Big file upload stop always at the same size

The problem is that I have a folder bigger > 60GB with > 50000 files that I want to upload to owncloud (localhost). The upload always stop at 12.3GB. I tried several times, and the behaviour is always the same. I don't have errors in owncloud log files too.

Steps to reproduce
1. Folder dragged&dropped in browser client (tried with several browser)
2. Folder get uploaded until 12.3GB

Expected behaviour
Should upload the whole folder (>60GB with > 50000 files)

Actual behaviour
Only 12.3GB are uploaded

Client configuration
Client version:
Client operating system: Debian 8 (pc is both client and server)

Server configuration
Operating system: Debian 8
Web server: nginx
Database: mariadb
PHP version: 5.6.30-0+deb8u1
ownCloud version (see ownCloud admin page): 9.3.1
Updated from an older ownCloud or fresh install: fresh
Special configurations (external storage, external authentication, reverse proxy, server-side-encryption): nas with 2TB mirror done with mdadm mounted at /home/cloud

ownCloud log (data/owncloud.log) and (/home/cloud/owncloud.log)
No errors

NGINX

nginx.conf

user www-data;
worker_processes 4;
pid /run/nginx.pid;
events {
	worker_connections 1768;
	# multi_accept on;
}
http {
    ##
# Basic Settings
##

sendfile on;
tcp_nopush on;
tcp_nodelay on;
keepalive_timeout 365;
types_hash_max_size 4096;
# server_tokens off;

# server_names_hash_bucket_size 64;
# server_name_in_redirect off;

include /etc/nginx/mime.types;
default_type application/octet-stream;

##
# SSL Settings
##

ssl_protocols TLSv1 TLSv1.1 TLSv1.2; # Dropping SSLv3, ref: POODLE
ssl_prefer_server_ciphers on;

##
# Logging Settings
##

access_log /var/log/nginx/access.log;
error_log /var/log/nginx/error.log;

##
# Gzip Settings
##

gzip on;
gzip_disable "msie6";

# gzip_vary on;
# gzip_proxied any;
# gzip_comp_level 6;
# gzip_buffers 16 8k;
# gzip_http_version 1.1;
# gzip_types text/plain text/css application/json application/javascript text/xml application/xml application/xml+rss text/javascript;

##
# Virtual Host Configs
##

include /etc/nginx/conf.d/*.conf;
include /etc/nginx/sites-enabled/*;
}
#mail {
#	# See sample authentication script at:
#	# http://wiki.nginx.org/ImapAuthenticateWithApachePhpScript
# 
#	# auth_http localhost/auth.php;
#	# pop3_capabilities "TOP" "USER";
#	# imap_capabilities "IMAP4rev1" "UIDPLUS";
# 
#	server {
#		listen     localhost:110;
#		protocol   pop3;
#		proxy      on;
#	}
# 
#	server {
#		listen     localhost:143;
#		protocol   imap;
#		proxy      on;
#	}
#}

sites-enabled/owncloud

server {
  listen 80;
  server_name 192.168.1.74;
  return 301 https://$server_name$request_uri;  # enforce https
}
server {
  listen 443 ssl;
  server_name 192.168.1.74;
  access_log /var/log/nginx/owncloud.access.log;
  error_log /var/log/nginx/owncloud.error.log;
  client_body_temp_path /home/cloud/tmp;
  proxy_temp_path /home/cloud/tmp;
  fastcgi_temp_path /home/cloud/tmp;
  uwsgi_temp_path /home/cloud/tmp;
  scgi_temp_path /home/cloud/tmp;
  ssl_certificate /etc/nginx/ssl/owncloud.crt;
  ssl_certificate_key /etc/nginx/ssl/owncloud.key;
  add_header Strict-Transport-Security "max-age=155520000; includeSubDomains";
  # Path to the root of your installation
  root /var/www;
  client_max_body_size 200G; # set max upload size
#  fastcgi_buffers 16 64K;
#  fastcgi_buffer_size 128k;
#  fastcgi_request_buffering off;
# Some rewrite rules, more to come later
  rewrite ^/owncloud/caldav((/|$).*)$ /owncloud/remote.php/caldav$1 last;
  rewrite ^/owncloud/carddav((/|$).*)$ /owncloud/remote.php/carddav$1 last;
  rewrite ^/owncloud/webdav((/|$).*)$ /owncloud/remote.php/webdav$1 last;
  # Protecting sensitive files from the evil outside world
  location ~ ^/owncloud/(data|config|\.ht|db_structure.xml|README) {
           deny all;
  }
  # Configure the root location with proper rewrite rules
  location /owncloud/ {
           rewrite ^/owncloud/.well-known/host-meta /public.php?service=host-meta last;
           rewrite ^/owncloud/.well-known/host-meta.json /public.php?service=host-meta-json last;
           rewrite ^/owncloud/.well-known/carddav /remote.php/carddav/ redirect;
           rewrite ^/owncloud/.well-known/caldav /remote.php/caldav/ redirect;
           rewrite ^/owncloud/apps/calendar/caldav.php /remote.php/caldav/ last;
           rewrite ^/owncloud/apps/contacts/carddav.php /remote.php/carddav/ last;
           rewrite ^/owncloud/apps/([^/]*)/(.*\.(css|php))$ /index.php?app=$1&getfile=$2 last;
           rewrite ^(/owncloud/core/doc[^\/]+/)$ $1/index.html;
           try_files $uri $uri/ index.php;
 }
location ~ \.php(?:$|/) {
  fastcgi_split_path_info ^(.+\.php)(/.+)$;
  include fastcgi_params;
  fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
  fastcgi_param PATH_INFO $fastcgi_path_info;
  fastcgi_param HTTPS on;
  fastcgi_connect_timeout 360000;
        fastcgi_send_timeout 360000;
        fastcgi_read_timeout 360000;
#  fastcgi_request_buffering off;
  fastcgi_pass unix:/var/run/php5-fpm.sock;
 }
# Optional: set long EXPIRES header on static assets
location ~* \.(?:jpg|jpeg|gif|bmp|ico|png|css|js|swf)$ {
expires 30d;
# Optional: Don't log access to assets
access_log off;
 }
}

PHP

/etc/php5/fpm/php.ini it's not the whole file, I think I've posted just what it's necessary and something more

