REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

I just ran HaplotypeCaller (GATK v4.2.3) on a per-chromosome basis for a bunch of samples, and am now trying to gather the outputted .g.vcf files back into one per individual before proceeding to the GenotypeGVCFs step. However, with multiple tools, I've gotten the same error. First, for CombineGVCFS:

gatk CombineGVCFs \
-R /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta \
-V GD_110-Concordia-SUPER1.g.vcf -V GD_110-Concordia-SUPER2.g.vcf \
-V GD_110-Concordia-SUPER3.g.vcf -V GD_110-Concordia-SUPER4.g.vcf \
-V GD_110-Concordia-SUPER5.g.vcf -V GD_110-Concordia-SUPER6.g.vcf \
-V GD_110-Concordia-SUPER7.g.vcf -V GD_110-Concordia-SUPER8.g.vcf \
-V GD_110-Concordia-SUPER9.g.vcf -V GD_110-Concordia-SUPER10.g.vcf \
-V GD_110-Concordia-SUPER11.g.vcf -V GD_110-Concordia-SUPER12.g.vcf \
-V GD_110-Concordia-SUPER13.g.vcf -V GD_110-Concordia-SUPER14.g.vcf \
-V GD_110-Concordia-SUPER15.g.vcf -V GD_110-Concordia-SUPER16.g.vcf \
-V GD_110-Concordia-SUPER17.g.vcf -V GD_110-Concordia-SUPER18.g.vcf \
-V GD_110-Concordia-SUPER19.g.vcf -V GD_110-Concordia-SUPER20.g.vcf \
-V GD_110-Concordia-SUPER21.g.vcf -V GD_110-Concordia-SUPER22.g.vcf \
-V GD_110-Concordia-SUPER23.g.vcf -V GD_110-Concordia-SUPER24.g.vcf \
\-V GD_110-Concordia-SUPER25.g.vcf -O GD_110-Concordia-ALL.g.vcf

This produced the output:

Using GATK jar /modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-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 -jar /modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-local.jar CombineGVCFs -R /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta -V GD_110-Concordia-SUPER1.g.vcf -V GD_110-Concordia-SUPER2.g.vcf -V GD_110-Concordia-SUPER3.g.vcf -V GD_110-Concordia-SUPER4.g.vcf -V GD_110-Concordia-SUPER5.g.vcf -V GD_110-Concordia-SUPER6.g.vcf -V GD_110-Concordia-SUPER7.g.vcf -V GD_110-Concordia-SUPER8.g.vcf -V GD_110-Concordia-SUPER9.g.vcf -V GD_110-Concordia-SUPER10.g.vcf -V GD_110-Concordia-SUPER11.g.vcf -V GD_110-Concordia-SUPER12.g.vcf -V GD_110-Concordia-SUPER13.g.vcf -V GD_110-Concordia-SUPER14.g.vcf -V GD_110-Concordia-SUPER15.g.vcf -V GD_110-Concordia-SUPER16.g.vcf -V GD_110-Concordia-SUPER17.g.vcf -V GD_110-Concordia-SUPER18.g.vcf -V GD_110-Concordia-SUPER19.g.vcf -V GD_110-Concordia-SUPER20.g.vcf -V GD_110-Concordia-SUPER21.g.vcf -V GD_110-Concordia-SUPER22.g.vcf -V GD_110-Concordia-SUPER23.g.vcf -V GD_110-Concordia-SUPER24.g.vcf -V GD_110-Concordia-SUPER25.g.vcf -O GD_110-Concordia-ALL.g.vcf
14:54:48.672 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 19, 2023 2:54:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:54:49.141 INFO  CombineGVCFs - ------------------------------------------------------------
14:54:49.141 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.2.3.0
14:54:49.141 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
14:54:49.141 INFO  CombineGVCFs - Executing as jessmclaughl_umass_edu@login1 on Linux v5.4.0-163-generic amd64
14:54:49.141 INFO  CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.20.1+1-post-Ubuntu-0ubuntu120.04
14:54:49.142 INFO  CombineGVCFs - Start Date/Time: December 19, 2023 at 2:54:48 PM UTC
14:54:49.142 INFO  CombineGVCFs - ------------------------------------------------------------
14:54:49.142 INFO  CombineGVCFs - ------------------------------------------------------------
14:54:49.142 INFO  CombineGVCFs - HTSJDK Version: 2.24.1
14:54:49.142 INFO  CombineGVCFs - Picard Version: 2.25.4
14:54:49.142 INFO  CombineGVCFs - Built for Spark Version: 2.4.5
14:54:49.142 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:54:49.142 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:54:49.142 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:54:49.142 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:54:49.143 INFO  CombineGVCFs - Deflater: IntelDeflater
14:54:49.143 INFO  CombineGVCFs - Inflater: IntelInflater
14:54:49.143 INFO  CombineGVCFs - GCS max retries/reopens: 20
14:54:49.143 INFO  CombineGVCFs - Requester pays: disabled
14:54:49.143 INFO  CombineGVCFs - Initializing engine
14:54:49.758 INFO  FeatureManager - Using codec VCFCodec to read file file:///nese/meclab/Jess/dorado/SNPs/GD_110-Concordia/GD_110-Concordia-SUPER1.g.vcf
14:54:49.830 INFO  CombineGVCFs - Shutting down engine
[December 19, 2023 at 2:54:49 PM UTC] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=83886080
org.broadinstitute.hellbender.exceptions.GATKException: Error initializing feature reader for path GD_110-Concordia-SUPER1.g.vcf
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:436)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:377)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:319)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:291)
 at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:226)
 at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$initializeDrivingVariants$0(MultiVariantWalker.java:86)
 at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1655)
 at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:658)
 at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(MultiVariantWalker.java:76)
 at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:67)
 at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:726)
 at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(MultiVariantWalker.java:49)
 at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
 at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
 at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
 at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
 at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
 at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: GD_110-Concordia-SUPER1.g.vcf
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:263)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:102)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:127)
 at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:433)
 ... 17 more
Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
 at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)
 ... 21 more

