java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3

GitHub | jpdna | 2 months ago
  1. 0

    gVCF - can't load multi-allelic sites

    GitHub | 2 months ago | jpdna
    java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3
  2. 0

    Raptor storing off bad last move in pgn file. Its rare has happened 1 time out of 3800+ games.

    GitHub | 11 months ago | cday-fics
    java.lang.IllegalArgumentException: Invalid move Rg8 emptyBB occupiedBB notColorToMoveBB color[WHITE] color[BLACK] 1 1 1 0 1 1 1 1 0 0 0 1 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 1 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 0 0 1 0 0 0 0 0 1 1 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 1 0 0 0 0 0 0 1 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 1 0 0 0 0 0 0 1 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 [WHITE][PAWN] [WHITE][KNIGHT] [WHITE][BISHOP] [WHITE][ROOK] [WHITE][QUEEN] [WHITE][KING] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [BLACK][PAWN] [BLACK][KNIGHT] [BLACK][BISHOP] [BLACK][ROOK] [BLACK][QUEEN] [BLACK][KING] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 |_|_|_|R|_|_|_|_| To Move: Black Last Move: d7 |_|_|_|P|_|_|_|_| Piece counts [WP=3 WN=0 WB=0 WR=1 WQ=0 WK=1][BP=0 BN= 0 BB=0 BR=1 BQ=0 BK=1] |_|_|k|_|_|_|_|_| Moves: 85 EP: - Castle: - |_|_|_|_|_|_|_|P| FEN: 3R4/3P4/2k5/7P/6K1/6P1/8/7r b - - 0 43 |_|_|_|_|_|_|K|_| State: 3072 Variant=lightning Result=0-1 |_|_|_|_|_|_|P|_| Event: 1 0 rated private lightning Site=freechess.org Date=2014.05.10 |_|_|_|_|_|_|_|_| WhiteName: cday BlackName=Vukvolan WhiteTime=-783 whiteLag=13483 blackRemainingTImeMillis = 9520 blackLag=11029 |_|_|_|_|_|_|*|r| initialWhiteClock: 00:01:00.0 initialBlackClocks=00:01:00.0 Legals=[Ra1, Rb1, Rc1, Rd1, Re1, Rf1, Rg1, Rh2, Rh3, Rh4, Kb5, Kc5, Kd5, Kb6, Kd6, Kb7, Kc7, Rxh5] Movelist=[e4, e5, f4, d5, exd5, e4, d3, f5, Nc3, Bd6, dxe4, fxe4, Nxe4, Qe7, Bd3, Nf6, Qe2, Nxe4, Qxe4, Qxe4+, Bxe4, O-O, Nf3, Bf5, Bxf5, Rxf5, O-O, h6, Nd4, Rf8, Ne6, Re8, Bd2, Nd7, Bc3, Nc5, Nxg7, Re4, Nf5, Rxf4, Nxd6, Rxf1+, Rxf1, cxd6, Rf6, Ne4, Rxh6, Kf7, Rh7+, Kg6, Rxb7, Nxc3, bxc3, Kf5, c4, Ke5, Rc7, Rb8, Rxa7, Rb1+, Kf2, Rb2, Kf3, Rxc2, Rc7, Rxa2, h4, Ra3+, Kg4, Ra2, g3, Re2, h5, Rh2, Re7+, Kd4, Re6, Kxc4, Rxd6, Kc5, Rd8, Rh1, d6, Kc6, d7] Squares with promote masks: []
  3. 0

