FailedConsole Output

Skipping 3,340 KB.. Full Log
erShuffleRegionJoinAndGroupByLeft.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/DefaultHeaderLines$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/converters/VariantContextConverter$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/javadocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/javadocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/python/DataFrameConversionWrapper.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToReadDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToCoverageDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToReadsConverter.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentRecordsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToAlignmentRecordsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentRecordsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentRecordDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentRecordsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToGenotypeDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentRecordsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentRecordsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToFragmentDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentRecordsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentRecordsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentRecordsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToSliceDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentRecordsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantContextConverter.html longer than 100 characters.
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[INFO] Building zip: /tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.12-0.28.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  9.201 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  4.856 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  5.011 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:10 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  9.989 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 12.256 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 17.498 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:30 min]
[INFO] ADAM_2.12: R APIs .................................. SUCCESS [ 55.306 s]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 44.437 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:20 min
[INFO] Finished at: 2019-06-28T15:39:57-07:00
[INFO] Final Memory: 66M/1495M
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ grep egg
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.12-0.28.0-SNAPSHOT-bin.tar.gz
drwxrwxr-x jenkins/jenkins        0 2019-06-28 15:36 adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 36792621 2019-06-28 15:36 adam-distribution-spark2_2.12-0.28.0-SNAPSHOT/repo/bdgenomics.adam-0.28.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/pyspark
2019-06-28 15:40:00 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-06-28 15:40:00 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-06-28 15:40:01 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2019-06-28 15:40:06 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3
++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y -n adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-3ba96dae-d13c-4aa2-b592-a4411e7516b3:

The following packages will be REMOVED:

    ca-certificates: 2019.5.15-0            
    certifi:         2019.6.16-py36_0       
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       9.1.0-hdf63c60_0       
    libstdcxx-ng:    9.1.0-hdf63c60_0       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1c-h7b6447c_1      
    pip:             19.1.1-py36_0          
    python:          3.6.8-h0371630_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py36_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.4-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ make clean
pip uninstall -y adam
Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
	
# define filenames
BAM=mouse_chrM.bam
+ BAM=mouse_chrM.bam
READS=${BAM}.reads.adam
+ READS=mouse_chrM.bam.reads.adam
SORTED_READS=${BAM}.reads.sorted.adam
+ SORTED_READS=mouse_chrM.bam.reads.sorted.adam
FRAGMENTS=${BAM}.fragments.adam
+ FRAGMENTS=mouse_chrM.bam.fragments.adam
    
# fetch our input dataset
echo "Fetching BAM file"
+ echo 'Fetching BAM file'
Fetching BAM file
rm -rf ${BAM}
+ rm -rf mouse_chrM.bam
wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}
+ wget -q https://s3.amazonaws.com/bdgenomics-test/mouse_chrM.bam

# once fetched, convert BAM to ADAM
echo "Converting BAM to ADAM read format"
+ echo 'Converting BAM to ADAM read format'
Converting BAM to ADAM read format
rm -rf ${READS}
+ rm -rf mouse_chrM.bam.reads.adam
${ADAM} transformAlignments ${BAM} ${READS}
+ ./bin/adam-submit transformAlignments mouse_chrM.bam mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/06/28 15:40:22 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/06/28 15:40:22 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/06/28 15:40:22 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/06/28 15:40:22 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "mouse_chrM.bam" "mouse_chrM.bam.reads.adam"
19/06/28 15:40:23 INFO spark.SparkContext: Running Spark version 2.4.3
19/06/28 15:40:23 INFO spark.SparkContext: Submitted application: transformAlignments
19/06/28 15:40:23 INFO spark.SecurityManager: Changing view acls to: jenkins
19/06/28 15:40:23 INFO spark.SecurityManager: Changing modify acls to: jenkins
19/06/28 15:40:23 INFO spark.SecurityManager: Changing view acls groups to: 
19/06/28 15:40:23 INFO spark.SecurityManager: Changing modify acls groups to: 
19/06/28 15:40:23 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/06/28 15:40:23 INFO util.Utils: Successfully started service 'sparkDriver' on port 42963.
19/06/28 15:40:23 INFO spark.SparkEnv: Registering MapOutputTracker
19/06/28 15:40:23 INFO spark.SparkEnv: Registering BlockManagerMaster
19/06/28 15:40:23 INFO storage.BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/06/28 15:40:23 INFO storage.BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/06/28 15:40:23 INFO storage.DiskBlockManager: Created local directory at /tmp/blockmgr-f0d7976c-df09-42ef-8063-487956109617
19/06/28 15:40:23 INFO memory.MemoryStore: MemoryStore started with capacity 366.3 MB
19/06/28 15:40:23 INFO spark.SparkEnv: Registering OutputCommitCoordinator
19/06/28 15:40:23 INFO util.log: Logging initialized @2321ms
19/06/28 15:40:23 INFO server.Server: jetty-9.3.z-SNAPSHOT, build timestamp: unknown, git hash: unknown
19/06/28 15:40:23 INFO server.Server: Started @2393ms
19/06/28 15:40:23 INFO server.AbstractConnector: Started ServerConnector@1af7f54a{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/06/28 15:40:23 INFO util.Utils: Successfully started service 'SparkUI' on port 4040.
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f0628de{/jobs,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@2b27cc70{/jobs/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6f6a7463{/jobs/job,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@79f227a9{/jobs/job/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6ca320ab{/stages,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50d68830{/stages/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@1e53135d{/stages/stage,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6754ef00{/stages/stage/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@619bd14c{/stages/pool,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@323e8306{/stages/pool/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@a23a01d{/storage,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4acf72b6{/storage/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@7561db12{/storage/rdd,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3301500b{/storage/rdd/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@24b52d3e{/environment,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@15deb1dc{/environment/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@6e9c413e{/executors,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@57a4d5ee{/executors/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@5af5def9{/executors/threadDump,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@3a45c42a{/executors/threadDump/json,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@36dce7ed{/static,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4b770e40{/,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@78e16155{/api,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@19868320{/jobs/job/kill,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@50b0bc4c{/stages/stage/kill,null,AVAILABLE,@Spark}
19/06/28 15:40:23 INFO ui.SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4040
19/06/28 15:40:23 INFO spark.SparkContext: Added JAR file:/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar at spark://192.168.10.27:42963/jars/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar with timestamp 1561761623803
19/06/28 15:40:23 INFO executor.Executor: Starting executor ID driver on host localhost
19/06/28 15:40:23 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 46635.
19/06/28 15:40:23 INFO netty.NettyBlockTransferService: Server created on 192.168.10.27:46635
19/06/28 15:40:23 INFO storage.BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/06/28 15:40:23 INFO storage.BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 46635, None)
19/06/28 15:40:23 INFO storage.BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:46635 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 46635, None)
19/06/28 15:40:23 INFO storage.BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 46635, None)
19/06/28 15:40:24 INFO storage.BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 46635, None)
19/06/28 15:40:24 INFO handler.ContextHandler: Started o.s.j.s.ServletContextHandler@4c9e38{/metrics/json,null,AVAILABLE,@Spark}
19/06/28 15:40:24 INFO rdd.ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
19/06/28 15:40:24 INFO rdd.ADAMContext: Loaded header from file:/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
19/06/28 15:40:25 INFO memory.MemoryStore: Block broadcast_0 stored as values in memory (estimated size 295.6 KB, free 366.0 MB)
19/06/28 15:40:25 INFO memory.MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 24.0 KB, free 366.0 MB)
19/06/28 15:40:25 INFO storage.BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.27:46635 (size: 24.0 KB, free: 366.3 MB)
19/06/28 15:40:25 INFO spark.SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2059
19/06/28 15:40:26 INFO read.RDDBoundAlignmentRecordDataset: Saving data in ADAM format
19/06/28 15:40:26 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/06/28 15:40:26 INFO input.FileInputFormat: Total input paths to process : 1
19/06/28 15:40:27 INFO spark.SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Parents of final stage: List()
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Missing parents: List()
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
19/06/28 15:40:27 INFO memory.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 85.6 KB, free 365.9 MB)
19/06/28 15:40:27 INFO memory.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.6 KB, free 365.9 MB)
19/06/28 15:40:27 INFO storage.BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.27:46635 (size: 31.6 KB, free: 366.2 MB)
19/06/28 15:40:27 INFO spark.SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
19/06/28 15:40:27 INFO scheduler.DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
19/06/28 15:40:27 INFO scheduler.TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
19/06/28 15:40:27 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7441 bytes)
19/06/28 15:40:27 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
19/06/28 15:40:27 INFO executor.Executor: Fetching spark://192.168.10.27:42963/jars/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar with timestamp 1561761623803
19/06/28 15:40:27 INFO client.TransportClientFactory: Successfully created connection to /192.168.10.27:42963 after 27 ms (0 ms spent in bootstraps)
19/06/28 15:40:27 INFO util.Utils: Fetching spark://192.168.10.27:42963/jars/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar to /tmp/spark-08e2ca69-8db4-4d69-8cab-332a627e1265/userFiles-9a2090f0-b880-4a46-9241-acfb01f89cc5/fetchFileTemp3206002033830503017.tmp
19/06/28 15:40:27 INFO executor.Executor: Adding file:/tmp/spark-08e2ca69-8db4-4d69-8cab-332a627e1265/userFiles-9a2090f0-b880-4a46-9241-acfb01f89cc5/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar to class loader
19/06/28 15:40:27 INFO rdd.NewHadoopRDD: Input split: file:/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
19/06/28 15:40:27 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/06/28 15:40:27 INFO codec.CodecConfig: Compression: GZIP
19/06/28 15:40:27 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Parquet block size to 134217728
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Parquet page size to 1048576
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Parquet dictionary page size to 1048576
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Dictionary is on
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Validation is off
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Writer version is: PARQUET_1_0
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Page size checking is: estimated
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Min row count for page size check is: 100
19/06/28 15:40:27 INFO hadoop.ParquetOutputFormat: Max row count for page size check is: 10000
19/06/28 15:40:27 INFO compress.CodecPool: Got brand-new compressor [.gz]
Ignoring SAM validation error: ERROR: Record 162622, Read name 613F0AAXX100423:3:58:9979:16082, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162624, Read name 613F0AAXX100423:6:13:3141:11793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162625, Read name 613F0AAXX100423:8:39:18592:13552, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162635, Read name 613F1AAXX100423:7:2:13114:10698, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162637, Read name 613F1AAXX100423:6:100:8840:11167, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162639, Read name 613F1AAXX100423:8:15:10944:11181, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162640, Read name 613F1AAXX100423:8:17:5740:10104, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162651, Read name 613F1AAXX100423:1:53:11097:8261, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162654, Read name 613F1AAXX100423:2:112:16779:19612, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162657, Read name 613F0AAXX100423:8:28:7084:17683, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162659, Read name 613F0AAXX100423:8:39:19796:12794, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162662, Read name 613F1AAXX100423:5:116:9339:3264, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162667, Read name 613F0AAXX100423:4:67:2015:3054, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162669, Read name 613F0AAXX100423:7:7:11297:11738, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162674, Read