[PHP]
;;;;;;;;;;;;;;;;;;;;
; php.ini Options  ;
;;;;;;;;;;;;;;;;;;;;
; Name for user-defined php.ini (.htaccess) files. Default is ".user.ini"
user_ini.filename = ".user.ini"
output_buffering = Off
; You can redirect all of the output of your scripts to a function.  For
; example, if you set output_handler to "mb_output_handler", character
; encoding will be transparently converted to the specified encoding.
; Setting any output handler automatically turns on output buffering.
; Note: People who wrote portable scripts should not depend on this ini
;   directive. Instead, explicitly set the output handler using ob_start().
;   Using this ini directive may cause problems unless you know what script
;   is doing.
; Note: You cannot use both "mb_output_handler" with "ob_iconv_handler"
;   and you cannot use both "ob_gzhandler" and "zlib.output_compression".
; Note: output_handler must be empty if this is set 'On' !!!!
;   Instead you must use zlib.output_handler.
; http://php.net/output-handler
;output_handler =
; Transparent output compression using the zlib library
; Valid values for this option are 'off', 'on', or a specific buffer size
; to be used for compression (default is 4KB)
; Note: Resulting chunk size may vary due to nature of compression. PHP
;   outputs chunks that are few hundreds bytes each as a result of
;   compression. If you prefer a larger chunk size for better
;   performance, enable output_buffering in addition.
; Note: You need to use zlib.output_handler instead of the standard
;   output_handler, or otherwise the output will be corrupted.
; http://php.net/zlib.output-compression
zlib.output_compression = Off
; http://php.net/zlib.output-compression-level
;zlib.output_compression_level = -1
; You cannot specify additional output handlers if zlib.output_compression
; is activated here. This setting does the same as output_handler but in
; a different order.
; http://php.net/zlib.output-handler
;zlib.output_handler =
; Implicit flush tells PHP to tell the output layer to flush itself
; automatically after every output block.  This is equivalent to calling the
; PHP function flush() after each and every call to print() or echo() and each
; and every HTML block.  Turning this option on has serious performance
; implications and is generally recommended for debugging purposes only.
; http://php.net/implicit-flush
; Note: This directive is hardcoded to On for the CLI SAPI
implicit_flush = Off
; The unserialize callback function will be called (with the undefined class'
; name as parameter), if the unserializer finds an undefined class
; which should be instantiated. A warning appears if the specified function is
; not defined, or if the function doesn't include/implement the missing class.
; So only set this entry, if you really want to implement such a
; callback-function.
unserialize_callback_func =
; When floats & doubles are serialized store serialize_precision significant
; digits after the floating point. The default value ensures that when floats
; are decoded with unserialize, the data will remain the same.
serialize_precision = 17
; This directive allows you to disable certain functions for security reasons.
; It receives a comma-delimited list of function names.
; http://php.net/disable-functions
disable_functions = pcntl_alarm,pcntl_fork,pcntl_waitpid,pcntl_wait,pcntl_wifexited,pcntl_wifstopped,pcntl_wifsignaled,pcntl_wexitstatus,pcntl_wtermsig,pcntl_wstopsig,pcntl_signal,pcntl_signal_dispatch,pcntl_get_last_error,pcntl_strerror,pcntl_sigprocmask,pcntl_sigwaitinfo,pcntl_sigtimedwait,pcntl_exec,pcntl_getpriority,pcntl_setpriority,
; This directive allows you to disable certain classes for security reasons.
; It receives a comma-delimited list of class names.
; http://php.net/disable-classes
disable_classes =
;;;;;;;;;;;;;;;;;
; Miscellaneous ;
;;;;;;;;;;;;;;;;;
; Decides whether PHP may expose the fact that it is installed on the server
; (e.g. by adding its signature to the Web server header).  It is no security
; threat in any way, but it makes it possible to determine whether you use PHP
; on your server or not.
; http://php.net/expose-php
expose_php = Off
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;
; Maximum execution time of each script, in seconds
; http://php.net/max-execution-time
; Note: This directive is hardcoded to 0 for the CLI SAPI
max_execution_time = 360000
; Maximum amount of time each script may spend parsing request data. It's a good
; idea to limit this time on productions servers in order to eliminate unexpectedly
; long running scripts.
; Note: This directive is hardcoded to -1 for the CLI SAPI
; Default Value: -1 (Unlimited)
; Development Value: 60 (60 seconds)
; Production Value: 60 (60 seconds)
; http://php.net/max-input-time
max_input_time = 360000
; Maximum input variable nesting level
; http://php.net/max-input-nesting-level
;max_input_nesting_level = 64
; How many GET/POST/COOKIE input variables may be accepted
max_input_vars = 100000
; Maximum amount of memory a script may consume (128MB)
; http://php.net/memory-limit
memory_limit = 256M
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Error handling and logging ;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
error_reporting = E_ALL & ~E_DEPRECATED & ~E_STRICT
display_errors = Off
; The display of errors which occur during PHP's startup sequence are handled
; separately from display_errors. PHP's default behavior is to suppress those
; errors from clients. Turning the display of startup errors on can be useful in
; debugging configuration problems. We strongly recommend you
; set this to 'off' for production servers.
; Default Value: Off
; Development Value: On
; Production Value: Off
; http://php.net/display-startup-errors
display_startup_errors = Off
; Besides displaying errors, PHP can also log errors to locations such as a
; server-specific log, STDERR, or a location specified by the error_log
; directive found below. While errors should not be displayed on productions
; servers they should still be monitored and logging is a great way to do that.
; Default Value: Off
; Development Value: On
; Production Value: On
; http://php.net/log-errors
log_errors = On
; Set maximum length of log_errors. In error_log information about the source is
; added. The default is 1024 and 0 allows to not apply any maximum length at all.
; http://php.net/log-errors-max-len
log_errors_max_len = 1024
; Do not log repeated messages. Repeated errors must occur in same file on same
; line unless ignore_repeated_source is set true.
; http://php.net/ignore-repeated-errors
ignore_repeated_errors = Off
; Ignore source of message when ignoring repeated messages. When this setting
; is On you will not log errors with repeated messages from different files or
; source lines.
; http://php.net/ignore-repeated-source
ignore_repeated_source = Off
; If this parameter is set to Off, then memory leaks will not be shown (on
; stdout or in the log). This has only effect in a debug compile, and if
; error reporting includes E_WARNING in the allowed list
; http://php.net/report-memleaks
report_memleaks = On
; This setting is on by default.
;report_zend_debug = 0
; Store the last error/warning message in $php_errormsg (boolean). Setting this value
; to On can assist in debugging and is appropriate for development servers. It should
; however be disabled on production servers.
; Default Value: Off
; Development Value: On
; Production Value: Off
; http://php.net/track-errors
track_errors = Off
; Turn off normal error reporting and emit XML-RPC error XML
; http://php.net/xmlrpc-errors
;xmlrpc_errors = 0
; An XML-RPC faultCode
;xmlrpc_error_number = 0
; When PHP displays or logs an error, it has the capability of formatting the
; error message as HTML for easier reading. This directive controls whether
; the error message is formatted as HTML or not.
; Note: This directive is hardcoded to Off for the CLI SAPI
; Default Value: On
; Development Value: On
; Production value: On
; http://php.net/html-errors
html_errors = On
; If html_errors is set to On *and* docref_root is not empty, then PHP
; produces clickable error messages that direct to a page describing the error
; or function causing the error in detail.
; You can download a copy of the PHP manual from http://php.net/docs
; and change docref_root to the base URL of your local copy including the
; leading '/'. You must also specify the file extension being used including
; the dot. PHP's default behavior is to leave these settings empty, in which
; case no links to documentation are generated.
; Note: Never use this feature for production boxes.
; http://php.net/docref-root
; Examples
;docref_root = "/phpmanual/"
; http://php.net/docref-ext
;docref_ext = .html
; String to output before an error message. PHP's default behavior is to leave
; this setting blank.
; http://php.net/error-prepend-string
; Example:
;error_prepend_string = "<span style='color: #ff0000'>"
; String to output after an error message. PHP's default behavior is to leave
; this setting blank.
; http://php.net/error-append-string
; Example:
;error_append_string = "</span>"
; Log errors to specified file. PHP's default behavior is to leave this value
; empty.
; http://php.net/error-log
; Example:
;error_log = php_errors.log
; Log errors to syslog (Event Log on Windows).
;error_log = syslog
;windows.show_crt_warning
; Default value: 0
; Development value: 0
; Production value: 0
;;;;;;;;;;;;;;;;;
; Data Handling ;
;;;;;;;;;;;;;;;;;
; The separator used in PHP generated URLs to separate arguments.
; PHP's default setting is "&".
; http://php.net/arg-separator.output
; Example:
;arg_separator.output = "&amp;"
; List of separator(s) used by PHP to parse input URLs into variables.
; PHP's default setting is "&".
; NOTE: Every character in this directive is considered as separator!
; http://php.net/arg-separator.input
; Example:
;arg_separator.input = ";&"
; This directive determines which super global arrays are registered when PHP
; starts up. G,P,C,E & S are abbreviations for the following respective super
; globals: GET, POST, COOKIE, ENV and SERVER. There is a performance penalty
; paid for the registration of these arrays and because ENV is not as commonly
; used as the others, ENV is not recommended on productions servers. You
