GATK version: 4.2.5.0

Commend used: 

gatk --java-options "-Xmx128G" \
MergeVcfs \
I=${interval_list} \
O=${output_Mutect}

${interval_list} is a .list file containing all the interval files' paths. All splited vcfs were created by Mutect2, and they belonged to the same sample. 

Running:

16:00:38.794 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/dssg/home/acct-medkwf/medkwf4/.conda/envs/dna/share/picard-2.27.4-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Aug 03 16:00:38 CST 2022] MergeVcfs INPUT=[/dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/interval.list] OUTPUT=/dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Aug 03 16:00:38 CST 2022] Executing as medkwf4@node030.pi.sjtu.edu.cn on Linux 4.18.0-240.el8.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.4-SNAPSHOT
[Wed Aug 03 16:00:38 CST 2022] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=514850816
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
        at java.net.URI.create(URI.java:852)
        at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1228)
        at htsjdk.samtools.util.IOUtil.lambda$unrollPaths$1(IOUtil.java:1182)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
        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:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
        at htsjdk.samtools.util.IOUtil.unrollPaths(IOUtil.java:1179)
        at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:171)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: java.net.URISyntaxException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
        at java.net.URI$Parser.fail(URI.java:2848)
        at java.net.URI$Parser.checkChars(URI.java:3021)
        at java.net.URI$Parser.parse(URI.java:3067)
        at java.net.URI.<init>(URI.java:588)
        at java.net.URI.create(URI.java:850)
        ... 18 more

For troubleshooting,  I used two specific vcf files in the list and reran the command

picard MergeVcfs I=/dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0001-scattered.interval I=/dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0002-scattered.interval O=test.txt

Running:

INFO    2022-08-03 15:26:49     MergeVcfs

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
**********
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
**********    MergeVcfs -I /dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0001-scattered.interval -I /dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0002-scattered.interval -O test.txt
**********

15:26:50.431 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/dssg/home/acct-medkwf/medkwf4/.conda/envs/dna/share/picard-2.27.4-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Aug 03 15:26:50 CST 2022] MergeVcfs INPUT=[/dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0001-scattered.interval, /dssg/home/acct-medkwf/medkwf4/results/MRD/CC_data/CC-H029C/Muetct2_test/CC-H029C.mutect2.vcf.gz.0002-scattered.interval] OUTPUT=test.txt    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Aug 03 15:26:50 CST 2022] Executing as medkwf4@sylogin1.pi.sjtu.edu.cn on Linux 4.18.0-240.el8.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.4-SNAPSHOT
[Wed Aug 03 15:26:50 CST 2022] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=514850816
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
        at java.net.URI.create(URI.java:852)
        at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1228)
        at htsjdk.samtools.util.IOUtil.lambda$unrollPaths$1(IOUtil.java:1182)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
        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:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
        at htsjdk.samtools.util.IOUtil.unrollPaths(IOUtil.java:1179)
        at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:171)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: java.net.URISyntaxException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
        at java.net.URI$Parser.fail(URI.java:2848)
        at java.net.URI$Parser.checkChars(URI.java:3021)
        at java.net.URI$Parser.parse(URI.java:3067)
        at java.net.URI.<init>(URI.java:588)
        at java.net.URI.create(URI.java:850)
        ... 18 more

It looks like issues with my VCF file header. Any idea about how to solve this problem?