These commands run well if metero deployed with mup tool. Mup creates docker for mongodb hence taking backup becomes easy with these commands.
Take backup of running app data from docker then copy to local folder out of docker.
docker exec -it mongodb mongodump --archive=/root/mongodump.gz --gzip
docker cp mongodb:/root/mongodump.gz mongodump_$(date +%Y-%m-%d_%H-%M-%S).gz
Move data to another server/local machine or a backup location
scp /path/to/dumpfile root@serverip:/path/to/backup
Get into mongo console running in docker then drop current database before getting new data.
docker exec -it mongodb mongo appName
db.runCommand( { dropDatabase: 1 } )
docker cp /path/to/dumpfile mongodb:/root/mongodump.gz
docker exec -it mongodb mongodump --archive=/root/mongodump.gz --gzip