How do I find which transaction is causing a "Waiting for table metadata lock" state?

SHOW ENGINE INNODB STATUS \G

Look for the Section -

TRANSACTIONS

We can use INFORMATION_SCHEMA Tables.

Useful Queries

To check about all the locks transactions are waiting for:

USE INFORMATION_SCHEMA;
SELECT * FROM INNODB_LOCK_WAITS;

A list of blocking transactions:

SELECT * 
FROM INNODB_LOCKS 
WHERE LOCK_TRX_ID IN (SELECT BLOCKING_TRX_ID FROM INNODB_LOCK_WAITS);

OR

SELECT INNODB_LOCKS.* 
FROM INNODB_LOCKS
JOIN INNODB_LOCK_WAITS
  ON (INNODB_LOCKS.LOCK_TRX_ID = INNODB_LOCK_WAITS.BLOCKING_TRX_ID);

A List of locks on particular table:

SELECT * FROM INNODB_LOCKS 
WHERE LOCK_TABLE = db_name.table_name;

A list of transactions waiting for locks:

SELECT TRX_ID, TRX_REQUESTED_LOCK_ID, TRX_MYSQL_THREAD_ID, TRX_QUERY
FROM INNODB_TRX
WHERE TRX_STATE = 'LOCK WAIT';

Reference - MySQL Troubleshooting: What To Do When Queries Don't Work, Chapter 6 - Page 96.

If you cannot find the process locking the table (cause it is alreay dead), it may be a thread still cleaning up like this

section TRANSACTION of

show engine innodb status;

at the end

---TRANSACTION 1135701157, ACTIVE 6768 sec
MySQL thread id 5208136, OS thread handle 0x7f2982e91700, query id 882213399 xxxIPxxx 82.235.36.49 my_user cleaning up

as mentionned in a comment in Clear transaction deadlock?

you can try killing the transaction thread directly, here with

 KILL 5208136;

worked for me.

mysql 5.7 exposes metadata lock information through the performance_schema.metadata_locks table.

Documentation here