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Originally posted by Teachh November 7, 2023
Hello guys!
Recently, I have been testing Nextflow with some public pipelines, and after playing a bit, I decided to run this pipelines to Kubernetes a local Kubernetes Cluster (K3S Dist.) that is more powerful.
The problem comes when following this tutorial from the official documentation doesn't work.
The logs show Invalid DER: object is not integer, more specifically:
java.io.IOException: Invalid DER: object is not integer
at nextflow.k8s.client.SSLUtils$Asn1Object.getInteger(SSLUtils.java:235)
at nextflow.k8s.client.SSLUtils.next(SSLUtils.java:166)
at nextflow.k8s.client.SSLUtils.decodePKCS1(SSLUtils.java:161)
at nextflow.k8s.client.SSLUtils.createKeyStore(SSLUtils.java:106)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44)
at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.call(StaticMetaMethodSite.java:89)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at nextflow.k8s.client.ConfigDiscovery.createKeyStore0(ConfigDiscovery.groovy:139)
at nextflow.k8s.client.ConfigDiscovery.createKeyStore(ConfigDiscovery.groovy:145)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:203)
at nextflow.k8s.client.ConfigDiscovery.createKeyManagers(ConfigDiscovery.groovy:161)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.k8s.client.ConfigDiscovery.fromKubeConfig(ConfigDiscovery.groovy:127)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:212)
at nextflow.k8s.client.ConfigDiscovery.discover(ConfigDiscovery.groovy:61)
at nextflow.k8s.client.ClientConfig.discover(ClientConfig.groovy:98)
at nextflow.k8s.K8sConfig.clientDiscovery(K8sConfig.groovy:260)
at nextflow.k8s.K8sConfig.memoizedMethodPriv$getClient(K8sConfig.groovy:213)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
at nextflow.k8s.K8sConfig$_closure2.doCall(K8sConfig.groovy)
at nextflow.k8s.K8sConfig$_closure2.doCall(K8sConfig.groovy)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.k8s.K8sConfig.getClient(K8sConfig.groovy)
at nextflow.k8s.K8sExecutor.register(K8sExecutor.groovy:66)
at nextflow.executor.Executor.init(Executor.groovy:67)
at nextflow.executor.ExecutorFactory.createExecutor(ExecutorFactory.groovy:210)
at nextflow.executor.ExecutorFactory.getExecutor(ExecutorFactory.groovy:201)
at nextflow.script.ProcessDef.run(ProcessDef.groovy:206)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
at nextflow.extension.ChannelEx.or(ChannelEx.groovy:132)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:54)
at org.codehaus.groovy.runtime.metaclass.NewInstanceMetaMethod.invoke(NewInstanceMetaMethod.java:54)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:64)
at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:44)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script_4518c005$_runScript_closure2$_closure4.doCall(Script_4518c005:16)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
at java.base/java.lang.reflect.Method.invoke(Method.java:578)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.script.BaseScript.run0(BaseScript.groovy:183)
at nextflow.script.BaseScript.run(BaseScript.groovy:192)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130)
at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
at nextflow.cli.Launcher.run(Launcher.groovy:494)
at nextflow.cli.Launcher.main(Launcher.groovy:653)
Some information:
Executing kubectl get nodes returns me the actual cluster correctly.
For anyone that is using a local K3S cluster, generate a new config file using your new Service Account instead of using the default config file generated by the master node. The decryption is generating this problem and it's not a good practice to share the admin config file.
Discussed in #4489
Originally posted by Teachh November 7, 2023
Hello guys!
Recently, I have been testing Nextflow with some public pipelines, and after playing a bit, I decided to run this pipelines to Kubernetes a local Kubernetes Cluster (K3S Dist.) that is more powerful.
The problem comes when following this tutorial from the official documentation doesn't work.
The logs show
Invalid DER: object is not integer
, more specifically:Some information:
kubectl get nodes
returns me the actual cluster correctly.nextflow run hello -work-dir s3://mybucket/scratch
Thanks in advance!
The text was updated successfully, but these errors were encountered: