If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.4.1
b) Exact command used:

docker run -v $(pwd):/2021 broadinstitute/gatk:4.1.4.1 gatk --java-options "-Xmx8G -XX:+UseParallelGC -XX:ParallelGCThreads=4" HaplotypeCaller \
-R 2021/bioinfo/lorena/bucket/reference/hg19_v0_Homo_sapiens_assembly19_v3.fasta -I 2021/scratch/bamro/ERR2880948.bam \
-L 2021/bioinfo/lorena/bucket/reference/Homo_sapiens_assembly19_v2.interval_list \
--native-pair-hmm-threads 8 \
-G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation \
-O 2021/scratch/output/$(basename $sample .bam).vcf.gz -ERC GVCF

c) Entire error log:

(base) tatianaalmeida@Auto 2021 % sh scratch/runHC.sh scratch/bamro/ERR2880948.bam

01:45:30.136 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default

01:45:30.136 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardHCAnnotation) is enabled for this tool by default

01:45:30.164 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

Jan 15, 2021 1:45:30 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

01:45:30.297 INFO  HaplotypeCaller - ------------------------------------------------------------

01:45:30.298 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.4.1

01:45:30.298 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/

01:45:30.298 INFO  HaplotypeCaller - Executing as root@ada861b931b3 on Linux v4.19.121-linuxkit amd64

01:45:30.298 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03

01:45:30.298 INFO  HaplotypeCaller - Start Date/Time: January 15, 2021 1:45:30 AM UTC

01:45:30.298 INFO  HaplotypeCaller - ------------------------------------------------------------

01:45:30.298 INFO  HaplotypeCaller - ------------------------------------------------------------

01:45:30.299 INFO  HaplotypeCaller - HTSJDK Version: 2.21.0

01:45:30.299 INFO  HaplotypeCaller - Picard Version: 2.21.2

01:45:30.299 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2

01:45:30.299 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

01:45:30.299 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

01:45:30.300 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

01:45:30.300 INFO  HaplotypeCaller - Deflater: IntelDeflater

01:45:30.300 INFO  HaplotypeCaller - Inflater: IntelInflater

01:45:30.300 INFO  HaplotypeCaller - GCS max retries/reopens: 20

01:45:30.300 INFO  HaplotypeCaller - Requester pays: disabled

01:45:30.301 INFO  HaplotypeCaller - Initializing engine

01:45:30.639 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///2021/scratch/reference/gatk/Homo_sapiens_assembly19_v2.interval_list

01:45:30.684 INFO  IntervalArgumentCollection - Processing 2864957093 bp from intervals

01:45:30.701 INFO  HaplotypeCaller - Done initializing engine

01:45:30.702 INFO  HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled

01:45:30.712 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output

01:45:30.712 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output

01:45:30.720 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so

01:45:30.721 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so

01:45:30.751 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM

01:45:30.751 INFO  IntelPairHmm - Available threads: 6

01:45:30.751 INFO  IntelPairHmm - Requested threads: 8

01:45:30.751 WARN  IntelPairHmm - Using 6 available threads, but 8 were requested

01:45:30.752 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation

01:45:30.786 INFO  ProgressMeter - Starting traversal

01:45:30.786 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute

01:45:30.848 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0

01:45:30.848 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0

01:45:30.848 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec

01:45:30.848 INFO  HaplotypeCaller - Shutting down engine

[January 15, 2021 1:45:30 AM UTC] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=180879360

***********************************************************************

A USER ERROR has occurred: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'

***********************************************************************

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Using GATK jar /gatk/gatk-package-4.1.4.1-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 -Xmx8G -XX:+UseParallelGC -XX:ParallelGCThreads=4 -jar /gatk/gatk-package-4.1.4.1-local.jar HaplotypeCaller --create-output-variant-index TRUE -R /2021/scratch/reference/gatk/hg19_v0_Homo_sapiens_assembly19_v3.fasta -I /2021/scratch/bamro/ERR2880948.bam -L /2021/scratch/reference/gatk/Homo_sapiens_assembly19_v2.interval_list --native-pair-hmm-threads 8 -G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation -O /2021/scratch/output/ERR2880948.g.vcf -ERC GVCF

I'm using a mac BigSur and I tried dos2unix without success. 
When I apply a search for non ATCGN it only came R and M. cat -e shows a '$' at the end of the lines.

I would like some help very much, 

Regards