 01-Nov-2018 10:06:53 [testng] processors available: 4 build 01-Nov-2018 10:06:53 [testng] useCommandThread: false build 01-Nov-2018 10:06:54 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:54 [testng] COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS build 01-Nov-2018 10:06:54 [testng] 1YCS build 01-Nov-2018 10:06:54 [testng] reading 10 atoms build 01-Nov-2018 10:06:54 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:54 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:54 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:54 [testng] 10 atoms created build 01-Nov-2018 10:06:54 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:54 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:54 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:54 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:54 [testng] >>> SIFTS File already downloaded for 1YCS build 01-Nov-2018 10:06:54 [testng] Getting SIFTS mapping for 1YCS|A: seq 1YCS|A build 01-Nov-2018 10:06:54 [testng] Getting SIFTS mapping for 1YCS|B: seq 1YCS|B build 01-Nov-2018 10:06:54 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:54 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:54 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:54 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:54 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:54 [testng] os.name: Linux build 01-Nov-2018 10:06:54 [testng] Access: ALL build 01-Nov-2018 10:06:54 [testng] memory: 33.4/150.5 build 01-Nov-2018 10:06:54 [testng] processors available: 4 build 01-Nov-2018 10:06:54 [testng] useCommandThread: false build 01-Nov-2018 10:06:54 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:54 [testng] HYDROLASE 09-SEP-09 3A6S build 01-Nov-2018 10:06:54 [testng] 3A6S build 01-Nov-2018 10:06:54 [testng] reading 5 atoms build 01-Nov-2018 10:06:54 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:54 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:54 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:54 [testng] 5 atoms created build 01-Nov-2018 10:06:54 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:54 [testng] Time for creating model: 0 ms build 01-Nov-2018 10:06:54 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:54 [testng] >>> SIFTS File already downloaded for 3A6S build 01-Nov-2018 10:06:54 [testng] Getting SIFTS mapping for 3A6S|B: seq 3A6S build 01-Nov-2018 10:06:54 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:54 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:54 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:54 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:54 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:54 [testng] os.name: Linux build 01-Nov-2018 10:06:54 [testng] Access: ALL build 01-Nov-2018 10:06:54 [testng] memory: 31.0/146.3 build 01-Nov-2018 10:06:54 [testng] processors available: 4 build 01-Nov-2018 10:06:54 [testng] useCommandThread: false build 01-Nov-2018 10:06:54 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:54 [testng] STRUCTURAL GENOMICS 04-MAR-03 1OOT build 01-Nov-2018 10:06:54 [testng] 1OOT build 01-Nov-2018 10:06:54 [testng] reading 5 atoms build 01-Nov-2018 10:06:54 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:54 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:54 [testng] model 1.1 alternative locations: A build 01-Nov-2018 10:06:54 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:54 [testng] 5 atoms created build 01-Nov-2018 10:06:54 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:54 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:54 [testng] >>> SIFTS File already downloaded for 1OOT build 01-Nov-2018 10:06:54 [testng] Source DBRef could not be determined. DBRefs might not have been retrieved. build 01-Nov-2018 10:06:54 [testng] Getting SIFTS mapping for 1OOT|A: seq 1OOT build 01-Nov-2018 10:06:54 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:54 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:54 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:54 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:54 