Class org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest
|
0%
successful |
Failed tests
testCohort
java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:228)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.onStartup(DetermineGermlineContigPloidy.java:301)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:148)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest.testCohort(DetermineGermlineContigPloidyIntegrationTest.java:38)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
at org.testng.TestRunner.privateRun(TestRunner.java:829)
at org.testng.TestRunner.run(TestRunner.java:602)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at org.testng.SuiteRunner.run(SuiteRunner.java:330)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at org.testng.TestNG.runSuites(TestNG.java:1099)
at org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python -c import gcnvkernel
Stdout:
Stderr: /opt/miniconda/envs/gatk/lib/python3.10/site-packages/arviz/__init__.py:39: FutureWarning:
ArviZ is undergoing a major refactor to improve flexibility and extensibility while maintaining a user-friendly interface.
Some upcoming changes may be backward incompatible.
For details and migration guidance, visit: https://python.arviz.org/en/latest/user_guide/migration_guide.html
warn(
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/gcnvkernel/__init__.py", line 1, in <module>
from pymc import __version__ as pymc_version
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/__init__.py", line 49, in <module>
from pymc import _version, gp, ode, sampling
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/__init__.py", line 15, in <module>
from pymc.sampling.forward import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/forward.py", line 38, in <module>
from fastprogress.fastprogress import progress_bar
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/__init__.py", line 2, in <module>
from .fastprogress import master_bar, progress_bar, force_console_behavior
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/fastprogress.py", line 15, in <module>
from fasthtml.common import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fasthtml/common.py", line 8, in <module>
from apswutils import Database
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/__init__.py", line 2, in <module>
from .db import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/db.py", line 21, in <module>
apsw.bestpractice.connection_optimize,
AttributeError: module 'apsw.bestpractice' has no attribute 'connection_optimize'
at app//org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at app//org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:119)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeCommand(PythonScriptExecutor.java:78)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:221)
... 56 more
testCohortDuplicateFiles
org.testng.TestException:
Expected exception of type class java.lang.IllegalArgumentException but got java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at app//org.testng.internal.invokers.ExpectedExceptionsHolder.wrongException(ExpectedExceptionsHolder.java:67)
at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:863)
at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
at app//org.testng.TestRunner.run(TestRunner.java:602)
at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at app//org.testng.TestNG.runSuites(TestNG.java:1099)
at app//org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:228)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.onStartup(DetermineGermlineContigPloidy.java:301)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:148)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest.testCohortDuplicateFiles(DetermineGermlineContigPloidyIntegrationTest.java:84)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
... 40 more
Caused by: org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python -c import gcnvkernel
Stdout:
Stderr: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/gcnvkernel/__init__.py", line 1, in <module>
from pymc import __version__ as pymc_version
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/__init__.py", line 49, in <module>
from pymc import _version, gp, ode, sampling
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/__init__.py", line 15, in <module>
from pymc.sampling.forward import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/forward.py", line 38, in <module>
from fastprogress.fastprogress import progress_bar
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/__init__.py", line 2, in <module>
from .fastprogress import master_bar, progress_bar, force_console_behavior
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/fastprogress.py", line 15, in <module>
from fasthtml.common import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fasthtml/common.py", line 8, in <module>
from apswutils import Database
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/__init__.py", line 2, in <module>
from .db import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/db.py", line 21, in <module>
apsw.bestpractice.connection_optimize,
AttributeError: module 'apsw.bestpractice' has no attribute 'connection_optimize'
at app//org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at app//org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:119)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeCommand(PythonScriptExecutor.java:78)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:221)
... 56 more
testCohortWithSingleSample
org.testng.TestException:
Expected exception of type class java.lang.IllegalArgumentException but got java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at app//org.testng.internal.invokers.ExpectedExceptionsHolder.wrongException(ExpectedExceptionsHolder.java:67)
at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:863)
at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
at app//org.testng.TestRunner.run(TestRunner.java:602)
at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at app//org.testng.TestNG.runSuites(TestNG.java:1099)
at app//org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:228)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.onStartup(DetermineGermlineContigPloidy.java:301)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:148)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest.testCohortWithSingleSample(DetermineGermlineContigPloidyIntegrationTest.java:72)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
... 40 more