Following the advice on other posts here and on other forums, I then checked the first input file, which produced the same error:

gatk ValidateVariants -V GD_110-Concordia-SUPER1.g.vcf
Using GATK jar /modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-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 -jar /modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-local.jar ValidateVariants -V GD_110-Concordia-SUPER1.g.vcf
14:57:58.141 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/modules/apps/gatk/4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 19, 2023 2:57:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:57:58.449 INFO  ValidateVariants - ------------------------------------------------------------
14:57:58.450 INFO  ValidateVariants - The Genome Analysis Toolkit (GATK) v4.2.3.0
14:57:58.450 INFO  ValidateVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
14:57:58.450 INFO  ValidateVariants - Executing as jessmclaughl_umass_edu@login1 on Linux v5.4.0-163-generic amd64
14:57:58.450 INFO  ValidateVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.20.1+1-post-Ubuntu-0ubuntu120.04
14:57:58.450 INFO  ValidateVariants - Start Date/Time: December 19, 2023 at 2:57:58 PM UTC
14:57:58.450 INFO  ValidateVariants - ------------------------------------------------------------
14:57:58.450 INFO  ValidateVariants - ------------------------------------------------------------
14:57:58.451 INFO  ValidateVariants - HTSJDK Version: 2.24.1
14:57:58.451 INFO  ValidateVariants - Picard Version: 2.25.4
14:57:58.451 INFO  ValidateVariants - Built for Spark Version: 2.4.5
14:57:58.451 INFO  ValidateVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:57:58.451 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:57:58.451 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:57:58.451 INFO  ValidateVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:57:58.451 INFO  ValidateVariants - Deflater: IntelDeflater
14:57:58.451 INFO  ValidateVariants - Inflater: IntelInflater
14:57:58.451 INFO  ValidateVariants - GCS max retries/reopens: 20
14:57:58.451 INFO  ValidateVariants - Requester pays: disabled
14:57:58.527 INFO  ValidateVariants - Initializing engine
14:57:58.845 INFO  FeatureManager - Using codec VCFCodec to read file file:///nese/meclab/Jess/dorado/SNPs/GD_110-Concordia/GD_110-Concordia-SUPER1.g.vcf
14:57:58.849 INFO  ValidateVariants - Shutting down engine
[December 19, 2023 at 2:57:58 PM UTC] org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=138412032
org.broadinstitute.hellbender.exceptions.GATKException: Error initializing feature reader for path GD_110-Concordia-SUPER1.g.vcf
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:436)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:377)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:319)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:291)
 at org.broadinstitute.hellbender.engine.VariantWalker.initializeDrivingVariants(VariantWalker.java:58)
 at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:67)
 at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:726)
 at org.broadinstitute.hellbender.engine.VariantWalker.onStartup(VariantWalker.java:45)
 at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
 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)
Caused by: htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: GD_110-Concordia-SUPER1.g.vcf
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:263)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:102)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:127)
 at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
 at org.broadinstitute.hellbender.engine.FeatureDataSource.getTribbleFeatureReader(FeatureDataSource.java:433)
 ... 13 more
Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
 at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)
 ... 17 more

