How to ensure database is cataloged I am planing to upgrade my database. I am referring to this website:
https://www.ibm.com/support/knowledgecenter/SSEPGG_11.5.0/com.ibm.db2.luw.qb.upgrade.doc/doc/t0007193.html

On the Before you begin part:
The second statement is Ensure that all the local databases that you want to upgrade are cataloged.

As my understanding, database is auto cataloged once its created. I run db2 list database directory and get some info, but not sure its consider cataloged or not:

[db2inst1@localhost bin]$ db2 list database directory

 System Database Directory

 Number of entries in the directory = 1

Database 1 entry:

 Database alias                       = MYDB
 Database name                        = MYDB
 Local database directory             = /home/db2inst1
 Database release level               = 10.00
 Comment                              =
 Directory entry type                 = Indirect
 Catalog database partition number    = 0
 Alternate server hostname            =
 Alternate server port number         =


Kindly advise.
There are 2 types of database directories in Db2 for LUW: system and local.
When you create a database on some path /some_path, the following directory structure is created for this local database directory (if it doesn't exist): /some_path/${DB2INSTANCE}/NODE0000/sqldbdir and the database is cataloged (or registered) in the system database directory automatically.
You may have many local directories in the system, but only one system directory.
You have an ability to uncatalog ("deregister") a database manually afterwards, which removes the corresponding entry from the system directory, but not from the local one. The only way to remove a database from its local directory is to drop it.  

So, the problem described in the doc is about such uncataloged databases, which Db2 instance is unaware of. If you uncataloged your databases previously, and forgot to catalog them again, you should find such databases and catalog them. If you don't remember their local database directory paths, you may use unix find /some_path -type d -name sqldbdir command, and db2 list db directory on /some_path, if you found the directory structure like /some_path/${DB2INSTANCE}/NODE0000/sqldbdir.