GenomicsDBImport does not recognize option --genomicsdb-update-workspace-path
Dear members GATK,
I used GenomicsDB import to joint GVCFs to an existing GenomicsDB datastore (e.g. database_all), by the option “--genomicsdb-update-workspace-path".
However, the option was not accepted by the version gatk-4.0.12.0. showing the following message :
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A USER ERROR has occurred: genomicsdb-update-workspace-path is not a recognized option
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Then, I tried with a recent version of GATK gatk-4.1.5.0, but now instead to update, the option tries to create a new folder.
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A USER ERROR has occurred: Error creating GenomicsDB workspace: database_all
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I appreciate any advice.
Best regards.
Jose-Luis
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Hi Jose Luis Gualdron thanks for your post.
The --genomicsdb-update-workspace-path option was added well after 4.0.12.0, which is why you see an error with that version. In the second step, If the GenomicsDB workspace was initially created with such an old version of GenomicsDBImport, it's possible that newer versions of the tool will be unable to do an incremental import into it, as support for incremental import was added fairly recently. Try wiping away anything left by the old GATK version and making sure the steps are all done using the latest version. -
Hi Anton,
thank you so much for reply. Recently, I downloaded the latest version of GATK (4.1.7.0) and I'm going to "Redo" all the steps to probe again GenomicsDB.
If I have any doubt or questions, I won't hesitate to contact you.
Best regards!
Jose Luis
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