BUILD FAILURE

[shibuvp]

i'm getting this error while building avocado

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 2.877 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [04:43 min]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:46 min
[INFO] Finished at: 2017-07-06T11:12:18+05:30
[INFO] Final Memory: 29M/502M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project avocado-core_2.10: There are test failures -> [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/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :avocado-core_2.10

[fnothaft]

Hi @shibuvp! Sorry for the confusion, docs are a bit out of date. Avocado needs to be built for Spark 2, due to a bug in Spark SQL in Spark 1.6.x.

[shibuvp]

thanks @fnothaft

[fnothaft]

No problem! Please leave this issue open; it'll remind me to update the docs.

[shibuvp]

ok, sure!
and can you share avocado submit command?
i'm looking to create vcf from a adam file

[fnothaft]

Sure, can do. What genome build are you on?

[shibuvp]

im using hg19.fa with paired fastq file on adam

[fnothaft]

Does your reference build have "chr" suffixes on the chromosome names?

[shibuvp]

no, but when i was trying to visualize the genome with sample adam file and test vcf file using mango genomic browser then i could see the "chr" like chr1, chr2, chr3 etc upto chr22

[fnothaft]

OK, interesting. BTW, what is the approximate coverage of your file?

[shibuvp]

you mean, which file?

[fnothaft]

The aligned reads or FASTQ.

[salimbakker]

