If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.1
b) Exact command used: (I downloaded and untared the GATK pre-packeged data sources)

$gatk Funcotator \
-R $ref/ucsc.hg19.fasta \
--data-sources-path /scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g \
--variant $execPath/GATK4teste_PASS_targets-file.vcf.gz \
--output $outPath/GATK4teste_func_annotations.vcf \
--output-file-format VCF \
--ref-version hg19;

c) Entire error log:

Using GATK jar /cephfs/scratch/6493700/programas/gatk-package-4.1.8.1-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 -jar /cephfs/scratch/6493700/programas/gatk-package-4.1.8.1-local.jar Funcotator -R /scratch/5644370/hg19/ucsc.hg19.fasta --data-sources-path /scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g --variant /scratch/6493700/GATK4_teste/in_out/avaliacao/out/GATK4teste_PASS_targets-file.vcf.gz --output /scratch/6493700/GATK4_teste/in_out/func_annot/out/GATK4teste_func_annotations.vcf --output-file-format VCF --ref-version hg19
17:06:44.598 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cephfs/scratch/6493700/programas/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 20, 2020 5:06:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
17:06:45.167 INFO Funcotator - ------------------------------------------------------------
17:06:45.168 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.1.8.1
17:06:45.168 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:06:45.169 INFO Funcotator - Executing as 6493700@aguia4-bm-0055.hpc.usp.br on Linux v4.17.6-1.el7.elrepo.x86_64 amd64
17:06:45.169 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_222-b10
17:06:45.173 INFO Funcotator - Start Date/Time: November 20, 2020 5:06:44 PM BRT
17:06:45.173 INFO Funcotator - ------------------------------------------------------------
17:06:45.173 INFO Funcotator - ------------------------------------------------------------
17:06:45.174 INFO Funcotator - HTSJDK Version: 2.23.0
17:06:45.174 INFO Funcotator - Picard Version: 2.22.8
17:06:45.174 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:06:45.174 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:06:45.174 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:06:45.174 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:06:45.174 INFO Funcotator - Deflater: IntelDeflater
17:06:45.174 INFO Funcotator - Inflater: IntelInflater
17:06:45.175 INFO Funcotator - GCS max retries/reopens: 20
17:06:45.175 INFO Funcotator - Requester pays: disabled
17:06:45.175 INFO Funcotator - Initializing engine
17:06:45.892 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/6493700/GATK4_teste/in_out/avaliacao/out/GATK4teste_PASS_targets-file.vcf.gz
17:06:46.142 INFO Funcotator - Done initializing engine
17:06:46.208 INFO Funcotator - Validating Sequence Dictionaries...
17:06:46.255 INFO Funcotator - Processing user transcripts/defaults/overrides...
17:06:46.366 INFO Funcotator - Initializing data sources...
17:06:46.400 INFO DataSourceUtils - Initializing data sources from directory: /scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g
17:06:46.485 INFO DataSourceUtils - Data sources version: 1.6.2019124g
17:06:46.515 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz
17:06:46.540 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124g.tar.gz
17:06:48.388 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/clinvar_20180401.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/clinvar/hg19/clinvar_20180401.vcf
17:06:48.534 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/acmg59_test_cleaned.txt -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/acmg_rec/hg19/acmg59_test_cleaned.txt
17:06:48.686 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/acmg_lof.tsv -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/acmg_lof/hg19/acmg_lof.tsv
17:06:48.810 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:06:48.970 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/gencode/hg19/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf
17:06:49.100 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/gencode.v19.pc_transcripts.fasta -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/gencode/hg19/gencode.v19.pc_transcripts.fasta
17:06:49.602 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
17:06:49.803 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000
17:06:53.492 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
17:07:04.976 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
17:07:06.162 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/clinvar_20180401.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/clinvar/hg19/clinvar_20180401.vcf
17:07:06.162 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000
17:07:06.241 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/clinvar/hg19/clinvar_20180401.vcf
17:07:06.553 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/clinvar_20180401.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/clinvar/hg19/clinvar_20180401.vcf
17:07:06.641 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/clinvar/hg19/clinvar_20180401.vcf
17:07:06.805 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/acmg59_test_cleaned.txt -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/acmg_rec/hg19/acmg59_test_cleaned.txt
17:07:06.829 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/acmg_lof.tsv -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/acmg_lof/hg19/acmg_lof.tsv
17:07:06.848 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:07:06.849 INFO DataSourceUtils - Setting lookahead cache for data source: LMMKnown : 100000
17:07:06.884 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:07:06.918 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:07:06.933 INFO FeatureManager - Using codec VCFCodec to read file file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/lmm_known/hg19/LMM_Path_LP_VUS5-variants-6-12-18.sorted.vcf
17:07:06.937 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/gencode/hg19/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf
17:07:06.937 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
17:07:07.011 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/gencode/hg19/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf
17:07:07.047 INFO DataSourceUtils - Resolved data source file path: file:///cephfs/scratch/6493700/GATK4_teste/scripts/func_annot/gencode.v19.pc_transcripts.fasta -> file:///scratch/6493700/GATK4_teste/in_out/func_annot/in/funcotator_dataSources.v1.6.20190124g/gencode/hg19/gencode.v19.pc_transcripts.fasta
17:07:14.948 INFO DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000
17:07:19.003 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
17:07:27.620 INFO FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
17:07:29.088 INFO Funcotator - Initializing Funcotator Engine...
17:07:29.194 INFO Funcotator - Creating a VCF file for output: file:/scratch/6493700/GATK4_teste/in_out/func_annot/out/GATK4teste_func_annotations.vcf
17:07:29.320 INFO ProgressMeter - Starting traversal
17:07:29.341 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:07:35.729 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:984456-984456 due to alternate allele: *
17:07:35.889 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:984491-984491 due to alternate allele: *
17:07:38.838 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463337-1463337 due to alternate allele: *
17:07:38.881 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463337-1463337 due to alternate allele: *
17:07:38.906 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463337-1463337 due to alternate allele: *
17:07:38.950 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463340-1463340 due to alternate allele: *
17:07:38.973 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463340-1463340 due to alternate allele: *
17:07:38.998 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1463340-1463340 due to alternate allele: *
17:07:39.708 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.735 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.823 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.856 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.910 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.962 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:39.996 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:40.187 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:40.391 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:40.535 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:40.689 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:07:40.798 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:1565596-1565596 due to alternate allele: *
17:08:02.106 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:19652132-19652133 due to alternate allele: *
17:08:02.407 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:19652132-19652133 due to alternate allele: *
17:08:02.448 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:19652132-19652133 due to alternate allele: *
17:08:05.304 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:22030121-22030121 due to alternate allele: *
17:08:05.594 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:22030121-22030121 due to alternate allele: *
17:08:05.652 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:22030121-22030121 due to alternate allele: *
17:08:05.727 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:22030121-22030121 due to alternate allele: *
17:08:14.960 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:29016716-29016716 due to alternate allele: *
17:08:14.977 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:29016716-29016716 due to alternate allele: *
17:08:15.034 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:29016716-29016716 due to alternate allele: *
17:08:15.060 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:29016716-29016716 due to alternate allele: *
17:08:21.181 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:32631614-32631619 due to alternate allele: *
17:08:21.212 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:32631614-32631619 due to alternate allele: *
17:08:21.242 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:32631614-32631619 due to alternate allele: *
17:08:21.271 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:32631614-32631619 due to alternate allele: *
17:08:24.379 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:24.410 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:24.443 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:24.468 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:24.493 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:24.519 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:36203722-36203722 due to alternate allele: *
17:08:44.626 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:44.644 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:44.644 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:44.644 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:44.644 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:44.644 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:53793511-53793511 due to alternate allele: *
17:08:47.890 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:55521906-55521906 due to alternate allele: *
17:08:47.891 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:55521906-55521906 due to alternate allele: *
17:08:47.891 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:55521906-55521906 due to alternate allele: *
17:08:55.000 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:65830297-65830300 due to alternate allele: *
17:08:55.000 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:65830297-65830300 due to alternate allele: *
17:08:55.000 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:65830297-65830300 due to alternate allele: *
17:09:02.525 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:76378359-76378362 due to alternate allele: *
17:09:02.534 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:76378360-76378360 due to alternate allele: *
17:09:02.540 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:76378361-76378361 due to alternate allele: *
17:09:03.710 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:77752549-77752549 due to alternate allele: *
17:09:03.710 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:77752549-77752549 due to alternate allele: *
17:09:03.710 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:77752549-77752549 due to alternate allele: *
17:09:18.806 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:94982785-94982785 due to alternate allele: *
17:09:18.807 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:94982785-94982785 due to alternate allele: *
17:09:18.807 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:94982785-94982785 due to alternate allele: *
17:09:18.807 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:94982785-94982785 due to alternate allele: *
17:09:18.807 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:94982785-94982785 due to alternate allele: *
17:09:30.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:109773705-109773710 due to alternate allele: *
17:09:30.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:109773705-109773710 due to alternate allele: *
17:09:32.701 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111890244-111890245 due to alternate allele: *
17:09:32.701 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111890244-111890245 due to alternate allele: *
17:09:32.701 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111890244-111890245 due to alternate allele: *
17:09:32.719 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111893793-111893793 due to alternate allele: *
17:09:32.720 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111893793-111893793 due to alternate allele: *
17:09:32.720 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:111893793-111893793 due to alternate allele: *
17:09:35.491 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.491 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.491 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.491 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.492 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.492 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449836-114449836 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:35.500 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:114449837-114449837 due to alternate allele: *
17:09:39.246 INFO ProgressMeter - chr1:118693217 2.2 1000 462.0
17:09:50.541 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000368801.2 for variant: chr1:152195728-152195730(ATT* -> A): Cannot yet handle indels starting outside an exon and ending within an exon.
