Hi. I have got gzip-compressed VCF file 1060142146_S31.vcf.gz using HaplotypeCaller. IndexFeatureFile works fine on 1060142146_S31.vcf.gz compressed by HaplotypeCaller. But after I inflated the same VCF file with gunzip and compressed with gzip, IndexFeatureFile exits with error when I try to index newly compressed 1060142146_S31.vcf.gz. How should I inflate and compress VCF files in a way that does not trigger an error?

GATK version:

The Genome Analysis Toolkit (GATK) v4.6.1.0
HTSJDK Version: 4.1.3
Picard Version: 3.3.0

Gzip version: 1.12

Gunzip version: 1.12

OS version: Ubuntu 24.04.1 LTS

Exact command used:

gatk IndexFeatureFile --input 1060142146_S31.vcf.gz

Entire program log:

Using GATK jar /home/administrator/tools/gatk/gatk-package-4.6.1.0-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 /home/administrator/tools/gatk/gatk-package-4.6.1.0-local.jar IndexFeatureFile --input 1060142146_S31.vcf.gz
13:28:23.495 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/administrator/tools/gatk/gatk-package-4.6.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
SLF4J(W): Class path contains multiple SLF4J providers.
SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@34279b8a]
SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@687389a6]
SLF4J(W): See https://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@34279b8a]
13:28:23.727 INFO  IndexFeatureFile - ------------------------------------------------------------
13:28:23.730 INFO  IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.6.1.0
13:28:23.731 INFO  IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
13:28:23.731 INFO  IndexFeatureFile - Executing as administrator@compute-vm-8-32-500-hdd-1736852799422 on Linux v6.8.0-51-generic amd64
13:28:23.731 INFO  IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+7-Ubuntu-124.04
13:28:23.731 INFO  IndexFeatureFile - Start Date/Time: February 19, 2025 at 1:28:23 PM ALMT
13:28:23.731 INFO  IndexFeatureFile - ------------------------------------------------------------
13:28:23.731 INFO  IndexFeatureFile - ------------------------------------------------------------
13:28:23.732 INFO  IndexFeatureFile - HTSJDK Version: 4.1.3
13:28:23.732 INFO  IndexFeatureFile - Picard Version: 3.3.0
13:28:23.733 INFO  IndexFeatureFile - Built for Spark Version: 3.5.0
13:28:23.735 INFO  IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:28:23.735 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:28:23.736 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:28:23.736 INFO  IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:28:23.736 INFO  IndexFeatureFile - Deflater: IntelDeflater
13:28:23.736 INFO  IndexFeatureFile - Inflater: IntelInflater
13:28:23.737 INFO  IndexFeatureFile - GCS max retries/reopens: 20
13:28:23.737 INFO  IndexFeatureFile - Requester pays: disabled
13:28:23.737 INFO  IndexFeatureFile - Initializing engine
13:28:23.737 INFO  IndexFeatureFile - Done initializing engine
13:28:23.829 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/administrator/varcall_results/gatk/1060142146_S31.vcf.gz
13:28:23.833 INFO  IndexFeatureFile - Shutting down engine
[February 19, 2025 at 1:28:23 PM ALMT] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=201326592
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A USER ERROR has occurred: Error while trying to create index for 1060142146_S31.vcf.gz. Error was: htsjdk.tribble.TribbleException.MalformedFeatureFile: Input file is not in valid block compressed format., for input source: /home/administrator/varcall_results/gatk/1060142146_S31.vcf.gz

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