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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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WARNING: Failed to detect whether we are running on Google Compute Engine. #5447

Closed sooheelee closed 5 years ago

sooheelee commented 5 years ago

Posting issue on @cmnbroad's request.

I see this stacktrace of a WARN for some GATK tools. The tools proceed to run successfully. For example, LearnReadOrientationModel gives this. I've been preparing for the GATK workshop and have been running a variety of tools.

For this particular message, I am running GATK v4.0.11.0 locally on my Mac laptop, in the 4.0.11.0 Docker. How can I deal with this WARN?

(gatk) root@3231a24c7afb:/gatk/my_data/3-somatic# gatk LearnReadOrientationModel -alt-table 13_tumor-alt.tsv -ref-hist 13_tumor-ref.metrics -alt-hist 13_tumor-alt-depth1.metrics -O tumor-artifact-prior-table.tsv 
Using GATK jar /gatk/gatk-package-4.0.11.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.0.11.0-local.jar LearnReadOrientationModel -alt-table 13_tumor-alt.tsv -ref-hist 13_tumor-ref.metrics -alt-hist 13_tumor-alt-depth1.metrics -O tumor-artifact-prior-table.tsv
16:20:57.885 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.0.11.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 26, 2018 4:20:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
WARNING: Failed to detect whether we are running on Google Compute Engine.
java.net.ConnectException: Connection refused (Connection refused)
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
    at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
    at java.net.Socket.connect(Socket.java:589)
    at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
    at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
    at sun.net.www.http.HttpClient.New(HttpClient.java:339)
    at sun.net.www.http.HttpClient.New(HttpClient.java:357)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
    at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
    at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104)
    at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)
    at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)
    at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)
    at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)
    at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)
    at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)
    at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)
    at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)
    at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)
    at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)
    at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)
    at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)
    at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:382)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:183)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