17:09:50.581 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000368801.2 for problem variant: chr1:152195728-152195730(ATT* -> A)
17:09:50.627 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000368801.2 for variant: chr1:152195728-152195730(ATT* -> AT): Cannot yet handle indels starting outside an exon and ending within an exon.
17:09:50.665 WARN GencodeFuncotationFactory - Creating default GencodeFuncotation on transcript ENST00000368801.2 for problem variant: chr1:152195728-152195730(ATT* -> AT)
17:10:08.828 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:165378735-165378735 due to alternate allele: *
17:10:41.034 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:205561494-205561498 due to alternate allele: *
17:10:41.035 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:205561494-205561498 due to alternate allele: *
17:10:41.035 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:205561494-205561498 due to alternate allele: *
17:10:41.036 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:205561494-205561498 due to alternate allele: *
17:10:46.818 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:213188876-213188876 due to alternate allele: *
17:10:46.818 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:213188876-213188876 due to alternate allele: *
17:10:46.818 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:213188876-213188876 due to alternate allele: *
17:10:46.818 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:213188876-213188876 due to alternate allele: *
17:10:46.818 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:213188876-213188876 due to alternate allele: *
17:10:48.937 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:215916732-215916732 due to alternate allele: *
17:10:48.937 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:215916732-215916732 due to alternate allele: *
17:11:06.443 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:237013551-237013551 due to alternate allele: *
17:11:06.444 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:237013551-237013551 due to alternate allele: *
17:11:38.966 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:246670298-246670313 due to alternate allele: *
17:11:38.967 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:246670298-246670313 due to alternate allele: *
17:11:38.967 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr1:246670298-246670313 due to alternate allele: *
17:12:23.500 INFO ProgressMeter - chr10:15559327 4.9 2000 408.0
17:12:24.584 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:16737157-16737157 due to alternate allele: *
17:12:24.640 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:16737157-16737157 due to alternate allele: *
17:12:24.690 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:16737157-16737157 due to alternate allele: *
17:12:24.735 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:16737157-16737157 due to alternate allele: *
17:12:25.683 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:25.726 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:25.758 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:25.864 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:25.916 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:25.958 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:26.024 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:26.052 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:17204248-17204248 due to alternate allele: *
17:12:28.010 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.155 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.216 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.250 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.275 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.298 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:28.429 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:29.074 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:29.342 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:29.369 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:29.404 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:18825193-18825204 due to alternate allele: *
17:12:32.285 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:22828832-22828832 due to alternate allele: *
17:12:32.470 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:22828832-22828832 due to alternate allele: *
17:12:32.570 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:22828832-22828832 due to alternate allele: *
17:12:35.355 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:25755736-25755736 due to alternate allele: *
17:13:09.706 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:74896743-74896743 due to alternate allele: *
17:13:09.712 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:74896743-74896743 due to alternate allele: *
17:13:09.712 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:74896743-74896743 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.843 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:13.844 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:81925798-81925800 due to alternate allele: *
17:13:42.559 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:42.589 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:42.590 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:42.590 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:42.590 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:42.590 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:112044560-112044560 due to alternate allele: *
17:13:48.117 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:118466670-118466670 due to alternate allele: *
17:13:52.622 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183688-124183688 due to alternate allele: *
17:13:52.622 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183688-124183688 due to alternate allele: *
17:13:52.622 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183688-124183688 due to alternate allele: *
17:13:52.622 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183688-124183688 due to alternate allele: *
17:13:52.622 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183688-124183688 due to alternate allele: *
17:13:52.630 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183689-124183689 due to alternate allele: *
17:13:52.631 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183689-124183689 due to alternate allele: *
17:13:52.631 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183689-124183689 due to alternate allele: *
17:13:52.631 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183689-124183689 due to alternate allele: *
17:13:52.631 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183689-124183689 due to alternate allele: *
17:13:52.638 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183690-124183690 due to alternate allele: *
