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The tool does not work with ipv6 only hosts.
In the log I see the following line:
[2017-05-22 15:38:29,314] [CRITICAL] [MainProcess] [Main:exception:218] Error setting up mongodb-consistent-backup: Could not resolve host 'myhostname', error: [Errno -2] Name or service not known
The problem is that the function validate_hostname() here does not support ipv6.
Mongodump tool supports ipv6 out of the box. For testing purposes I simply commented out this check and backups were done without problems.
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