CombineGVCFs outputs null genotypes for all samples
CombineGVCFs generates ./. for all samples. Individual GVCFs have 0/0 or 0/1 sites but when combined they are all ./. and doesnt generate variant information (AC, AN or AF).
These GVCFs were created using 4.2.0.0 Haplotypecaller (-ERC GVCF)
REQUIRED for all errors and issues:
a) GATK version used: 4.2.0.0
b) Exact command used:
gatk --java-options -Xmx36g CombineGVCFs
--reference human_g1k_v37_decoy.fasta
-V gvcf.list
--output TGCTn100_chr13.gvcf
-L 13
-D dbsnp_138.b37.vcf
c) Entire program log:
Using GATK jar gatk-4.2.2.0/gatk-package-4.2.2.0-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 -Xmx36g -jar gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar CombineGVCFs --reference human_g1k_v37_decoy.fasta -V gvcf.list --output /TGCTn100_chr13.gvcf -L 13 -D dbsnp_138.b37.vcf
10:14:36.169 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 28, 2023 10:14:36 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:14:36.479 INFO CombineGVCFs - ------------------------------------------------------------
10:14:36.480 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.2.2.0
10:14:36.480 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
10:14:36.480 INFO CombineGVCFs - Executing as ravichav@ji08 on Linux v3.10.0-1160.45.1.el7.x86_64 amd64
10:14:36.480 INFO CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v11.0.11+9-LTS-194
10:14:36.481 INFO CombineGVCFs - Start Date/Time: June 28, 2023 at 10:14:36 AM EDT
10:14:36.481 INFO CombineGVCFs - ------------------------------------------------------------
10:14:36.481 INFO CombineGVCFs - ------------------------------------------------------------
10:14:36.481 INFO CombineGVCFs - HTSJDK Version: 2.24.1
10:14:36.481 INFO CombineGVCFs - Picard Version: 2.25.4
10:14:36.481 INFO CombineGVCFs - Built for Spark Version: 2.4.5
10:14:36.482 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:14:36.482 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:14:36.482 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:14:36.482 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:14:36.482 INFO CombineGVCFs - Deflater: IntelDeflater
10:14:36.482 INFO CombineGVCFs - Inflater: IntelInflater
10:14:36.482 INFO CombineGVCFs - GCS max retries/reopens: 20
10:14:36.483 INFO CombineGVCFs - Requester pays: disabled
10:14:36.484 INFO CombineGVCFs - Initializing engine
10:14:36.807 INFO FeatureManager - Using codec VCFCodec to read file file://dbsnp_138.b37.vcf
10:14:37.027 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_10.gvcf
10:14:37.441 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_11.gvcf
10:14:37.606 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_12.gvcf
10:14:37.844 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_13.gvcf
10:14:38.069 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_14.gvcf
10:14:38.562 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_15.gvcf
10:14:38.758 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_16.gvcf
10:14:39.044 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_17.gvcf
10:14:39.225 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_18.gvcf
10:14:39.698 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_19.gvcf
10:14:39.861 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_1.gvcf
10:14:39.979 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_20.gvcf
10:14:40.168 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_21.gvcf
10:14:41.673 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_22.gvcf
10:14:41.887 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_23.gvcf
10:14:42.030 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_24.gvcf
10:14:42.304 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_25.gvcf
10:14:42.474 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_26.gvcf
10:14:42.646 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_27.gvcf
10:14:42.811 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_28.gvcf
10:14:42.967 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_2.gvcf
10:14:43.112 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_3.gvcf
10:14:44.182 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_4.gvcf
10:14:44.344 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_5.gvcf
10:14:44.566 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_6.gvcf
10:14:44.758 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_7.gvcf
10:14:44.887 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_8.gvcf
10:14:45.024 INFO FeatureManager - Using codec VCFCodec to read file file://12665_B_9.gvcf
10:14:45.163 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_29.gvcf
10:14:45.298 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_30.gvcf
10:14:45.426 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_31.gvcf
10:14:45.557 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_32.gvcf
10:14:49.233 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_33.gvcf
10:14:49.346 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_34.gvcf
10:14:49.476 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_35.gvcf
10:14:49.640 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_36.gvcf
10:14:49.764 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_37.gvcf
10:14:50.008 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_38.gvcf
10:14:50.156 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_39.gvcf
10:14:50.302 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_40.gvcf
10:14:50.430 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_41.gvcf
10:14:50.581 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_42.gvcf
10:14:50.695 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_43.gvcf
10:14:50.846 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_44.gvcf
10:14:50.992 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_45.gvcf
10:14:51.131 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_46.gvcf
10:14:51.280 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_47.gvcf
10:14:51.408 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_48.gvcf
10:14:51.544 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_49.gvcf
10:14:51.706 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_50.gvcf
10:14:51.902 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_51.gvcf
10:14:52.048 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_52.gvcf
10:14:52.175 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_53.gvcf
10:14:54.409 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_54.gvcf
10:14:54.537 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_55.gvcf
10:14:54.675 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_56.gvcf
10:14:54.817 INFO FeatureManager - Using codec VCFCodec to read file file://12665_C_57.gvcf
10:14:54.935 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3623.gvcf
10:14:55.348 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3624.gvcf
10:14:55.636 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3625.gvcf
10:14:55.968 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3626.gvcf
10:14:56.298 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3627.gvcf
10:14:56.709 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3628.gvcf
10:14:56.966 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3629.gvcf
10:14:57.138 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3630.gvcf
10:14:57.309 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3631.gvcf
10:15:04.614 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3632.gvcf
10:15:04.906 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3633.gvcf
10:15:05.281 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3634.gvcf
10:15:05.659 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3635.gvcf
10:15:05.959 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3636.gvcf
10:15:06.203 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3637.gvcf
10:15:06.511 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3638.gvcf
10:15:06.886 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3639.gvcf
10:15:07.296 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3640.gvcf
10:15:07.624 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3641.gvcf
10:15:07.882 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3642.gvcf
10:15:08.193 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3643.gvcf
10:15:08.481 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3644.gvcf
10:15:08.834 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3645.gvcf
10:15:09.116 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3646.gvcf
10:15:09.401 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3647.gvcf
10:15:09.822 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3648.gvcf
10:15:10.138 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3649.gvcf
10:15:10.377 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3650.gvcf
10:15:10.745 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3651.gvcf
10:15:10.996 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3652.gvcf
10:15:11.263 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3653.gvcf
10:15:16.138 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3654.gvcf
10:15:16.493 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3655.gvcf
10:15:16.923 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3720.gvcf
10:15:17.036 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3721.gvcf
10:15:17.156 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3722.gvcf
10:15:17.271 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3723.gvcf
10:15:17.397 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3724.gvcf
10:15:17.514 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3725.gvcf
10:15:17.643 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3726.gvcf
10:15:17.782 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3728.gvcf
10:15:17.913 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3739.gvcf
10:15:18.056 INFO FeatureManager - Using codec VCFCodec to read file file://CGRBG3740.gvcf
10:16:05.049 INFO IntervalArgumentCollection - Processing 115169878 bp from intervals
10:16:05.118 INFO CombineGVCFs - Done initializing engine
10:16:05.143 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "gvcf". Defaulting to VCF.
10:16:05.159 INFO ProgressMeter - Starting traversal
10:16:05.169 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
10:16:10.478 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 13:19020145 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
10:16:28.769 INFO ProgressMeter - 13:19021224 0.4 1000 2542.4
10:16:55.435 INFO ProgressMeter - 13:19024554 0.8 2000 2387.3
10:17:21.325 INFO ProgressMeter - 13:19028057 1.3 3000 2363.6
10:17:45.380 INFO ProgressMeter - 13:19030542 1.7 4000 2395.0
