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GatherVcfsCloud in GATK v4.0.1.0 docker container returns Unable to parse header error

YatrosYatros Seattle, WA, USAMember ✭✭


I'm trying to merge some GVCF files from WES data. After making a hard filtering step, the GatherVcfsCloud command in GATK docker image returns the following error stating that it can not parse the header of the input files:

Picked up _JAVA_OPTIONS:
20:52:51.762 INFO  NativeLibraryLoader - Loading from jar:file:/gatk/build/install/gatk/lib/gkl-0.8.2.jar!/com/intel/gkl/native/
20:52:52.089 INFO  GatherVcfsCloud - ------------------------------------------------------------
20:52:52.090 INFO  GatherVcfsCloud - The Genome Analysis Toolkit (GATK) v4.0.1.0
20:52:52.090 INFO  GatherVcfsCloud - For support and documentation go to
20:52:52.091 INFO  GatherVcfsCloud - Executing as [email protected] on Linux v4.4.0-116-generic amd64
20:52:52.091 INFO  GatherVcfsCloud - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_131-8u131-b11-2ubuntu1.16.04.3-b11
20:52:52.091 INFO  GatherVcfsCloud - Start Date/Time: March 12, 2018 8:52:51 PM UTC
20:52:52.091 INFO  GatherVcfsCloud - ------------------------------------------------------------
20:52:52.092 INFO  GatherVcfsCloud - ------------------------------------------------------------
20:52:52.092 INFO  GatherVcfsCloud - HTSJDK Version: 2.14.1
20:52:52.092 INFO  GatherVcfsCloud - Picard Version: 2.17.2
20:52:52.093 INFO  GatherVcfsCloud - HTSJDK Defaults.COMPRESSION_LEVEL : 1
20:52:52.093 INFO  GatherVcfsCloud - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:52:52.093 INFO  GatherVcfsCloud - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:52:52.093 INFO  GatherVcfsCloud - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:52:52.093 INFO  GatherVcfsCloud - Deflater: IntelDeflater
20:52:52.094 INFO  GatherVcfsCloud - Inflater: IntelInflater
20:52:52.094 INFO  GatherVcfsCloud - GCS max retries/reopens: 20
20:52:52.094 INFO  GatherVcfsCloud - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from
20:52:52.094 INFO  GatherVcfsCloud - Initializing engine
20:52:52.094 INFO  GatherVcfsCloud - Done initializing engine
20:52:52.094 INFO  GatherVcfsCloud - Checking inputs.
20:52:52.146 INFO  GatherVcfsCloud - Shutting down engine
[March 12, 2018 8:52:52 PM UTC] done. Elapsed time: 0.01 minutes.
htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /mnt/user/Project/GVCFS/cromwell-executions/JointGenotyping/6958b134-2439-49ef-a41d-d7ed33e11170/call-HardFilterAndMakeSitesOnlyVcf/shard-0/execution/IPD1515.0.sites_only.variant_filtered.vcf.gz, for input source: file:///mnt/user/Project/GVCFS/cromwell-executions/JointGenotyping/6958b134-2439-49ef-a41d-d7ed33e11170/call-HardFilterAndMakeSitesOnlyVcf/shard-0/execution/Project.0.sites_only.variant_filtered.vcf.gz
    at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(
    at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(
    at org.broadinstitute.hellbender.Main.mainEntry(
    at org.broadinstitute.hellbender.Main.main(
Caused by: java.nio.file.NoSuchFileException: /mnt/user/Project/GVCFS/cromwell-executions/JointGenotyping/6958b134-2439-49ef-a41d-d7ed33e11170/call-HardFilterAndMakeSitesOnlyVcf/shard-0/execution/Project.0.sites_only.variant_filtered.vcf.gz
    at sun.nio.fs.UnixException.translateToIOException(
    at sun.nio.fs.UnixException.rethrowAsIOException(
    at sun.nio.fs.UnixException.rethrowAsIOException(
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(
    at java.nio.file.Files.newByteChannel(
    at java.nio.file.Files.newByteChannel(
    at htsjdk.samtools.seekablestream.SeekablePathStream.<init>(
    at htsjdk.tribble.util.ParsingUtils.openInputStream(
    at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(
    ... 12 more
Using GATK wrapper script /gatk/build/install/gatk/bin/gatk
    /gatk/build/install/gatk/bin/gatk GatherVcfsCloud --ignore-safety-checks --gather-type BLOCK --input inputs.list --output Project.sites_only.vcf.gz

However, if I run exactly the same command with GATK with the same inputs.list file, the Project.sites_only.vcf.gz file is generated correctly and the headers of the different files do not give any parsing errors.

Can you have a look at this issue for the next release of the GATK docker container?

Thank you very much,



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