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GenomicsDBImport too slow on local server

dbeckerdbecker MunichMember ✭✭✭

Hi,

I tried using GenomicsDBImport for our data. In my testcase I tried importing Chromosome 1 for 223 samples. Since most samples are panels and we have only a few genomes and exomes, I thought it would be best to always call anything together.
My commandline:

opt/gatk/4.0.0.0/gatk --java-options "-Xmx8G -Xms8G" GenomicsDBImport
 --sample-name-map[...]/all_samples.sample_map 
--genomicsdb-workspace-path [...]/germline_snp_database_1
 --batch-size 50 
-L NC_000001 
--reader-threads 5

I only use 5 reader threads because I plan on parallelizing with scatter gather later on. The command is running since 14 hours on a local server. Is there something wrong, or something I can do to mae it reasonable fast? So far the GATK 3.8 pipeline is way faster.

Thanks & best regards,
Daniel

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