16:20:59.204 INFO  LearnReadOrientationModel - ------------------------------------------------------------
16:20:59.205 INFO  LearnReadOrientationModel - The Genome Analysis Toolkit (GATK) v4.0.11.0
16:20:59.205 INFO  LearnReadOrientationModel - For support and documentation go to https://software.broadinstitute.org/gatk/
16:20:59.206 INFO  LearnReadOrientationModel - Executing as root@3231a24c7afb on Linux v4.9.125-linuxkit amd64
16:20:59.206 INFO  LearnReadOrientationModel - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_181-8u181-b13-0ubuntu0.16.04.1-b13
16:20:59.207 INFO  LearnReadOrientationModel - Start Date/Time: November 26, 2018 4:20:57 PM UTC
16:20:59.207 INFO  LearnReadOrientationModel - ------------------------------------------------------------
16:20:59.207 INFO  LearnReadOrientationModel - ------------------------------------------------------------
16:20:59.208 INFO  LearnReadOrientationModel - HTSJDK Version: 2.16.1
16:20:59.208 INFO  LearnReadOrientationModel - Picard Version: 2.18.13
16:20:59.208 INFO  LearnReadOrientationModel - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:20:59.208 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:20:59.209 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:20:59.209 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:20:59.209 INFO  LearnReadOrientationModel - Deflater: IntelDeflater
16:20:59.209 INFO  LearnReadOrientationModel - Inflater: IntelInflater
16:20:59.209 INFO  LearnReadOrientationModel - GCS max retries/reopens: 20
16:20:59.209 INFO  LearnReadOrientationModel - Requester pays: disabled
16:20:59.209 INFO  LearnReadOrientationModel - Initializing engine
16:20:59.352 INFO  LearnReadOrientationModel - Done initializing engine
16:21:00.402 INFO  LearnReadOrientationModel - Context AAC: with 217930 ref and 1616 alt examples, EM converged in 12 steps
16:21:01.086 INFO  LearnReadOrientationModel - Context AAG: with 354938 ref and 3337 alt examples, EM converged in 12 steps
16:21:01.611 INFO  LearnReadOrientationModel - Context AAT: with 252561 ref and 1308 alt examples, EM converged in 11 steps
16:21:02.365 INFO  LearnReadOrientationModel - Context ACA: with 323210 ref and 5248 alt examples, EM converged in 13 steps
16:21:03.088 INFO  LearnReadOrientationModel - Context ACC: with 284921 ref and 4351 alt examples, EM converged in 13 steps
16:21:03.785 INFO  LearnReadOrientationModel - Context ACG: with 83185 ref and 2548 alt examples, EM converged in 13 steps
16:21:04.441 INFO  LearnReadOrientationModel - Context ACT: with 257420 ref and 3512 alt examples, EM converged in 13 steps
16:21:05.269 INFO  LearnReadOrientationModel - Context AGA: with 393111 ref and 6728 alt examples, EM converged in 13 steps
16:21:06.090 INFO  LearnReadOrientationModel - Context AGC: with 358648 ref and 6527 alt examples, EM converged in 13 steps
16:21:06.995 INFO  LearnReadOrientationModel - Context AGG: with 494947 ref and 7682 alt examples, EM converged in 14 steps
16:21:07.497 INFO  LearnReadOrientationModel - Context ATA: with 180560 ref and 1078 alt examples, EM converged in 12 steps
16:21:07.964 INFO  LearnReadOrientationModel - Context ATC: with 213079 ref and 1522 alt examples, EM converged in 11 steps
16:21:08.549 INFO  LearnReadOrientationModel - Context ATG: with 282561 ref and 2106 alt examples, EM converged in 12 steps
16:21:09.030 INFO  LearnReadOrientationModel - Context CAA: with 284942 ref and 1909 alt examples, EM converged in 11 steps
16:21:09.635 INFO  LearnReadOrientationModel - Context CAC: with 351720 ref and 3718 alt examples, EM converged in 12 steps
16:21:10.322 INFO  LearnReadOrientationModel - Context CAG: with 547234 ref and 5940 alt examples, EM converged in 12 steps
16:21:11.103 INFO  LearnReadOrientationModel - Context CCA: with 464164 ref and 8212 alt examples, EM converged in 13 steps
16:21:11.899 INFO  LearnReadOrientationModel - Context CCC: with 512128 ref and 7580 alt examples, EM converged in 13 steps
16:21:12.719 INFO  LearnReadOrientationModel - Context CCG: with 143118 ref and 4274 alt examples, EM converged in 14 steps
16:21:13.361 INFO  LearnReadOrientationModel - Context CGA: with 74445 ref and 2480 alt examples, EM converged in 14 steps
16:21:14.122 INFO  LearnReadOrientationModel - Context CGC: with 115334 ref and 3741 alt examples, EM converged in 14 steps
16:21:14.667 INFO  LearnReadOrientationModel - Context CTA: with 173673 ref and 1472 alt examples, EM converged in 13 steps
16:21:15.238 INFO  LearnReadOrientationModel - Context CTC: with 439622 ref and 3855 alt examples, EM converged in 12 steps
16:21:15.709 INFO  LearnReadOrientationModel - Context GAA: with 333082 ref and 2101 alt examples, EM converged in 11 steps
16:21:16.222 INFO  LearnReadOrientationModel - Context GAC: with 227508 ref and 2090 alt examples, EM converged in 12 steps
16:21:17.015 INFO  LearnReadOrientationModel - Context GCA: with 340865 ref and 6507 alt examples, EM converged in 14 steps
16:21:17.906 INFO  LearnReadOrientationModel - Context GCC: with 404793 ref and 8210 alt examples, EM converged in 14 steps
16:21:18.677 INFO  LearnReadOrientationModel - Context GGA: with 409382 ref and 6784 alt examples, EM converged in 13 steps
16:21:19.182 INFO  LearnReadOrientationModel - Context GTA: with 153202 ref and 1568 alt examples, EM converged in 12 steps
16:21:19.680 INFO  LearnReadOrientationModel - Context TAA: with 208518 ref and 1131 alt examples, EM converged in 12 steps
16:21:20.459 INFO  LearnReadOrientationModel - Context TCA: with 325628 ref and 6437 alt examples, EM converged in 13 steps
16:21:21.008 INFO  LearnReadOrientationModel - Context AAA: with 426193 ref and 2055 alt examples, EM converged in 12 steps
16:21:21.044 INFO  LearnReadOrientationModel - Shutting down engine
[November 26, 2018 4:21:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel done. Elapsed time: 0.39 minutes.
Runtime.totalMemory()=780140544
Tool returned:
SUCCESS
sooheelee commented 5 years ago