name 613F0AAXX100423:6:59:10490:20829, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162678, Read name 613F1AAXX100423:8:11:17603:4766, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162682, Read name 613F0AAXX100423:5:86:10814:10257, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162683, Read name 613F0AAXX100423:5:117:14178:6111, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162685, Read name 613F0AAXX100423:2:3:13563:6720, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162689, Read name 613F0AAXX100423:7:59:16009:15799, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162696, Read name 613F0AAXX100423:5:31:9663:18252, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162698, Read name 613F1AAXX100423:2:27:12264:14626, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162699, Read name 613F0AAXX100423:1:120:19003:6647, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162702, Read name 613F1AAXX100423:3:37:6972:18407, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162704, Read name 613F1AAXX100423:3:77:6946:3880, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162706, Read name 613F0AAXX100423:7:48:2692:3492, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162708, Read name 613F1AAXX100423:7:80:8790:1648, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162710, Read name 6141AAAXX100423:5:30:15036:17610, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162712, Read name 613F1AAXX100423:8:80:6261:4465, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162713, Read name 6141AAAXX100423:5:74:5542:6195, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162715, Read name 613F1AAXX100423:5:14:14844:13639, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162718, Read name 613F1AAXX100423:7:112:14569:8480, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162725, Read name 613F1AAXX100423:4:56:10160:9879, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162727, Read name 6141AAAXX100423:7:89:12209:9221, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162731, Read name 6141AAAXX100423:6:55:1590:19793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162732, Read name 6141AAAXX100423:7:102:16679:12368, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162734, Read name 613F1AAXX100423:2:7:4909:18472, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162737, Read name 6141AAAXX100423:4:73:6574:10572, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162741, Read name 6141AAAXX100423:1:8:14113:12655, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162743, Read name 6141AAAXX100423:3:40:7990:5056, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162744, Read name 6141AAAXX100423:4:36:15793:3411, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162745, Read name 6141AAAXX100423:8:83:1139:18985, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162746, Read name 6141AAAXX100423:5:7:18196:13562, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162748, Read name 6141AAAXX100423:3:114:5639:7123, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162751, Read name 6141AAAXX100423:7:47:4898:8640, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162753, Read name 6141AAAXX100423:3:64:8064:8165, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162756, Read name 613F1AAXX100423:1:105:14386:1684, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162757, Read name 613F1AAXX100423:6:98:1237:19470, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162761, Read name 613F1AAXX100423:7:106:19658:9261, MAPQ should be 0 for unmapped read.
19/06/28 15:40:37 INFO hadoop.InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
19/06/28 15:40:38 INFO output.FileOutputCommitter: Saved output of task 'attempt_20190628154026_0002_r_000000_0' to file:/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20190628154026_0002_r_000000
19/06/28 15:40:38 INFO mapred.SparkHadoopMapRedUtil: attempt_20190628154026_0002_r_000000_0: Committed
19/06/28 15:40:38 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 856 bytes result sent to driver
19/06/28 15:40:38 INFO scheduler.TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 10927 ms on localhost (executor driver) (1/1)
19/06/28 15:40:38 INFO scheduler.TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
19/06/28 15:40:38 INFO scheduler.DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 11.063 s
19/06/28 15:40:38 INFO scheduler.DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.130683 s
19/06/28 15:40:38 INFO hadoop.ParquetFileReader: Initiating action with parallelism: 5
19/06/28 15:40:38 INFO io.SparkHadoopWriter: Job job_20190628154026_0002 committed.
