Added an optimisation to spare not required shuffle of unpaired reads by benraha · Pull Request #2282 · bigdatagenomics/adam

benraha · 2020-11-18T15:06:34Z

This PR adds an option to avoid shuffling the entire alignment dataset when transforming to FragmentDataset.

This adds a boolean parameter to the function toFragments() that, when specified, the FragmentDataset is created with one read per Fragment record.

This resolved issue #2281 .

…when they are unpaired

benraha · 2020-11-18T15:07:50Z

Jenkins, test this please

AmplabJenkins · 2020-11-18T15:39:59Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 1654f45 # timeout=10Checking out Revision 1654f45 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 1654f4582adc31c44bbf7eae908934548ba29afdFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2020-11-18T17:00:40Z

The Jenkins failure logs are a bit much to go through, this is the relevant part

...
[INFO] ------------< org.bdgenomics.adam:adam-python-spark2_2.11 >-------------
[INFO] Building ADAM_2.11: Python APIs 0.33.0-SNAPSHOT                    [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
...
=================================== 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: 
...
E                   py4j.protocol.Py4JError: An error occurred while calling o1728.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)

benraha · 2020-11-18T19:12:37Z

@heuermh Thanks! The tests should pass now, I'm ready to review and merge :)

AmplabJenkins · 2020-11-18T19:42:46Z

Test FAILed.
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Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c # timeout=10Checking out Revision f142e4c (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

benraha · 2020-11-19T08:27:17Z

Jenkins, test this please

AmplabJenkins · 2020-11-19T09:08:34Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c # timeout=10Checking out Revision f142e4c (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

benraha · 2020-11-19T18:30:35Z

Jenkins, test this please

AmplabJenkins · 2020-11-19T19:12:18Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3134/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains f142e4c # timeout=10Checking out Revision f142e4c (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f142e4c93b3a8733c1f790ac4c73fb6d138ee442First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result FAILUREADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2020-11-19T21:06:21Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3135/

Build result: FAILURE

[...truncated 5 lines...]Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2282/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains bb2f078 # timeout=10Checking out Revision bb2f078 (origin/pr/2282/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f bb2f0780be008639963f08cff4fdddfaab8a37c4First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.12,3.0.1,ubuntuTriggering ADAM-prb ? 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb ? 2.7.5,2.12,2.4.7,ubuntuADAM-prb ? 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSADAM-prb ? 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb ? 2.7.5,2.12,2.4.7,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

benraha · 2020-11-19T21:08:28Z

There seems to be some kind of issue unpacking the hadoop tar gz

https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3135/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.7,label=ubuntu/console

heuermh · 2020-11-19T22:10:46Z

Sorry for all the trouble with Jenkins, I have seen something similar recently on another project

https://amplab.cs.berkeley.edu/jenkins/job/mango-prb/1002/HADOOP_VERSION=2.7.5,SCALAVER=2.12,SPARK_VERSION=2.4.7,label=amp-jenkins-staging-worker-02/console

That Apache mirror download link 404s, not sure what the actual issue is. Also odd that 2.7.7 doesn't match $HADOOP_VERSION . . . that will cause trouble when we add Hadoop 3.x to the build matrix (#2267).

heuermh · 2020-11-20T01:49:53Z

And a note from our admin staff:

i'm going to be upgrading jenkins to something more reasonable, and there will definitely be
some downtime as i get things sorted.

we should be back up and building by monday.

benraha · 2020-11-24T19:06:38Z

Jenkins, test this please

AmplabJenkins · 2020-11-24T20:01:31Z

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3136/

Build result: FAILURE

[...truncated 717 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 1.7.1' > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef^{commit} # timeout=30Checking out Revision e6332ef (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef # timeout=30Commit message: "code format fix"First time build. Skipping changelog.Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3136/ and message: 'Build finished. '

heuermh · 2020-11-24T20:08:05Z

re: Jenkins, might want to follow these threads

http://apache-spark-developers-list.1001551.n3.nabble.com/jenkins-downtime-tomorrow-evening-weekend-td30405.html

http://apache-spark-developers-list.1001551.n3.nabble.com/build-system-IMPORTANT-UPDATE-td30430.html

benraha · 2020-12-02T19:18:53Z

Jenkins, test this please

AmplabJenkins · 2020-12-02T20:14:18Z

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3137/

Build result: FAILURE

[...truncated 717 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef^{commit} # timeout=30Checking out Revision e6332ef (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef # timeout=30Commit message: "code format fix" > git rev-list --no-walk e6332ef # timeout=30Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3137/ and message: 'Build finished. '

heuermh · 2020-12-02T20:20:33Z

Re

The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
Build step 'Execute shell' marked build as failure

