Closed sooheelee closed 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
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 - ------------------------------------------------------------
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.
We need to wait for google cloud dependency updates in order for the fix to be incorporated into gatk.
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.
Can we close this then @lbergelson?
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?
@vortexing This is fixed in master, and will be part of the next GATK release.
Excellent, thank you!!!! (and my log files thank you too!!)
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
"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 Files\Java\jdk1.8.0_121\jre\lib\ext\nashorn.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\sunec.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\sunjce_provider.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\sunmscapi.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\sunpkcs11.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\ext\zipfs.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\javaws.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\jce.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\jfr.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\jfxswt.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\jsse.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\management-agent.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\plugin.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\resources.jar;D:\Program Files\Java\jdk1.8.0_121\jre\lib\rt.jar;C:\project\push\target\classes;E:\repository\org\springframework\boot\spring-boot-starter-jdbc\2.3.0.RELEASE\spring-boot-starter-jdbc-2.3.0.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot-starter\2.3.0.RELEASE\spring-boot-starter-2.3.0.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot\2.3.0.RELEASE\spring-boot-2.3.0.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot-autoconfigure\2.3.0.RELEASE\spring-boot-autoconfigure-2.3.0.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot-starter-logging\2.3.0.RELEASE\spring-boot-starter-logging-2.3.0.RELEASE.jar;E:\repository\ch\qos\logback\logback-classic\1.2.3\logback-classic-1.2.3.jar;E:\repository\ch\qos\logback\logback-core\1.2.3\logback-core-1.2.3.jar;E:\repository\org\apache\logging\log4j\log4j-to-slf4j\2.13.2\log4j-to-slf4j-2.13.2.jar;E:\repository\org\apache\logging\log4j\log4j-api\2.13.2\log4j-api-2.13.2.jar;E:\repository\org\slf4j\jul-to-slf4j\1.7.30\jul-to-slf4j-1.7.30.jar;E:\repository\jakarta\annotation\jakarta.annotation-api\1.3.5\jakarta.annotation-api-1.3.5.jar;E:\repository\org\yaml\snakeyaml\1.26\snakeyaml-1.26.jar;E:\repository\com\zaxxer\HikariCP\3.4.5\HikariCP-3.4.5.jar;E:\repository\org\springframework\spring-jdbc\5.2.6.RELEASE\spring-jdbc-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-beans\5.2.6.RELEASE\spring-beans-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-tx\5.2.6.RELEASE\spring-tx-5.2.6.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot-starter-web\2.3.0.RELEASE\spring-boot-starter-web-2.3.0.RELEASE.jar;E:\repository\org\springframework\boot\spring-boot-starter-json\2.3.0.RELEASE\spring-boot-starter-json-2.3.0.RELEASE.jar;E:\repository\com\fasterxml\jackson\core\jackson-databind\2.11.0\jackson-databind-2.11.0.jar;E:\repository\com\fasterxml\jackson\core\jackson-annotations\2.11.0\jackson-annotations-2.11.0.jar;E:\repository\com\fasterxml\jackson\core\jackson-core\2.11.0\jackson-core-2.11.0.jar;E:\repository\com\fasterxml\jackson\datatype\jackson-datatype-jdk