FailedConsole Output

Skipping 2,719 KB.. Full Log
ibution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/python/DataFrameConversionWrapper.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToAlignmentDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToSequenceDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToCoverageDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToVariantContextDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToReadDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFragmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantContextsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToGenotypeDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ToSliceDatasetConversion.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantContextsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToFeaturesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToSlicesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToFragmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToFeatureConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/JavaADAMContext$.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SlicesToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/SequencesToCoverageDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToAlignmentsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FragmentsToSequencesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToSequencesDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToCoverageConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/CoverageToGenotypesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToAlignmentsConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToReadsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/ReadsToSlicesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/FeaturesToVariantContextConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/GenotypesToVariantsDatasetConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/AlignmentsToFeaturesConverter.html longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/api/java/VariantsToAlignmentsConverter.html longer than 100 characters.
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[INFO] Building zip: /tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.30.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  8.977 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  4.859 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:22 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  8.964 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 11.099 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 11.463 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:41 min]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [01:03 min]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 46.581 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:39 min
[INFO] Finished at: 2020-01-24T10:35:08-08:00
[INFO] Final Memory: 88M/1401M
[INFO] ------------------------------------------------------------------------
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.30.0-SNAPSHOT-bin.tar.gz
+ grep bdgenomics.adam
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-01-24 10:31 adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 57067251 2020-01-24 10:31 adam-distribution-spark2_2.11-0.30.0-SNAPSHOT/repo/bdgenomics.adam-0.30.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/pyspark
2020-01-24 10:35:11 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2020-01-24 10:35:11 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-01-24 10:35:12 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).
2020-01-24 10:35:19 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-d1992d4a-f0b3-49b9-9230-f76d5405efe8/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8/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/2.11/SPARK_VERSION/2.4.4/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 $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8
++ 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-d1992d4a-f0b3-49b9-9230-f76d5405efe8 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-d1992d4a-f0b3-49b9-9230-f76d5405efe8:

The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2019.11.27-0           
    certifi:          2019.11.28-py36_0      
    ld_impl_linux-64: 2.33.1-h53a641e_7      
    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:          1.1.1d-h7b6447c_3      
    pip:              19.3.1-py36_0          
    python:           3.6.10-h0371630_0      
    readline:         7.0-h7b6447c_5         
    setuptools:       44.0.0-py36_0          
    sqlite:           3.30.1-h7b6447c_0      
    tk:               8.6.8-hbc83047_0       
    wheel:            0.33.6-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/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
pip uninstall -y adam
Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
rm -rf dist/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit
20/01/24 10:35:35 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
20/01/24 10:35:35 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/01/24 10:35:36 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/01/24 10:35:36 INFO SparkContext: Running Spark version 2.4.4
20/01/24 10:35:36 INFO SparkContext: Submitted application: transformAlignments
20/01/24 10:35:36 INFO SecurityManager: Changing view acls to: jenkins
20/01/24 10:35:36 INFO SecurityManager: Changing modify acls to: jenkins
20/01/24 10:35:36 INFO SecurityManager: Changing view acls groups to: 
20/01/24 10:35:36 INFO SecurityManager: Changing modify acls groups to: 
20/01/24 10:35:36 INFO 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()
20/01/24 10:35:37 INFO Utils: Successfully started service 'sparkDriver' on port 38379.
20/01/24 10:35:37 INFO SparkEnv: Registering MapOutputTracker
20/01/24 10:35:37 INFO SparkEnv: Registering BlockManagerMaster
20/01/24 10:35:37 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/01/24 10:35:37 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/01/24 10:35:37 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-00fe8f31-e7a8-4c0b-85a9-313723415f2f
20/01/24 10:35:37 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/01/24 10:35:37 INFO SparkEnv: Registering OutputCommitCoordinator
20/01/24 10:35:37 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/01/24 10:35:37 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.32:4040
20/01/24 10:35:37 INFO SparkContext: Added JAR file:/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar at spark://192.168.10.32:38379/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1579890937571
20/01/24 10:35:37 INFO Executor: Starting executor ID driver on host localhost
20/01/24 10:35:37 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 38802.