I build avocado, build failed and get this error

`- score snp in a read with no evidence of the snp

• score snp in a read with evidence of the snp
• build genotype for het snp
• force call possible STR/indel !!! IGNORED !!!
• log space factorial
• fisher test for strand bias
  2017-07-06 12:15:11 WARN BiallelicGenotyper:149 - Input RDD is not persisted. Performance may be degraded.
• discover and call simple SNP *** FAILED ***
  java.lang.UnsupportedOperationException:
  at org.apache.spark.sql.catalyst.expressions.PrettyAttribute.nullable(namedExpressions.scala:293)
  at org.apache.spark.sql.catalyst.expressions.CreateArray$$anonfun$dataType$3.apply(complexTypeCreator.scala:40)
  at org.apache.spark.sql.catalyst.expressions.CreateArray$$anonfun$dataType$3.apply(complexTypeCreator.scala:40)
  at scala.collection.Iterator$class.exists(Iterator.scala:753)
  at scala.collection.AbstractIterator.exists(Iterator.scala:1157)
  at scala.collection.IterableLike$class.exists(IterableLike.scala:77)
  at scala.collection.AbstractIterable.exists(Iterable.scala:54)
  at org.apache.spark.sql.catalyst.expressions.CreateArray.dataType(complexTypeCreator.scala:40)
  at org.apache.spark.sql.catalyst.expressions.Alias.dataType(namedExpressions.scala:136)
  at org.apache.spark.sql.catalyst.expressions.NamedExpression$class.typeSuffix(namedExpressions.scala:84)
  at org.apache.spark.sql.catalyst.expressions.Alias.typeSuffix(namedExpressions.scala:120)
  at org.apache.spark.sql.catalyst.expressions.Alias.toString(namedExpressions.scala:155)
  at java.lang.String.valueOf(String.java:2994)
  at scala.collection.mutable.StringBuilder.append(StringBuilder.scala:197)
  at scala.collection.TraversableOnce$$anonfun$addString$1.apply(TraversableOnce.scala:327)
  at scala.collection.Iterator$class.foreach(Iterator.scala:727)
  at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
  at scala.collection.TraversableOnce$class.addString(TraversableOnce.scala:320)
  at scala.collection.AbstractIterator.addString(Iterator.scala:1157)
  at scala.collection.TraversableOnce$class.mkString(TraversableOnce.scala:286)
  at scala.collection.AbstractIterator.mkString(Iterator.scala:1157)
  at org.apache.spark.sql.catalyst.expressions.Expression.toString(Expression.scala:219)
  at org.apache.spark.sql.catalyst.expressions.Expression.prettyString(Expression.scala:209)
  at org.apache.spark.sql.Column.named(Column.scala:144)
  at org.apache.spark.sql.DataFrame$$anonfun$select$1$$anonfun$apply$9.apply(DataFrame.scala:708)
  at org.apache.spark.sql.DataFrame$$anonfun$select$1$$anonfun$apply$9.apply(DataFrame.scala:708)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:34)
  at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
  at scala.collection.AbstractTraversable.map(Traversable.scala:105)
  at org.apache.spark.sql.DataFrame$$anonfun$select$1.apply(DataFrame.scala:708)
  at org.apache.spark.sql.DataFrame$$anonfun$select$1.apply(DataFrame.scala:708)
  at org.apache.spark.sql.DataFrame.org$apache$spark$sql$DataFrame$$withPlan(DataFrame.scala:2127)
  at org.apache.spark.sql.DataFrame.select(DataFrame.scala:707)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$readsToObservations$1.apply(BiallelicGenotyper.scala:426)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$readsToObservations$1.apply(BiallelicGenotyper.scala:320)
  at scala.Option.fold(Option.scala:157)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.readsToObservations(BiallelicGenotyper.scala:320)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$call$1.apply(BiallelicGenotyper.scala:109)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$$anonfun$call$1.apply(BiallelicGenotyper.scala:88)
  at scala.Option.fold(Option.scala:157)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.call(BiallelicGenotyper.scala:88)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyper$.discoverAndCall(BiallelicGenotyper.scala:158)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite$$anonfun$11.apply$mcV$sp(BiallelicGenotyperSuite.scala:239)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
  at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
  at org.scalatest.Transformer.apply(Transformer.scala:22)
  at org.scalatest.Transformer.apply(Transformer.scala:20)
  at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
  at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
  at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$runTest(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.runTest(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
  at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
  at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413)
  at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401)
  at scala.collection.immutable.List.foreach(List.scala:318)
  at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401)
  at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396)
  at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483)
  at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208)
  at org.scalatest.FunSuite.runTests(FunSuite.scala:1555)
  at org.scalatest.Suite$class.run(Suite.scala:1424)
  at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.org$scalatest$BeforeAndAfter$$super$run(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.avocado.genotyping.BiallelicGenotyperSuite.run(BiallelicGenotyperSuite.scala:43)
  at org.scalatest.Suite$class.callExecuteOnSuite$1(Suite.scala:1492)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1528)
  at org.scalatest.Suite$$anonfun$runNestedSuites$1.apply(Suite.scala:1526)
  at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
  at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
  at org.scalatest.Suite$class.runNestedSuites(Suite.scala:1526)
  at org.scalatest.tools.DiscoverySuite.runNestedSuites(DiscoverySuite.scala:29)
  at org.scalatest.Suite$class.run(Suite.scala:1421)
  at org.scalatest.tools.DiscoverySuite.run(DiscoverySuite.scala:29)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:318)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  2017-07-06 12:15:18 WARN BiallelicGenotyper:149 - Input RDD is not persisted. Performance may be degraded.
  `

[shibuvp]

sry sir, i really don't know what the approximate coverage is, i'm newbud in the genomics

[fnothaft]

That error is expected on Spark 1.6.2. Can you run ./scripts/move_to_spark2.sh and rebuild?

No worries about the coverage. I'll pull together some default parameters for you in a sec.

[shibuvp]

okey sir

[fnothaft]

https://gist.github.com/fnothaft/627f4e295f9400cff453b6c3f671fd7d should be a reasonable set of default parameters. Let me know if you run into any problems!

[shibuvp]

okey thanks sir!

[shibuvp]

can i use adam file as input reads?

[fnothaft]

Yup, ADAM and SAM/BAM/CRAM are both fine.

[shibuvp]

ok, i will try
and i'm looking to load reads from hdfs, i think it wouldn't be a problem, ryt?

[salimbakker]

Thanks sir avocado build success

[fnothaft]

You're welcome—glad to hear it!