8\2.11.0\jackson-datatype-jdk8-2.11.0.jar;E:\repository\com\fasterxml\jackson\datatype\jackson-datatype-jsr310\2.11.0\jackson-datatype-jsr310-2.11.0.jar;E:\repository\com\fasterxml\jackson\module\jackson-module-parameter-names\2.11.0\jackson-module-parameter-names-2.11.0.jar;E:\repository\org\springframework\boot\spring-boot-starter-tomcat\2.3.0.RELEASE\spring-boot-starter-tomcat-2.3.0.RELEASE.jar;E:\repository\org\apache\tomcat\embed\tomcat-embed-core\9.0.35\tomcat-embed-core-9.0.35.jar;E:\repository\org\glassfish\jakarta.el\3.0.3\jakarta.el-3.0.3.jar;E:\repository\org\apache\tomcat\embed\tomcat-embed-websocket\9.0.35\tomcat-embed-websocket-9.0.35.jar;E:\repository\org\springframework\spring-web\5.2.6.RELEASE\spring-web-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-webmvc\5.2.6.RELEASE\spring-webmvc-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-aop\5.2.6.RELEASE\spring-aop-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-context\5.2.6.RELEASE\spring-context-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-expression\5.2.6.RELEASE\spring-expression-5.2.6.RELEASE.jar;E:\repository\org\mybatis\spring\boot\mybatis-spring-boot-starter\2.1.2\mybatis-spring-boot-starter-2.1.2.jar;E:\repository\org\mybatis\spring\boot\mybatis-spring-boot-autoconfigure\2.1.2\mybatis-spring-boot-autoconfigure-2.1.2.jar;E:\repository\org\mybatis\mybatis\3.5.4\mybatis-3.5.4.jar;E:\repository\org\mybatis\mybatis-spring\2.0.4\mybatis-spring-2.0.4.jar;E:\repository\mysql\mysql-connector-java\8.0.20\mysql-connector-java-8.0.20.jar;E:\repository\org\springframework\boot\spring-boot-configuration-processor\2.3.0.RELEASE\spring-boot-configuration-processor-2.3.0.RELEASE.jar;E:\repository\org\springframework\spring-core\5.2.6.RELEASE\spring-core-5.2.6.RELEASE.jar;E:\repository\org\springframework\spring-jcl\5.2.6.RELEASE\spring-jcl-5.2.6.RELEASE.jar;E:\repository\com\google\firebase\firebase-admin\6.8.1\firebase-admin-6.8.1.jar;E:\repository\com\google\api-client\google-api-client\1.25.0\google-api-client-1.25.0.jar;E:\repository\com\google\oauth-client\google-oauth-client\1.25.0\google-oauth-client-1.25.0.jar;E:\repository\com\google\http-client\google-http-client-jackson2\1.25.0\google-http-client-jackson2-1.25.0.jar;E:\repository\com\google\api-client\google-api-client-gson\1.25.0\google-api-client-gson-1.25.0.jar;E:\repository\com\google\http-client\google-http-client-gson\1.25.0\google-http-client-gson-1.25.0.jar;E:\repository\com\google\code\gson\gson\2.8.6\gson-2.8.6.jar;E:\repository\com\google\http-client\google-http-client\1.25.0\google-http-client-1.25.0.jar;E:\repository\com\google\code\findbugs\jsr305\3.0.2\jsr305-3.0.2.jar;E:\repository\org\apache\httpcomponents\httpclient\4.5.12\httpclient-4.5.12.jar;E:\repository\org\apache\httpcomponents\httpcore\4.4.13\httpcore-4.4.13.jar;E:\repository\commons-codec\commons-codec\1.14\commons-codec-1.14.jar;E:\repository\com\google\j2objc\j2objc-annotations\1.1\j2objc-annotations-1.1.jar;E:\repository\com\google\api\api-common\1.7.0\api-common-1.7.0.jar;E:\repository\com\google\auth\google-auth-library-oauth2-http\0.11.0\google-auth-library-oauth2-http-0.11.0.jar;E:\repository\com\google\auth\google-auth-library-credentials\0.11.0\google-auth-library-credentials-0.11.0.jar;E:\repository\com\google\cloud\google-cloud-storage\1.43.0\google-cloud-storage-1.43.0.jar;E:\repository\com\google\cloud\google-cloud-core\1.43.0\google-cloud-core-1.43.0.jar;E:\repository\joda-time\joda-time\2.9.2\joda-time-2.9.2.jar;E:\repository\com\google\api\gax\1.30.0\gax-1.30.0.jar;E:\repository\com\google\protobuf\protobuf-java-util\3.6.0\protobuf-java-util-3.6.0.jar;E:\repository