-2

I was using the command yesterday and it worked perfectly. I may have installed a different perl or ava but I'm not sure why this would cause the error. I've looked at the other examples of this on StackOverflow but it appears that they are applicable to web browsers.

How can I fix this on a remote server using my conda enivornment? 

(bbmap_env) -bash-4.1$ sendsketch.sh in=scaffolds.fasta out=sketch.txt outsketch=sketch overwrite=t
Adding /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/bbmap_env/opt/bbmap-38.58-0/resources/blacklist_refseq_species_250.sketch to blacklist.
0.036 seconds.
Loaded 1 sketch in 6.969 seconds.
javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.ssl.Alert.createSSLException(Alert.java:128)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:321)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:264)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:259)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:642)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.onCertificate(CertificateMessage.java:461)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.consume(CertificateMessage.java:361)
    at java.base/sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:392)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:444)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:421)
    at java.base/sun.security.ssl.TransportContext.dispatch(TransportContext.java:178)
    at java.base/sun.security.ssl.SSLTransport.decode(SSLTransport.java:164)
    at java.base/sun.security.ssl.SSLSocketImpl.decode(SSLSocketImpl.java:1152)
    at java.base/sun.security.ssl.SSLSocketImpl.readHandshakeRecord(SSLSocketImpl.java:1063)
    at java.base/sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:402)
    at java.base/sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:567)
    at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:185)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getOutputStream0(HttpURLConnection.java:1356)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:1331)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(HttpsURLConnectionImpl.java:241)
    at server.ServerTools.sendAndReceive(ServerTools.java:98)
    at sketch.SendSketch.processRemote(SendSketch.java:386)
    at sketch.SendSketch.process(SendSketch.java:308)
    at sketch.SendSketch.main(SendSketch.java:53)
Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:385)
    at java.base/sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:290)
    at java.base/sun.security.validator.Validator.validate(Validator.java:264)
    at java.base/sun.security.ssl.X509TrustManagerImpl.validate(X509TrustManagerImpl.java:321)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:221)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:129)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:626)
    ... 19 more
Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.build(SunCertPathBuilder.java:141)
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:126)
    at java.base/java.security.cert.CertPathBuilder.build(CertPathBuilder.java:297)
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:380)
    ... 25 more
javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
    at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1963)
    at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1958)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1957)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1525)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1509)
    at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:329)
    at server.ServerTools.sendAndReceive(ServerTools.java:134)
    at sketch.SendSketch.processRemote(SendSketch.java:386)
    at sketch.SendSketch.process(SendSketch.java:308)
    at sketch.SendSketch.main(SendSketch.java:53)
Caused by: javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.ssl.Alert.createSSLException(Alert.java:128)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:321)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:264)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:259)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:642)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.onCertificate(CertificateMessage.java:461)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.consume(CertificateMessage.java:361)
    at java.base/sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:392)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:444)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:421)
    at java.base/sun.security.ssl.TransportContext.dispatch(TransportContext.java:178)
    at java.base/sun.security.ssl.SSLTransport.decode(SSLTransport.java:164)
    at java.base/sun.security.ssl.SSLSocketImpl.decode(SSLSocketImpl.java:1152)
    at java.base/sun.security.ssl.SSLSocketImpl.readHandshakeRecord(SSLSocketImpl.java:1063)
    at java.base/sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:402)
    at java.base/sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:567)
    at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:185)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1581)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1509)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:245)
    at server.ServerTools.sendAndReceive(ServerTools.java:127)
    ... 3 more
Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:385)
    at java.base/sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:290)
    at java.base/sun.security.validator.Validator.validate(Validator.java:264)
    at java.base/sun.security.ssl.X509TrustManagerImpl.validate(X509TrustManagerImpl.java:321)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:221)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:129)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:626)
