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

YatrosYatros Seattle, WA, USAMember ✭✭

Hello,

I'm trying to merge some GVCF files from WES data. After making a hard filtering step, the GatherVcfsCloud command in GATK 4.0.1.0 docker image returns the following error stating that it can not parse the header of the input files:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/JointGenotyping/6958b134-2439-49ef-a41d-d7ed33e11170/call-SitesOnlyGatherVcf/execution/tmp.KqtDKJ
20:52:51.762 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/build/install/gatk/lib/gkl-0.8.2.jar!/com/intel/gkl/native/libgkl_compression.so
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 https://software.broadinstitute.org/gatk/
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 https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
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] org.broadinstitute.hellbender.tools.GatherVcfsCloud done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=6174015488
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(TribbleIndexedFeatureReader.java:262)
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:101)
    at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:126)
    at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:110)
    at org.broadinstitute.hellbender.tools.GatherVcfsCloud.getReaderFromVCFUri(GatherVcfsCloud.java:226)
    at org.broadinstitute.hellbender.tools.GatherVcfsCloud.getHeader(GatherVcfsCloud.java:200)
    at org.broadinstitute.hellbender.tools.GatherVcfsCloud.doWork(GatherVcfsCloud.java:153)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
    at org.broadinstitute.hellbender.Main.main(Main.java:275)
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(UnixException.java:86)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
    at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
    at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
    at java.nio.file.Files.newByteChannel(Files.java:361)
    at java.nio.file.Files.newByteChannel(Files.java:407)
    at htsjdk.samtools.seekablestream.SeekablePathStream.<init>(SeekablePathStream.java:41)
    at htsjdk.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:108)
    at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:252)
    ... 12 more
Using GATK wrapper script /gatk/build/install/gatk/bin/gatk
Running:
    /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 4.0.2.1 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,

Best,

Yatros

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