Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

gVCF ALT Column Showing Only <NON_REF> #8974

Open
kotchanipar opened this issue Sep 9, 2024 · 0 comments
Open

gVCF ALT Column Showing Only <NON_REF> #8974

kotchanipar opened this issue Sep 9, 2024 · 0 comments

Comments

@kotchanipar
Copy link

kotchanipar commented Sep 9, 2024

I use gatk CombineGVCFs to merge *gvcf files after running Haplotypecaller using command below

gatk CombineGVCFs -R ${ref} -V merge.list -O comnine_all.gvcf.gz

but it has the following warning message

`The following have been reloaded with a version change:

  1. GCCcore/11.2.0 => GCCcore/12.2.0

WARNING: GATK v4.1.4.1 support for Java 11 is in beta state. Use at your own risk.

The following have been reloaded with a version change:

  1. GATK/4.5.0-java-17 => GATK/4.1.4.1-GCCcore-8.3.0-Java-11
  2. GCCcore/12.2.0 => GCCcore/8.3.0
  3. GMP/6.2.1-GCCcore-11.2.0 => GMP/6.1.2-GCCcore-8.3.0
  4. Java/17.0.4 => Java/11.0.16
  5. Python/3.9.6-GCCcore-11.2.0 => Python/3.7.4-GCCcore-8.3.0
  6. SQLite/3.36-GCCcore-11.2.0 => SQLite/3.29.0-GCCcore-8.3.0
  7. Tcl/8.6.11-GCCcore-11.2.0 => Tcl/8.6.9-GCCcore-8.3.0
  8. XZ/5.2.5-GCCcore-11.2.0 => XZ/5.2.4-GCCcore-8.3.0
  9. binutils/2.37-GCCcore-11.2.0 => binutils/2.32-GCCcore-8.3.0
  10. bzip2/1.0.8-GCCcore-11.2.0 => bzip2/1.0.8-GCCcore-8.3.0
  11. libffi/3.4.2-GCCcore-11.2.0 => libffi/3.2.1-GCCcore-8.3.0
  12. libreadline/8.1-GCCcore-11.2.0 => libreadline/8.0-GCCcore-8.3.0
  13. ncurses/6.2-GCCcore-11.2.0 => ncurses/6.1-GCCcore-8.3.0
  14. zlib/1.2.11-GCCcore-11.2.0 => zlib/1.2.11-GCCcore-8.3.0

13:26:41.785 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nbt_main/share/module_new/modules/software/GATK/4.1.4.1-GCCcore-8.3.0-Java-11/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Sep 09, 2024 1:26:42 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:26:42.114 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.115 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.4.1
13:26:42.115 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
13:26:42.115 INFO CombineGVCFs - Executing as [email protected] on Linux v4.18.0-305.el8.x86_64 amd64
13:26:42.115 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.16+8
13:26:42.115 INFO CombineGVCFs - Start Date/Time: September 9, 2024 at 1:26:41 PM ICT
13:26:42.115 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.115 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.116 INFO CombineGVCFs - HTSJDK Version: 2.21.0
13:26:42.116 INFO CombineGVCFs - Picard Version: 2.21.2
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:26:42.116 INFO CombineGVCFs - Deflater: IntelDeflater
13:26:42.116 INFO CombineGVCFs - Inflater: IntelInflater
13:26:42.116 INFO CombineGVCFs - GCS max retries/reopens: 20
13:26:42.116 INFO CombineGVCFs - Requester pays: disabled
13:26:42.116 INFO CombineGVCFs - Initializing engine
13:26:42.404 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam1.gvcf.gz
13:26:42.569 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam2.gvcf.gz
13:26:42.757 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam3.gvcf.gz
13:26:42.891 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam4.gvcf.gz
13:26:43.003 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam5.gvcf.gz
13:26:43.160 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam6.gvcf.gz
13:26:43.246 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam7.gvcf.gz
13:26:43.316 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam8.gvcf.gz
13:26:43.456 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam9.gvcf.gz
13:26:43.527 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam10.gvcf.gz
13:26:43.631 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam11.gvcf.gz
13:26:43.770 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam12.gvcf.gz
13:26:43.858 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam13.gvcf.gz
13:26:44.623 INFO CombineGVCFs - Done initializing engine
13:26:44.681 INFO ProgressMeter - Starting traversal
13:26:44.681 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:26:45.034 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location NC_080782.1:78723 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
13:26:54.683 INFO ProgressMeter - NC_080782.1:3768890 0.2 571000 3425657.4
13:27:04.683 INFO ProgressMeter - NC_080782.1:17827068 0.3 1391000 4172791.4
13:27:14.694 INFO ProgressMeter - NC_080782.1:44855178 0.5 2086000 4170192.9
13:27:24.706 INFO ProgressMeter - NC_080782.1:67560924 0.7 2761000 4138913.2
13:27:34.715 INFO ProgressMeter - NC_080782.1:106975576 0.8 3384000 4058121.6`

and the result shows that all entries in the ALT column are <NON_REF>.

image

Could you help me figure out this problem?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant