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A problem about GenomicsDBImport and CombineGVCFs

danriadanria chinaMember
Hello, I used GenomicsDBImport to consolidate GVCFs for a trio family exome data, the command GenomicsDBImport step as follows :

java -Xmx4g -Xms4g -jar gatk-package-4.1.2.0-local.jar GenomicsDBImport -R GRCh38.fa -L chr10.bed --variant father_chr10.g.vcf.gz --variant mother_chr10.g.vcf.gz --variant child_chr10.g.vcf.gz --genomicsdb-workspace-path chr10_database.db

I used chr10 as a test, but this step has been running more than 24 hours, no error message. The log file as folows:

21:58:19.589 INFO GenomicsDBImport - Importing batch 1 with 3 samples
21:58:44.235 INFO GenomicsDBImport - Importing batch 1 with 3 samples
21:59:14.939 INFO GenomicsDBImport - Importing batch 1 with 3 samples
21:59:48.823 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:00:12.540 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:00:30.240 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:00:52.077 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:01:27.475 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:01:50.316 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:02:23.183 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:02:49.333 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:03:24.300 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:03:50.376 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:04:25.497 INFO GenomicsDBImport - Importing batch 1 with 3 samples
22:04:52.138 INFO GenomicsDBImport - Importing batch 1 with 3 samples

So I am a bit confused. Generally, GenomicsDBImport is the preferred tool than CombineGVCFs, but why did it take a long period of time? What is the reason for this? how should I fix my command?

I then tried running CombineGVCFs using the following command to test:
java -Xmx4g -jar gatk-package-4.1.2.0-local.jar CombineGVCFs -R GRCh38.fa -L chr10.bed --variant father_chr10.g.vcf.gz --variant mother_chr10.g.vcf.gz --variant child_chr10.g.vcf.gz -O family_chr10.g.vcf.gz

CombineGVCFs ran successfully and only took less than five minutes. I know I can use CombineGVCFs to consolidate my GVCFs, but I am still confused for GenomicsDBImport.

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