2 added 7329 characters in body
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I've found the logs from mysql error logs, please find it below

2019-01-16T17:28:40.035857Z 12 [ERROR] [MY-012856] [InnoDB] InnoDB: MySQL is trying to perform a consistent read but the read view is not assigned!
TRANSACTION 281479774522976, ACTIVE 0 sec fetching rows
mysql tables in use 8, locked 0
0 lock struct(s), heap size 1136, 0 row lock(s)
MySQL thread id 12, OS thread handle 123145382744064, query id 149 localhost root Opening tables
SHOW INDEXES FROM catalog_category_product_index_tmp WHERE `Non_unique` = 1

2019-01-16T17:28:40.036096Z 12 [ERROR] [MY-000000] [InnoDB] InnoDB: Assertion failure: row0sel.cc:4630
InnoDB: thread 123145382744064
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/8.0/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
17:28:40 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=8388608
read_buffer_size=131072
max_used_connections=3
max_threads=1024
thread_count=4
connection_count=3
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 412896 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x7f8ee3216a00
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 700004cb4e90 thread_stack 0x46000
0   mysqld                              0x000000010a837504 my_print_stacktrace(unsigned char*, unsigned long) + 60
1   mysqld                              0x0000000109ed5afa handle_fatal_signal + 688
2   libsystem_platform.dylib            0x00007fff64eeaf5a _sigtramp + 26
3   ???                                 0x000000011c671558 0x0 + 4771485016
4   libsystem_c.dylib                   0x00007fff64d15312 abort + 127
5   mysqld                              0x000000010ab18d8b basename_index(char const*, int) + 0
6   mysqld                              0x000000010aac6939 row_search_mvcc(unsigned char*, page_cur_mode_t, row_prebuilt_t*, unsigned long, unsigned long) + 3812
7   mysqld                              0x000000010a9d6467 ha_innobase::general_fetch(unsigned char*, unsigned int, unsigned int) + 115
8   mysqld                              0x0000000109be0514 handler::ha_index_next_same(unsigned char*, unsigned char const*, unsigned int) + 202
9   mysqld                              0x0000000109da82ab join_read_next_same(READ_RECORD*) + 39
10  mysqld                              0x0000000109da4e65 sub_select(JOIN*, QEP_TAB*, bool) + 617
11  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
12  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
13  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
14  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
15  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
16  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
17  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
18  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
19  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
20  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
21  mysqld                              0x0000000109da1172 JOIN::exec() + 770
22  mysqld                              0x0000000109e17e98 handle_query(THD*, LEX*, Query_result*, unsigned long long, unsigned long long) + 536
23  mysqld                              0x0000000109de7056 execute_show(THD*, TABLE_LIST*) + 568
24  mysqld                              0x0000000109d76484 Sql_cmd_show::execute(THD*) + 72
25  mysqld                              0x0000000109de292f mysql_execute_command(THD*, bool) + 2938
26  mysqld                              0x0000000109de0f83 mysql_parse(THD*, Parser_state*) + 901
27  mysqld                              0x0000000109ddfabf dispatch_command(THD*, COM_DATA const*, enum_server_command) + 5353
28  mysqld                              0x0000000109de0817 do_command(THD*) + 293
29  mysqld                              0x0000000109ec4503 handle_connection(void*) + 372
30  mysqld                              0x000000010ab6e0b6 pfs_spawn_thread(void*) + 318
31  libsystem_pthread.dylib             0x00007fff64ef46c1 _pthread_body + 340
32  libsystem_pthread.dylib             0x00007fff64ef456d _pthread_body + 0
33  libsystem_pthread.dylib             0x00007fff64ef3c5d thread_start + 13