This in Jenkins Build: Execute shell is apparently no longer correct

export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export CONDA_BIN=/home/anaconda/bin/
export PATH=${JAVA_HOME}/bin/:${CONDA_BIN}:${PATH}

shaneknapp · 2020-12-03T00:27:17Z

test this please

shaneknapp · 2020-12-03T00:27:44Z

Re

The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
Build step 'Execute shell' marked build as failure

This in Jenkins Build: Execute shell is apparently no longer correct

export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export CONDA_BIN=/home/anaconda/bin/
export PATH=${JAVA_HOME}/bin/:${CONDA_BIN}:${PATH}

i fixed JAVA_HOME to point to /usr/java/latest (java 8)

AmplabJenkins · 2020-12-03T01:15:08Z

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3138/

Build result: FAILURE

[...truncated 713 B...][WARNING] Reference path does not exist: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=30 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=30 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=30Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef^{commit} # timeout=30Checking out Revision e6332ef (detached) > git config core.sparsecheckout # timeout=30 > git checkout -f e6332ef # timeout=30Commit message: "code format fix" > git rev-list --no-walk e6332ef # timeout=30Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3138/ and message: 'Build finished. '

shaneknapp · 2020-12-03T02:59:24Z

test this please

shaneknapp · 2020-12-03T02:59:50Z

(i also updated the build config so that the main prb build runs on the workers, and not the primary node)

AmplabJenkins · 2020-12-03T04:15:38Z

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3139/

Build result: FAILURE

[...truncated 1.02 KB...]Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef^{commit} # timeout=10Checking out Revision e6332ef (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef # timeout=10Commit message: "code format fix" > git rev-list --no-walk e6332ef # timeout=10Triggering ADAM-prb » 2.7.5,2.12,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.11,2.4.7,ubuntuTriggering ADAM-prb » 2.7.5,2.12,3.0.1,ubuntuADAM-prb » 2.7.5,2.12,2.4.7,ubuntu completed with result FAILUREADAM-prb » 2.7.5,2.11,2.4.7,ubuntu completed with result SUCCESSADAM-prb » 2.7.5,2.12,3.0.1,ubuntu completed with result SUCCESSNotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3139/ and message: 'Build finished. '

benraha · 2021-02-28T09:50:55Z

Jenkins, test this please

AmplabJenkins · 2021-02-28T10:41:43Z

Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/3157/

Build result: FAILURE

[...truncated 905 B...]Wiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Using reference repository: /home/jenkins/gitcaches/adam.referenceFetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse e6332ef^{commit} # timeout=10Checking out Revision e6332ef (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef # timeout=10Commit message: "code format fix" > git rev-list --no-walk a895649 # timeout=10Triggering ADAM-prb » 3.2.1,2.12,3.0.2,ubuntuADAM-prb » 3.2.1,2.12,3.0.2,ubuntu completed with result FAILURENotifying endpoint with url 'https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'Setting status of e6332ef to FAILURE with url https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/3157/ and message: 'Build finished. '

Added an optimisation to not spare not required shuffle of the reads …

cc4a711

…when they are unpaired

added mergePairedReads as a parameter to Python API

d6a6678

code format fix

e6332ef

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benraha commented Nov 18, 2020

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benraha commented Nov 18, 2020

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AmplabJenkins commented Nov 18, 2020

Build result: FAILURE

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heuermh commented Nov 18, 2020

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benraha commented Nov 18, 2020

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AmplabJenkins commented Nov 18, 2020

Build result: FAILURE

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benraha commented Nov 19, 2020

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AmplabJenkins commented Nov 19, 2020

Build result: FAILURE

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benraha commented Nov 19, 2020

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AmplabJenkins commented Nov 19, 2020

Build result: FAILURE

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AmplabJenkins commented Nov 19, 2020

Build result: FAILURE

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benraha commented Nov 19, 2020

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heuermh commented Nov 19, 2020

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heuermh commented Nov 20, 2020

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benraha commented Nov 24, 2020

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AmplabJenkins commented Nov 24, 2020

Build result: FAILURE

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heuermh commented Nov 24, 2020

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benraha commented Dec 2, 2020

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AmplabJenkins commented Dec 2, 2020

Build result: FAILURE

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heuermh commented Dec 2, 2020

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shaneknapp commented Dec 3, 2020

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shaneknapp commented Dec 3, 2020

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AmplabJenkins commented Dec 3, 2020

Build result: FAILURE

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shaneknapp commented Dec 3, 2020

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shaneknapp commented Dec 3, 2020

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AmplabJenkins commented Dec 3, 2020

Build result: FAILURE

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benraha commented Feb 28, 2021

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AmplabJenkins commented Feb 28, 2021

Build result: FAILURE

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