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gatk-package-4.0.9.0-local.jar, GenomicsDBImport

manolismanolis Member ✭✭
edited September 2018 in Ask the GATK team
Hi, I have this error ... I'm working with a linux server with simply bash codes. With the older versions I did not have this problem



Using GATK jar /home/manolis/bin/gatk-4.0.9.0/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 -Xmx10
g -jar /home/manolis/bin/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar GenomicsDBImport --genomicsdb-workspace-path /home/manolis/GATK4/germlineVariants/3.genomicsDB/PROVA/
21 --batch-size 1 -L chr21 --sample-name-map gVCF.list --reader-threads 1 -ip 100
08:44:49.154 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/manolis/bin/gatk-4.0.9.0/gatk-package-4.0.9.0-local.jar!/com/intel/gkl/native/l
ibgkl_compression.so
Sep 28, 2018 8:44:49 AM 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:432)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
        at sun.net.www.http.HttpClient.<init>(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 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)

Sep 28, 2018 8:44:49 AM 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:432)
        at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
        at sun.net.www.http.HttpClient.<init>(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 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)

Best Answer

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @manolis

    Would you please give me the exact command you are using, the dataset you are using the tool on and the version of gatk please.
    Thank you.

    Regards
    Bhanu

  • manolismanolis Member ✭✭
    edited October 2018

    Hi,

    this "warning" is totally random, sometimes I have this warning another times no ...

    gatk-4.0.9.0

    ${GATK4} --java-options "-Xmx10g" GenomicsDBImport --genomicsdb-workspace-path /home/${variantdb}/21 --batch-size 1 -L chr21 --sample-name-map gVCF.list --reader-threads 1 -ip 100

    gVCF.list is a list of 105 gVCF

    Thanks

  • manolismanolis Member ✭✭

    just some more informations... for GenomicsDBImport are available totally 25G RAM (10G for java, -Xmx) and I also tried with --batch-size 5 and --reader-threads 5.

    The same warning is always random also sometimes with BQSR, ApplyBQSR, HaplotypeCaller ... Maybe it depends from my server setting?

    Could you tell me under what conditions I must have this warning?

    Thanks

  • manolismanolis Member ✭✭

    Hi, considering that I always have a final output file from each command, I would like to know if I can use it for downstream analysis even I have this warning.

    In the post October 8, the command is --batch-size 50 not --batch-size 5

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