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:54 [testng] os.name: Linux build 01-Nov-2018 10:06:54 [testng] Access: ALL build 01-Nov-2018 10:06:54 [testng] memory: 29.9/149.4 build 01-Nov-2018 10:06:54 [testng] processors available: 4 build 01-Nov-2018 10:06:54 [testng] useCommandThread: false build 01-Nov-2018 10:06:54 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:54 [testng] HYDROLASE 09-SEP-09 3A6S build 01-Nov-2018 10:06:54 [testng] 3A6S build 01-Nov-2018 10:06:54 [testng] reading 10 atoms build 01-Nov-2018 10:06:54 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:54 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:54 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:54 [testng] 10 atoms created build 01-Nov-2018 10:06:54 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:54 [testng] Time for creating model: 1 ms build 01-Nov-2018 10:06:54 [testng] Error reading author details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:54 [testng] Error reading build details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:54 [testng] Jalview Version: Test build 01-Nov-2018 10:06:54 [testng] Java version: 1.8.0_171 build 01-Nov-2018 10:06:54 [testng] amd64 Linux 3.10.0-862.3.3.el7.x86_64 build 01-Nov-2018 10:06:54 [testng] Error reading author details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:54 [testng] Error reading build details: java.io.FileNotFoundException: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB1-JOB1/cloverclasses (Is a directory) build 01-Nov-2018 10:06:54 [testng] Jalview Version: Test build 01-Nov-2018 10:06:55 [testng] Nov 01, 2018 10:06:55 AM compbio.ws.client.Jws2Client connectToRegistry build 01-Nov-2018 10:06:55 [testng] INFO: Connected to RegistryWS successfully! build 01-Nov-2018 10:06:55 [testng] registry.getSupportedServices: [GLprobsWS, MuscleWS, ClustalOWS, ClustalWS, MSAprobsWS, AAConWS, RNAalifoldWS, ProbconsWS, GlobPlotWS, IUPredWS, MafftWS, TcoffeeWS, JronnWS, DisemblWS] build 01-Nov-2018 10:06:55 [testng] Attempting to connect with MafftWS... build 01-Nov-2018 10:06:55 [testng] Nov 01, 2018 10:06:55 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:55 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:55 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@16ee7957 build 01-Nov-2018 10:06:55 [testng] Attempting to connect with MuscleWS... build 01-Nov-2018 10:06:55 [testng] Nov 01, 2018 10:06:55 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:55 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:55 [testng] Warning - overwriting a sequenceSetId for a viewport! build 01-Nov-2018 10:06:55 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@705273f8 build 01-Nov-2018 10:06:55 [testng] Attempting to connect with ClustalWS... build 01-Nov-2018 10:06:55 [testng] Nov 01, 2018 10:06:55 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:55 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:55 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@35b8ea59 build 01-Nov-2018 10:06:55 [testng] Attempting to connect with ClustalOWS... build 01-Nov-2018 10:06:56 [testng] Nov 01, 2018 10:06:55 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:56 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:56 [testng] Allocating Jmol Viewer: build 01-Nov-2018 10:06:56 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@e527bca build 01-Nov-2018 10:06:56 [testng] Attempting to connect with TcoffeeWS... build 01-Nov-2018 10:06:56 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:56 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:56 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:56 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:56 [testng] os.name: Linux build 01-Nov-2018 10:06:56 [testng] Access: ALL build 01-Nov-2018 10:06:56 [testng] memory: 91.4/146.3 build 01-Nov-2018 10:06:56 [testng] processors available: 4 build 01-Nov-2018 10:06:56 [testng] useCommandThread: false build 01-Nov-2018 10:06:56 [testng] >>Jmol>> History on build 01-Nov-2018 10:06:56 [testng] <>Jmol>> # Jmol state version 12.2.4 2011-10-11 21:29;function _setWindowState() {# width 339;# height 297; stateVersion = 1202004; background [x000000]; axis1Color = "[xff0000]"; axis2Color = "[x007f00]"; axis3Color = "[x0000ff]"; set ambientPercent 45; set diffusePercent 84; set specular true; set specularPercent 22; set specularPower 40; set specularExponent 6; set zShadePower 1; statusReporting = true;}function _setFileState() { set allowEmbeddedScripts false; set appendNew true; set appletProxy ""; set applySymmetryToBonds false; set autoBond true; set bondRadiusMilliAngstroms 150; set bondTolerance 0.45; set defaultLattice {0.0 0.0 0.0}; set defaultLoadFilter ""; set defaultLoadScript ""; set defaultStructureDssp true; set defaultVDW Jmol; set forceAutoBond false; #set defaultDirectory "/Users/jimp"; #set loadFormat "http://www.rcsb.org/pdb/files/%FILE.pdb.gz"; #set loadLigandFormat "http://www.rcsb.org/pdb/files/ligand/%FILE.cif"; #set smilesUrlFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True"; #set nihResolverFormat "http://cactus.nci.nih.gov/chemical/structure/%FILE"; #set edsUrlFormat "http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap"; #set edsUrlCutoff "load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split(' ')[2]"; set legacyAutoBonding false; set minBondDistance 0.4; set minimizationCriterion 0.0010; set minimizationSteps 100; set pdbAddHydrogens false; set pdbGetHeader false; set pdbSequential false; set percentVdwAtom 20; set smallMoleculeMaxAtoms 40000; set smartAromatic true; load /*file*/"/tmp/jalview_pdb3226739938478340499.txt";}function _setVariableState() { set defaultanglelabel "%VALUE %UNITS"; set defaultcolorscheme "jmol"; set defaultdistancelabel "%VALUE %UNITS"; set defaultdrawarrowscale 0.5; set defaultlabelpdb "%m%r"; set defaultlabelxyz "%a"; set defaultlattice "{0.0 0.0 0.0}"; set defaultloadfilter ""; set defaultloadscript ""; set defaulttorsionlabel "%VALUE %UNITS"; set defaulttranslucent 0.5; set defaultvdw "Jmol"; set allowembeddedscripts true; set allowmoveatoms false; set allowrotateselected false; set appletproxy ""; set applysymmetrytobonds false; set atompicking true; set atomtypes ""; set autobond true; set autofps false; set axes window; set axesmode 0; set axesscale 2.0; set bondmodeor false; set bondradiusmilliangstroms 150; set bondtolerance 0.45; set cartoonbaseedges false; set cartoonrockets false; set chaincasesensitive false; set dataseparator "~~~"; set defaultstructuredssp true; set delaymaximumms 0; set dipolescale 1.0; set disablepopupmenu false; set displaycellparameters true; set dotdensity 3; set dotscale 1; set dotsselectedonly false; set dotsurface true; set dragselected false; set drawhover false; set drawpicking false; set dsspcalculatehydrogenalways true; set dynamicmeasurements false; set ellipsoidarcs false; set ellipsoidaxes false; set ellipsoidaxisdiameter 0.02; set ellipsoidball true; set ellipsoiddotcount 200; set ellipsoiddots false; set ellipsoidfill false; set forceautobond false; set fractionalrelative false; set gestureswipefactor 1.0; set greyscalerendering false; set hbondsangleminimum 90.0; set hbondsbackbone false; set hbondsdistancemaximum 3.25; set hbondsrasmol true; set hbondssolid false; set helixstep 1; set helppath "http://chemapps.stolaf.edu/jmol/docs/index.htm"; set hermitelevel 0; set hidenameinpopup false; set hidenavigationpoint false; set highresolution false; set historylevel 0; set hoverdelay 0.5; set imagestate true; set iskiosk false; set isosurfacekey false; set isosurfacepropertysmoothing true; set isosurfacepropertysmoothingpower 7; set justifymeasurements false; set loadatomdatatolerance 0.01; set measureallmodels false; set measurementlabels true; set messagestylechime false; set minbonddistance 0.4; set minimizationcriterion 0.0010; set minimizationrefresh true; set minimizationsilent false; set minimizationsteps 100; set minpixelselradius 6; set monitorenergy false; set multiplebondradiusfactor 0.0; set multiplebondspacing -1.0; set navigatesurface false; set navigationperiodic false; set navigationspeed 5.0; set partialdots false; set pdbaddhydrogens false; set