19/06/28 15:40:38 INFO cli.TransformAlignments: Overall Duration: 15.3 secs
19/06/28 15:40:38 INFO spark.SparkContext: Invoking stop() from shutdown hook
19/06/28 15:40:38 INFO server.AbstractConnector: Stopped Spark@1af7f54a{HTTP/1.1,[http/1.1]}{0.0.0.0:4040}
19/06/28 15:40:38 INFO ui.SparkUI: Stopped Spark web UI at http://192.168.10.27:4040
19/06/28 15:40:38 INFO spark.MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/06/28 15:40:38 INFO memory.MemoryStore: MemoryStore cleared
19/06/28 15:40:38 INFO storage.BlockManager: BlockManager stopped
19/06/28 15:40:38 INFO storage.BlockManagerMaster: BlockManagerMaster stopped
19/06/28 15:40:38 INFO scheduler.OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/06/28 15:40:38 INFO spark.SparkContext: Successfully stopped SparkContext
19/06/28 15:40:38 INFO util.ShutdownHookManager: Shutdown hook called
19/06/28 15:40:38 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-0082255e-bbbf-4359-84ff-e997803a838a
19/06/28 15:40:38 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-08e2ca69-8db4-4d69-8cab-332a627e1265

# then, sort the BAM
echo "Converting BAM to ADAM read format with sorting"
+ echo 'Converting BAM to ADAM read format with sorting'
Converting BAM to ADAM read format with sorting
rm -rf ${SORTED_READS}
+ rm -rf mouse_chrM.bam.reads.sorted.adam
${ADAM} transformAlignments -sort_reads ${READS} ${SORTED_READS}
+ ./bin/adam-submit transformAlignments -sort_reads mouse_chrM.bam.reads.adam mouse_chrM.bam.reads.sorted.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestJ8GJ19q/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/bin/spark-submit
19/06/28 15:40:40 WARN util.Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/06/28 15:40:40 WARN util.Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/06/28 15:40:40 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
19/06/28 15:40:40 INFO cli.ADAMMain: ADAM invoked with args: "transformAlignments" "-sort_reads" "mouse_chrM.bam.reads.adam" "mouse_chrM.bam.reads.sorted.adam"
"-sort_reads" is not a valid option
 INPUT                                                                     : The ADAM, BAM or SAM file to apply the transforms to
 OUTPUT                                                                    : Location to write the transformed data in ADAM/Parquet format
 -add_md_tags VAL                                                          : Add MD Tags to reads based on the FASTA (or equivalent) file passed to
                                                                             this option.
 -aligned_read_predicate                                                   : Only load aligned reads. Only works for Parquet files. Exclusive of
                                                                             region predicate. (default: false)
 -bin_quality_scores VAL                                                   : Rewrites quality scores of reads into bins from a string of bin
                                                                             descriptions, e.g. 0,20,10;20,40,30.
 -cache                                                                    : Cache data to avoid recomputing between stages. (default: false)
 -coalesce N                                                               : Set the number of partitions written to the ADAM output directory
                                                                             (default: -1)
 -concat VAL                                                               : Concatenate this file with <INPUT> and write the result to <OUTPUT>
 -defer_merging                                                            : Defers merging single file output (default: false)
 -disable_fast_concat                                                      : Disables the parallel file concatenation engine. (default: false)
 -disable_pg                                                               : Disable writing a new @PG line. (default: false)
 -force_load_bam                                                           : Forces TransformAlignments to load from BAM/SAM. (default: false)
 -force_load_fastq                                                         : Forces TransformAlignments to load from unpaired FASTQ. (default: false)
 -force_load_ifastq                                                        : Forces TransformAlignments to load from interleaved FASTQ. (default:
                                                                             false)
 -force_load_parquet                                                       : Forces TransformAlignments to load from Parquet. (default: false)
 -force_shuffle_coalesce                                                   : Even if the repartitioned RDD has fewer partitions, force a shuffle.
                                                                             (default: false)
 -h (-help, --help, -?)                                                    : Print help (default: false)
 -known_indels VAL                                                         : VCF file including locations of known INDELs. If none is provided,
                                                                             default consensus model will be used.
 -known_snps VAL                                                           : Sites-only VCF giving location of known SNPs
 -limit_projection                                                         : Only project necessary fields. Only works for Parquet files. (default:
                                                                             false)
 -log_odds_threshold N                                                     : The log-odds threshold for accepting a realignment. Default value is
                                                                             5.0. (default: 5.0)
 -mark_duplicate_reads                                                     : Mark duplicate reads (default: false)
 -max_consensus_number N                                                   : The maximum number of consensus to try realigning a target region to.
                                                                             Default value is 30. (default: 30)
 -max_indel_size N                                                         : The maximum length of an INDEL to realign to. Default value is 500.
