第4类错误：连接超时

错误包：vcfucsc、vcfcadd

1、vcfucsc

输出结果：

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
Removing 0 daemon stop events from registry
Starting a Gradle Daemon, 1 busy Daemon could not be reused, use --status for details
Starting process 'Gradle build daemon'. Working directory: /root/.gradle/daemon/7.4.2 Command: /root/install_path/bisheng-jdk-11.0.15/bin/java --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.base/java.nio.charset=ALL-UNNAMED --add-opens java.base/java.net=ALL-UNNAMED --add-opens java.base/java.util.concurrent.atomic=ALL-UNNAMED -XX:MaxMetaspaceSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xms256m -Xmx512m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /root/.gradle/wrapper/dists/gradle-7.4.2-bin/48ivgl02cpt2ed3fh9dbalvx8/gradle-7.4.2/lib/gradle-launcher-7.4.2.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 7.4.2
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 0.979 secs.
The client will now receive all logging from the daemon (pid: 2260769). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-2260769.out.log
Starting build in new daemon [memory: 512 MiB]
Using 4 worker leases.
Watching the file system is configured to be enabled if available
Now considering [/root/jvarkit] as hierarchies to watch
File system watching is active
Starting Build
Settings evaluated using settings file '/root/jvarkit/settings.gradle'.
Projects loaded. Root project using build file '/root/jvarkit/build.gradle'.
Included projects: [root project 'jvarkit']> Configure project :
Evaluating root project 'jvarkit' using build file '/root/jvarkit/build.gradle'.
All projects evaluated.
Selected primary task 'vcfucsc' from project :
Tasks to be executed: [vcfucsc com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc]
Tasks that were excluded: []
:vcfucsc (Thread[Execution worker for ':' Thread 2,5,main]) started.
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning> Task :vcfucsc
Starting process 'command 'git''. Working directory: /root/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for vcfucsc com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc because:Build cache is disabled
Vcfucsc com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc is not up-to-date because:Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/jvarkit/tmp/com/github/lindenb/jvarkit/tools/vcfucsc
Starting process 'command 'which''. Working directory: /root/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/jvarkit/tmp
[ant:copy] Copying 1 file to /root/jvarkit/tmp/com/github/lindenb/jvarkit/tools/vcfucsc
copy to /root/jvarkit/src/main/resources/so/so-simple.owl
[ant:copy] Copying 1 file to /root/jvarkit/tmp/META-INF/so
[ant:mkdir] Created dir: /root/jvarkit/tmp/META-INF/chromnames
[ant:copy] Copying 1 file to /root/jvarkit/tmp/META-INF/chromnames
[ant:unzip] Expanding: /root/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar into /root/jvarkit/tmp
[ant:unzip] Expanding: /root/jvarkit/lib/mysql/mysql-connector-java/5.1.47/mysql-connector-java-5.1.47.jar into /root/jvarkit/tmp
Starting process 'command 'git''. Working directory: /root/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
[ant:jar] Building jar: /root/jvarkit/dist/vcfucsc.jar
[ant:delete] Deleting directory /root/jvarkit/tmp
jar file generated :/root/jvarkit/dist/vcfucsc.jar
[ant:mkdir] Created dir: /root/jvarkit/tmp
Test will be executed in /root/jvarkit/tests-output/vcfucsc/index.html
[ant:javac] Compiling 2 source files to /root/jvarkit/tmp[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcscTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.jcommander.LauncherTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.io.IOUtilsTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.LineIteratorsTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.StringUtilsTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.AbstractCharSequenceTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.DelegateCharSequenceTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.VCFUtilsTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.CharSplitterTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.SequenceDictionaryUtilsTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.fasta.ContigNameConverterTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.IntervalParserFactoryTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.SimpleIntervalTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.AFExtractorFactoryTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.vcftrios.DeNovoDetectorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.CounterTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.bed.BedLineCodecTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.log.ProgressFactoryTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.samtools.ContigDictComparatorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.SmartComparatorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.EqualRangeIteratorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.FilterIteratorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.MergingIteratorTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.samfilter.SamRecordFilterFactoryTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.reference.TwoBitSequenceFileTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.math.DiscreteMedianTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.IntArrayTest
[ant:java] Nov 11, 2022 10:23:54 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.DoubleArrayTest
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:7 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:4 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=11. That took:6 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=477. That took:21 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:34 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:16 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:19 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:12 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:11 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:0 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:2 millisecs
[ant:java] [INFO][VcfUcsc]Getting jdbc-driver
[ant:java] [SEVERE][VcfUcsc]Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java] com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:342)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2197)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2230)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2025)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:778)
[ant:java]      at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386)
[ant:java]      at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:677)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:251)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc.beforeVcf(VcfUcsc.java:407)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcscTest.test01(VcfUcscTest.java:35)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
[ant:java]      at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:412)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:255)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:237)
[ant:java]      at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
[ant:java]      at java.base/java.net.Socket.connect(Socket.java:609)
[ant:java]      at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:211)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:301)
[ant:java]      ... 42 more
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [INFO][VcfUcsc]Getting jdbc-driver
[ant:java] [SEVERE][VcfUcsc]Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java] com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:342)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2197)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2230)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2025)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:778)
[ant:java]      at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386)
[ant:java]      at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:677)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:251)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc.beforeVcf(VcfUcsc.java:407)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcscTest.test01(VcfUcscTest.java:35)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
[ant:java]      at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:412)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:255)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:237)
[ant:java]      at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
[ant:java]      at java.base/java.net.Socket.connect(Socket.java:609)
[ant:java]      at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:211)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:301)
[ant:java]      ... 42 more
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java]
[ant:java] ===============================================
[ant:java] Command line suite
[ant:java] Total tests run: 100, Failures: 2, Skips: 0
[ant:java] ===============================================
[ant:java] > Task :vcfucsc
[ant:java] Java Result: 255
[ant:delete] Deleting directory /root/jvarkit/tmp
:vcfucsc (Thread[Execution worker for ':' Thread 2,5,main]) completed. Took 4 mins 49.957 secs.BUILD SUCCESSFUL in 4m 55s
1 actionable task: 1 executed

