HaplotypeCaller Incompatible Contigs DNASeq

I'm using GATK 4.0.11 and I'm getting the following error message when I run HaplotypeCaller on DNAseq data:

10:19:17.089 INFO HaplotypeCaller - ------------------------------------------------------------

10:19:17.089 INFO HaplotypeCaller - ------------------------------------------------------------

10:19:17.090 INFO HaplotypeCaller - HTSJDK Version: 2.16.1

10:19:17.090 INFO HaplotypeCaller - Picard Version: 2.18.13

10:19:17.091 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2

10:19:17.091 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

10:19:17.091 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

10:19:17.091 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

10:19:17.091 INFO HaplotypeCaller - Deflater: IntelDeflater

10:19:17.091 INFO HaplotypeCaller - Inflater: IntelInflater

10:19:17.091 INFO HaplotypeCaller - GCS max retries/reopens: 20

10:19:17.092 INFO HaplotypeCaller - Requester pays: disabled

10:19:17.092 INFO HaplotypeCaller - Initializing engine

10:19:17.536 INFO HaplotypeCaller - Shutting down engine

[January 5, 2019 10:19:17 AM EST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.12 minutes.


Runtime.totalMemory()=311427072



A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.

reference contigs = [chr17:c43125483-43044295]

reads contigs = []



I then tried another file from NCBI:



A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.

reference contigs = [chr17:c43125483-43044295]


reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]

The proceeding steps were FastqToSam, BWA, and MarkDuplicates.

Any suggestions?

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