                                                                             (default: 500)
 -max_read_length N                                                        : Maximum FASTQ read length, defaults to 10,000 base pairs (bp). (default:
                                                                             0)
 -max_reads_per_target N                                                   : The maximum number of reads attached to a target considered for
                                                                             realignment. Default is 20000. (default: 20000)
 -max_target_size N                                                        : The maximum length of a target region to attempt realigning. Default
                                                                             length is 3000. (default: 3000)
 -md_tag_fragment_size N                                                   : When adding MD tags to reads, load the reference in fragments of this
                                                                             size. (default: 1000000)
 -md_tag_overwrite                                                         : When adding MD tags to reads, overwrite existing incorrect tags.
                                                                             (default: false)
 -min_acceptable_quality N                                                 : Minimum acceptable quality for recalibrating a base in a read. Default
                                                                             is 5. (default: 5)
 -paired_fastq VAL                                                         : When converting two (paired) FASTQ files to ADAM, pass the path to the
                                                                             second file here.
 -parquet_block_size N                                                     : Parquet block size (default = 128mb) (default: 134217728)
 -parquet_compression_codec [UNCOMPRESSED | SNAPPY | GZIP | LZO | BROTLI   : Parquet compression codec (default: GZIP)
 | LZ4 | ZSTD]                                                                
 -parquet_disable_dictionary                                               : Disable dictionary encoding (default: false)
 -parquet_logging_level VAL                                                : Parquet logging level (default = severe) (default: SEVERE)
 -parquet_page_size N                                                      : Parquet page size (default = 1mb) (default: 1048576)
 -partition_bin_size N                                                     : Partition bin size used in Hive-style partitioning. Defaults to 1Mbp
                                                                             (1,000,000) base pairs). (default: 1000000)
 -partition_by_start_pos                                                   : Save the data partitioned by genomic range bins based on start pos using
                                                                             Hive-style partitioning. (default: false)
 -print_metrics                                                            : Print metrics to the log on completion (default: false)
 -read_group VAL                                                           : Set converted FASTQs' read-group identifiers to this value; if
                                                                             empty-string is passed, use the basename of the input file, minus the
                                                                             extension.
 -realign_indels                                                           : Locally realign indels present in reads. (default: false)
 -recalibrate_base_qualities                                               : Recalibrate the base quality scores (ILLUMINA only) (default: false)
 -reference VAL                                                            : Path to a reference file to use for indel realignment.
 -region_predicate VAL                                                     : Only load a specific range of regions. Mutually exclusive with aligned
                                                                             read predicate.
 -repartition N                                                            : Set the number of partitions to map data to (default: -1)
 -sampling_fraction N                                                      : Fraction of reads to sample during recalibration; omitted by default.
                                                                             (default: 0.0)
 -sampling_seed N                                                          : Seed to use when sampling during recalibration; omitted by default by
                                                                             setting to 0 (thus, 0 is an invalid seed). (default: 0)
 -single                                                                   : Saves OUTPUT as single file (default: false)
 -sort_by_read_name                                                        : Sort alignments by read name. (default: false)
 -sort_by_reference_position                                               : Sort alignments by reference position, with references ordered by name.
                                                                             (default: false)
 -sort_by_reference_position_and_index                                     : Sort alignments by reference position, with references ordered by index.
                                                                             (default: false)
 -sort_fastq_output                                                        : Sets whether to sort the FASTQ output, if saving as FASTQ. False by
                                                                             default. Ignored if not saving as FASTQ. (default: false)
 -storage_level VAL                                                        : Set the storage level to use for caching. (default: MEMORY_ONLY)
 -stringency VAL                                                           : Stringency level for various checks; can be SILENT, LENIENT, or STRICT.
                                                                             Defaults to LENIENT (default: LENIENT)
 -unclip_reads                                                             : If true, unclips reads during realignment. (default: false)
19/06/28 15:40:40 INFO util.ShutdownHookManager: Shutdown hook called
19/06/28 15:40:40 INFO util.ShutdownHookManager: Deleting directory /tmp/spark-1801f72b-023d-415c-9589-01812046c605
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/c4ae03ebb16f949fccd194b443f390e0d2bd9db1
Finished: FAILURE