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java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at net.sf.cram.CramTools.invoke(CramTools.java:93) at net.sf.cram.CramTools.main(CramTools.java:123)Caused by: java.lang.RuntimeException: java.net.ConnectException: Connection timed out at net.sf.cram.ref.ReferenceSource.findBases(ReferenceSource.java:183) at net.sf.cram.ref.ReferenceSource.getReferenceBases(ReferenceSource.java:127) at net.sf.cram.Bam2Cram.main(Bam2Cram.java:282) ... 6 moreCaused by: java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:382) at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:241) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:228) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:365) at java.net.Socket.connect(Socket.java:527) at java.net.Socket.connect(Socket.java:476) at sun.net.NetworkClient.doConnect(NetworkClient.java:163) at sun.net.www.http.HttpClient.openServer(HttpClient.java:424) at sun.net.www.http.HttpClient.openServer(HttpClient.java:538) at sun.net.www.http.HttpClient.<init>(HttpClient.java:214) at sun.net.www.http.HttpClient.New(HttpClient.java:300) at sun.net.www.http.HttpClient.New(HttpClient.java:319) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:987) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:923) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:841) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1195) at java.net.URL.openStream(URL.java:1010) at net.sf.cram.ref.ReferenceSource.loadFromPath(ReferenceSource.java:249) at net.sf.cram.ref.ReferenceSource.findBasesByMD5(ReferenceSource.java:283) at net.sf.cram.ref.ReferenceSource.findBases(ReferenceSource.java:179) ... 8 more