pdbgetheader false; set pdbsequential false; set percentvdwatom 20; set pickingspinrate 10; set picklabel ""; set pointgroupdistancetolerance 0.2; set pointgrouplineartolerance 8.0; set propertyatomnumbercolumncount 0; set propertyatomnumberfield 0; set propertycolorscheme "roygb"; set propertydatacolumncount 0; set propertydatafield 0; set quaternionframe "p"; set rangeselected false; set ribbonaspectratio 16; set ribbonborder false; set rocketbarrels false; set saveproteinstructurestate true; set selectallmodels true; set selecthetero true; set selecthydrogen true; set sheetsmoothing 1.0; set showhiddenselectionhalos false; set showhydrogens true; set showkeystrokes true; set showmeasurements true; set showmultiplebonds true; set shownavigationpointalways false; set slabbyatom false; set slabbymolecule false; set smallmoleculemaxatoms 40000; set smartaromatic true; set solventprobe false; set solventproberadius 1.2; set ssbondsbackbone false; set stereodegrees -5.0; set strandcountformeshribbon 7; set strandcountforstrands 5; set strutdefaultradius 0.3; set strutlengthmaximum 7.0; set strutsmultiple false; set strutspacing 6; set testflag1 false; set testflag2 false; set testflag3 false; set testflag4 false; set tracealpha true; set usearcball false; set useminimizationthread true; set usenumberlocalization true; set vectorscale 1.0; set vibrationscale 1.0; set wireframerotation false; set zdepth 0; set zoomlarge true; set zslab 0;# label defaults; select none; color label none; background label none; set labelOffset 4 4; set labelAlignment left; set labelPointer off; font label 13.0 SansSerif Plain;}function _setModelState() { select ({659:665}); color atoms opaque [xc88395]; select ({0:44 53:84 93:340 347:731 736:816}); Spacefill 0.0; select ({285:290 449:454 773 797}); color atoms opaque [xb974a5]; select ({5:66 81:141 297:316 347:392 536:564 588:619 628:658 737:744 747:754 775:777 783:789 808:810}); color atoms opaque [x25c54c]; select ({291:296 323:328 341:346 572:577 774 779 782 812}); color atoms opaque [x70686e]; select ({0:4 67:80 142:164 229:265 393:448 455:481 532:535 583:587 620:627 666:684 712:731 736 745 746 755:757 766:770 790:796 798:800 807 814}); color atoms opaque [xffffff]; select ({177:228 482:531 565:571 578:582 694:711 759:765 801:806 811 813}); color atoms opaque [xd4d189]; select ({815 816}); color atoms opaque [x24c44b]; select ({732:735}); Spacefill 2.0; select ({45:52 85:92 341:346}); Spacefill 0.8; select ({266:284 317:322 329:340 771 772 778 780 781}); color atoms opaque [x988d43]; select ({165:176 758}); color atoms opaque [x7d3881]; select BONDS ({58:61 63:65 95:101 130 307 356 357 359:361}); wireframe 0.4; select BONDS ({0:57 62 66:94 102:129 131:306 308:355 358 362:751}); wireframe 0.0; select ({661}); label "%n %r"; measures delete; measure (({734})) (({664})); # distance 13.28 1.328 nm [FES]1602.S1 #736 [THR]89.OG1 #665; select *; set measures nanometers; font measures 15.0 SansSerif Plain; select ({0:4 67:80 142:176 229:346 389:481 532:535 583:627 659:684 712:731}); Cartoon 0.25; select ({5:66 81:141 177:228 347:388 482:531 536:582 628:649 685:711}); Cartoon 1.5; boundBox off; font boundBox 14.0 SansSerif Plain; boundBox off; unitcell off; font unitcell 14.0 SansSerif Plain; unitcell off; hover "%U"; frank on; font frank 16.0 SansSerif Bold; select *; frame 1.1; set unitcell {0.0 0.0 0.0}; unitcell OFF; set fontScaling false;}function _setPerspectiveState() { set perspectiveModel 11; set scaleAngstromsPerInch 0.0; set perspectiveDepth true; set visualRange 5.0; set cameraDepth 3.0; boundbox corners {-6.196001 -11.645 -3.927} {29.28 29.978 28.44} # volume = 47793.684; center {11.542 9.166499 12.2565}; moveto -1.0 {0 0 1 0} 100.0 0.85 0.17 {11.542 9.166499 12.2565} 26.6833 {0.0 0.0 0.0} -19.47622 18.289658 0.0; save orientation "default"; moveto 0.0 {0 0 1 0} 100.0 0.85 0.17 {11.542 9.166499 12.2565} 26.6833 {0.0 0.0 0.0} -19.47622 18.289658 0.0;; slab 100;depth 0; set slabRange 0.0; set spinX 0; set spinY 30; set spinZ 0; set spinFps 30; set navX 0; set navY 0; set navZ 0; set navFps 