Hi, I am trying to merge a couple of GVCF files generated using HaplotypeCaller but getting Caused by: java.util.zip.ZipException: Not in GZIP format

When I do the below command, the header seems ok but the file is not gzipped since I could directly cat it (even though it has the .gz extension)

cat file.g.vcf.gz

Here's the full stack trace

04:12:01.153 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/gitc/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Jun 16 04:12:01 UTC 2021] MergeVcfs INPUT=[/io/batch/1d0a29/inputs/zWl8g/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_10scattered.g.vcf.gz, /io/batch/1d0a29/inputs/eZmhB/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_11scattered.g.vcf.gz, /io/batch/1d0a29/inputs/mixos/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_12scattered.g.vcf.gz, /io/batch/1d0a29/inputs/XyL3V/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_13scattered.g.vcf.gz, /io/batch/1d0a29/inputs/WKN0l/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_14scattered.g.vcf.gz, /io/batch/1d0a29/inputs/O8dCZ/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_15scattered.g.vcf.gz, /io/batch/1d0a29/inputs/tsqqu/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_16scattered.g.vcf.gz, /io/batch/1d0a29/inputs/P2fu4/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_17scattered.g.vcf.gz, /io/batch/1d0a29/inputs/4cgYv/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_18scattered.g.vcf.gz, /io/batch/1d0a29/inputs/CjEZA/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_19scattered.g.vcf.gz, /io/batch/1d0a29/inputs/eZxWU/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_1scattered.g.vcf.gz, /io/batch/1d0a29/inputs/UO18W/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_20scattered.g.vcf.gz, /io/batch/1d0a29/inputs/IsGAN/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_21scattered.g.vcf.gz, /io/batch/1d0a29/inputs/6I4Jo/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_22scattered.g.vcf.gz, /io/batch/1d0a29/inputs/0MX9c/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_23scattered.g.vcf.gz, /io/batch/1d0a29/inputs/rZXJM/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_24scattered.g.vcf.gz, /io/batch/1d0a29/inputs/YOzTA/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_25scattered.g.vcf.gz, /io/batch/1d0a29/inputs/6I41q/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_26scattered.g.vcf.gz, /io/batch/1d0a29/inputs/pH9XX/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_27scattered.g.vcf.gz, /io/batch/1d0a29/inputs/7GT0m/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_28scattered.g.vcf.gz, /io/batch/1d0a29/inputs/dYObh/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_29scattered.g.vcf.gz, /io/batch/1d0a29/inputs/VSHWZ/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_2scattered.g.vcf.gz, /io/batch/1d0a29/inputs/0SZZP/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_30scattered.g.vcf.gz, /io/batch/1d0a29/inputs/sEyUP/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_31scattered.g.vcf.gz, /io/batch/1d0a29/inputs/eeCDa/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_32scattered.g.vcf.gz, /io/batch/1d0a29/inputs/dgvUR/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_33scattered.g.vcf.gz, /io/batch/1d0a29/inputs/Z9qhc/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_34scattered.g.vcf.gz, /io/batch/1d0a29/inputs/ZtZ4r/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_35scattered.g.vcf.gz, /io/batch/1d0a29/inputs/Hn2AR/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_36scattered.g.vcf.gz, /io/batch/1d0a29/inputs/ydwjH/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_37scattered.g.vcf.gz, /io/batch/1d0a29/inputs/qrQfZ/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_38scattered.g.vcf.gz, /io/batch/1d0a29/inputs/rGVqz/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_39scattered.g.vcf.gz, /io/batch/1d0a29/inputs/XaUHE/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_3scattered.g.vcf.gz, /io/batch/1d0a29/inputs/ef7sM/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_40scattered.g.vcf.gz, /io/batch/1d0a29/inputs/H4LOi/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_41scattered.g.vcf.gz, /io/batch/1d0a29/inputs/knAVw/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_42scattered.g.vcf.gz, /io/batch/1d0a29/inputs/BdJT3/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_43scattered.g.vcf.gz, /io/batch/1d0a29/inputs/4U4HT/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_44scattered.g.vcf.gz, /io/batch/1d0a29/inputs/vdMUw/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_45scattered.g.vcf.gz, /io/batch/1d0a29/inputs/aSRUq/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_46scattered.g.vcf.gz, /io/batch/1d0a29/inputs/QBAeT/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_47scattered.g.vcf.gz, /io/batch/1d0a29/inputs/wprQc/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_48scattered.g.vcf.gz, /io/batch/1d0a29/inputs/6ryKW/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_49scattered.g.vcf.gz, /io/batch/1d0a29/inputs/UR6zm/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_4scattered.g.vcf.gz, /io/batch/1d0a29/inputs/vcWDz/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_50scattered.g.vcf.gz, /io/batch/1d0a29/inputs/5Iwwt/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_5scattered.g.vcf.gz, /io/batch/1d0a29/inputs/sMTDW/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_6scattered.g.vcf.gz, /io/batch/1d0a29/inputs/MCh9G/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_7scattered.g.vcf.gz, /io/batch/1d0a29/inputs/fUtSw/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_8scattered.g.vcf.gz, /io/batch/1d0a29/inputs/CV4Vb/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_9scattered.g.vcf.gz] OUTPUT=SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.g.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 Jun 16 04:12:01 UTC 2021] Executing as root@a43602a413f7 on Linux 5.4.0-1042-gcp amd64; OpenJDK 64-Bit Server VM 1.8.0_222-8u222-b10-1~deb9u1-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.4-SNAPSHOT
[Wed Jun 16 04:12:01 UTC 2021] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2027290624
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Not in GZIP format, for input source: file:///io/batch/1d0a29/inputs/zWl8g/SC_GMFUL5306375.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov_10scattered.g.vcf.gz
	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:120)
	at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:80)
	at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:140)
	at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:92)
	at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:174)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: java.util.zip.ZipException: Not in GZIP format
	at java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165)
	at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:79)
	at java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:91)
	at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:257)
	... 10 more