Troubleshooting GATK GenomicsDBImport Workspace Creation Error

gatk GenomicsDBImport A USER ERROR has occurred: Error creating GenomicsDB workspace:

The error message "A USER ERROR has occurred: Error creating GenomicsDB workspace" in GATK's GenomicsDBImport tool typically indicates that there was an issue with creating or accessing the directory where the GenomicsDB workspace is supposed to be stored. Here are some common reasons and solutions for this error:

1. Permissions Issue:

   • Ensure that you have the necessary read and write permissions for the directory where you are trying to create the GenomicsDB workspace.
   • You can check and modify permissions using commands like chmod and chown in Unix-based systems.

2. Existing Directory:

   • If a directory with the same name already exists, it might cause conflicts. Try specifying a different directory name or delete the existing directory if it is not needed.

3. Path Issues:

   • Ensure that the path you provided is correct and that all parent directories exist.
   • Avoid using special characters or spaces in the directory path.

4. Disk Space:

   • Check if there is enough disk space available on the drive where you are trying to create the workspace.

5. File System Issues:

   • Ensure that the file system is not corrupted and is functioning correctly.

6. Cluster Environment:

   • If you are running this on a cluster, ensure that the shared file system is accessible from all nodes.

Here is an example command for GenomicsDBImport:

gatk GenomicsDBImport \
   --genomicsdb-workspace-path my_database \
   --batch-size 50 \
   -L interval_list.interval_list \
   --sample-name-map sample_map.txt \
   --reader-threads 5

Troubleshooting Steps

1. Check Permissions:

   ls -ld /path/to/my_database
   

2. Create a New Directory:

   mkdir /path/to/new_database
   

3. Check Disk Space:

   df -h /path/to/my_database
   

4. Verify Path:

   cd /path/to/my_database
   

Example Command with Correct Path and Permissions

gatk GenomicsDBImport \
   --genomicsdb-workspace-path /path/to/new_database \
   --batch-size 50 \
   -L interval_list.interval_list \
   --sample-name-map sample_map.txt \
   --reader-threads 5

If you continue to face issues, you can enable more detailed logging by adding the --verbosity DEBUG flag to your command to get more information about what might be going wrong.

gatk --java-options "-Xmx4g" GenomicsDBImport \
   --genomicsdb-workspace-path /path/to/new_database \
   --batch-size 50 \
   -L interval_list.interval_list \
   --sample-name-map sample_map.txt \
   --reader-threads 5 \
   --verbosity DEBUG

This should help you pinpoint the exact cause of the error.