my version and error info:
a) GATK version 18.104.22.168
b) Exact command used:
gatk --java-options "-Xmx200g -Xms200g" \
--genomicsdb-workspace-path Neo_96_GATK_dbase \
--batch-size 50 \
-L Chr2_nm_RagTag \
--sample-name-map Neo_96sample_map.txt \
--tmp-dir /tmp \
c) Entire error log: A USER ERROR has occurred: Error creating GenomicsDB workspace: Neo_96_GATK_dbase already exists
How do I append and existing GenomcsDB?
I ran GenomicsDBImport for 96 genome samples and 29 chromosomes, but the run died after 2 months and completed 23 chromosomes and started on two others, but those two were terminated when the server went down. I deleted those two DB directories and tried to run GenomicsDBImport on one chromosome at a time (in parallel), but I am getting the above "workspace already exists". Is there a way to append the database?
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