; can still get access to the environment variables through getenv() should you
; need to.
; Default Value: "EGPCS"
; Development Value: "GPCS"
; Production Value: "GPCS";
; http://php.net/variables-order
variables_order = "EGPCS"
; This directive determines which super global data (G,P & C) should be
; registered into the super global array REQUEST. If so, it also determines
; the order in which that data is registered. The values for this directive
; are specified in the same manner as the variables_order directive,
; EXCEPT one. Leaving this value empty will cause PHP to use the value set
; in the variables_order directive. It does not mean it will leave the super
; globals array REQUEST empty.
; Default Value: None
; Development Value: "GP"
; Production Value: "GP"
; http://php.net/request-order
request_order = "GP"
; This directive determines whether PHP registers $argv & $argc each time it
; runs. $argv contains an array of all the arguments passed to PHP when a script
; is invoked. $argc contains an integer representing the number of arguments
; that were passed when the script was invoked. These arrays are extremely
; useful when running scripts from the command line. When this directive is
; enabled, registering these variables consumes CPU cycles and memory each time
; a script is executed. For performance reasons, this feature should be disabled
; on production servers.
; Note: This directive is hardcoded to On for the CLI SAPI
; Default Value: On
; Development Value: Off
; Production Value: Off
; http://php.net/register-argc-argv
register_argc_argv = Off
; When enabled, the ENV, REQUEST and SERVER variables are created when they're
; first used (Just In Time) instead of when the script starts. If these
; variables are not used within a script, having this directive on will result
; in a performance gain. The PHP directive register_argc_argv must be disabled
; for this directive to have any affect.
; http://php.net/auto-globals-jit
auto_globals_jit = On
; Whether PHP will read the POST data.
; This option is enabled by default.
; Most likely, you won't want to disable this option globally. It causes $_POST
; and $_FILES to always be empty; the only way you will be able to read the
; POST data will be through the php://input stream wrapper. This can be useful
; to proxy requests or to process the POST data in a memory efficient fashion.
; http://php.net/enable-post-data-reading
;enable_post_data_reading = Off
; Maximum size of POST data that PHP will accept.
; Its value may be 0 to disable the limit. It is ignored if POST data reading
; is disabled through enable_post_data_reading.
; http://php.net/post-max-size
post_max_size = 200G
; Automatically add files before PHP document.
; http://php.net/auto-prepend-file
auto_prepend_file =
; Automatically add files after PHP document.
; http://php.net/auto-append-file
auto_append_file =
; By default, PHP will output a media type using the Content-Type header. To
; disable this, simply set it to be empty.
;
; PHP's built-in default media type is set to text/html.
; http://php.net/default-mimetype
default_mimetype = "text/html"
; PHP's default character set is set to UTF-8.
; http://php.net/default-charset
default_charset = "UTF-8"
; PHP internal character encoding is set to empty.
; If empty, default_charset is used.
; http://php.net/internal-encoding
;internal_encoding =
; PHP input character encoding is set to empty.
; If empty, default_charset is used.
; http://php.net/input-encoding
;input_encoding =
; PHP output character encoding is set to empty.
; If empty, default_charset is used.
; See also output_buffer.
; http://php.net/output-encoding
;output_encoding =
; Always populate the $HTTP_RAW_POST_DATA variable. PHP's default behavior is
; to disable this feature and it will be removed in a future version.
; If post reading is disabled through enable_post_data_reading,
; $HTTP_RAW_POST_DATA is *NOT* populated.
; http://php.net/always-populate-raw-post-data
always_populate_raw_post_data = -1
;;;;;;;;;;;;;;;;
; File Uploads ;
;;;;;;;;;;;;;;;;
; Whether to allow HTTP file uploads.
; http://php.net/file-uploads
file_uploads = On
; Temporary directory for HTTP uploaded files (will use system default if not
; specified).
; http://php.net/upload-tmp-dir
upload_tmp_dir = /home/cloud/tmp
; Maximum allowed size for uploaded files.
; http://php.net/upload-max-filesize
upload_max_filesize = 200G
; Maximum number of files that can be uploaded via a single request
max_file_uploads = 160000
;;;;;;;;;;;;;;;;;;
; Fopen wrappers ;
;;;;;;;;;;;;;;;;;;
; Whether to allow the treatment of URLs (like http:// or ftp://) as files.
; http://php.net/allow-url-fopen
allow_url_fopen = On
; Whether to allow include/require to open URLs (like http:// or ftp://) as files.
; http://php.net/allow-url-include
allow_url_include = Off
; Define the anonymous ftp password (your email address). PHP's default setting
; for this is empty.
; http://php.net/from
;from="john@doe.com"
; Define the User-Agent string. PHP's default setting for this is empty.
; http://php.net/user-agent
;user_agent="PHP"