10;}function _setSelectionState() { set hideNotSelected false;}function _setState() { initialize; set refreshing false; _setWindowState; _setFileState; _setVariableState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay false; set antialiasTranslucent true; set antialiasImages true;}_setState; build 01-Nov-2018 10:06:56 [testng] build 01-Nov-2018 10:06:56 [testng] Nov 01, 2018 10:06:56 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:56 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:56 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3ca8cb37 build 01-Nov-2018 10:06:56 [testng] build 01-Nov-2018 10:06:56 [testng] FileManager.getAtomSetCollectionFromFile(/tmp/jalview_pdb3226739938478340499.txt) build 01-Nov-2018 10:06:56 [testng] FileManager opening file /tmp/jalview_pdb3226739938478340499.txt build 01-Nov-2018 10:06:56 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:56 [testng] IRON-SULFUR PROTEIN 19-MAR-98 1A70 build 01-Nov-2018 10:06:56 [testng] SPINACH FERREDOXIN build 01-Nov-2018 10:06:56 [testng] FES = FE2/S2 (INORGANIC) CLUSTER build 01-Nov-2018 10:06:56 [testng] Setting space group name to P 21 21 21 build 01-Nov-2018 10:06:56 [testng] 1A70 build 01-Nov-2018 10:06:56 [testng] Time for openFile(/tmp/jalview_pdb3226739938478340499.txt): 275 ms build 01-Nov-2018 10:06:56 [testng] reading 817 atoms build 01-Nov-2018 10:06:56 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:56 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:56 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:56 [testng] 817 atoms created build 01-Nov-2018 10:06:56 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:56 [testng] Attempting to connect with ProbconsWS... build 01-Nov-2018 10:06:56 [testng] Operating headless display=null nographicsallowed=true build 01-Nov-2018 10:06:56 [testng] (C) 2015 Jmol Development build 01-Nov-2018 10:06:56 [testng] Jmol Version: 14.29.17 2018-06-15 14:15 build 01-Nov-2018 10:06:56 [testng] java.vendor: Java: Oracle Corporation build 01-Nov-2018 10:06:56 [testng] java.version: Java 1.8.0_171 build 01-Nov-2018 10:06:56 [testng] os.name: Linux build 01-Nov-2018 10:06:56 [testng] Access: ALL build 01-Nov-2018 10:06:56 [testng] memory: 46.5/148.9 build 01-Nov-2018 10:06:56 [testng] processors available: 4 build 01-Nov-2018 10:06:56 [testng] useCommandThread: false build 01-Nov-2018 10:06:56 [testng] The Resolver thinks Pdb build 01-Nov-2018 10:06:56 [testng] IRON-SULFUR PROTEIN 19-MAR-98 1A70 build 01-Nov-2018 10:06:56 [testng] SPINACH FERREDOXIN build 01-Nov-2018 10:06:56 [testng] FES = FE2/S2 (INORGANIC) CLUSTER build 01-Nov-2018 10:06:56 [testng] Setting space group name to P 21 21 21 build 01-Nov-2018 10:06:56 [testng] 1A70 build 01-Nov-2018 10:06:56 [testng] Nov 01, 2018 10:06:56 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:56 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:56 [testng] reading 817 atoms build 01-Nov-2018 10:06:56 [testng] ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false build 01-Nov-2018 10:06:56 [testng] 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. build 01-Nov-2018 10:06:56 [testng] Default Van der Waals type for model set to Jmol build 01-Nov-2018 10:06:56 [testng] 817 atoms created build 01-Nov-2018 10:06:56 [testng] ModelSet: autobonding; use autobond=false to not generate bonds automatically build 01-Nov-2018 10:06:56 [testng] Time for creating model: 11 ms build 01-Nov-2018 10:06:56 [testng] Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@71e2790a build 01-Nov-2018 10:06:56 [testng] >>Jmol>> model *; select backbone;restrict;cartoon;wireframe off;spacefill off build 01-Nov-2018 10:06:56 [testng] Nov 01, 2018 10:06:56 AM compbio.ws.client.Jws2Client connect build 01-Nov-2018 10:06:56 [testng] INFO: Connected successfully! build 01-Nov-2018 10:06:56 [testng] <>Jmol>> History on build 01-Nov-2018 10:06:56 [testng] <>Jmol>> History on build 01-Nov-2018 10:06:56 [testng] <>Jmol>> set hoverDelay=0.1 build 01-Nov-2018 10:06:56 [testng] build 01-Nov-2018 10:06:56 [testng] <>Jmol>> History on build 01-Nov-2018 10:06:56 [testng] <