mysql 5.6 – Table is full even with innodb_file_per_table

I am trying to create an index to my table using alter query.
My my.cnf file

innodb_data_home_dir = /usr/local/mysql5/data
innodb_data_file_path = ibdata1:60021538816;ibdata2:300M;ibdata3:30000M;ibdata4:10000M;ibdata5:10000M:autoextend
innodb_buffer_pool_instances = 3
innodb_buffer_pool_size = 3G
innodb_additional_mem_pool_size = 8M
# Set .._log_file_size to 25 % of buffer pool size
innodb_log_file_size = 256M
innodb_additional_mem_pool_size = 128M
innodb_log_buffer_size = 8M
innodb_flush_log_at_trx_commit = 2
innodb_lock_wait_timeout = 100
innodb_file_per_table
innodb_flush_method=O_DIRECT

Still every time my alter query

alter table user add unique index idx_emailHash (emailHash);

giving Table ‘user’ is full?
What am I missing. I am using MySQL 5.6

Some more info

(root@db data)# ll | grep user
    -rw-rw----. 1 mysql mysql       19551 Jun 10 14:33 user.frm
    -rw-rw----. 1 mysql mysql 28412215296 Jun 10 22:58 user.ibd

(root@db data)# ll | grep ibd
-rwxr-xr-x. 1 mysql mysql 60021538816 Jun 10 22:58 ibdata1
-rw-rw----. 1 mysql mysql   314572800 Jun 10 22:20 ibdata2
-rw-rw----. 1 mysql mysql 31457280000 Jun 10 22:33 ibdata3
-rw-rw----. 1 mysql mysql 10485760000 Jun 10 22:51 ibdata4
-rw-rw----. 1 mysql mysql 10485760000 Jun 10 22:51 ibdata5