    ... 19 more
Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.build(SunCertPathBuilder.java:141)
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:126)
    at java.base/java.security.cert.CertPathBuilder.build(CertPathBuilder.java:297)
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:380)
    ... 25 more
javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.ssl.Alert.createSSLException(Alert.java:128)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:321)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:264)
    at java.base/sun.security.ssl.TransportContext.fatal(TransportContext.java:259)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:642)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.onCertificate(CertificateMessage.java:461)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.consume(CertificateMessage.java:361)
    at java.base/sun.security.ssl.SSLHandshake.consume(SSLHandshake.java:392)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:444)
    at java.base/sun.security.ssl.HandshakeContext.dispatch(HandshakeContext.java:421)
    at java.base/sun.security.ssl.TransportContext.dispatch(TransportContext.java:178)
    at java.base/sun.security.ssl.SSLTransport.decode(SSLTransport.java:164)
    at java.base/sun.security.ssl.SSLSocketImpl.decode(SSLSocketImpl.java:1152)
    at java.base/sun.security.ssl.SSLSocketImpl.readHandshakeRecord(SSLSocketImpl.java:1063)
    at java.base/sun.security.ssl.SSLSocketImpl.startHandshake(SSLSocketImpl.java:402)
    at java.base/sun.net.www.protocol.https.HttpsClient.afterConnect(HttpsClient.java:567)
    at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:185)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1581)
    at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1509)
    at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:245)
    at server.ServerTools.sendAndReceive(ServerTools.java:127)
    at sketch.SendSketch.processRemote(SendSketch.java:386)
    at sketch.SendSketch.process(SendSketch.java:308)
    at sketch.SendSketch.main(SendSketch.java:53)
Caused by: sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:385)
    at java.base/sun.security.validator.PKIXValidator.engineValidate(PKIXValidator.java:290)
    at java.base/sun.security.validator.Validator.validate(Validator.java:264)
    at java.base/sun.security.ssl.X509TrustManagerImpl.validate(X509TrustManagerImpl.java:321)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkTrusted(X509TrustManagerImpl.java:221)
    at java.base/sun.security.ssl.X509TrustManagerImpl.checkServerTrusted(X509TrustManagerImpl.java:129)
    at java.base/sun.security.ssl.CertificateMessage$T12CertificateConsumer.checkServerCerts(CertificateMessage.java:626)
    ... 19 more
Caused by: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.build(SunCertPathBuilder.java:141)
    at java.base/sun.security.provider.certpath.SunCertPathBuilder.engineBuild(SunCertPathBuilder.java:126)
    at java.base/java.security.cert.CertPathBuilder.build(CertPathBuilder.java:297)
    at java.base/sun.security.validator.PKIXValidator.doBuild(PKIXValidator.java:380)
    ... 25 more
ERROR: Server returned code 1 and this message:
null
java.lang.Exception: Aborting.
    at shared.KillSwitch.kill(KillSwitch.java:108)
    at sketch.SendSketch.processRemote(SendSketch.java:389)
    at sketch.SendSketch.process(SendSketch.java:308)
    at sketch.SendSketch.main(SendSketch.java:53)
O.rka
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  • Check this link. https://stackoverflow.com/questions/1828775/how-to-handle-invalid-ssl-certificates-with-apache-httpclient – Sambit Jul 26 '19 at 18:02
  • Hi @Sambit Thanks for the link. My knowledge of Java and OpenSSL is limited but I'm trying to understand the solution. It appears the issue is that I don't have the proper certificates. Are these Java or OpenSSL certificates (apologies if that is a dumb question)? For fixing this on a linux server, is the easiest fix using the following tool: https://github.com/escline/InstallCert ? I know how to find my $HOSTNAME but how can I get my `path to system keystore` and `port`? – O.rka Jul 26 '19 at 18:14
  • If you do not have a certificate, no problem, you can skip it , for this I have given the link. If you post the code, probably people will be able to help you. – Sambit Jul 26 '19 at 18:16

1 Answers1

-3

The server was down. It works now. https://www.biostars.org/p/391551/#392603 explains.

O.rka
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  • The server was not down. You established a TCP connection to it, initiated an SSL handshake with it, received a certificate from it, and failed to establish a trust relationship with the certificate. None of that would have been possible if the server was down. – user207421 Aug 22 '19 at 23:50
  • It wasn't working, I asked the developer of the tool and they said the server was down. The next week when the server was back up I tried again and it worked. I can't reproduce this because the server is up. – O.rka Aug 23 '19 at 00:44
  • It doesn't matter what they told you. If the server was down it couldn't have sent you a certificate. You would have got 'connection refused' or a connect timeout, instead of all this. – user207421 Aug 23 '19 at 00:47
  • So should I just delete this post? – O.rka Aug 23 '19 at 00:50
  • I think so, yes. It's answered in the duplicate, and this answer wouldnt' help anybody even it if was true. A chat with the developer might be in order, too. What really happened was that they fixed the certificate. – user207421 Aug 23 '19 at 00:54