Trying to track this down, but I was trying to follow the breadcrumbs to make my own sketches to use for BBSketch, using fetchNt.sh, and am getting the following.
it is possible that this is internal to our networking, but it feels like it might be related to NCBI constantly changing servers. Any thoughts on this?
Thank you.
]$ bash /cm/shared/easybuild-modules/software/BBTools/40.01-Java-17/pipelines/fetch/fetchNt.sh
java -ea --add-modules jdk.incubator.vector -Xmx1g -Xms1g -cp /cm/shared/easybuild-modules/software/BBTools/40.01-Java-17/cur bgzip zl=8 server ow shrinknames maxbadheaders=5000 badheaders=badHeaders.txt taxpath=auto
WARNING: Using incubator modules: jdk.incubator.vector
Executing tax.RenameGiToTaxid [-Xmx1g, in=stdin.fa.gz, out=renamed.fa.gz, pigz=32, unpigz, bgzip, zl=8, server, ow, shrinkname
javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: un
at java.net.http/jdk.internal.net.http.HttpClientImpl.send(HttpClientImpl.java:579)
at java.net.http/jdk.internal.net.http.HttpClientFacade.send(HttpClientFacade.java:123)
at server.ServerTools.sendAndReceive_httpClient(ServerTools.java:225)
at server.ServerTools.sendAndReceive(ServerTools.java:123)
at tax.TaxClient.sendAndReceiveOnceSpecificServer(TaxClient.java:349)
at tax.TaxClient.sendAndReceiveSpecificServer(TaxClient.java:315)
at tax.TaxClient.sendAndReceive(TaxClient.java:291)
at tax.TaxClient.accessionToTaxidArray(TaxClient.java:190)
at tax.RenameGiToTaxid.translateToTaxIDs(RenameGiToTaxid.java:718)
at tax.RenameGiToTaxid.updateHeadersFromServer_fasta(RenameGiToTaxid.java:628)
at tax.RenameGiToTaxid.updateHeadersFromServer(RenameGiToTaxid.java:589)
at tax.RenameGiToTaxid.processInner_server(RenameGiToTaxid.java:859)
at tax.RenameGiToTaxid.process(RenameGiToTaxid.java:275)
at tax.RenameGiToTaxid.main(RenameGiToTaxid.java:42)
Caused by: javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderEx
at java.base/sun.security.ssl.Alert.createSSLException(Alert.java:131)
at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:383)
at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:326)
at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:321)
at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.checkServerCerts(CertificateMessage.java:1351)
at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.onConsumeCertificate(CertificateMessage.java:1
at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.consume(CertificateMessage.java:1169)
at java.base/sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:396)
at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:480)
at java.base/sun.security.ssl.SSLEngineImpl$DelegatedTask$DelegatedAction.run(SSLEngineImpl.java:1277)
at java.base/sun.security.ssl.SSLEngineImpl$DelegatedTask$DelegatedAction.run(SSLEngineImpl.java:1264)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:712)
at java.base/sun.security.ssl.SSLEngineImpl$DelegatedTask.run(SSLEngineImpl.java:1209)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at java.net.http/jdk.internal.net.http.common.SSLFlowDelegate.lambda$executeTasks$3(SSLFlowDelegate.java:1132)
at java.net.http/jdk.internal.net.http.HttpClientImpl$DelegatingExecutor.execute(HttpClientImpl.java:158)
at java.net.http/jdk.internal.net.http.common.SSLFlowDelegate.executeTasks(SSLFlowDelegate.java:1127)
at java.net.http/jdk.internal.net.http.common.SSLFlowDelegate.doHandshake(SSLFlowDelegate.java:1093)
at java.net.http/jdk.internal.net.http.common.SSLFlowDelegate$Reader.processData(SSLFlowDelegate.java:498)
at java.net.http/jdk.internal.net.http.common.SSLFlowDelegate$Reader$ReaderDownstreamPusher.run(SSLFlowDelegate.java:2
at java.net.http/jdk.internal.net.http.common.SequentialScheduler$LockingRestartableTask.run(SequentialScheduler.java:
at java.net.http/jdk.internal.net.http.common.SequentialScheduler$CompleteRestartableTask.run(SequentialScheduler.java
at java.net.http/jdk.internal.net.http.common.SequentialScheduler$TryEndDeferredCompleter.complete(SequentialScheduler
at java.net.http/jdk.internal.net.http.common.SequentialScheduler$CompleteRestartableTask.run(SequentialScheduler.java
at java.net.http/jdk.internal.net.http.common.SequentialScheduler$SchedulableTask.run(SequentialScheduler.java:230)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBui
at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:439)
at java.base/sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:306)
at java.base/sun.security.validator.Validator.validate(Validator.java:264)
at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:285)
at java.base/sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:144)
at java.base/sun.security.ssl.CertificateMessage$T13CertificateConsumer.checkServerCerts(CertificateMessage.java:1329)
... 23 more
Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested ta
at java.base/sun.security.provider.certpath.SunCertPathBuilder.build(SunCertPathBuilder.java:148)
at java.base/sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:129)
at java.base/java.security.cert.CertPathBuilder.build(CertPathBuilder.java:297)
at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:434)
... 28 more
Trying to track this down, but I was trying to follow the breadcrumbs to make my own sketches to use for BBSketch, using fetchNt.sh, and am getting the following.
it is possible that this is internal to our networking, but it feels like it might be related to NCBI constantly changing servers. Any thoughts on this?
Thank you.