    h3. Reproducible Case The following code works in 6.0.2 but fails in 6.5.0. Originally reported on forum http://www.zkoss.org/forum/listComment/19974 {code:xml} <decimalbox class="currency" width="200px" value="15000" locale="de" format="#,##0.00" ></decimalbox> {code} h3. Error Message The error message showed under 6.5.0 is: {code:java} Malformed pattern "#,##0.00" Caused by: java.lang.IllegalArgumentException: Malformed pattern "#,##0.00" at java.text.DecimalFormat.applyPattern(DecimalFormat.java:2561) at java.text.DecimalFormat.applyLocalizedPattern(DecimalFormat.java:2283) at org.zkoss.zul.impl.NumberInputElement.formatNumber(NumberInputElement.java:219) at org.zkoss.zul.Decimalbox.coerceToString(Decimalbox.java:164) at org.zkoss.zul.impl.InputElement.renderProperties(InputElement.java:838) at org.zkoss.zul.impl.FormatInputElement.renderProperties(FormatInputElement.java:52) at org.zkoss.zul.impl.NumberInputElement.renderProperties(NumberInputElement.java:172) at org.zkoss.zul.Decimalbox.renderProperties(Decimalbox.java:174) at org.zkoss.zk.ui.AbstractComponent.redraw(AbstractComponent.java:1805) at org.zkoss.zk.ui.sys.HtmlPageRenders.outPageContent(HtmlPageRenders.java:609) at org.zkoss.zul.impl.PageRenderer.renderDesktop(PageRenderer.java:98) at org.zkoss.zul.impl.PageRenderer.render(PageRenderer.java:56) at org.zkoss.zk.ui.impl.PageImpl.redraw(PageImpl.java:854) at org.zkoss.zk.ui.impl.UiEngineImpl.execNewPage0(UiEngineImpl.java:490) at org.zkoss.zk.ui.impl.UiEngineImpl.execNewPage(UiEngineImpl.java:316) at org.zkoss.zk.ui.http.DHtmlLayoutServlet.process(DHtmlLayoutServlet.java:215) at org.zkoss.zk.ui.http.DHtmlLayoutServlet.doGet(DHtmlLayoutServlet.java:135) at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) at javax.servlet.http.HttpServlet.service(HttpServlet.java:820) at org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:401) at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766) at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:450) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) at org.mortbay.jetty.Server.handle(Server.java:326) at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:928) at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549) at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212) at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) {code}

    ZK-Tracker | 4 years ago | hawk
    java.lang.IllegalArgumentException: Malformed pattern "#,##0.00"
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    Automated exception search integrated into your IDE

  5. 0

    Java recursive "find median" algorithm exception errors

    Stack Overflow | 3 years ago | mharris7190
    java.lang.IllegalArgumentException: 4 &gt; 0
  6. 0

    After logging into our Archiva instance, I can click on the Edit Details button to change the password. I enter the existing password and the new password (twice) and click the OK button. The dialog remains on screen with no indication of what has happened. After a while, I closed by web browser window and opened a new one - I then attempted to login with the new password, only to find that the password change had not occurred. After an investigation, I found that the change password dialog was making a POST to "/restServices/redbackServices/userService/updateMe", which was failing with a 500 Internal Server Error. The stack trace follows... {quote} java.lang.RuntimeException: org.apache.cxf.interceptor.Fault: fromIndex(0) &gt; toIndex(-1) at org.apache.cxf.interceptor.AbstractFaultChainInitiatorObserver.onMessage(AbstractFaultChainInitiatorObserver.java:116) at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:371) at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:251) at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:223) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:197) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:149) at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:171) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:290) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPost(AbstractHTTPServlet.java:209) at javax.servlet.http.HttpServlet.service(HttpServlet.java:755) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:265) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1496) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1476) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:499) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) Caused by: org.apache.cxf.interceptor.Fault: fromIndex(0) &gt; toIndex(-1) at org.apache.cxf.service.invoker.AbstractInvoker.createFault(AbstractInvoker.java:163) at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:129) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:200) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:99) at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:59) at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:96) at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:307) ... 39 more Caused by: java.lang.IllegalArgumentException: fromIndex(0) &gt; toIndex(-1) at java.util.ArrayList.subListRangeCheck(ArrayList.java:964) at java.util.ArrayList.subList(ArrayList.java:954) at org.apache.archiva.redback.policy.DefaultUserSecurityPolicy.extensionChangePassword(DefaultUserSecurityPolicy.java:317) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:343) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:327) at org.apache.archiva.web.security.ArchivaConfigurableUsersManager.updateUser(ArchivaConfigurableUsersManager.java:392) at org.apache.archiva.redback.rest.services.DefaultUserService.updateUser(DefaultUserService.java:386) at org.apache.archiva.redback.rest.services.DefaultUserService.updateMe(DefaultUserService.java:367) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:181) at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:97) ... 44 more </pre> <h3>Caused by:</h3><pre>org.apache.cxf.interceptor.Fault: fromIndex(0) &gt; toIndex(-1) at org.apache.cxf.service.invoker.AbstractInvoker.createFault(AbstractInvoker.java:163) at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:129) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:200) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:99) at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:59) at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:96) at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:307) at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:251) at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:223) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:197) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:149) at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:171) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:290) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPost(AbstractHTTPServlet.java:209) at javax.servlet.http.HttpServlet.service(HttpServlet.java:755) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:265) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1496) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1476) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:499) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.IllegalArgumentException: fromIndex(0) &gt; toIndex(-1) at java.util.ArrayList.subListRangeCheck(ArrayList.java:964) at java.util.ArrayList.subList(ArrayList.java:954) at org.apache.archiva.redback.policy.DefaultUserSecurityPolicy.extensionChangePassword(DefaultUserSecurityPolicy.java:317) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:343) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:327) at org.apache.archiva.web.security.ArchivaConfigurableUsersManager.updateUser(ArchivaConfigurableUsersManager.java:392) at org.apache.archiva.redback.rest.services.DefaultUserService.updateUser(DefaultUserService.java:386) at org.apache.archiva.redback.rest.services.DefaultUserService.updateMe(DefaultUserService.java:367) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:181) at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:97) ... 44 more </pre> <h3>Caused by:</h3><pre>java.lang.IllegalArgumentException: fromIndex(0) &gt; toIndex(-1) at java.util.ArrayList.subListRangeCheck(ArrayList.java:964) at java.util.ArrayList.subList(ArrayList.java:954) at org.apache.archiva.redback.policy.DefaultUserSecurityPolicy.extensionChangePassword(DefaultUserSecurityPolicy.java:317) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:343) at org.apache.archiva.redback.users.jdo.JdoUserManager.updateUser(JdoUserManager.java:327) at org.apache.archiva.web.security.ArchivaConfigurableUsersManager.updateUser(ArchivaConfigurableUsersManager.java:392) at org.apache.archiva.redback.rest.services.DefaultUserService.updateUser(DefaultUserService.java:386) at org.apache.archiva.redback.rest.services.DefaultUserService.updateMe(DefaultUserService.java:367) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:181) at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:97) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:200) at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:99) at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:59) at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:96) at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:307) at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:251) at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:223) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:197) at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:149) at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:171) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:290) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPost(AbstractHTTPServlet.java:209) at javax.servlet.http.HttpServlet.service(HttpServlet.java:755) at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:265) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1496) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1476) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:499) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255) at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) at org.eclipse.jetty.server.Server.handle(Server.java:370) at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494) at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982) at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043) at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865) at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240) at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82) at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667) at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) at java.lang.Thread.run(Thread.java:745) {quote}

    Apache's JIRA Issue Tracker | 1 year ago | Jasvinder Bahra
    java.lang.RuntimeException: org.apache.cxf.interceptor.Fault: fromIndex(0) &gt; toIndex(-1)

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    Root Cause Analysis

    1. java.lang.IllegalArgumentException

      Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3

      at org.bdgenomics.adam.converters.VariantContextConverter.convert()
    2. org.bdgenomics.adam
      ADAMContext$$anonfun$loadVcf$1.apply
      1. org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:214)
      2. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
      3. org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
      3 frames
    3. Scala
      Iterator$$anon$13.hasNext
      1. scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
      1 frame
    4. Spark
      Executor$TaskRunner.run
      1. org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595)
      2. org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
      3. org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
      4. org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
      5. org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
      6. org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
      7. org.apache.spark.scheduler.Task.run(Task.scala:89)
      8. org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
      8 frames
    5. Java RT
      Thread.run
      1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
      2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
      3. java.lang.Thread.run(Thread.java:745)
      3 frames