17:13:52.638 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183690-124183690 due to alternate allele: *
17:13:52.638 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183690-124183690 due to alternate allele: *
17:13:52.638 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183690-124183690 due to alternate allele: *
17:13:52.638 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183690-124183690 due to alternate allele: *
17:13:52.646 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183691-124183691 due to alternate allele: *
17:13:52.646 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183691-124183691 due to alternate allele: *
17:13:52.646 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183691-124183691 due to alternate allele: *
17:13:52.646 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183691-124183691 due to alternate allele: *
17:13:52.646 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:124183691-124183691 due to alternate allele: *
17:14:01.133 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:133954118-133954118 due to alternate allele: *
17:14:01.134 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr10:133954118-133954118 due to alternate allele: *
17:14:05.776 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:640051-640051 due to alternate allele: *
17:14:07.974 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.974 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.975 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.976 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.977 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.977 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:07.977 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:1481691-1481699 due to alternate allele: *
17:14:35.143 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:26724995-26724995 due to alternate allele: *
17:14:35.167 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:26724995-26724995 due to alternate allele: *
17:14:38.558 INFO ProgressMeter - chr11:27401743 7.2 3000 419.4
17:14:39.015 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:30358033-30358034 due to alternate allele: *
17:14:44.987 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:36425014-36425014 due to alternate allele: *
17:14:44.987 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:36425014-36425014 due to alternate allele: *
17:14:44.987 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:36425014-36425014 due to alternate allele: *
17:14:44.987 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:36425014-36425014 due to alternate allele: *
17:14:44.987 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:36425014-36425014 due to alternate allele: *
17:14:47.360 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:43413158-43413162 due to alternate allele: *
17:14:47.360 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:43413158-43413162 due to alternate allele: *
17:14:47.361 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:43413158-43413162 due to alternate allele: *
17:14:47.366 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:43413158-43413162 due to alternate allele: *
17:14:53.032 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.032 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.032 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.032 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.033 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47267410-47267410 due to alternate allele: *
17:14:53.428 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47372738-47372738 due to alternate allele: *
17:14:53.428 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47372738-47372738 due to alternate allele: *
17:14:53.428 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:47372738-47372738 due to alternate allele: *
17:14:59.951 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:57479731-57479732 due to alternate allele: *
17:14:59.951 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:57479731-57479732 due to alternate allele: *
17:14:59.951 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:57479731-57479732 due to alternate allele: *
17:14:59.951 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:57479731-57479732 due to alternate allele: *
17:14:59.951 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:57479731-57479732 due to alternate allele: *
17:15:20.118 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:68773810-68773812 due to alternate allele: *
17:15:20.136 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:68773810-68773812 due to alternate allele: *
17:15:20.137 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:68773810-68773812 due to alternate allele: *
17:15:23.369 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:73670795-73670800 due to alternate allele: *
17:15:27.741 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:76833583-76833583 due to alternate allele: *
17:15:27.741 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:76833583-76833583 due to alternate allele: *
17:15:27.741 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:76833583-76833583 due to alternate allele: *
17:15:27.741 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:76833583-76833583 due to alternate allele: *
17:15:39.026 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:89914894-89914901 due to alternate allele: *
17:15:39.027 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:89914894-89914901 due to alternate allele: *
17:15:39.027 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:89914894-89914901 due to alternate allele: *
17:15:48.519 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:102199611-102199613 due to alternate allele: *
17:15:48.519 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:102199611-102199613 due to alternate allele: *
17:16:04.667 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:118769032-118769032 due to alternate allele: *
17:16:04.667 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:118769032-118769032 due to alternate allele: *
17:16:06.883 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:120175680-120175684 due to alternate allele: *
17:16:06.883 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr11:120175680-120175684 due to alternate allele: *
17:16:24.394 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:6562931-6562931 due to alternate allele: *
17:16:24.394 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:6562931-6562931 due to alternate allele: *
17:16:24.394 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:6562931-6562931 due to alternate allele: *
17:16:24.394 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:6562931-6562931 due to alternate allele: *
17:16:24.394 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:6562931-6562931 due to alternate allele: *