定位到报错位置：

[ant:java] [INFO][VcfUcsc]Getting jdbc-driver
[ant:java] [SEVERE][VcfUcsc]Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java] com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
[ant:java]
[ant:java] The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:990)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:342)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2197)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2230)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2025)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:778)
[ant:java]      at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
[ant:java]      at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
[ant:java]      at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
[ant:java]      at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:386)
[ant:java]      at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:330)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:677)
[ant:java]      at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:251)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcsc.beforeVcf(VcfUcsc.java:407)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.vcfucsc.VcfUcscTest.test01(VcfUcscTest.java:35)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] Caused by: java.net.ConnectException: Connection timed out (Connection timed out)
[ant:java]      at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:412)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:255)
[ant:java]      at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:237)
[ant:java]      at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
[ant:java]      at java.base/java.net.Socket.connect(Socket.java:609)
[ant:java]      at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:211)
[ant:java]      at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:301)
[ant:java]      ... 42 more
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport

从报错可以得知，是连接到某个数据库失败，定位到代码中：


这是一个国外学校的数据库地址（无法直接访问，但是有可以访问该校官网）：

"hg19"应该是具体的数据库

2、vcfcadd

输出结果：

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
Removing 0 daemon stop events from registry
Starting a Gradle Daemon (subsequent builds will be faster)
Starting process 'Gradle build daemon'. Working directory: /root/.gradle/daemon/7.4.2 Command: /root/install_path/bisheng-jdk-11.0.15/bin/java --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.base/java.nio.charset=ALL-UNNAMED --add-opens java.base/java.net=ALL-UNNAMED --add-opens java.base/java.util.concurrent.atomic=ALL-UNNAMED -XX:MaxMetaspaceSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xms256m -Xmx512m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /root/.gradle/wrapper/dists/gradle-7.4.2-bin/48ivgl02cpt2ed3fh9dbalvx8/gradle-7.4.2/lib/gradle-launcher-7.4.2.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 7.4.2
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 4.372 secs.
The client will now receive all logging from the daemon (pid: 3766898). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-3766898.out.log
Starting build in new daemon [memory: 512 MiB]
Using 4 worker leases.
Watching the file system is configured to be enabled if available
Now considering [/root/jvarkit_old] as hierarchies to watch
File system watching is active
Starting Build
Settings evaluated using settings file '/root/jvarkit_old/settings.gradle'.
Projects loaded. Root project using build file '/root/jvarkit_old/build.gradle'.
Included projects: [root project 'jvarkit']> Configure project :
Evaluating root project 'jvarkit' using build file '/root/jvarkit_old/build.gradle'.
All projects evaluated.
Selected primary task 'vcfcadd' from project :
Tasks to be executed: [vcfcadd com.github.lindenb.jvarkit.tools.cadd.VcfCadd]
Tasks that were excluded: []
:vcfcadd (Thread[Execution worker for ':',5,main]) started.> Task :vcfcadd
Starting process 'command 'git''. Working directory: /root/jvarkit_old Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for vcfcadd com.github.lindenb.jvarkit.tools.cadd.VcfCadd because:Build cache is disabled
Vcfcadd com.github.lindenb.jvarkit.tools.cadd.VcfCadd is not up-to-date because:Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/jvarkit_old/tmp/META-INF
