search

pstawinski / pygenebe

PyGeneBe: A Python client seamlessly integrating with the GeneBe platform, offering efficient annotation of genetic variants through its API, while supporting pandas, VCF file formats, and HGVS parsing
https://genebe.net
6 stars 0 forks source link

Error 500 while trying to annotate a VCF #3

Open menyawino opened 3 hours ago

menyawino commented 3 hours ago

I use this command

genebe annotate --input /mnt/d/omar_wsl/555.vcf --output out.vcf.gz --username XXXX --api_key XXXX --genome hg19

I keep getting the error below although I have checked everything, my username, api, integrity of the vcf, and internet connection

INFO:root:Welcome. Annotating VCF file for genome hg19. Ensure that VCF file has biallelic form. 0it [00:00, ?it/s]INFO:root:I will try to log in as menyawino@gmail.com ERROR:root:Got response with code 500 with body {"timestamp":1728913665558,"status":500,"error":"Internal Server Error","trace":"java.lang.NullPointerException: Cannot invoke \"String.equals(Object)\" because the return value of \"am.genebe.annotation.model.VariantAnnotated.getChr()\" is null\n\tat pl.genebeam.service.VariantService.variantInformationBulk(VariantService.java:893)\n\tat pl.genebeam.web.api_public.VariantPublicController.variant(VariantPublicController.java:135)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(Unknown Source)\n\tat java.base/java.lang.reflect.Method.invoke(Unknown Source)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)\n\tat org.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:174)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)\n\tat org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)\n\tat pl.genebeam.web.api_public.VariantPublicController$$SpringCGLIB$$0.variant(<generated>)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(Unknown Source)\n\tat java.base/java.lang.reflect.Method.invoke(Unknown Source)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:255)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:188)\n\tat org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:926)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:831)\n\tat org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\tat org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1089)\n\tat org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:979)\n\tat org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1014)\n\tat org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590)\n\tat org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:195)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.AbstractRequestLoggingFilter.doFilterInternal(AbstractRequestLoggingFilter.java:289)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:108)\n\tat org.springframework.security.web.FilterChainProxy.lambda$doFilterInternal$3(FilterChainProxy.java:231)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:365)\n\tat org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:120)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:131)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:85)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:100)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:179)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:213)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:107)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:93)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:82)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:69)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:62)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.session.DisableEncodeUrlFilter.doFilterInternal(DisableEncodeUrlFilter.java:42)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:233)\n\tat org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:191)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:113)\n\tat org.springframework.web.servlet.handler.HandlerMappingIntrospector.lambda$createCacheFilter$3(HandlerMappingIntrospector.java:195)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:113)\n\tat org.springframework.web.filter.CompositeFilter.doFilter(CompositeFilter.java:74)\n\tat org.springframework.security.config.annotation.web.configuration.WebMvcSecurityConfiguration$CompositeFilterChainProxy.doFilter(WebMvcSecurityConfiguration.java:230)\n\tat org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:352)\n\tat org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:268)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.session.web.http.SessionRepositoryFilter.doFilterInternal(SessionRepositoryFilter.java:142)\n\tat org.springframework.session.web.http.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:82)\n\tat org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:352)\n\tat org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:268)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.ForwardedHeaderFilter.doFilterInternal(ForwardedHeaderFilter.java:173)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)\n\tat org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:731)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:344)\n\tat org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:384)\n\tat org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)\n\tat org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:905)\n\tat org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1741)\n\tat org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)\n\tat java.base/java.lang.VirtualThread.run(Unknown Source)\n","path":"/cloud/api-public/v1/variants"} 0it [00:02, ?it/s] Traceback (most recent call last): File "/home/cardioinform/miniconda3/envs/yarab/bin/genebe", line 8, in <module> sys.exit(main()) ^^^^^^ File "/home/cardioinform/miniconda3/envs/yarab/lib/python3.12/site-packages/genebe/entrypoint.py", line 147, in main annotate_vcf( File "/home/cardioinform/miniconda3/envs/yarab/lib/python3.12/site-packages/genebe/vcf_simple_annotator.py", line 145, in annotate_vcf annotated_variants = annotate( ^^^^^^^^^ File "/home/cardioinform/miniconda3/envs/yarab/lib/python3.12/site-packages/genebe/client.py", line 343, in annotate raise WrongServerResponseError( genebe.client.WrongServerResponseError: Got response with code 500 with body {"timestamp":1728913665558,"status":500,"error":"Internal Server Error","trace":"java.lang.NullPointerException: Cannot invoke \"String.equals(Object)\" because the return value of \"am.genebe.annotation.model.VariantAnnotated.getChr()\" is null\n\tat pl.genebeam.service.VariantService.variantInformationBulk(VariantService.java:893)\n\tat pl.genebeam.web.api_public.VariantPublicController.variant(VariantPublicController.java:135)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(Unknown Source)\n\tat java.base/java.lang.reflect.Method.invoke(Unknown Source)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:355)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)\n\tat org.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:174)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:768)\n\tat org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:720)\n\tat pl.genebeam.web.api_public.VariantPublicController$$SpringCGLIB$$0.variant(<generated>)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(Unknown Source)\n\tat java.base/java.lang.reflect.Method.invoke(Unknown Source)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:255)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:188)\n\tat org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:926)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:831)\n\tat org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\tat org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1089)\n\tat org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:979)\n\tat org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1014)\n\tat org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590)\n\tat org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:195)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.AbstractRequestLoggingFilter.doFilterInternal(AbstractRequestLoggingFilter.java:289)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:108)\n\tat org.springframework.security.web.FilterChainProxy.lambda$doFilterInternal$3(FilterChainProxy.java:231)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:365)\n\tat org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:120)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:131)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:85)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:100)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:179)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:213)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:107)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:93)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:82)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:69)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:62)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.session.DisableEncodeUrlFilter.doFilterInternal(DisableEncodeUrlFilter.java:42)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:374)\n\tat org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:233)\n\tat org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:191)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:113)\n\tat org.springframework.web.servlet.handler.HandlerMappingIntrospector.lambda$createCacheFilter$3(HandlerMappingIntrospector.java:195)\n\tat org.springframework.web.filter.CompositeFilter$VirtualFilterChain.doFilter(CompositeFilter.java:113)\n\tat org.springframework.web.filter.CompositeFilter.doFilter(CompositeFilter.java:74)\n\tat org.springframework.security.config.annotation.web.configuration.WebMvcSecurityConfiguration$CompositeFilterChainProxy.doFilter(WebMvcSecurityConfiguration.java:230)\n\tat org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:352)\n\tat org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:268)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.session.web.http.SessionRepositoryFilter.doFilterInternal(SessionRepositoryFilter.java:142)\n\tat org.springframework.session.web.http.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:82)\n\tat org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:352)\n\tat org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:268)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.springframework.web.filter.ForwardedHeaderFilter.doFilterInternal(ForwardedHeaderFilter.java:173)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:164)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:140)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)\n\tat org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:731)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:344)\n\tat org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:384)\n\tat org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)\n\tat org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:905)\n\tat org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1741)\n\tat org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)\n\tat java.base/java.lang.VirtualThread.run(Unknown Source)\n","path":"/cloud/api-public/v1/variants"}

pstawinski commented 2 hours ago

The error you get says:

Ensure that VCF file has biallelic form

Is your vcf in biallelic form? If not, use convert your vcf with f.ex. bcftools norm and please check again.