10:18:07.153 INFO ProgressMeter - 13:19033566 2.0 5000 2459.3
10:18:34.593 INFO ProgressMeter - 13:19036274 2.5 7000 2810.8
10:19:23.555 INFO ProgressMeter - 13:19041610 3.3 8000 2419.5
10:19:34.433 INFO ProgressMeter - 13:19042217 3.5 9000 2580.5
10:19:45.083 INFO ProgressMeter - 13:19042539 3.7 12000 3274.0
10:19:55.220 INFO ProgressMeter - 13:19058043 3.8 31000 8085.3
10:20:05.347 INFO ProgressMeter - 13:19242864 4.0 162000 40470.2
10:20:15.356 INFO ProgressMeter - 13:19348611 4.2 296000 70986.9
10:20:25.375 INFO ProgressMeter - 13:19462073 4.3 513000 118290.9
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10:20:45.565 INFO ProgressMeter - 13:19686233 4.7 983000 210345.4
10:20:55.627 INFO ProgressMeter - 13:19766588 4.8 1310000 270607.1
10:21:05.659 INFO ProgressMeter - 13:19897474 5.0 1461000 291724.5
10:21:15.744 INFO ProgressMeter - 13:19984766 5.2 1742000 336538.2
10:21:25.787 INFO ProgressMeter - 13:20103487 5.3 1978000 370161.3
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10:21:45.843 INFO ProgressMeter - 13:20322522 5.7 2399000 422516.6
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10:22:05.950 INFO ProgressMeter - 13:20529223 6.0 2705000 449857.4
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10:23:06.046 INFO ProgressMeter - 13:21184258 7.0 3841000 547570.9
10:23:16.062 INFO ProgressMeter - 13:21295244 7.2 4059000 565198.3
10:23:26.080 INFO ProgressMeter - 13:21401606 7.3 4327000 588826.3
10:23:36.103 INFO ProgressMeter - 13:21516421 7.5 4494000 597958.9
10:23:46.123 INFO ProgressMeter - 13:21617307 7.7 4693000 610863.6
10:23:56.141 INFO ProgressMeter - 13:21721614 7.8 4868000 620165.6
10:24:06.159 INFO ProgressMeter - 13:21833935 8.0 5070000 632445.6
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10:24:26.212 INFO ProgressMeter - 13:22054893 8.4 5490000 657429.9
10:24:36.221 INFO ProgressMeter - 13:22177408 8.5 5693000 668386.0
10:24:46.281 INFO ProgressMeter - 13:22299874 8.7 5845000 672983.9
10:24:56.384 INFO ProgressMeter - 13:22440758 8.9 5968000 674077.4
10:25:06.482 INFO ProgressMeter - 13:22561648 9.0 6099000 676022.9
10:25:16.560 INFO ProgressMeter - 13:22702902 9.2 6211000 675854.3
10:25:26.643 INFO ProgressMeter - 13:22845242 9.4 6338000 677288.7
10:25:36.662 INFO ProgressMeter - 13:23023524 9.5 6435000 675600.0
10:25:46.763 INFO ProgressMeter - 13:23196294 9.7 6543000 675007.0
10:25:56.854 INFO ProgressMeter - 13:23329413 9.9 6719000 681342.3
10:26:06.867 INFO ProgressMeter - 13:23471401 10.0 6863000 684364.4
10:26:16.961 INFO ProgressMeter - 13:23588647 10.2 7026000 689057.7
10:26:26.995 INFO ProgressMeter - 13:23734039 10.4 7160000 690868.5
10:26:37.009 INFO ProgressMeter - 13:23869373 10.5 7322000 695302.6
10:26:47.064 INFO ProgressMeter - 13:23993330 10.7 7537000 704507.7
10:26:57.115 INFO ProgressMeter - 13:24136216 10.9 7657000 704691.3
10:27:07.135 INFO ProgressMeter - 13:24270753 11.0 7841000 710701.2
10:27:17.147 INFO ProgressMeter - 13:24399083 11.2 8005000 714755.5
10:27:27.149 INFO ProgressMeter - 13:24515614 11.4 8247000 725563.8
10:27:37.153 INFO ProgressMeter - 13:24629624 11.5 8394000 727820.3
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10:28:07.204 INFO ProgressMeter - 13:24966506 12.0 8933000 742318.6
10:28:17.212 INFO ProgressMeter - 13:25056629 12.2 9209000 754791.7
10:28:27.220 INFO ProgressMeter - 13:25158256 12.4 9454000 764421.9
10:28:37.232 INFO ProgressMeter - 13:25264273 12.5 9650000 769882.3
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10:29:07.270 INFO ProgressMeter - 13:25544490 13.0 10529000 807747.3
10:29:17.271 INFO ProgressMeter - 13:25671009 13.2 10681000 809062.5
10:29:27.299 INFO ProgressMeter - 13:25789841 13.4 10838000 810691.5
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10:30:07.384 INFO ProgressMeter - 13:26253455 14.0 11688000 832661.5
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10:31:07.662 INFO ProgressMeter - 13:27040026 15.0 12669000 842266.9
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10:34:08.484 INFO ProgressMeter - 13:29138590 18.1 15839000 877251.8
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12:05:33.666 INFO ProgressMeter - 13:114618561 109.5 99027000 904563.1
12:05:43.677 INFO ProgressMeter - 13:114789314 109.6 99330000 905950.1
12:05:53.737 INFO ProgressMeter - 13:114875588 109.8 99533000 906415.5
12:06:03.764 INFO ProgressMeter - 13:114985026 110.0 99675000 906329.3
12:06:13.786 INFO ProgressMeter - 13:115072362 110.1 99975000 907678.6
12:06:16.959 INFO ProgressMeter - 13:115109340 110.2 100019850 907650.0
12:06:16.959 INFO ProgressMeter - Traversal complete. Processed 100019850 total variants in 110.2 minutes.
12:06:17.835 INFO CombineGVCFs - Shutting down engine
[June 28, 2023 at 12:06:17 PM EDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 111.70 minutes.
Runtime.totalMemory()=32984694784
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Following up on this request GATK Team
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No-calls are expected behavior for CombineGVCFs. Since these variants haven't been through GenotypeGVCFs (or GnarlyGenotyper), they haven't had quality filters applied yet, so we don't want users working with low quality variants. You should run GenotypeGVCFs on the output from CombineGVCFs as in the joint calling best practices: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
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