demonstrate multi-allelic gVCF failure - test added #1205

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jpdna commented Oct 11, 2016

This PR does not pass tests - this is as intended as purpose is to demonstrate problem.

Test added in ADAMContextSuite
and related test vcf file, which demonstrates that we currently cannot import gVCF variants which have a
Multi-allelic site with non-ref symbolic allele

error reported when running tests is:

2016-10-11 11:30:03 ERROR TaskSetManager:74 - Task 0 in stage 0.0 failed 1 times; aborting job
- load gvcf which contains a multi-allelic row from a directory *** FAILED ***
  org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost): java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18030096-18030099 Q564.73 of type=MIXED alleles=[TAAA*, <NON_REF>, T, TA, TAA] attr={BaseQRankSum=-0.133, ClippingRankSum=-1.438, DP=114, MLEAC=[0, 1, 1, 0], MLEAF=[0.00, 0.500, 0.500, 0.00], MQ=69.72, MQ0=0, MQRankSum=-0.686, ReadPosRankSum=-0.013} GT=GT:AD:DP:GQ:PL 2/3:13,3,17,17,0:50:86:602,508,1628,86,678,553,137,342,0,281,467,744,353,309,659
    at org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:214)
    at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
    at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
    at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
    at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
    at org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595)
    at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
    at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)

@jpdna jpdna changed the title from Added multi-alleleic gVCF test which currently fails to demonstrate multi-allelic gVCF failure - test added Oct 11, 2016

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Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1531/

Build result: FAILURE

GitHub pull request #1205 of commit cd05b74 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1205/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 9830f50 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1205/merge^{commit} # timeout=10Checking out Revision 9830f50 (origin/pr/1205/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9830f5063012db134a809f62c43e78373ba3f81eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1531/

Build result: FAILURE

GitHub pull request #1205 of commit cd05b74 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prb > /home/jenkins/git2/bin/git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > /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 --version # timeout=10 > /home/jenkins/git2/bin/git -c core.askpass=true 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/1205/merge^{commit} # timeout=10 > /home/jenkins/git2/bin/git branch -a --contains 9830f50 # timeout=10 > /home/jenkins/git2/bin/git rev-parse remotes/origin/pr/1205/merge^{commit} # timeout=10Checking out Revision 9830f50 (origin/pr/1205/merge) > /home/jenkins/git2/bin/git config core.sparsecheckout # timeout=10 > /home/jenkins/git2/bin/git checkout -f 9830f5063012db134a809f62c43e78373ba3f81eFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.0,2.11,1.5.2,centosTriggering ADAM-prb ? 2.6.0,2.10,1.5.2,centosTouchstone configurations resulted in FAILURE, so aborting...Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

@fnothaft fnothaft referenced this pull request Nov 7, 2016

Merged

Miscellaneous VCF fixes #1247

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ok to close in favor of #1247?

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heuermh commented Nov 7, 2016

ok to close in favor of #1247?

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Closed as merged in #1247.

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fnothaft commented Nov 8, 2016

Closed as merged in #1247.

@fnothaft fnothaft closed this Nov 8, 2016

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