20/01/24 10:35:37 INFO NettyBlockTransferService: Server created on 192.168.10.32:38802
20/01/24 10:35:37 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/01/24 10:35:37 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.32, 38802, None)
20/01/24 10:35:37 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.32:38802 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.32, 38802, None)
20/01/24 10:35:37 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.32, 38802, None)
20/01/24 10:35:37 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.32, 38802, None)
20/01/24 10:35:38 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/01/24 10:35:38 INFO ADAMContext: Loaded header from file:/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/01/24 10:35:39 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
20/01/24 10:35:39 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
20/01/24 10:35:39 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.10.32:38802 (size: 23.1 KB, free: 366.3 MB)
20/01/24 10:35:39 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2058
20/01/24 10:35:41 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/01/24 10:35:41 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/24 10:35:41 INFO FileInputFormat: Total input paths to process : 1
20/01/24 10:35:41 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/01/24 10:35:41 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/01/24 10:35:41 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/01/24 10:35:41 INFO DAGScheduler: Parents of final stage: List()
20/01/24 10:35:41 INFO DAGScheduler: Missing parents: List()
20/01/24 10:35:41 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814), which has no missing parents
20/01/24 10:35:41 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.0 KB, free 365.9 MB)
20/01/24 10:35:41 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.2 KB, free 365.9 MB)
20/01/24 10:35:41 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.10.32:38802 (size: 30.2 KB, free: 366.2 MB)
20/01/24 10:35:41 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1161
20/01/24 10:35:41 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3814) (first 15 tasks are for partitions Vector(0))
20/01/24 10:35:41 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/01/24 10:35:41 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
20/01/24 10:35:41 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/01/24 10:35:41 INFO Executor: Fetching spark://192.168.10.32:38379/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar with timestamp 1579890937571
20/01/24 10:35:42 INFO TransportClientFactory: Successfully created connection to /192.168.10.32:38379 after 273 ms (0 ms spent in bootstraps)
20/01/24 10:35:42 INFO Utils: Fetching spark://192.168.10.32:38379/jars/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to /tmp/spark-030a2694-a0cc-4b8b-9776-9a23221004fa/userFiles-80527dfb-9079-4cb9-a3a2-1b2a21dca6f0/fetchFileTemp6669183595505826167.tmp
20/01/24 10:35:42 INFO Executor: Adding file:/tmp/spark-030a2694-a0cc-4b8b-9776-9a23221004fa/userFiles-80527dfb-9079-4cb9-a3a2-1b2a21dca6f0/adam-assembly-spark2_2.11-0.30.0-SNAPSHOT.jar to class loader
20/01/24 10:35:42 INFO NewHadoopRDD: Input split: file:/tmp/adamTestq6PY3D0/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/01/24 10:35:42 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/24 10:35:42 INFO CodecConfig: Compression: GZIP
20/01/24 10:35:42 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/01/24 10:35:42 INFO ParquetOutputFormat: Parquet block size to 134217728
20/01/24 10:35:42 INFO ParquetOutputFormat: Parquet page size to 1048576
20/01/24 10:35:42 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/01/24 10:35:42 INFO ParquetOutputFormat: Dictionary is on
20/01/24 10:35:42 INFO ParquetOutputFormat: Validation is off
20/01/24 10:35:42 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/01/24 10:35:42 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/01/24 10:35:42 INFO ParquetOutputFormat: Page size checking is: estimated
20/01/24 10:35:42 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/01/24 10:35:42 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/01/24 10:35:42 ERROR Executor: Exception in task 0.0 in stage 0.0 (TID 0)
java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
20/01/24 10:35:42 WARN TaskSetManager: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

20/01/24 10:35:42 ERROR TaskSetManager: Task 0 in stage 0.0 failed 1 times; aborting job
20/01/24 10:35:42 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/01/24 10:35:42 INFO TaskSchedulerImpl: Cancelling stage 0
20/01/24 10:35:42 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage cancelled
20/01/24 10:35:42 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) failed in 1.114 s due to Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
20/01/24 10:35:42 INFO DAGScheduler: Job 0 failed: runJob at SparkHadoopWriter.scala:78, took 1.210570 s
20/01/24 10:35:42 ERROR SparkHadoopWriter: Aborting job job_20200124103541_0002.