Caused by: org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python -c import gcnvkernel
Stdout:
Stderr: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/gcnvkernel/__init__.py", line 1, in <module>
from pymc import __version__ as pymc_version
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/__init__.py", line 49, in <module>
from pymc import _version, gp, ode, sampling
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/__init__.py", line 15, in <module>
from pymc.sampling.forward import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/forward.py", line 38, in <module>
from fastprogress.fastprogress import progress_bar
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/__init__.py", line 2, in <module>
from .fastprogress import master_bar, progress_bar, force_console_behavior
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/fastprogress.py", line 15, in <module>
from fasthtml.common import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fasthtml/common.py", line 8, in <module>
from apswutils import Database
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/__init__.py", line 2, in <module>
from .db import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/db.py", line 21, in <module>
apsw.bestpractice.connection_optimize,
AttributeError: module 'apsw.bestpractice' has no attribute 'connection_optimize'
at app//org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at app//org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:119)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeCommand(PythonScriptExecutor.java:78)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:221)
... 56 more
testCohortWithoutContigPloidyPriors
org.testng.TestException:
Expected exception of type class org.broadinstitute.hellbender.exceptions.UserException$BadInput but got java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at app//org.testng.internal.invokers.ExpectedExceptionsHolder.wrongException(ExpectedExceptionsHolder.java:67)
at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:863)
at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
at java.base@17.0.12/java.util.ArrayList.forEach(ArrayList.java:1511)
at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
at app//org.testng.TestRunner.run(TestRunner.java:602)
at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
at app//org.testng.TestNG.runSuites(TestNG.java:1099)
at app//org.testng.TestNG.run(TestNG.java:1067)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:153)
at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:63)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base@17.0.12/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base@17.0.12/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base@17.0.12/java.lang.reflect.Method.invoke(Method.java:569)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:92)
at jdk.proxy1/jdk.proxy1.$Proxy4.stop(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:200)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:132)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:103)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:63)
at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:121)
at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
Caused by: java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:228)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.onStartup(DetermineGermlineContigPloidy.java:301)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:148)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:152)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:193)
at org.broadinstitute.hellbender.CommandLineProgramTest.runCommandLine(CommandLineProgramTest.java:27)
at org.broadinstitute.hellbender.testutils.CommandLineProgramTester.runCommandLine(CommandLineProgramTester.java:112)
at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest.testCohortWithoutContigPloidyPriors(DetermineGermlineContigPloidyIntegrationTest.java:63)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
... 40 more
Caused by: org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
python exited with 1
Command Line: python -c import gcnvkernel
Stdout:
Stderr: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/gcnvkernel/__init__.py", line 1, in <module>
from pymc import __version__ as pymc_version
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/__init__.py", line 49, in <module>
from pymc import _version, gp, ode, sampling
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/__init__.py", line 15, in <module>
from pymc.sampling.forward import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/pymc/sampling/forward.py", line 38, in <module>
from fastprogress.fastprogress import progress_bar
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/__init__.py", line 2, in <module>
from .fastprogress import master_bar, progress_bar, force_console_behavior
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fastprogress/fastprogress.py", line 15, in <module>
from fasthtml.common import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/fasthtml/common.py", line 8, in <module>
from apswutils import Database
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/__init__.py", line 2, in <module>
from .db import *
File "/opt/miniconda/envs/gatk/lib/python3.10/site-packages/apswutils/db.py", line 21, in <module>
apsw.bestpractice.connection_optimize,
AttributeError: module 'apsw.bestpractice' has no attribute 'connection_optimize'
at app//org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
at app//org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:119)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:193)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeCommand(PythonScriptExecutor.java:78)
at app//org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:221)
... 56 more
Tests
| Test | Duration | Result |
|---|---|---|
| testCase | - | ignored |
| testCaseWithContigPloidyPrior | - | ignored |
| testCohort | 4.665s | failed |
| testCohortDuplicateFiles | 2.249s | failed |
| testCohortWithSingleSample | 2.050s | failed |
| testCohortWithoutContigPloidyPriors | 2.089s | failed |
Standard error
[January 23, 2026 at 5:19:10 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.05 minutes. Runtime.totalMemory()=524288000 [January 23, 2026 at 5:19:13 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=524288000 [January 23, 2026 at 5:19:15 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=524288000 [January 23, 2026 at 5:19:17 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=524288000