Just tested this locally outside of the Docker. I do not see the WARN:

WMCF9-CB5:shlee$ gatk40110 LearnReadOrientationModel -alt-table 13_tumor-alt.tsv -ref-hist 13_tumor-ref.metrics -alt-hist 13_tumor-alt-depth1.metrics -O 13_tumor-artifact-prior-table.tsv 
Using GATK jar /Applications/genomicstools/gatk/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/genomicstools/gatk/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar LearnReadOrientationModel -alt-table 13_tumor-alt.tsv -ref-hist 13_tumor-ref.metrics -alt-hist 13_tumor-alt-depth1.metrics -O 13_tumor-artifact-prior-table.tsv
12:16:19.960 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/genomicstools/gatk/gatk-4.0.11.0/gatk-package-4.0.11.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
Nov 26, 2018 12:16:20 PM shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider warnAboutProblematicCredentials
WARNING: Your application has authenticated using end user credentials from Google Cloud SDK. We recommend that most server applications use service accounts instead. If your application continues to use end user credentials from Cloud SDK, you might receive a "quota exceeded" or "API not enabled" error. For more information about service accounts, see https://cloud.google.com/docs/authentication/.
12:16:20.176 INFO  LearnReadOrientationModel - ------------------------------------------------------------
12:16:20.177 INFO  LearnReadOrientationModel - The Genome Analysis Toolkit (GATK) v4.0.11.0
12:16:20.177 INFO  LearnReadOrientationModel - For support and documentation go to https://software.broadinstitute.org/gatk/
12:16:20.177 INFO  LearnReadOrientationModel - Executing as shlee@WMCF9-CB5 on Mac OS X v10.13.6 x86_64
12:16:20.177 INFO  LearnReadOrientationModel - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_111-b14
12:16:20.177 INFO  LearnReadOrientationModel - Start Date/Time: November 26, 2018 12:16:19 PM EST
12:16:20.177 INFO  LearnReadOrientationModel - ------------------------------------------------------------
12:16:20.177 INFO  LearnReadOrientationModel - ------------------------------------------------------------
12:16:20.178 INFO  LearnReadOrientationModel - HTSJDK Version: 2.16.1
12:16:20.178 INFO  LearnReadOrientationModel - Picard Version: 2.18.13
12:16:20.178 INFO  LearnReadOrientationModel - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:16:20.178 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:16:20.178 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:16:20.178 INFO  LearnReadOrientationModel - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:16:20.178 INFO  LearnReadOrientationModel - Deflater: IntelDeflater
12:16:20.178 INFO  LearnReadOrientationModel - Inflater: IntelInflater
12:16:20.178 INFO  LearnReadOrientationModel - GCS max retries/reopens: 20
12:16:20.179 INFO  LearnReadOrientationModel - Requester pays: disabled
12:16:20.179 INFO  LearnReadOrientationModel - Initializing engine
12:16:20.264 INFO  LearnReadOrientationModel - Done initializing engine
12:16:22.006 INFO  LearnReadOrientationModel - Context AAC: with 217930 ref and 1616 alt examples, EM converged in 12 steps
12:16:22.710 INFO  LearnReadOrientationModel - Context AAG: with 354938 ref and 3337 alt examples, EM converged in 12 steps
12:16:23.278 INFO  LearnReadOrientationModel - Context AAT: with 252561 ref and 1308 alt examples, EM converged in 11 steps
12:16:24.064 INFO  LearnReadOrientationModel - Context ACA: with 323210 ref and 5248 alt examples, EM converged in 13 steps
12:16:24.802 INFO  LearnReadOrientationModel - Context ACC: with 284921 ref and 4351 alt examples, EM converged in 13 steps