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7f8ee2899028): SHOW INDEXES FROM catalog_category_product_index_tmp WHERE `Non_unique` = 1
Connection ID (thread ID): 12
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
2019-01-16T17:28:40.6NZ mysqld_safe mysqld restarted
2019-01-16T17:28:40.389018Z 0 [Warning] [MY-011071] [Server] option 'max_allowed_packet': unsigned value 4294967296 adjusted to 1073741824
2019-01-16T17:28:40.389333Z 0 [System] [MY-010116] [Server] /usr/local/opt/mysql/bin/mysqld (mysqld 8.0.12) starting as process 41668
2019-01-16T17:28:40.392737Z 0 [Warning] [MY-010159] [Server] Setting lower_case_table_names=2 because file system for /usr/local/var/mysql/ is case insensitive
[warn] kq_init: detected broken kqueue; not using.: Undefined error: 0
2019-01-16T17:28:40.911155Z 0 [System] [MY-010229] [Server] Starting crash recovery...
2019-01-16T17:28:40.911246Z 0 [System] [MY-010232] [Server] Crash recovery finished.
2019-01-16T17:28:40.916273Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.
2019-01-16T17:28:40.935211Z 0 [System] [MY-010931] [Server] /usr/local/opt/mysql/bin/mysqld: ready for connections. Version: '8.0.12'  socket: '/tmp/mysql.sock'  port: 3306  Homebrew.

I've found the logs from mysql error logs, please find it below

2019-01-16T17:28:40.035857Z 12 [ERROR] [MY-012856] [InnoDB] InnoDB: MySQL is trying to perform a consistent read but the read view is not assigned!
TRANSACTION 281479774522976, ACTIVE 0 sec fetching rows
mysql tables in use 8, locked 0
0 lock struct(s), heap size 1136, 0 row lock(s)
MySQL thread id 12, OS thread handle 123145382744064, query id 149 localhost root Opening tables
SHOW INDEXES FROM catalog_category_product_index_tmp WHERE `Non_unique` = 1

2019-01-16T17:28:40.036096Z 12 [ERROR] [MY-000000] [InnoDB] InnoDB: Assertion failure: row0sel.cc:4630
InnoDB: thread 123145382744064
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/8.0/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
17:28:40 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=8388608
read_buffer_size=131072
max_used_connections=3
max_threads=1024
thread_count=4
connection_count=3
It is possible that mysqld could use up to 
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 412896 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x7f8ee3216a00
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 700004cb4e90 thread_stack 0x46000
0   mysqld                              0x000000010a837504 my_print_stacktrace(unsigned char*, unsigned long) + 60
1   mysqld                              0x0000000109ed5afa handle_fatal_signal + 688
2   libsystem_platform.dylib            0x00007fff64eeaf5a _sigtramp + 26
3   ???                                 0x000000011c671558 0x0 + 4771485016
4   libsystem_c.dylib                   0x00007fff64d15312 abort + 127
5   mysqld                              0x000000010ab18d8b basename_index(char const*, int) + 0
6   mysqld                              0x000000010aac6939 row_search_mvcc(unsigned char*, page_cur_mode_t, row_prebuilt_t*, unsigned long, unsigned long) + 3812
7   mysqld                              0x000000010a9d6467 ha_innobase::general_fetch(unsigned char*, unsigned int, unsigned int) + 115
8   mysqld                              0x0000000109be0514 handler::ha_index_next_same(unsigned char*, unsigned char const*, unsigned int) + 202
9   mysqld                              0x0000000109da82ab join_read_next_same(READ_RECORD*) + 39
10  mysqld                              0x0000000109da4e65 sub_select(JOIN*, QEP_TAB*, bool) + 617
11  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
12  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
13  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
14  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
15  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
16  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
17  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
18  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
19  mysqld                              0x0000000109da5505 evaluate_join_record(JOIN*, QEP_TAB*) + 586
20  mysqld                              0x0000000109da4f2c sub_select(JOIN*, QEP_TAB*, bool) + 816
21  mysqld                              0x0000000109da1172 JOIN::exec() + 770
22  mysqld                              0x0000000109e17e98 handle_query(THD*, LEX*, Query_result*, unsigned long long, unsigned long long) + 536
23  mysqld                              0x0000000109de7056 execute_show(THD*, TABLE_LIST*) + 568
24  mysqld                              0x0000000109d76484 Sql_cmd_show::execute(THD*) + 72
25  mysqld                              0x0000000109de292f mysql_execute_command(THD*, bool) + 2938
26  mysqld                              0x0000000109de0f83 mysql_parse(THD*, Parser_state*) + 901
27  mysqld                              0x0000000109ddfabf dispatch_command(THD*, COM_DATA const*, enum_server_command) + 5353
28  mysqld                              0x0000000109de0817 do_command(THD*) + 293
29  mysqld                              0x0000000109ec4503 handle_connection(void*) + 372
30  mysqld                              0x000000010ab6e0b6 pfs_spawn_thread(void*) + 318
31  libsystem_pthread.dylib             0x00007fff64ef46c1 _pthread_body + 340
32  libsystem_pthread.dylib             0x00007fff64ef456d _pthread_body + 0
33  libsystem_pthread.dylib             0x00007fff64ef3c5d thread_start + 13

