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Failed to detect whether we are running on google compute engine ???

SkyWarriorSkyWarrior TurkeyMember ✭✭✭
Gokalps-Mac-mini:1000GVCFs sky$ gatk SelectVariants -V 1000G_CEU_chr16.vcf.gz -O 1000G_CEU_AFfilt_chr16.vcf.gz -select "AF > 0.0"
Using GATK jar /Users/sky/scripts/gatk-package-4.0.9.0-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 /Users/sky/scripts/gatk-package-4.0.9.0-local.jar SelectVariants -V 1000G_CEU_chr16.vcf.gz -O 1000G_CEU_AFfilt_chr16.vcf.gz -select AF > 0.0
14:35:45.842 INFO  NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sky/scripts/gatk-package-4.0.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
Sep 24, 2018 2:35:47 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: No route to host (connect failed)
    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:360)
    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)

14:35:47.079 INFO  SelectVariants - ------------------------------------------------------------
14:35:47.079 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.0.9.0
14:35:47.080 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
14:35:47.080 INFO  SelectVariants - Executing as [email protected] on Mac OS X v10.13.6 x86_64
14:35:47.080 INFO  SelectVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_181-b13
14:35:47.080 INFO  SelectVariants - Start Date/Time: September 24, 2018 2:35:45 PM EET
14:35:47.080 INFO  SelectVariants - ------------------------------------------------------------
14:35:47.081 INFO  SelectVariants - ------------------------------------------------------------
14:35:47.082 INFO  SelectVariants - HTSJDK Version: 2.16.1
14:35:47.082 INFO  SelectVariants - Picard Version: 2.18.13
14:35:47.082 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:35:47.082 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:35:47.082 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:35:47.082 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:35:47.082 INFO  SelectVariants - Deflater: IntelDeflater
14:35:47.082 INFO  SelectVariants - Inflater: IntelInflater

I am getting this strange error message from time to time. It is clear that I am using the gatk local however something is wrong with google compute engine checks I guess.

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