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NullPointerException in FastaReferenceMaker.closeTool

I want to use FastaAlternateReferenceMaker, however, it is giving me null pointer exception in FastaReferenceMaker.closeTool. To isolate the problem I replicated the same error by running the simpler `gatk FastaReferenceMaker -R example.fasta -O test.out` where example.fasta is from the GATK test folder and it is accompanied by the .dict in the same folder.

src/test/resources/org/broadinstitute/hellbender/tools/examples/ExampleReferenceWalker/example.fasta

Unfortunately, the error doesn't really tell me much, could someone point me in the right direction to fixing this issue? Thanks

I am running GATK 4.1.0.0.

```
$ gatk FastaReferenceMaker -R example.fasta -O test.out
Using GATK jar /Users/brianlandry/bto/resources/gatk/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar defined in environment variable GATK_LOCAL_JAR
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Users/brianlandry/bto/resources/gatk/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar FastaReferenceMaker -R example.fasta -O test.out
13:15:26.283 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/brianlandry/bto/resources/gatk/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib
13:15:27.972 INFO FastaReferenceMaker - ------------------------------------------------------------
13:15:27.973 INFO FastaReferenceMaker - The Genome Analysis Toolkit (GATK) v4.1.0.0
13:15:27.973 INFO FastaReferenceMaker - For support and documentation go to *EDITED TO REMOVE HYPLINK SO I COULD POST*
13:15:27.973 INFO FastaReferenceMaker - Executing as [email protected] on Mac OS X v10.14.5 x86_64
13:15:27.973 INFO FastaReferenceMaker - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_181-b13
13:15:27.974 INFO FastaReferenceMaker - Start Date/Time: July 24, 2019 1:15:26 PM PDT
13:15:27.974 INFO FastaReferenceMaker - ------------------------------------------------------------
13:15:27.974 INFO FastaReferenceMaker - ------------------------------------------------------------
13:15:27.974 INFO FastaReferenceMaker - HTSJDK Version: 2.18.2
13:15:27.974 INFO FastaReferenceMaker - Picard Version: 2.18.25
13:15:27.974 INFO FastaReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:15:27.974 INFO FastaReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:15:27.974 INFO FastaReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:15:27.974 INFO FastaReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:15:27.975 INFO FastaReferenceMaker - Deflater: IntelDeflater
13:15:27.975 INFO FastaReferenceMaker - Inflater: IntelInflater
13:15:27.975 INFO FastaReferenceMaker - GCS max retries/reopens: 20
13:15:27.975 INFO FastaReferenceMaker - Requester pays: disabled
13:15:27.975 INFO FastaReferenceMaker - Initializing engine
13:15:28.297 INFO FastaReferenceMaker - Done initializing engine
13:15:28.298 INFO FastaReferenceMaker - Shutting down engine
[July 24, 2019 1:15:28 PM PDT] org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=373293056
java.lang.NullPointerException
at org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker.closeTool(FastaReferenceMaker.java:137)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:970)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
```

Answers

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