Console Output

Skipping 1,034 KB.. Full Log
            fi
        fi
    fi

    # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation
    _CONDA_D="${CONDA_PREFIX}/etc/conda/activate.d"
    if [[ -d "$_CONDA_D" ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi
    unset _CONDA_PYTHON
else
    unset _CONDA_PYTHON
    return $?
fi
++ ((  0 == 0  ))
++ export CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ export CONDA_PS1_BACKUP=
++ CONDA_PS1_BACKUP=
++ [[ /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
++ export PATH=/home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ [[ '' == */* ]]
++ export CONDA_DEFAULT_ENV=adam-build-51926fa8-c191-4e17-aa5c-a183d965739e
++ CONDA_DEFAULT_ENV=adam-build-51926fa8-c191-4e17-aa5c-a183d965739e
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e
"$_CONDA_DIR/conda" ..changeps1
+++ /home/anaconda/bin/conda ..changeps1
++ '[' 1 = 1 ']'
grep -q CONDA_DEFAULT_ENV <<<$PS1
+++ grep -q CONDA_DEFAULT_ENV
grep -q "POWERLINE" <<<$PS1
+++ grep -q POWERLINE
++ export 'PS1=(adam-build-51926fa8-c191-4e17-aa5c-a183d965739e) '
++ PS1='(adam-build-51926fa8-c191-4e17-aa5c-a183d965739e) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/etc/conda/activate.d ]]
++ unset _CONDA_PYTHON

