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