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All of the uses of org.apache.hadoop.fs.FileSystem.get use the single argument version that takes a job configuration. This will always return the default file system type (which is usually HDFS), rather than using the file system type used in the URIs for the input or output paths. This is particularly a problem on Amazon's Elastic MapReduce where the input and output data typically reside in a org.apache.hadoop.fs.s3native.NativeS3FileSystem.
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