I am using ShiftFasta to create the following files for the mitochondrial analysis

1. shifted dictionary file

2. shifted fasta file

3. shifted fasta index

4. shift back chain

5. intervals file

6. shifted intervals file

While the files 1,2, 3, and 4 get generated as expected, intervals and shifted.intervals files are empty. I am not sure what I am doing wrong, and I would appreciate any pointers to fix this.

a) GATK version used: version 4.3.0.0

b) Exact command used:

gatk --java-options "-Xmx3g" ShiftFasta \
    --reference hg38.chrM.fa \
    --output mito_shift.fasta \
    --shift-back-output mito_shift.back_chain \
    --intervals chrM:576-16024 --shift-offset-list 8000 --interval-file-name mito \
    --sequence-dictionary hg38.chrM.dict \
    --tmp-dir .

 
c) Entire program log:

Using GATK jar /usr/local/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 -Xmx3g -jar /usr/local/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ShiftFasta --reference hg38.chrM.fa --output mito_shift.fasta --shift-back-output mito_shift.back_chain --intervals chrM:576-16024 --shift-offset-list 8000 --interval-file-name mito --sequence-dictionary hg38.chrM.dict --tmp-dir .
14:40:49.732 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:40:50.138 INFO  ShiftFasta - ------------------------------------------------------------
14:40:50.140 INFO  ShiftFasta - The Genome Analysis Toolkit (GATK) v4.3.0.0
14:40:50.140 INFO  ShiftFasta - For support and documentation go to https://software.broadinstitute.org/gatk/
14:40:50.140 INFO  ShiftFasta - Executing as ram@hasta on Linux v3.10.0-1160.53.1.el7.x86_64 amd64
14:40:50.141 INFO  ShiftFasta - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src
14:40:50.142 INFO  ShiftFasta - Start Date/Time: October 20, 2022 at 2:40:49 PM GMT
14:40:50.142 INFO  ShiftFasta - ------------------------------------------------------------
14:40:50.142 INFO  ShiftFasta - ------------------------------------------------------------
14:40:50.144 INFO  ShiftFasta - HTSJDK Version: 3.0.1
14:40:50.144 INFO  ShiftFasta - Picard Version: 2.27.5
14:40:50.144 INFO  ShiftFasta - Built for Spark Version: 2.4.5
14:40:50.144 INFO  ShiftFasta - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:40:50.144 INFO  ShiftFasta - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:40:50.145 INFO  ShiftFasta - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:40:50.145 INFO  ShiftFasta - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:40:50.145 INFO  ShiftFasta - Deflater: IntelDeflater
14:40:50.146 INFO  ShiftFasta - Inflater: IntelInflater
14:40:50.146 INFO  ShiftFasta - GCS max retries/reopens: 20
14:40:50.146 INFO  ShiftFasta - Requester pays: disabled
14:40:50.146 WARN  ShiftFasta -

ESC[1mESC[31m   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: ShiftFasta is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!ESC[0m


14:40:50.146 INFO  ShiftFasta - Initializing engine
14:40:50.327 INFO  IntervalArgumentCollection - Processing 15449 bp from intervals
14:40:50.329 INFO  ShiftFasta - Done initializing engine
14:40:50.340 INFO  ProgressMeter - Starting traversal
14:40:50.341 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Records Processed   Records/Minute
14:40:50.353 INFO  ProgressMeter -             unmapped              0.0                     0              0.0
14:40:50.353 INFO  ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
14:40:50.355 INFO  ShiftFasta - Shutting down engine
[October 20, 2022 at 2:40:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648