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Adding ReadRDD, SequenceRDD, and SliceRDD. #1895

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commented Jan 30, 2018

Work in progress.

Todo:

  • Refactor FragmentConverterSliceConverter
  • Refactor FastaSliceConverter & FastaSequenceConverter into a single class/object
  • Clarify method names on ADAMContext, see below
  • Integrate avro.formats.Alphabet and models.Alphabet
  • Increase unit test coverage
  • Python and R APIs
  • Update docs

Proposal for new ADAMContext API methods:

class ADAMContext {

// existing methods
def loadFastq(pathName: String, optPathName2: Option[String] = None, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordRDD = {}

def loadPairedFastq(pathName1: String, pathName2: String, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordRDD = {}

def loadUnpairedFastq(pathName: String, setFirstOfPair: Boolean = false, setSecondOfPair: Boolean = false, optRecordGroup: Option[String] = None, stringency: ValidationStringency = ValidationStringency.STRICT): AlignmentRecordRDD = {}

def loadInterleavedFastqAsFragments(pathName: String): FragmentRDD = {}

// new methods (other PRs)
def loadPairedFastqAsFragments(pathName1: String, pathName2: String): FragmentRDD = {}

// new methods (this PR)
def loadFastaDna(pathName: String): SequenceRDD = {}

def loadFastaProtein(pathName: String): SequenceRDD = {}

def loadFastaRna(pathName: String): SequenceRDD = {}

def loadFastaDna(pathName: String, maximumLength: Long = 10000L): SliceRDD = {}

def loadParquetReads(...): ReadRDD = {}

def loadParquetSequences(...): SequenceRDD = {}

def loadParquetSlices(...): SliceRDD = {}

def loadReads(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): ReadRDD = {}

def loadDnaSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceRDD = {}

def loadProteinSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceRDD = {}

def loadRnaSequences(pathName: String, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SequenceRDD = {}

// or loadDnaSlices?
def loadSlices(pathName: String, maximumLength: Long = 10000L, optPredicate: Option[FilterPredicate], optProjection: Option[Schema] = None): SliceRDD = {}

External methods that extend ADAMContext

def loadGenbankDna(pathName: String): SequenceRDD = {}

def loadGenbankProtein(pathName: String): SequenceRDD = {}

def loadGenbankRna(pathName: String): SequenceRDD = {}

def loadGenbankDna(pathName: String, maximumLength: Long = 10000L): SliceRDD = {}

etc.

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commented Jan 30, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2623/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 6055632 # timeout=10Checking out Revision 6055632 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 6055632860706831bdf2c08ead110639ee1381daFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Jan 30, 2018

Coverage Status

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

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commented Jan 30, 2018

Coverage Status

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

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commented Jan 30, 2018

Coverage Status

Coverage decreased (-3.3%) to 75.827% when pulling 38cb59c on heuermh:sequence-rdd-two into 429680e on bigdatagenomics:master.

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commented Jan 30, 2018

Coverage Status

Coverage decreased (-3.4%) to 79.258% when pulling 3383a3c on heuermh:sequence-rdd-two into adff336 on bigdatagenomics:master.

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commented Jan 31, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2624/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 723d1cf # timeout=10Checking out Revision 723d1cf (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 723d1cf855c29160ec818e3995e1e08984f60319First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Jan 31, 2018

Test PASSed.
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Test PASSed.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from 460f6bf to 12285a1 Feb 2, 2018

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commented Feb 2, 2018

Test FAILed.
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Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 70594c6 # timeout=10Checking out Revision 70594c6 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 70594c69954117a0b0f479803d9042fd26a1e067First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from 12285a1 to 1ea3984 Feb 3, 2018

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commented Feb 4, 2018

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

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 3fccb8f # timeout=10Checking out Revision 3fccb8f (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 3fccb8f27e0a59f77df4597277bac891fc852148First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from 1ea3984 to e381016 Feb 7, 2018

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commented Feb 7, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2653/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 74766f0 # timeout=10Checking out Revision 74766f0 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 74766f0375c433ff60fa5dc296336f6bf91f1996First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Feb 10, 2018

Is it the PR that should solve my FastConverter problems?

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commented Feb 10, 2018

Is it the PR that should solve my FastConverter problems?

That is the intent; it doesn't yet. It does allow for https://github.com/heuermh/biojava-adam as a workaround. I will run some performance comparisons on our cluster on Monday.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from e381016 to 50c34ae Feb 14, 2018

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commented Feb 14, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2666/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 93a07ac # timeout=10Checking out Revision 93a07ac (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 93a07ac9bd72d891152c1a38b18851af66553f88First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from 50c34ae to cb0ba2f Mar 5, 2018

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commented Mar 5, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2694/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 0a4e4d6 # timeout=10Checking out Revision 0a4e4d6 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 0a4e4d6849da43ca07dab1933a15f5a390bbab81First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented Apr 12, 2018

I do not see this very important issue in the roadmap for 0.25, do you want to release it later?

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commented Apr 12, 2018

Sorry, as evident from all the conflicting files, this is a large change and is sensitive to further refactoring. #1981 is another large one that needs to go first. I'd like to have this in 0.25.0, which has a due date of May 1st.

@heuermh heuermh force-pushed the heuermh:sequence-rdd-two branch from cb0ba2f to ee44ce1 Apr 25, 2018

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commented Apr 25, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2761/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 646b91f # timeout=10Checking out Revision 646b91f (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 646b91f44a78729620c138f1407d5ab20b02e93aFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented May 1, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2762/

Build result: ABORTED

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 4a8e4fb # timeout=10Checking out Revision 4a8e4fb (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 4a8e4fb45e86a4deb6db2a5a4b5f1c64e36cd9ddFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result ABORTEDADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented May 6, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2763/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 9a88e8d # timeout=10Checking out Revision 9a88e8d (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9a88e8dc1d05545b87a37946cc6a0da7f1c8ce21First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented May 6, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2764/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains d163c58 # timeout=10Checking out Revision d163c58 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f d163c58a08ab92c6df4df83823e9fa1c9ae635b3First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented May 7, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2765/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 454da56 # timeout=10Checking out Revision 454da56 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 454da56226d67ffced14877bff56c14d60f298caFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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commented May 7, 2018

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2766/

Build result: FAILURE

[...truncated 7 lines...] > /home/jenkins/git2/bin/git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git --version # timeout=10 > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > /home/jenkins/git2/bin/git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > /home/jenkins/git2/bin/git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > /home/jenkins/git2/bin/git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > /home/jenkins/git2/bin/git rev-parse origin/pr/1895/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a -v --no-abbrev --contains 7c91b67 # timeout=10Checking out Revision 7c91b67 (origin/pr/1895/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 7c91b67e9eb492e041874713dc96c371bd8ca599First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.10,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.10,2.2.1,centosTriggering ADAM-prb ? 2.7.3,2.11,2.2.1,centosTriggering ADAM-prb ? 2.6.2,2.11,2.2.1,centosADAM-prb ? 2.7.3,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.6.2,2.10,2.2.1,centos completed with result SUCCESSADAM-prb ? 2.7.3,2.11,2.2.1,centos completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.1,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

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