unset CONDA_PATH
++ unset CONDA_PATH

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ pushd adam-python
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Using cached pytest-3.9.1-py2.py3-none-any.whl (213 kB)
Collecting py>=1.5.0
  Using cached py-1.9.0-py2.py3-none-any.whl (99 kB)
Collecting six>=1.10.0
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting atomicwrites>=1.0
  Using cached atomicwrites-1.4.0-py2.py3-none-any.whl (6.8 kB)
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/lib/python3.6/site-packages (from pytest==3.9.1) (50.3.1.post20201107)
Collecting more-itertools>=4.0.0
  Using cached more_itertools-8.6.0-py3-none-any.whl (45 kB)
Collecting attrs>=17.4.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)
Collecting pluggy>=0.7
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Using cached importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB)
Collecting zipp>=0.5
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Installing collected packages: py, six, atomicwrites, more-itertools, attrs, zipp, importlib-metadata, pluggy, pytest
Successfully installed atomicwrites-1.4.0 attrs-20.3.0 importlib-metadata-2.0.0 more-itertools-8.6.0 pluggy-0.13.1 py-1.9.0 pytest-3.9.1 six-1.15.0 zipp-3.4.0
+ popd
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
+ mvn -U -P python,distribution package '-Dsuites=select.no.suites*' -Dhadoop.version=2.7.5
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
[INFO] ADAM_2.12: Python APIs                                             [jar]
[INFO] ADAM_2.12: Distribution                                            [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >-------------
[INFO] Building ADAM_2.12 0.33.0-SNAPSHOT                                 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.12 ---
[INFO] Modified 129 of 439 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.33.0-SNAPSHOT              [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.8/classes at 1605713735167
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.8/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.12 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark3_2.12 ---
[INFO] 
Loading source files for package org.bdgenomics.adam.shade...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT  [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.12.8/classes at 1605713742457
[WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.12 ---
Discovery starting.
Discovery completed in 65 milliseconds.
Run starting. Expected test count is: 0
Run completed in 71 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark3_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.33.0-SNAPSHOT                           [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes at 1605713758459
[WARNING] warning: there were 21 deprecation warnings
[WARNING] warning: there were 31 deprecation warnings (since 0.21.0)
[WARNING] warning: there was one deprecation warning (since 1.0.6)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 174 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 229 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 25 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 153 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/test-classes at 1605713785283
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                          ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName)
[WARNING]                                             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
[WARNING]                                                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val samIter = asScalaIterator(newSAMReader.iterator())
[WARNING]                     ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G")))
[WARNING]                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes))
[WARNING]                                                           ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
[WARNING]                   ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T"))))
[WARNING]                     ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer))
[WARNING]                                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) {
[WARNING]                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G")))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true)))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
[WARNING]                   ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getNonReferenceLikelihoods
[WARNING]                   ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 1)
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 2)
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       genotypeAttributes)))((bldr, fn) => {
[WARNING]       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]                                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(0) === 10)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(1) === 12)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(2) === 14)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(3) === 16)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER")
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER1")
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(1) === "FAILED_FILTER2")
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(2) === "FAILED_FILTER3")
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(d => d: java.lang.Double))
[WARNING]             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]           .map(i => i: java.lang.Integer))
[WARNING]               ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(i => i: java.lang.Integer))
[WARNING]             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq"))
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq", "lowdp"))
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 1)
[WARNING]              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 2)
[WARNING]              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         vcb.filters(Set("FAILED1", "FAILED2", "FAILED3"))
[WARNING]                        ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val failedSet = v.getFiltersFailed.toSet
[WARNING]                       ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name"))
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name1", "name2"))
[WARNING]                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED"))
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED1", "FAILED2"))
[WARNING]                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10).map(i => i: java.lang.Integer)
[WARNING]              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                      ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f).map(i => i: java.lang.Float)
[WARNING]                ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("+Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("-Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)
[WARNING]                               ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M")
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M", "100M", "90M10D")
[WARNING]                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("ONE_INT", "42")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("A_INT", "10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_INT", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_STRING", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("STRING_G", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId))
[WARNING]                                                                         ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(read.mdTag.get.end === read.getEnd)
[WARNING]            ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] 168 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 27 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark3_2.12 ---
Discovery starting.
Discovery completed in 627 milliseconds.
Run starting. Expected test count is: 0
Run completed in 633 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark3_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark3_2.12 ---
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala:846: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 283 documentable templates
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:747: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:748: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:749: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3464: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1859: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1839: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1810: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException".
    /**
    ^
24 warnings found
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.33.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.33.0-SNAPSHOT          [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/classes at 1605713850939
[WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes at 1605713858168
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 8 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark3_2.12 ---
Discovery starting.
Discovery completed in 186 milliseconds.
Run starting. Expected test count is: 0
Run completed in 193 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark3_2.12 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 192 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.33.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.33.0-SNAPSHOT                            [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes at 1605713876022
[WARNING] warning: there was one deprecation warning
[WARNING] warning: there was one deprecation warning (since 2.12.0)
[WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/test-classes at 1605713884628
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark3_2.12 ---
Discovery starting.
Discovery completed in 132 milliseconds.
Run starting. Expected test count is: 0
Run completed in 137 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark3_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark3_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.33.0-SNAPSHOT                       [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.12.8/classes at 1605713903281
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.8 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.30 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-python-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Python APIs 0.33.0-SNAPSHOT                    [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-python-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark3_2.12 ---
pip install -e .
Obtaining file:///tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python
Requirement already satisfied: pyspark>=1.6.0 in /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python (from bdgenomics.adam==0.32.0a0) (3.0.1)
Collecting py4j==0.10.9
  Using cached py4j-0.10.9-py2.py3-none-any.whl (198 kB)
Installing collected packages: bdgenomics.adam, py4j
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.9
python setup.py bdist_egg
running bdist_egg
running egg_info
writing bdgenomics.adam.egg-info/PKG-INFO
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/rdd.py to rdd.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantDataset_test.py to variantDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentDataset_test.py to alignmentDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/coverageDataset_test.py to coverageDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeDataset_test.py to genotypeDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying deps/bin/find-spark.sh -> build/scripts-3.6
copying deps/bin/find-adam-assembly.sh -> build/scripts-3.6
copying deps/bin/adam-submit -> build/scripts-3.6
copying deps/bin/adam-shell -> build/scripts-3.6
copying deps/bin/find-adam-egg.sh -> build/scripts-3.6
copying deps/bin/adamR -> build/scripts-3.6
copying deps/bin/pyadam -> build/scripts-3.6
copying deps/bin/find-adam-home -> build/scripts-3.6
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-3.6
changing mode of build/scripts-3.6/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find_adam_home.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.adam.__pycache__.find_adam_home.cpython-36: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.32.0a0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark3_2.12 ---
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.12, pytest-3.9.1, py-1.9.0, pluggy-0.13.1 -- /home/jenkins/anaconda2/envs/adam-build-51926fa8-c191-4e17-aa5c-a183d965739e/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 63 items

bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_alignments PASSED [  1%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_bed PASSED [  3%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_coverage PASSED [  4%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_dna_sequences PASSED [  6%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_genotypes PASSED [  7%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_gtf PASSED [  9%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_indexed_bam PASSED [ 11%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_interval_list PASSED [ 12%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_narrowPeak PASSED [ 14%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_slices PASSED [ 15%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_variants PASSED [ 17%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_inner_join PASSED [ 19%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_right_outer_join PASSED [ 20%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_caching PASSED [ 22%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_count_kmers PASSED [ 23%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegion PASSED [ 25%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegions PASSED [ 26%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_load_indexed_bam PASSED [ 28%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_persisting PASSED [ 30%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_pipe_as_sam PASSED [ 31%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_known_indels PASSED [ 33%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_reads PASSED [ 34%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_as_bam PASSED [ 36%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_sorted_sam PASSED [ 38%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_unordered_sam PASSED [ 39%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_full_outer_join PASSED [ 41%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join PASSED [ 42%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join_groupBy_left PASSED [ 44%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_left_outer_join PASSED [ 46%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join PASSED [ 47%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 49%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_coverage PASSED [ 50%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_fragments FAILED [ 52%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transform PASSED [ 53%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transmute_to_coverage PASSED [ 55%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_union PASSED [ 57%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_aggregatedCoverage PASSED [ 58%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_collapse PASSED [ 60%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_flatten PASSED [ 61%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_save PASSED [ 63%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_toFeatures PASSED [ 65%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_bed PASSED [ 66%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_gtf PASSED [ 68%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_interval_list PASSED [ 69%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_narrowPeak PASSED [ 71%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_transform PASSED [ 73%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_to_variants PASSED [ 74%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_transform PASSED [ 76%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_filter PASSED [ 77%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_all_array PASSED [ 79%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_alts_array PASSED [ 80%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_array PASSED [ 82%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_genotype_array PASSED [ 84%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_scalar PASSED [ 85%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_all_array PASSED [ 87%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_alts_array PASSED [ 88%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_array PASSED [ 90%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_scalar PASSED [ 92%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_round_trip PASSED [ 93%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort PASSED [ 95%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort_lex PASSED [ 96%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_transform PASSED [ 98%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_vcf_round_trip PASSED [100%]

=================================== FAILURES ===================================
____________________ AlignmentDatasetTest.test_to_fragments ____________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_to_fragments>

    def test_to_fragments(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
        reads = ac.loadAlignments(readsPath)
    
>       fragments = reads.toFragments()

bdgenomics/adam/test/alignmentDataset_test.py:169: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/rdd.py:882: in toFragments
    return FragmentDataset(self._jvmRdd.toFragments(), self.sc)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py:1305: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/utils.py:128: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xspy4j.Py4JException: Method toFragments([]) does not exist\\n\tat py4j.reflection.ReflectionEngine.getMethod(Reflect...java:79)\\n\tat py4j.GatewayConnection.run(GatewayConnection.java:238)\\n\tat java.lang.Thread.run(Thread.java:748)\\n'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7fd8aa9ade80>
target_id = 'o1571', name = 'toFragments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
                        format(target_id, ".", name), value)
                else:
                    raise Py4JError(
                        "An error occurred while calling {0}{1}{2}. Trace:\n{3}\n".
>                       format(target_id, ".", name, value))
E                   py4j.protocol.Py4JError: An error occurred while calling o1571.toFragments. Trace:
E                   py4j.Py4JException: Method toFragments([]) does not exist
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:318)
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:326)
E                   	at py4j.Gateway.invoke(Gateway.java:274)
E                   	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
E                   	at py4j.commands.CallCommand.execute(CallCommand.java:79)
E                   	at py4j.GatewayConnection.run(GatewayConnection.java:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py:332: Py4JError
- generated xml file: /tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/alignmentDataset_test.py:143: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(readsAsCoverage.toDF().count(), 5)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/coverageDataset_test.py:59: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(features.toDF().count(), coverage.toDF().count())

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestYO4Orx5/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
============== 1 failed, 62 passed, 113 warnings in 71.89 seconds ==============
make: *** [test] Error 1
Makefile:83: recipe for target 'test' failed
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
    at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:764)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:711)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:289)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    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.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  8.480 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.584 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  9.588 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:38 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 24.281 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 28.281 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 16.528 s]
[INFO] ADAM_2.12: Python APIs ............................. FAILURE [01:16 min]
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:29 min
[INFO] Finished at: 2020-11-18T07:39:55-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-python) on project adam-python-spark3_2.12: Command execution failed.: Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :adam-python-spark3_2.12
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/1654f4582adc31c44bbf7eae908934548ba29afd
Finished: FAILURE