GATK gradlew bundle Error

Question

[Abdul Rafay Khan]

While building gatk

sudo ./gradlew bundle

Downloading https://services.gradle.org/distributions/gradle-3.1-bin.zip

Exception in thread "main" javax.net.ssl.SSLException: java.security.ProviderException: java.security.InvalidKeyException: EC parameters error at sun.security.ssl.Alerts.getSSLException(Alerts.java:208) at sun.security.ssl.SSLSocketImpl.fatal(SSLSocketImpl.java:1914) at sun.security.ssl.SSLSocketImpl.fatal(SSLSocketImpl.java:1872) at sun.security.ssl.SSLSocketImpl.handleException(SSLSocketImpl.java:1855) at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1376) at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1353) at sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:559) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:185) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1366) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263) at org.gradle.wrapper.Download.downloadInternal(Download.java:58) at org.gradle.wrapper.Download.download(Download.java:44) at org.gradle.wrapper.Install$1.call(Install.java:61) at org.gradle.wrapper.Install$1.call(Install.java:48) at org.gradle.wrapper.ExclusiveFileAccessManager.access(ExclusiveFileAccessManager.java:69) at org.gradle.wrapper.Install.createDist(Install.java:48) at org.gradle.wrapper.WrapperExecutor.execute(WrapperExecutor.java:107) at org.gradle.wrapper.GradleWrapperMain.main(GradleWrapperMain.java:61) Caused by: java.security.ProviderException: java.security.InvalidKeyException: EC parameters error at sun.security.pkcs11.P11Key$P11ECPublicKey.getEncodedInternal(P11Key.java:1024) at sun.security.pkcs11.P11Key.equals(P11Key.java:158) at java.util.ArrayList.indexOf(ArrayList.java:302) at java.util.ArrayList.contains(ArrayList.java:285) at sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:239) at sun.security.validator.Validator.validate(Validator.java:260) at sun.security.ssl.X509TrustManagerImpl.validate(X509TrustManagerImpl.java:326) at sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:231) at sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:126) at sun.security.ssl.ClientHandshaker.serverCertificate(ClientHandshaker.java:1459) at sun.security.ssl.ClientHandshaker.processMessage(ClientHandshaker.java:213) at sun.security.ssl.Handshaker.processLoop(Handshaker.java:961) at sun.security.ssl.Handshaker.process_record(Handshaker.java:897) at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:1033) at sun.security.ssl.SSLSocketImpl.performInitialHandshake(SSLSocketImpl.java:1342) at sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:1369) ... 13 more Caused by: java.security.InvalidKeyException: EC parameters error at sun.security.ec.ECParameters.getAlgorithmParameters(ECParameters.java:284) at sun.security.ec.ECPublicKeyImpl.(ECPublicKeyImpl.java:59) at sun.security.pkcs11.P11Key$P11ECPublicKey.getEncodedInternal(P11Key.java:1021) ... 28 more Caused by: java.security.NoSuchProviderException: no such provider: SunEC at sun.security.jca.GetInstance.getService(GetInstance.java:83) at sun.security.jca.GetInstance.getInstance(GetInstance.java:206) at java.security.Security.getImpl(Security.java:697) at java.security.AlgorithmParameters.getInstance(AlgorithmParameters.java:199) at sun.security.ec.ECParameters.getAlgorithmParameters(ECParameters.java:279)

Answer 1

[dariober]

I surmise this has nothing to do with GATK but with gradle. Googling java.security.ProviderException: java.security.InvalidKeyException: EC parameters leads to this issue which suggests OpenJDK7 is the culprit. As suggested there, try upgrading to OpenJDK8 in case you are also on 7. This is, of course, a wild guess from me...!

[Abdul Rafay Khan]

Thank you dariober, it works

sudo apt-get update
sudo apt-get install openjdk-8-jdk

sudo update-alternatives --config java
sudo update-alternatives --config javac

and enter the number for which JDK to use of your choice.