12:16:25.586 INFO  LearnReadOrientationModel - Context ACG: with 83185 ref and 2548 alt examples, EM converged in 13 steps
12:16:26.245 INFO  LearnReadOrientationModel - Context ACT: with 257420 ref and 3512 alt examples, EM converged in 13 steps
12:16:27.027 INFO  LearnReadOrientationModel - Context AGA: with 393111 ref and 6728 alt examples, EM converged in 13 steps
12:16:27.911 INFO  LearnReadOrientationModel - Context AGC: with 358648 ref and 6527 alt examples, EM converged in 13 steps
12:16:28.813 INFO  LearnReadOrientationModel - Context AGG: with 494947 ref and 7682 alt examples, EM converged in 14 steps
12:16:29.461 INFO  LearnReadOrientationModel - Context ATA: with 180560 ref and 1078 alt examples, EM converged in 12 steps
12:16:29.940 INFO  LearnReadOrientationModel - Context ATC: with 213079 ref and 1522 alt examples, EM converged in 11 steps
12:16:30.524 INFO  LearnReadOrientationModel - Context ATG: with 282561 ref and 2106 alt examples, EM converged in 12 steps
12:16:31.007 INFO  LearnReadOrientationModel - Context CAA: with 284942 ref and 1909 alt examples, EM converged in 11 steps
12:16:31.710 INFO  LearnReadOrientationModel - Context CAC: with 351720 ref and 3718 alt examples, EM converged in 12 steps
12:16:32.407 INFO  LearnReadOrientationModel - Context CAG: with 547234 ref and 5940 alt examples, EM converged in 12 steps
12:16:33.215 INFO  LearnReadOrientationModel - Context CCA: with 464164 ref and 8212 alt examples, EM converged in 13 steps
12:16:34.070 INFO  LearnReadOrientationModel - Context CCC: with 512128 ref and 7580 alt examples, EM converged in 13 steps
12:16:34.860 INFO  LearnReadOrientationModel - Context CCG: with 143118 ref and 4274 alt examples, EM converged in 14 steps
12:16:35.567 INFO  LearnReadOrientationModel - Context CGA: with 74445 ref and 2480 alt examples, EM converged in 14 steps
12:16:36.368 INFO  LearnReadOrientationModel - Context CGC: with 115334 ref and 3741 alt examples, EM converged in 14 steps
12:16:36.931 INFO  LearnReadOrientationModel - Context CTA: with 173673 ref and 1472 alt examples, EM converged in 13 steps
12:16:37.537 INFO  LearnReadOrientationModel - Context CTC: with 439622 ref and 3855 alt examples, EM converged in 12 steps
12:16:38.010 INFO  LearnReadOrientationModel - Context GAA: with 333082 ref and 2101 alt examples, EM converged in 11 steps
12:16:38.546 INFO  LearnReadOrientationModel - Context GAC: with 227508 ref and 2090 alt examples, EM converged in 12 steps
12:16:39.384 INFO  LearnReadOrientationModel - Context GCA: with 340865 ref and 6507 alt examples, EM converged in 14 steps
12:16:40.330 INFO  LearnReadOrientationModel - Context GCC: with 404793 ref and 8210 alt examples, EM converged in 14 steps
12:16:41.107 INFO  LearnReadOrientationModel - Context GGA: with 409382 ref and 6784 alt examples, EM converged in 13 steps
12:16:41.620 INFO  LearnReadOrientationModel - Context GTA: with 153202 ref and 1568 alt examples, EM converged in 12 steps
12:16:42.114 INFO  LearnReadOrientationModel - Context TAA: with 208518 ref and 1131 alt examples, EM converged in 12 steps
12:16:42.902 INFO  LearnReadOrientationModel - Context TCA: with 325628 ref and 6437 alt examples, EM converged in 13 steps
12:16:43.443 INFO  LearnReadOrientationModel - Context AAA: with 426193 ref and 2055 alt examples, EM converged in 12 steps
12:16:43.452 INFO  LearnReadOrientationModel - Shutting down engine
[November 26, 2018 12:16:43 PM EST] org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel done. Elapsed time: 0.39 minutes.
Runtime.totalMemory()=1543503872
Tool returned:
SUCCESS
jjfarrell commented 5 years ago