Figuring that perhaps I was using the wrong tool, I then tried the GatherVcfs tool on Picard, only to have the same output yet again:

gatk GatherVcfs -R /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta -I GD_110-Concordia-SUPER1.g.vcf -I GD_110-Concordia-SUPER2.g.vcf -I GD_110-Concordia-SUPER3.g.vcf -I GD_110-Concordia-SUPER4.g.vcf -I GD_110-Concordia-SUPER5.g.vcf -I GD_110-Concordia-SUPER6.g.vcf -I GD_110-Concordia-SUPER7.g.vcf -I GD_110-Concordia-SUPER8.g.vcf -I GD_110-Concordia-SUPER9.g.vcf -I GD_110-Concordia-SUPER10.g.vcf -I GD_110-Concordia-SUPER11.g.vcf -I GD_110-Concordia-SUPER12.g.vcf -I GD_110-Concordia-SUPER13.g.vcf -I GD_110-Concordia-SUPER14.g.vcf -I GD_110-Concordia-SUPER15.g.vcf -I GD_110-Concordia-SUPER16.g.vcf -I GD_110-Concordia-SUPER17.g.vcf -I GD_110-Concordia-SUPER18.g.vcf -I GD_110-Concordia-SUPER19.g.vcf -I GD_110-Concordia-SUPER20.g.vcf -I GD_110-Concordia-SUPER21.g.vcf -I GD_110-Concordia-SUPER22.g.vcf -I GD_110-Concordia-SUPER23.g.vcf -I GD_110-Concordia-SUPER24.g.vcf -I GD_110-Concordia-SUPER25.g.vcf -O GD_110-Concordia-ALL.g.vcf
Using GATK jar /modules/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-9.4.0/gatk-4.4.0.0-v4vuf3ny7cfdslxnvr5doajufikgfm7q/bin/gatk-package-4.4.0.0-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 -jar /modules/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-9.4.0/gatk-4.4.0.0-v4vuf3ny7cfdslxnvr5doajufikgfm7q/bin/gatk-package-4.4.0.0-local.jar GatherVcfs -R /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta -I GD_110-Concordia-SUPER1.g.vcf -I GD_110-Concordia-SUPER2.g.vcf -I GD_110-Concordia-SUPER3.g.vcf -I GD_110-Concordia-SUPER4.g.vcf -I GD_110-Concordia-SUPER5.g.vcf -I GD_110-Concordia-SUPER6.g.vcf -I GD_110-Concordia-SUPER7.g.vcf -I GD_110-Concordia-SUPER8.g.vcf -I GD_110-Concordia-SUPER9.g.vcf -I GD_110-Concordia-SUPER10.g.vcf -I GD_110-Concordia-SUPER11.g.vcf -I GD_110-Concordia-SUPER12.g.vcf -I GD_110-Concordia-SUPER13.g.vcf -I GD_110-Concordia-SUPER14.g.vcf -I GD_110-Concordia-SUPER15.g.vcf -I GD_110-Concordia-SUPER16.g.vcf -I GD_110-Concordia-SUPER17.g.vcf -I GD_110-Concordia-SUPER18.g.vcf -I GD_110-Concordia-SUPER19.g.vcf -I GD_110-Concordia-SUPER20.g.vcf -I GD_110-Concordia-SUPER21.g.vcf -I GD_110-Concordia-SUPER22.g.vcf -I GD_110-Concordia-SUPER23.g.vcf -I GD_110-Concordia-SUPER24.g.vcf -I GD_110-Concordia-SUPER25.g.vcf -O GD_110-Concordia-ALL.g.vcf
14:01:47.834 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/modules/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-9.4.0/gatk-4.4.0.0-v4vuf3ny7cfdslxnvr5doajufikgfm7q/bin/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Dec 19 14:01:47 UTC 2023] GatherVcfs --INPUT GD_110-Concordia-SUPER1.g.vcf --INPUT GD_110-Concordia-SUPER2.g.vcf --INPUT GD_110-Concordia-SUPER3.g.vcf --INPUT GD_110-Concordia-SUPER4.g.vcf --INPUT GD_110-Concordia-SUPER5.g.vcf --INPUT GD_110-Concordia-SUPER6.g.vcf --INPUT GD_110-Concordia-SUPER7.g.vcf --INPUT GD_110-Concordia-SUPER8.g.vcf --INPUT GD_110-Concordia-SUPER9.g.vcf --INPUT GD_110-Concordia-SUPER10.g.vcf --INPUT GD_110-Concordia-SUPER11.g.vcf --INPUT GD_110-Concordia-SUPER12.g.vcf --INPUT GD_110-Concordia-SUPER13.g.vcf --INPUT GD_110-Concordia-SUPER14.g.vcf --INPUT GD_110-Concordia-SUPER15.g.vcf --INPUT GD_110-Concordia-SUPER16.g.vcf --INPUT GD_110-Concordia-SUPER17.g.vcf --INPUT GD_110-Concordia-SUPER18.g.vcf --INPUT GD_110-Concordia-SUPER19.g.vcf --INPUT GD_110-Concordia-SUPER20.g.vcf --INPUT GD_110-Concordia-SUPER21.g.vcf --INPUT GD_110-Concordia-SUPER22.g.vcf --INPUT GD_110-Concordia-SUPER23.g.vcf --INPUT GD_110-Concordia-SUPER24.g.vcf --INPUT GD_110-Concordia-SUPER25.g.vcf --OUTPUT GD_110-Concordia-ALL.g.vcf --REFERENCE_SEQUENCE /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Tue Dec 19 14:01:47 UTC 2023] Executing as jessmclaughl_umass_edu@login1 on Linux 5.4.0-163-generic amd64; OpenJDK 64-Bit Server VM 17.0.5+8; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2023-12-19 14:01:47 GatherVcfs Checking inputs.
[Tue Dec 19 14:01:47 UTC 2023] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=98566144
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: file:///nese/meclab/Jess/dorado/SNPs/GD_110-Concordia/GD_110-Concordia-SUPER1.g.vcf
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:264)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:103)
 at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:128)
 at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
 at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:81)
 at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:145)
 at htsjdk.variant.vcf.VCFFileReader.getSequenceDictionary(VCFFileReader.java:122)
 at picard.vcf.GatherVcfs.doWork(GatherVcfs.java:101)
 at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
 at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
 at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
 at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
 at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file
 at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:115)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
 at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
 at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:262)
... 12 more

The catch is that I checked my vcfs, and they do in fact all appear to have the #CHROM line, without any other obvious errors:

##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --min-base-quality-score 20 --emit-ref-confidence GVCF --output /nese/meclab/Jess/dorado/SNPs/GD_110_SUPER_1^M.g.vcf.g.vcf --intervals SUPER_1^M --input /nese/meclab/Jess/dorado/align_genomeH2_Sept2023/IR-bams/GD_110_SORT_DR_CL_RG_IR.bam --reference /nese/meclab/Shared/reference_genomes/GD_reference_genome/fSalBra1.hap2.cur.20230512.fasta --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --max-mnp-distance 0 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.2.3.0",Date="December 1, 2023 at 2:42:44 PM UTC">
##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)
##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)
##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)
##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)
##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)
##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)
##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)
##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)
##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)
##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)
##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)
##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)
##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)
##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)
##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive)
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##contig=<ID=SUPER_1,length=99388286>
##contig=<ID=SUPER_2,length=60494693>
##contig=<ID=SUPER_3,length=52544285>
##contig=<ID=SUPER_4,length=50283246>
##contig=<ID=SUPER_5,length=46574413>
##contig=<ID=SUPER_6,length=46419030>
##contig=<ID=SUPER_7,length=44467116>
##contig=<ID=SUPER_8,length=43347643>
##contig=<ID=SUPER_9,length=42620587>
##contig=<ID=SUPER_10,length=41637409>
##contig=<ID=SUPER_11,length=40765202>
##contig=<ID=SUPER_12,length=40068765>
##contig=<ID=SUPER_13,length=38865264>
##contig=<ID=SUPER_14,length=37349020>
##contig=<ID=SUPER_15,length=36871833>
##contig=<ID=SUPER_16,length=36840974>
##contig=<ID=SUPER_17,length=36758898>
##contig=<ID=SUPER_18,length=36616962>
##contig=<ID=SUPER_19,length=36202799>
##contig=<ID=SUPER_20,length=33995598>
##contig=<ID=SUPER_20_unloc_1,length=406135>
##contig=<ID=SUPER_20_unloc_2,length=310195>
##contig=<ID=SUPER_20_unloc_3,length=193154>
##contig=<ID=SUPER_20_unloc_4,length=189741>
##contig=<ID=SUPER_21,length=34019765>
##contig=<ID=SUPER_22,length=33960001>
##contig=<ID=SUPER_23,length=32802579>
##contig=<ID=SUPER_24,length=29456005>
##contig=<ID=SUPER_25,length=28888514>
##contig=<ID=scaffold_146,length=38845>
##contig=<ID=scaffold_156,length=34718>
##contig=<ID=scaffold_155,length=34850>
##contig=<ID=scaffold_145,length=39058>
##contig=<ID=scaffold_120,length=56971>
##contig=<ID=scaffold_131,length=52264>
##contig=<ID=scaffold_128,length=52845>
##contig=<ID=scaffold_149,length=37989>
##contig=<ID=scaffold_159,length=34518>
##contig=<ID=scaffold_147,length=38801>
##contig=<ID=scaffold_157,length=34645>
##contig=<ID=scaffold_130,length=52423>