[ant:mkdir] Created dir: /root/jvarkit_old/dist
Downloading https://repo1.maven.org/maven2/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar to /root/jvarkit_old/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/com/github/samtools/htsjdk/3.0.0
[ant:get] Getting: https://repo1.maven.org/maven2/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar
[ant:get] To: /root/jvarkit_old/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar[ant:get] ....................................................
[ant:get] ....................................................
[ant:get] ............................
[ant:get] ....
[ant:get] .....
[ant:get] .................
[ant:get] ......................................> Task :vcfcadd
Downloading https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar to /root/jvarkit_old/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/commons-logging/commons-logging/1.1.1
[ant:get] Getting: https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[ant:get] To: /root/jvarkit_old/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
Downloading https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /root/jvarkit_old/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0
[ant:get] Getting: https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[ant:get] To: /root/jvarkit_old/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
Downloading https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /root/jvarkit_old/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/apache/commons/commons-jexl/2.1.1
[ant:get] Getting: https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[ant:get] To: /root/jvarkit_old/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
Downloading https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar to /root/jvarkit_old/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/apache/commons/commons-compress/1.19
[ant:get] Getting: https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar
[ant:get] To: /root/jvarkit_old/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar
Downloading https://repo1.maven.org/maven2/org/tukaani/xz/1.8/xz-1.8.jar to /root/jvarkit_old/lib/org/tukaani/xz/1.8/xz-1.8.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/tukaani/xz/1.8
[ant:get] Getting: https://repo1.maven.org/maven2/org/tukaani/xz/1.8/xz-1.8.jar
[ant:get] To: /root/jvarkit_old/lib/org/tukaani/xz/1.8/xz-1.8.jar[ant:get] .......
[ant:get] .....
[ant:get] ....................................................
[ant:get] ....................................................
[ant:get] ..................
[ant:get] .....
[ant:get] ....................................................
[ant:get] .
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8> Task :vcfcadd
Downloading https://repo1.maven.org/maven2/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar to /root/jvarkit_old/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/sharegov/mjson/1.4.1
[ant:get] Getting: https://repo1.maven.org/maven2/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
[ant:get] To: /root/jvarkit_old/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
Downloading https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar to /root/jvarkit_old/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/xerial/snappy/snappy-java/1.1.8.4
[ant:get] Getting: https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
[ant:get] To: /root/jvarkit_old/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
Downloading https://repo1.maven.org/maven2/com/beust/jcommander/1.72/jcommander-1.72.jar to /root/jvarkit_old/lib/com/beust/jcommander/1.72/jcommander-1.72.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/com/beust/jcommander/1.72
[ant:get] Getting: https://repo1.maven.org/maven2/com/beust/jcommander/1.72/jcommander-1.72.jar
[ant:get] To: /root/jvarkit_old/lib/com/beust/jcommander/1.72/jcommander-1.72.jar
Downloading https://repo1.maven.org/maven2/org/testng/testng/6.14.3/testng-6.14.3.jar to /root/jvarkit_old/lib/org/testng/testng/6.14.3/testng-6.14.3.jar
[ant:mkdir] Created dir: /root/jvarkit_old/lib/org/testng/testng/6.14.3