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7f8ee2899028): SHOW INDEXES FROM catalog_category_product_index_tmp WHERE `Non_unique` = 1
Connection ID (thread ID): 12
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
2019-01-16T17:28:40.6NZ mysqld_safe mysqld restarted
2019-01-16T17:28:40.389018Z 0 [Warning] [MY-011071] [Server] option 'max_allowed_packet': unsigned value 4294967296 adjusted to 1073741824
2019-01-16T17:28:40.389333Z 0 [System] [MY-010116] [Server] /usr/local/opt/mysql/bin/mysqld (mysqld 8.0.12) starting as process 41668
2019-01-16T17:28:40.392737Z 0 [Warning] [MY-010159] [Server] Setting lower_case_table_names=2 because file system for /usr/local/var/mysql/ is case insensitive
[warn] kq_init: detected broken kqueue; not using.: Undefined error: 0
2019-01-16T17:28:40.911155Z 0 [System] [MY-010229] [Server] Starting crash recovery...
2019-01-16T17:28:40.911246Z 0 [System] [MY-010232] [Server] Crash recovery finished.
2019-01-16T17:28:40.916273Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.
2019-01-16T17:28:40.935211Z 0 [System] [MY-010931] [Server] /usr/local/opt/mysql/bin/mysqld: ready for connections. Version: '8.0.12'  socket: '/tmp/mysql.sock'  port: 3306  Homebrew.
1
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Mysql error in setup:upgrade

I'm getting error in bin/magento setup:upgrade in macOS High Sierra.

$ php bin/magento setup:upgrade
Cache cleared successfully
File system cleanup:
/Users/rab/php-apps/magentoCE2/generated/code/Composer
/Users/rab/php-apps/magentoCE2/generated/code/MSP
/Users/rab/php-apps/magentoCE2/generated/code/Magento
/Users/rab/php-apps/magentoCE2/generated/code/Symfony
The directory '/Users/rab/php-apps/magentoCE2/generated/metadata/' doesn't exist - skipping cleanup
Updating modules:
Schema creation/updates:
Warning: PDOStatement::execute(): MySQL server has gone away 
in /Users/rab/php-apps/magentoCE2/vendor/magento/zendframework1/
library/Zend/Db/Statement/Pdo.php on line 228

I've tried to change mysql settings in my.cnf, please see mysql settings below.

mysql> show global variables like 'max_%';
+----------------------------+----------------------+
| Variable_name              | Value                |
+----------------------------+----------------------+
| max_allowed_packet         | 1073741824           |
| max_binlog_cache_size      | 18446744073709547520 |
| max_binlog_size            | 1073741824           |
| max_binlog_stmt_cache_size | 18446744073709547520 |
| max_connect_errors         | 100                  |
| max_connections            | 1024                 |
| max_delayed_threads        | 20                   |
| max_digest_length          | 1024                 |
| max_error_count            | 1024                 |
| max_execution_time         | 8                    |
| max_heap_table_size        | 16777216             |
| max_insert_delayed_threads | 20                   |
| max_join_size              | 18446744073709551615 |
| max_length_for_sort_data   | 4096                 |
| max_points_in_geometry     | 65536                |
| max_prepared_stmt_count    | 16382                |
| max_relay_log_size         | 0                    |
| max_seeks_for_key          | 18446744073709551615 |
| max_sort_length            | 1024                 |
| max_sp_recursion_depth     | 0                    |
| max_user_connections       | 0                    |
| max_write_lock_count       | 18446744073709551615 |
+----------------------------+----------------------+
22 rows in set (0.01 sec)

I'm still getting the same error. Please help!!