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:78)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1083)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:1000)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:991)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply$mcV$sp(GenomicDataset.scala:3816)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply(GenomicDataset.scala:3800)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply(GenomicDataset.scala:3800)
	at scala.Option.fold(Option.scala:158)
	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveRddAsParquet(GenomicDataset.scala:3800)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveAsParquet(GenomicDataset.scala:3882)
	at org.bdgenomics.adam.rdd.GenomicDataset$class.saveAsParquet(GenomicDataset.scala:322)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveAsParquet(GenomicDataset.scala:3771)
	at org.bdgenomics.adam.rdd.read.AlignmentDataset.save(AlignmentDataset.scala:639)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:646)
	at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:204)
	at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:126)
	at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:65)
	at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
	at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:845)
	at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:161)
	at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:184)
	at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86)
	at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:920)
	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:929)
	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Command body threw exception:
org.apache.spark.SparkException: Job aborted.
20/01/24 10:35:42 INFO TransformAlignments: Overall Duration: 6.28 secs
Exception in thread "main" org.apache.spark.SparkException: Job aborted.
	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:100)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1083)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1081)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:1000)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:991)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
	at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:991)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply$mcV$sp(GenomicDataset.scala:3816)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply(GenomicDataset.scala:3800)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset$$anonfun$saveRddAsParquet$1.apply(GenomicDataset.scala:3800)
	at scala.Option.fold(Option.scala:158)
	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveRddAsParquet(GenomicDataset.scala:3800)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveAsParquet(GenomicDataset.scala:3882)
	at org.bdgenomics.adam.rdd.GenomicDataset$class.saveAsParquet(GenomicDataset.scala:322)
	at org.bdgenomics.adam.rdd.AvroGenomicDataset.saveAsParquet(GenomicDataset.scala:3771)
	at org.bdgenomics.adam.rdd.read.AlignmentDataset.save(AlignmentDataset.scala:639)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:646)
	at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
	at org.bdgenomics.adam.cli.TransformAlignments.run(TransformAlignments.scala:204)
	at org.bdgenomics.adam.cli.ADAMMain.apply(ADAMMain.scala:126)
	at org.bdgenomics.adam.cli.ADAMMain$.main(ADAMMain.scala:65)
	at org.bdgenomics.adam.cli.ADAMMain.main(ADAMMain.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
	at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:845)
	at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:161)
	at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:184)
	at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:86)
	at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:920)
	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:929)
	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1889)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
	at org.apache.spark.internal.io.SparkHadoopWriter$.write(SparkHadoopWriter.scala:78)
	... 42 more
Caused by: java.lang.NoSuchMethodError: org.apache.parquet.schema.Types$PrimitiveBuilder.as(Lorg/apache/parquet/schema/LogicalTypeAnnotation;)Lorg/apache/parquet/schema/Types$Builder;
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:161)
	at org.apache.parquet.avro.AvroSchemaConverter.convertUnion(AvroSchemaConverter.java:226)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:182)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:141)
	at org.apache.parquet.avro.AvroSchemaConverter.convertField(AvroSchemaConverter.java:244)
	at org.apache.parquet.avro.AvroSchemaConverter.convertFields(AvroSchemaConverter.java:135)
	at org.apache.parquet.avro.AvroSchemaConverter.convert(AvroSchemaConverter.java:126)
	at org.apache.parquet.avro.AvroWriteSupport.init(AvroWriteSupport.java:121)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:388)
	at org.apache.parquet.hadoop.ParquetOutputFormat.getRecordWriter(ParquetOutputFormat.java:349)
	at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
	at org.apache.spark.internal.io.HadoopMapReduceWriteConfigUtil.initWriter(SparkHadoopWriter.scala:350)
	at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:120)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:83)
	at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:123)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
20/01/24 10:35:42 INFO SparkContext: Invoking stop() from shutdown hook
20/01/24 10:35:42 INFO SparkUI: Stopped Spark web UI at http://192.168.10.32:4040
20/01/24 10:35:42 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/01/24 10:35:42 INFO MemoryStore: MemoryStore cleared
20/01/24 10:35:42 INFO BlockManager: BlockManager stopped
20/01/24 10:35:42 INFO BlockManagerMaster: BlockManagerMaster stopped
20/01/24 10:35:42 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/01/24 10:35:42 INFO SparkContext: Successfully stopped SparkContext
20/01/24 10:35:42 INFO ShutdownHookManager: Shutdown hook called
20/01/24 10:35:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-89a04d73-980c-4dd0-8680-6b4b46ec0a6d
20/01/24 10:35:42 INFO ShutdownHookManager: Deleting directory /tmp/spark-030a2694-a0cc-4b8b-9776-9a23221004fa
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/07e6b1a39af5863a6c67f63690416da161096882
Finished: FAILURE