[ant:get] Getting: https://repo1.maven.org/maven2/org/testng/testng/6.14.3/testng-6.14.3.jar
[ant:get] To: /root/jvarkit_old/lib/org/testng/testng/6.14.3/testng-6.14.3.jar
[ant:mkdir] Created dir: /root/jvarkit_old/tmp/com/github/lindenb/jvarkit/tools/cadd
Starting process 'command 'which''. Working directory: /root/jvarkit_old Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/jvarkit_old Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/jvarkit_old Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/jvarkit_old/tmp[ant:javac] 1 warning> Task :vcfcadd
[ant:copy] Copying 1 file to /root/jvarkit_old/tmp/com/github/lindenb/jvarkit/tools/cadd
[ant:mkdir] Created dir: /root/jvarkit_old/tmp/META-INF/chromnames
[ant:copy] Copying 1 file to /root/jvarkit_old/tmp/META-INF/chromnames
[ant:unzip] Expanding: /root/jvarkit_old/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/org/tukaani/xz/1.8/xz-1.8.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar into /root/jvarkit_old/tmp
[ant:unzip] Expanding: /root/jvarkit_old/lib/com/beust/jcommander/1.72/jcommander-1.72.jar into /root/jvarkit_old/tmp
Starting process 'command 'git''. Working directory: /root/jvarkit_old Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
[ant:jar] Building jar: /root/jvarkit_old/dist/vcfcadd.jar
[ant:delete] Deleting directory /root/jvarkit_old/tmp
jar file generated :/root/jvarkit_old/dist/vcfcadd.jar
[ant:mkdir] Created dir: /root/jvarkit_old/tmp
Test will be executed in /root/jvarkit_old/tests-output/vcfcadd/index.html
[ant:javac] Compiling 2 source files to /root/jvarkit_old/tmp[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning
[ant:java] Nov 18, 2022 11:54:08 AM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest> Task :vcfcadd
[ant:mkdir] Created dir: /root/jvarkit_old/tests-output/vcfcadd[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java] [SEVERE][VcfCadd]Invalid GZIP header
[ant:java] htsjdk.samtools.SAMFormatException: Invalid GZIP header
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:121)
[ant:java]      at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
[ant:java]      at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:233)
[ant:java]      at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:287)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:165)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:147)
[ant:java]      at htsjdk.tribble.readers.TabixReader.<init>(TabixReader.java:109)
[ant:java]      at com.github.lindenb.jvarkit.util.tabix.TabixFileReader.<init>(TabixFileReader.java:61)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCadd.beforeVcf(VcfCadd.java:459)
[ant:java]      at com.github.lindenb.jvarkit.jcommander.OnePassVcfLauncher.doWork(OnePassVcfLauncher.java:123)
[ant:java]      at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:795)
[ant:java]      at com.github.lindenb.jvarkit.tools.cadd.VcfCaddTest.test01(VcfCaddTest.java:32)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ant:java]      at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ant:java]      at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ant:java]      at java.base/java.lang.reflect.Method.invoke(Method.java:566)
[ant:java]      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:124)
[ant:java]      at org.testng.internal.Invoker.invokeMethod(Invoker.java:583)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:719)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:989)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] [SEVERE][OnePassVcfLauncher]initialization failed
[ant:java] [TEST] end TestSupport
[ant:java]
[ant:java] ===============================================
[ant:java] Command line suite
[ant:java] Total tests run: 14, Failures: 14, Skips: 0
[ant:java] ===============================================
[ant:java] > Task :vcfcadd
[ant:java] Java Result: 255
[ant:delete] Deleting directory /root/jvarkit_old/tmp
:vcfcadd (Thread[Execution worker for ':',5,main]) completed. Took 3 mins 38.658 secs.BUILD SUCCESSFUL in 3m 54s
1 actionable task: 1 executed

从输出结果可以得知，他在不断的尝试初始化一个GZIP工具包。
定位到源码：

传入了一个链接。



国外的一个教育网站，所以链接超时，初始化包失败。

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