I am also seeing this warning 3x with 4.0.11.0 on a cluster but outside of docker (centos 6). 

18:05:08.861 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/pkg/gatk/4.0.11.0/install/bin/gatk-package-4.0.11.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 24, 2018 6:05:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
WARNING: Failed to detect whether we are running on Google Compute Engine.
java.net.NoRouteToHostException: No route to host (Host unreachable)
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.net.Socket.connect(Socket.java:589)
        at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
        at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
        at sun.net.www.http.HttpClient.New(HttpClient.java:339)
        at sun.net.www.http.HttpClient.New(HttpClient.java:357)
        at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
        at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104)
        at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)
        at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)
        at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)
        at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)
        at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)
        at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:382)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:183)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

Nov 24, 2018 6:05:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
WARNING: Failed to detect whether we are running on Google Compute Engine.
java.net.NoRouteToHostException: No route to host (Host unreachable)
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.net.Socket.connect(Socket.java:589)
        at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
        at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
        at sun.net.www.http.HttpClient.New(HttpClient.java:339)
        at sun.net.www.http.HttpClient.New(HttpClient.java:357)
        at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
        at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104)
        at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)
        at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)
        at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)
        at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)
        at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)
        at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:382)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:183)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

Nov 24, 2018 6:05:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
WARNING: Failed to detect whether we are running on Google Compute Engine.
java.net.NoRouteToHostException: No route to host (Host unreachable)
        at java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
        at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
        at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
        at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.net.Socket.connect(Socket.java:589)
        at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
        at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
        at sun.net.www.http.HttpClient.New(HttpClient.java:339)
        at sun.net.www.http.HttpClient.New(HttpClient.java:357)
        at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
        at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
        at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
        at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104)
        at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)
        at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)
        at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)
        at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)
        at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)
        at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)
        at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)
        at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)
        at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:382)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:183)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

18:05:09.067 INFO  HaplotypeCaller - ------------------------------------------------------------
18:05:09.067 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.11.0
18:05:09.067 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
18:05:09.067 INFO  HaplotypeCaller - Executing as farrell@scc-wr4.scc.bu.edu on Linux v2.6.32-754.6.3.el6.x86_64 amd64
18:05:09.067 INFO  HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_151-b12
18:05:09.067 INFO  HaplotypeCaller - Start Date/Time: November 24, 2018 6:05:08 PM EST
18:05:09.067 INFO  HaplotypeCaller - ------------------------------------------------------------
18:05:09.067 INFO  HaplotypeCaller - ------------------------------------------------------------
lbergelson commented 5 years ago

There was a change to auth library so this should now be an info level output. I'm going to try to push for the stack trace to be emitted on debug output only.

lbergelson commented 5 years ago

We need to wait for google cloud dependency updates in order for the fix to be incorporated into gatk.

lbergelson commented 5 years ago

This will be fixed once https://github.com/googleapis/google-auth-library-java/pull/214 is incorporated into gatk, but we're waiting on another release of the google auth library and then the nio library which might take a bit.

sooheelee commented 5 years ago

Can we close this then @lbergelson?

vortexing commented 5 years ago

Is this actually fixed? Is there a version of GATK tools that incorporates this change so I can stop having the majority of my logs when run locally be filled up by this exact error message?

droazen commented 5 years ago

@vortexing This is fixed in master, and will be part of the next GATK release.

vortexing commented 5 years ago

Excellent, thank you!!!! (and my log files thank you too!!)

angelnmara commented 4 years ago

I have the seam problem with app engine and Mac OS INFORMACIÓN: Failed to detect whether we are running on Google Compute Engine. I init cloud, I am SU my IDE is Eclipse. Run as - App Engine, I don't have a problem with ubuntu, just MAC

a1043710306 commented 4 years ago

"D:\Program Files\Java\jdk1.8.0_121\bin\java.exe" -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:62530,suspend=y,server=n -XX:TieredStopAtLevel=1 -noverify -Dspring.output.ansi.enabled=always -Dcom.sun.management.jmxremote -Dspring.jmx.enabled=true -Dspring.liveBeansView.mbeanDomain -Dspring.application.admin.enabled=true -javaagent:C:\Users\Sweet\AppData\Local\JetBrains\IntelliJIdea2020.1\captureAgent\debugger-agent.jar -Dfile.encoding=UTF-8 -classpath "D:\Program Files\Java\jdk1.8.0_121\jre\lib\charsets.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\deploy.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\access-bridge-64.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\cldrdata.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\dnsns.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\jaccess.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\jfxrt.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\localedata.jar;D:\Program 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Files\JetBrains\IntelliJ IDEA 2020.1\lib\idea_rt.jar" com.luz.push.PushApplication Connected to the target VM, address: '127.0.0.1:62530', transport: 'socket'