[shibuvp]

i'm getting this error while running avocado

command is,

./bin/avocado-submit biallelicGenotyper hdfs://master.hdp:8020/sample/salim3.adam hdfs://master.hdp:8020/vcfoutput/salim3.vcf -is_not_grc -min_genotype_quality 10 -min_phred_to_discover_variant 15 -min_observations_to_discover_variant 3 -min_het_indel_quality_by_depth -1.0 -min_hom_indel_quality_by_depth -1.0 -min_het_indel_allelic_fraction 0.2 -min_het_snp_allelic_fraction 0.125 -max_het_snp_allelic_fraction 0.8 -max_het_indel_allelic_fraction 0.85 -min_indel_rms_mapping_quality 30 -min_het_snp_quality_by_depth 2.5

[shibuvp]

is it the problem of scala version?

[fnothaft]

That's an odd error; I don't think I've seen it before. Did you compile for Scala 2.10 or 2.11? The Spark 2.x pre-built distributions are packaged for Scala 2.11, so I'd generally recommend building for Scala 2.11.

[shibuvp]

oh .. i have scala 2.10 on my cluster

[shibuvp]

@fnothaft i was changed the scala version into 2.11.8 for spark 2.1.0, but the error is still same!

[shibuvp]

the issue i found in my cluster was, the version of scala. It was 2.11.8 whereas pom.xml in avocado contains scala of 2.10.4 . So i had changed the pom.xml file scala version into 2.11.8 and give rebuild , but it shows error and build getting failed.