17:16:27.897 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:7805511-7805511 due to alternate allele: *
17:16:31.715 WARN FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3. Dropping bases from the end: 1 (size=451, ref allele: A)
17:16:31.715 WARN FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3. Dropping bases from the end: 1 (size=451, alt allele: G)
17:16:38.108 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626322-19626322 due to alternate allele: *
17:16:38.108 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626322-19626322 due to alternate allele: *
17:16:38.109 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626322-19626322 due to alternate allele: *
17:16:38.109 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626322-19626322 due to alternate allele: *
17:16:38.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626326-19626326 due to alternate allele: *
17:16:38.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626326-19626326 due to alternate allele: *
17:16:38.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626326-19626326 due to alternate allele: *
17:16:38.116 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:19626326-19626326 due to alternate allele: *
17:16:38.360 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:20522126-20522126 due to alternate allele: *
17:16:38.360 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:20522126-20522126 due to alternate allele: *
17:16:39.156 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:21201572-21201582 due to alternate allele: *
17:16:39.156 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:21201572-21201582 due to alternate allele: *
17:16:39.156 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:21201572-21201582 due to alternate allele: *
17:16:39.156 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:21201572-21201582 due to alternate allele: *
17:16:39.157 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:21201572-21201582 due to alternate allele: *
17:16:42.798 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:25673079-25673079 due to alternate allele: *
17:16:42.798 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:25673079-25673079 due to alternate allele: *
17:16:42.799 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:25673079-25673079 due to alternate allele: *
17:16:42.799 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:25673079-25673079 due to alternate allele: *
17:16:42.799 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:25673079-25673079 due to alternate allele: *
17:16:47.231 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:30822240-30822240 due to alternate allele: *
17:16:47.244 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:30822240-30822240 due to alternate allele: *
17:16:47.281 INFO ProgressMeter - chr12:30867794 9.3 4000 430.2
17:16:55.950 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:16:56.093 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:16:56.128 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:16:56.176 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:16:56.204 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:16:56.229 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:45797401-45797406 due to alternate allele: *
17:17:04.669 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.706 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.748 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.777 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.810 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.831 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.877 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.913 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386528-51386530 due to alternate allele: *
17:17:04.946 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:04.972 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:04.997 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.022 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.047 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.072 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.097 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.129 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386529-51386530 due to alternate allele: *
17:17:05.169 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.197 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.238 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.263 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.288 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.313 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.338 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:05.363 WARN GencodeFuncotationFactory - Cannot create complete funcotation for variant at chr12:51386530-51386530 due to alternate allele: *
17:17:25.784 INFO VcfFuncotationFactory - ClinVar_VCF 20180401 cache hits/total: 0/127
17:17:25.792 INFO VcfFuncotationFactory - LMMKnown 20180612 cache hits/total: 0/0
17:17:25.792 INFO VcfFuncotationFactory - gnomAD_exome 2.1 cache hits/total: 24/1534
17:17:25.792 INFO VcfFuncotationFactory - gnomAD_genome 2.1 cache hits/total: 46/4178
17:17:26.091 INFO Funcotator - Shutting down engine
[November 20, 2020 5:17:26 PM BRT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 10.70 minutes.
Runtime.totalMemory()=11558453248
java.lang.StringIndexOutOfBoundsException: String index out of range: 545
at java.lang.String.substring(String.java:1963)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.initializeForInsertion(ProteinChangeInfo.java:256)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.<init>(ProteinChangeInfo.java:93)
at org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.create(ProteinChangeInfo.java:371)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createSequenceComparison(GencodeFuncotationFactory.java:2045)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotationForProteinCodingFeature(GencodeFuncotationFactory.java:1235)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createExonFuncotation(GencodeFuncotationFactory.java:1086)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnSingleTranscript(GencodeFuncotationFactory.java:1020)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:847)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:831)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:508)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:509)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:564)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:243)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:147)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:157)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:904)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:858)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

Would anyone be able to help me understand why I'm getting these warnings/errors?