. _ _ /\ / '_ () \ \ \ \ ( ( )\ | ' | '| | ' \/ ` | \ \ \ \ \/ _)| |)| | | | | || (| | ) ) ) ) ' |__| .|| ||| |\, | / / / / =========|_|==============|__/=//// :: Spring Boot :: (v2.3.0.RELEASE)

2020-05-29 15:14:30.695 INFO 12904 --- [ main] com.luz.push.PushApplication : Starting PushApplication on DESKTOP-05L3FQL with PID 12904 (C:\project\push\target\classes started by Sweet in C:\project\push) 2020-05-29 15:14:30.712 INFO 12904 --- [ main] com.luz.push.PushApplication : No active profile set, falling back to default profiles: default 2020-05-29 15:14:32.088 WARN 12904 --- [ main] o.m.s.mapper.ClassPathMapperScanner : No MyBatis mapper was found in '[com.luz.push]' package. Please check your configuration. 2020-05-29 15:14:32.662 INFO 12904 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 8282 (http) 2020-05-29 15:14:32.675 INFO 12904 --- [ main] o.a.coyote.http11.Http11NioProtocol : Initializing ProtocolHandler ["http-nio-8282"] 2020-05-29 15:14:32.676 INFO 12904 --- [ main] o.apache.catalina.core.StandardService : Starting service [Tomcat] 2020-05-29 15:14:32.677 INFO 12904 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.35] 2020-05-29 15:14:32.802 INFO 12904 --- [ main] o.a.c.c.C.[Tomcat].[localhost].[/] : Initializing Spring embedded WebApplicationContext 2020-05-29 15:14:32.802 INFO 12904 --- [ main] o.s.web.context.ContextLoader : Root WebApplicationContext: initialization completed in 1944 ms 2020-05-29 15:14:32.899 INFO 12904 --- [ main] com.luz.push.utils.GcmUtils : start init gcm server 2020-05-29 15:14:33.029 WARN 12904 --- [ main] c.g.a.oauth2.ComputeEngineCredentials : Failed to detect whether we are running on Google Compute Engine.

java.net.SocketException: Network is unreachable: connect at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1202) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:966) at com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104) at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981) at com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210) at com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100) at com.luz.push.utils.GcmUtils.init(GcmUtils.java:31) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:416) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1788) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:595) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:895) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:878) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226) at com.luz.push.PushApplication.main(PushApplication.java:10)

2020-05-29 15:14:33.032 WARN 12904 --- [ main] c.g.a.oauth2.ComputeEngineCredentials : Failed to detect whether we are running on Google Compute Engine.

java.net.SocketException: Network is unreachable: connect at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1202) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:966) at com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104) at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981) at com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210) at com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100) at com.luz.push.utils.GcmUtils.init(GcmUtils.java:31) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:416) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1788) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:595) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:895) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:878) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226) at com.luz.push.PushApplication.main(PushApplication.java:10)

2020-05-29 15:14:33.035 WARN 12904 --- [ main] c.g.a.oauth2.ComputeEngineCredentials : Failed to detect whether we are running on Google Compute Engine.

java.net.SocketException: Network is unreachable: connect at java.net.DualStackPlainSocketImpl.waitForConnect(Native Method) at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:85) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:589) at sun.net.NetworkClient.doConnect(NetworkClient.java:175) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1202) at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:966) at com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104) at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981) at com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210) at com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207) at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100) at com.luz.push.utils.GcmUtils.init(GcmUtils.java:31) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:416) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1788) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:595) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:895) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:878) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226) at com.luz.push.PushApplication.main(PushApplication.java:10)

java.io.IOException: The Application Default Credentials are not available. They are available if running in Google Compute Engine. Otherwise, the environment variable GOOGLE_APPLICATION_CREDENTIALS must be defined pointing to a file defining the credentials. See https://developers.google.com/accounts/docs/application-default-credentials for more information. at com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:131) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127) at com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100) at com.luz.push.utils.GcmUtils.init(GcmUtils.java:31) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:389) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:333) at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:157) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:416) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1788) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:595) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:517) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:323) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:226) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:321) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:895) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:878) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:143) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:758) at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397) at org.springframework.boot.SpringApplication.run(SpringApplication.java:315) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1237) at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226) at com.luz.push.PushApplication.main(PushApplication.java:10) Disconnected from the target VM, address: '127.0.0.1:62530', transport: 'socket'

Process finished with exit code 1

ashwini06 commented 4 years ago

I am having problems running Mutect2 using gatk v4.1.8.0. Any suggestions?