[root@master avocado]# mvn package
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core-spark2_2.10:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.10 ---
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.10 ---
[INFO] Source directory: /opt/avocado/src/main/scala added.
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.10 ---
[INFO] Modified 0 of 47 .scala files
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.10 ---
[INFO] No sources to compile
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.10 ---
[INFO] Test Source directory: /opt/avocado/src/test/scala added.
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.10 ---
[INFO] No sources to compile
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core-spark2_2.10 ---
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core-spark2_2.10 ---
[INFO] Source directory: /opt/avocado/avocado-core/src/main/scala added.
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core-spark2_2.10 ---
[INFO] Modified 0 of 41 .scala files
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /opt/avocado/avocado-core/src/main/resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core-spark2_2.10 ---
[WARNING] Expected all dependencies to require Scala version: 2.11.8
[WARNING] org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core-spark2_2.10 ---
[INFO] Test Source directory: /opt/avocado/avocado-core/src/test/scala added.
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 25 resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core-spark2_2.10 ---
[WARNING] Expected all dependencies to require Scala version: 2.11.8
[WARNING] org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] /opt/avocado/avocado-core/src/test/scala:-1: info: compiling
[INFO] Compiling 19 source files to /opt/avocado/avocado-core/target/scala-2.11.8/test-classes at 1499681179372
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:81: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(state === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:82: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(qual, 20.0, tol = 1e-3))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:89: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(state === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:90: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(qual, 30.0, tol = 1e-3))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:97: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(state === 3)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:98: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(qual, 40.0, tol = 1e-3))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:103: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(perfectScores.isEmpty)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:106: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpScores.isEmpty)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:112: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(scores.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:116: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpVariant.toVariant === snp)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:117: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.squareMapQ === 50 * 50)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:118: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.alleleCoverage === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:119: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.otherCoverage === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:120: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.alleleForwardStrand === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:121: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.otherForwardStrand === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:122: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.copyNumber === 2)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:123: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.referenceLogLikelihoods(0), os.logL(0, 2, 0.9999, 0.99999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:124: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.referenceLogLikelihoods(1), os.logL(1, 2, 0.9999, 0.99999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:125: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.referenceLogLikelihoods(2), os.logL(2, 2, 0.9999, 0.99999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:131: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(scores.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:135: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpVariant.toVariant === snp)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:136: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.squareMapQ === 40 * 40)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:137: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.alleleCoverage === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:138: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.otherCoverage === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:139: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.alleleForwardStrand === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:140: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.otherForwardStrand === 0)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:141: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(snpObservation.copyNumber === 2)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:142: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.alleleLogLikelihoods(0), os.logL(0, 2, 0.9999, 0.9999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:143: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.alleleLogLikelihoods(1), os.logL(1, 2, 0.9999, 0.9999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:144: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(snpObservation.alleleLogLikelihoods(2), os.logL(2, 2, 0.9999, 0.9999)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:157: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getVariant === snp)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:158: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStart === snp.getStart)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:159: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getEnd === snp.getEnd)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:160: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getContigName === snp.getContigName)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:161: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getSampleId === "sample")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:162: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getGenotypeQuality === 73)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:163: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getAlleles.size === 2)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:164: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getAlleles.get(0) === GenotypeAllele.ALT)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:165: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getAlleles.get(1) === GenotypeAllele.REF)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:166: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getReferenceReadDepth === 9)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:167: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getAlternateReadDepth === 7)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:168: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStrandBiasComponents.size === 4)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:169: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStrandBiasComponents.get(0) === 5)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:170: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStrandBiasComponents.get(1) === 4)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:171: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStrandBiasComponents.get(2) === 3)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:172: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getStrandBiasComponents.get(3) === 4)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:173: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(genotype.getGenotypeLikelihoods.size === 3)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:187: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(variants.rdd.count === 3)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:194: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gts.size === 3)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:195: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gts.map(.getReadDepth).toSet.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:199: error: can't expand macros compiled by previous versions of Scala
[ERROR] }) === 2)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:205: error: can't expand macros compiled by previous versions of Scala
[ERROR] .length === 9)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:210: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(fact0, 0.0))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:213: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(fact1, 0.0))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:216: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(fact5, log(120.0)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:220: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(fact10, log(6227020800L.toDouble)))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:226: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(phredPBias1, 22.185272))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:229: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(MathUtils.fpEquals(phredPBias2, 44.729904))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:250: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gts.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:252: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getStart === 225057L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:253: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getEnd === 225058L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:254: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getReferenceAllele === "A")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:255: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getAlternateAllele === "G")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:256: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.count( == GenotypeAllele.REF) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:257: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.count(_ == GenotypeAllele.ALT) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:283: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gts.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:285: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getStart === 832735L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:286: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getEnd === 832736L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:287: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getReferenceAllele === "A")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:288: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getAlternateAllele === "AGTTTT")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:289: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.count(_ == GenotypeAllele.REF) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:290: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.count(_ == GenotypeAllele.ALT) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:328: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(homGt.getVariant.getStart === 839355L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:329: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(homGt.getVariant.getEnd === 839356L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:330: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(homGt.getVariant.getReferenceAllele === "A")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:331: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(homGt.getVariant.getAlternateAllele === "C")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:341: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(reads.rdd.count === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:352: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(variants.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:357: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(obs.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:377: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(variants.rdd.count === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:381: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:384: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:403: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(variants.rdd.count === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:407: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:410: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:422: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:425: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getStart === 1777262L)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:426: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getReferenceAllele === "TACACACACACACACACACACACACACACAC")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:427: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getVariant.getAlternateAllele === "T")
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:428: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:440: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:443: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:458: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:461: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:476: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:479: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:495: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gtArray.size === 2)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:501: error: can't expand macros compiled by previous versions of Scala
[ERROR] }) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:507: error: can't expand macros compiled by previous versions of Scala
[ERROR] }) === 1)
[ERROR] ^
[ERROR] /opt/avocado/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala:509: error: can't expand macros compiled by previous versions of Scala
[ERROR] assert(gt.getAlleles.forall(_ == GenotypeAllele.ALT))
[ERROR] ^
[ERROR] 836 errors found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] avocado: A Variant Caller, Distributed ............. SUCCESS [ 2.267 s]
[INFO] avocado-core: Core variant calling algorithms ...... FAILURE [ 8.429 s]
[INFO] avocado-cli: Command line interface for a distributed variant caller SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 10.820 s
[INFO] Finished at: 2017-07-10T15:36:24+05:30
[INFO] Final Memory: 31M/570M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) on project avocado-core-spark2_2.10: wrap: org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1) -> [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 -rf :avocado-core-spark2_2.10
[root@master avocado]#

can you please check it @fnothaft ?