##contig=<ID=scaffold_138,length=42068>
##contig=<ID=scaffold_93,length=82598>
##contig=<ID=scaffold_49,length=212306>
##contig=<ID=scaffold_103,length=71558>
##contig=<ID=scaffold_154,length=35170>
##contig=<ID=scaffold_144,length=39185>
##contig=<ID=scaffold_122,length=56206>
##contig=<ID=scaffold_113,length=63397>
##contig=<ID=scaffold_97,length=75088>
##contig=<ID=scaffold_143,length=39864>
##contig=<ID=scaffold_153,length=35235>
##contig=<ID=scaffold_170,length=19025>
##contig=<ID=scaffold_114,length=59890>
##contig=<ID=scaffold_96,length=78734>
##contig=<ID=scaffold_168,length=22635>
##contig=<ID=scaffold_98,length=74449>
##contig=<ID=scaffold_160,length=33725>
##contig=<ID=scaffold_161,length=33198>
##contig=<ID=scaffold_117,length=58146>
##contig=<ID=scaffold_119,length=58252>
##contig=<ID=scaffold_107,length=68638>
##contig=<ID=scaffold_106,length=69016>
##contig=<ID=scaffold_115,length=59762>
##contig=<ID=scaffold_116,length=58699>
##contig=<ID=scaffold_162,length=33184>
##contig=<ID=scaffold_101,length=72300>
##contig=<ID=scaffold_110,length=65330>
##contig=<ID=scaffold_58,length=161626>
##contig=<ID=scaffold_164,length=31261>
##contig=<ID=scaffold_118,length=58104>
##contig=<ID=scaffold_78,length=99882>
##contig=<ID=scaffold_112,length=63411>
##contig=<ID=scaffold_165,length=28521>
##contig=<ID=scaffold_123,length=55308>
##contig=<ID=scaffold_166,length=27683>
##contig=<ID=scaffold_77,length=101252>
##contig=<ID=scaffold_169,length=19072>
##contig=<ID=scaffold_133,length=50369>
##contig=<ID=scaffold_167,length=22690>
##contig=<ID=scaffold_134,length=46622>
##contig=<ID=scaffold_53,length=190417>
##contig=<ID=scaffold_124,length=55295>
##contig=<ID=scaffold_142,length=40066>
##contig=<ID=scaffold_152,length=35375>
##contig=<ID=scaffold_163,length=33108>
##contig=<ID=scaffold_125,length=54343>
##contig=<ID=scaffold_126,length=54042>
##contig=<ID=scaffold_139,length=41197>
##contig=<ID=scaffold_158,length=34546>
##contig=<ID=scaffold_148,length=38303>
##contig=<ID=scaffold_95,length=79166>
##contig=<ID=scaffold_140,length=40969>
##contig=<ID=scaffold_150,length=37182>
##contig=<ID=scaffold_137,length=44488>
##contig=<ID=scaffold_135,length=46575>
##contig=<ID=scaffold_73,length=110434>
##contig=<ID=scaffold_136,length=45293>
##contig=<ID=scaffold_88,length=89068>
##contig=<ID=scaffold_129,length=52821>
##contig=<ID=scaffold_151,length=37087>
##contig=<ID=scaffold_141,length=40449>
##contig=<ID=scaffold_127,length=53965>
##source=HaplotypeCaller
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  GD_110
SUPER_1 1       .       T       <NON_REF>       .       .       END=686 GT:DP:GQ:MIN_DP:PL      0/0:0:0:0:0,0,0
SUPER_1 687     .       C       <NON_REF>       .       .       END=710 GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,30

I also ran all of these in GATK v4.4.0 to see if it was an issue that was perhaps specific to that version, but received the same errors. For additional context (not sure if this really matters), these are all being run on the computing cluster at my institution.

Am I missing some obvious error in the formation of my headers? Or is there another option I should be adding to my commands? 

Thanks in advance!