Using GATK jar /home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar Mutect2 -R /home/proj/stage/cancer/reference/GRCh37/genome/human_g1k_v37_decoy.fasta -L /home/proj/stage/cancer/reference/target_capture_bed/production/balsamic/gicfdna_3.1_hg19_design.bed -I consensus/concatenated_ACC5611A5_XXXXXX_consensusalign_ss_r2.bam --germline-resource /home/proj/stage/cancer/reference/GRCh37/variants/dbsnp_grch37_b138.vcf.gz -O mutect2/concatenated_ACC5611A5_XXXXXX_mutect2_unfiltered_ss_r2.vcf.gz
11:47:50.850 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 02, 2020 11:47:51 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:47:51.054 INFO  Mutect2 - ------------------------------------------------------------
11:47:51.055 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.8.0
11:47:51.055 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
11:47:51.055 INFO  Mutect2 - Executing as ashwini.jeggari@compute-0-0.local on Linux v3.10.0-1062.4.1.el7.x86_64 amd64
11:47:51.055 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
11:47:51.055 INFO  Mutect2 - Start Date/Time: July 2, 2020 11:47:50 AM CEST
11:47:51.056 INFO  Mutect2 - ------------------------------------------------------------
11:47:51.056 INFO  Mutect2 - ------------------------------------------------------------
11:47:51.056 INFO  Mutect2 - HTSJDK Version: 2.22.0
11:47:51.056 INFO  Mutect2 - Picard Version: 2.22.8
11:47:51.056 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:47:51.056 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:47:51.056 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:47:51.057 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:47:51.057 INFO  Mutect2 - Deflater: IntelDeflater
11:47:51.057 INFO  Mutect2 - Inflater: IntelInflater
11:47:51.057 INFO  Mutect2 - GCS max retries/reopens: 20
11:47:51.057 INFO  Mutect2 - Requester pays: disabled
11:47:51.057 INFO  Mutect2 - Initializing engine
11:47:51.372 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/proj/stage/cancer/reference/GRCh37/variants/dbsnp_grch37_b138.vcf.gz
11:47:51.457 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/proj/stage/cancer/reference/target_capture_bed/production/balsamic/gicfdna_3.1_hg19_design.bed
11:47:51.465 INFO  IntervalArgumentCollection - Processing 74592 bp from intervals
11:47:51.474 INFO  Mutect2 - Done initializing engine
11:47:51.487 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
11:47:51.489 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
11:47:51.534 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
11:47:51.534 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
11:47:51.534 INFO  IntelPairHmm - Available threads: 16
11:47:51.534 INFO  IntelPairHmm - Requested threads: 4
11:47:51.534 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
11:47:51.557 INFO  ProgressMeter - Starting traversal
11:47:51.557 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
11:47:52.683 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
11:47:52.683 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
11:47:52.683 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.24 sec
11:47:52.684 INFO  Mutect2 - Shutting down engine
[July 2, 2020 11:47:52 AM CEST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=2511863808
java.lang.IllegalArgumentException: Read bases and read quality arrays aren't the same size: Bases: 38 vs Base Q's: 38 vs Insert Q's: 146 vs Delete Q's: 146.
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:734)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.createQualityModifiedRead(PairHMMLikelihoodCalculationEngine.java:205)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.modifyReadQualities(PairHMMLikelihoodCalculationEngine.java:268)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngine.java:236)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeReadLikelihoods(PairHMMLikelihoodCalculationEngine.java:164)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:246)
    at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:299)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
    at org.broadinstitute.hellbender.Main.main(Main.java:292)
compute-0-0 /home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/ACC5611A1-A9/hotfish/UMI_run Conda env: D_UMI_APJ Git repo: None Git branch: None

$gatk --version Using GATK jar /home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/proj/bin/conda/envs/D_UMI_APJ/share/gatk4-4.1.8.0-0/gatk-package-4.1.8.0-local.jar --version The Genome Analysis Toolkit (GATK) v4.1.8.0 HTSJDK Version: 2.22.0 Picard Version: 2.22.8

lbergelson commented 4 years ago

Hi @ashwini06 Could you open this in a new issue instead of at the end of this unrelated one?