Help with GenotypeGVCFs in GATK4
I am trying to run GenotypeGVCFs on a database I just created using GenomicsDBImport. However, I am getting an error I don't know how to fix. The error is:
A USER ERROR has occurred: n is not a recognized option
The script I'm using is here:
singularity exec gatk-4.img \
/opt/gatk/gatk GenotypeGVCFs \
-R $REFERENCE/Gasterosteus_aculeatus_gasAcu1.fasta \
-V gendb://$DATA_DIR/genomicsdb_array \
-G StandardAnnotation -newQual \
I have to use GATK in a singularity image on the cluster I have access to. To me, it's unclear what 'n' is referring to. Also, during the GenomicsDBImport step, I used the line below:
--genomicsdb-workspace-path $path/chr1/DE_M_chr1_DB \
Yet, there is no directory called "DE_M_chr1_DB", instead there is only a directory called genomicsdb_array, and 4 files. Is this correct?
Thanks for your help!