\com\google\api\grpc\proto-google-common-protos\1.12.0\proto-google-common-protos-1.12.0.jar;E:\repository\com\google\api\grpc\proto-google-iam-v1\0.12.0\proto-google-iam-v1-0.12.0.jar;E:\repository\com\google\cloud\google-cloud-core-http\1.43.0\google-cloud-core-http-1.43.0.jar;E:\repository\com\google\http-client\google-http-client-appengine\1.24.1\google-http-client-appengine-1.24.1.jar;E:\repository\com\google\http-client\google-http-client-jackson\1.24.1\google-http-client-jackson-1.24.1.jar;E:\repository\org\codehaus\jackson\jackson-core-asl\1.9.11\jackson-core-asl-1.9.11.jar;E:\repository\com\google\api\gax-httpjson\0.47.0\gax-httpjson-0.47.0.jar;E:\repository\io\opencensus\opencensus-contrib-http-util\0.15.0\opencensus-contrib-http-util-0.15.0.jar;E:\repository\com\google\apis\google-api-services-storage\v1-rev135-1.24.1\google-api-services-storage-v1-rev135-1.24.1.jar;E:\repository\com\google\cloud\google-cloud-firestore\0.61.0-beta\google-cloud-firestore-0.61.0-beta.jar;E:\repository\com\google\cloud\google-cloud-core-grpc\1.43.0\google-cloud-core-grpc-1.43.0.jar;E:\repository\com\google\protobuf\protobuf-java\3.6.0\protobuf-java-3.6.0.jar;E:\repository\io\grpc\grpc-protobuf\1.13.1\grpc-protobuf-1.13.1.jar;E:\repository\io\grpc\grpc-protobuf-lite\1.13.1\grpc-protobuf-lite-1.13.1.jar;E:\repository\io\grpc\grpc-context\1.13.1\grpc-context-1.13.1.jar;E:\repository\com\google\api\gax-grpc\1.30.0\gax-grpc-1.30.0.jar;E:\repository\org\threeten\threetenbp\1.3.3\threetenbp-1.3.3.jar;E:\repository\com\google\api\grpc\proto-google-cloud-firestore-v1beta1\0.26.0\proto-google-cloud-firestore-v1beta1-0.26.0.jar;E:\repository\com\google\auto\value\auto-value\1.4\auto-value-1.4.jar;E:\repository\io\grpc\grpc-netty-shaded\1.13.1\grpc-netty-shaded-1.13.1.jar;E:\repository\io\grpc\grpc-core\1.13.1\grpc-core-1.13.1.jar;E:\repository\com\google\errorprone\error_prone_annotations\2.1.2\error_prone_annotations-2.1.2.jar;E:\repository\io\opencensus\opencensus-contrib-grpc-metrics\0.12.3\opencensus-contrib-grpc-metrics-0.12.3.jar;E:\repository\io\grpc\grpc-stub\1.13.1\grpc-stub-1.13.1.jar;E:\repository\io\grpc\grpc-auth\1.13.1\grpc-auth-1.13.1.jar;E:\repository\io\opencensus\opencensus-api\0.15.0\opencensus-api-0.15.0.jar;E:\repository\io\opencensus\opencensus-contrib-grpc-util\0.15.0\opencensus-contrib-grpc-util-0.15.0.jar;E:\repository\com\google\guava\guava\20.0\guava-20.0.jar;E:\repository\org\slf4j\slf4j-api\1.7.30\slf4j-api-1.7.30.jar;E:\repository\io\netty\netty-codec-http\4.1.49.Final\netty-codec-http-4.1.49.Final.jar;E:\repository\io\netty\netty-common\4.1.49.Final\netty-common-4.1.49.Final.jar;E:\repository\io\netty\netty-buffer\4.1.49.Final\netty-buffer-4.1.49.Final.jar;E:\repository\io\netty\netty-codec\4.1.49.Final\netty-codec-4.1.49.Final.jar;E:\repository\io\netty\netty-handler\4.1.49.Final\netty-handler-4.1.49.Final.jar;E:\repository\io\netty\netty-resolver\4.1.49.Final\netty-resolver-4.1.49.Final.jar;E:\repository\io\netty\netty-transport\4.1.49.Final\netty-transport-4.1.49.Final.jar;E:\repository\com\alibaba\druid\1.1.6\druid-1.1.6.jar;E:\repository\redis\clients\jedis\3.1.0\jedis-3.1.0.jar;E:\repository\org\apache\commons\commons-pool2\2.8.0\commons-pool2-2.8.0.jar;C:\Program 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.
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.
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.
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
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
Hi @ashwini06 Could you open this in a new issue instead of at the end of this unrelated one?
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?