; Default timeout for socket based streams (seconds)
; http://php.net/default-socket-timeout
default_socket_timeout = 360000
; If your scripts have to deal with files from Macintosh systems,
; or you are running on a Mac and need to deal with files from
; unix or win32 systems, setting this flag will cause PHP to
; automatically detect the EOL character in those files so that
; fgets() and file() will work regardless of the source of the file.
; http://php.net/auto-detect-line-endings
;auto_detect_line_endings = Off
;;;;;;;;;;;;;;;;;;;
; Module Settings ;
;;;;;;;;;;;;;;;;;;;
[CLI Server]
; Whether the CLI web server uses ANSI color coding in its terminal output.
cli_server.color = On
[intl]
;intl.default_locale =
; This directive allows you to produce PHP errors when some error
; happens within intl functions. The value is the level of the error produced.
; Default is 0, which does not produce any errors.
;intl.error_level = E_WARNING
;intl.use_exceptions = 0
[sqlite3]
;sqlite3.extension_dir =
[Pdo]
; Whether to pool ODBC connections. Can be one of "strict", "relaxed" or "off"
; http://php.net/pdo-odbc.connection-pooling
;pdo_odbc.connection_pooling=strict
;pdo_odbc.db2_instance_name
[Pdo_mysql]
; If mysqlnd is used: Number of cache slots for the internal result set cache
; http://php.net/pdo_mysql.cache_size
pdo_mysql.cache_size = 2000
; Default socket name for local MySQL connects.  If empty, uses the built-in
; MySQL defaults.
; http://php.net/pdo_mysql.default-socket
pdo_mysql.default_socket=
[SQL]
; http://php.net/sql.safe-mode
sql.safe_mode = Off
[MySQL]
; Allow accessing, from PHP's perspective, local files with LOAD DATA statements
; http://php.net/mysql.allow_local_infile
mysql.allow_local_infile = On
; Allow or prevent persistent links.
; http://php.net/mysql.allow-persistent
mysql.allow_persistent = On
; If mysqlnd is used: Number of cache slots for the internal result set cache
; http://php.net/mysql.cache_size
mysql.cache_size = 2000
; Maximum number of persistent links.  -1 means no limit.
; http://php.net/mysql.max-persistent
mysql.max_persistent = -1
; Maximum number of links (persistent + non-persistent).  -1 means no limit.
; http://php.net/mysql.max-links
mysql.max_links = -1
; Default port number for mysql_connect().  If unset, mysql_connect() will use
; the $MYSQL_TCP_PORT or the mysql-tcp entry in /etc/services or the
; compile-time value defined MYSQL_PORT (in that order).  Win32 will only look
; at MYSQL_PORT.
; http://php.net/mysql.default-port
mysql.default_port =
; Default socket name for local MySQL connects.  If empty, uses the built-in
; MySQL defaults.
; http://php.net/mysql.default-socket
mysql.default_socket =
; Default host for mysql_connect() (doesn't apply in safe mode).
; http://php.net/mysql.default-host
mysql.default_host =
; Default user for mysql_connect() (doesn't apply in safe mode).
; http://php.net/mysql.default-user
mysql.default_user =
; Default password for mysql_connect() (doesn't apply in safe mode).
; Note that this is generally a *bad* idea to store passwords in this file.
; *Any* user with PHP access can run 'echo get_cfg_var("mysql.default_password")
; and reveal this password!  And of course, any users with read access to this
; file will be able to reveal the password as well.
; http://php.net/mysql.default-password
mysql.default_password =
; Maximum time (in seconds) for connect timeout. -1 means no limit
; http://php.net/mysql.connect-timeout
mysql.connect_timeout = 60
; Trace mode. When trace_mode is active (=On), warnings for table/index scans and
; SQL-Errors will be displayed.
; http://php.net/mysql.trace-mode
mysql.trace_mode = Off
[MySQLi]
; Maximum number of persistent links.  -1 means no limit.
; http://php.net/mysqli.max-persistent
mysqli.max_persistent = -1
; Allow accessing, from PHP's perspective, local files with LOAD DATA statements
; http://php.net/mysqli.allow_local_infile
;mysqli.allow_local_infile = On
; Allow or prevent persistent links.
; http://php.net/mysqli.allow-persistent
mysqli.allow_persistent = On
; Maximum number of links.  -1 means no limit.
; http://php.net/mysqli.max-links
mysqli.max_links = -1
; If mysqlnd is used: Number of cache slots for the internal result set cache
; http://php.net/mysqli.cache_size
mysqli.cache_size = 2000
; Default port number for mysqli_connect().  If unset, mysqli_connect() will use
; the $MYSQL_TCP_PORT or the mysql-tcp entry in /etc/services or the
; compile-time value defined MYSQL_PORT (in that order).  Win32 will only look
; at MYSQL_PORT.
; http://php.net/mysqli.default-port
mysqli.default_port = 3306
; Default socket name for local MySQL connects.  If empty, uses the built-in
; MySQL defaults.
; http://php.net/mysqli.default-socket
mysqli.default_socket =
; Default host for mysql_connect() (doesn't apply in safe mode).
; http://php.net/mysqli.default-host
mysqli.default_host =
; Default user for mysql_connect() (doesn't apply in safe mode).
; http://php.net/mysqli.default-user
mysqli.default_user =
; Default password for mysqli_connect() (doesn't apply in safe mode).
; Note that this is generally a *bad* idea to store passwords in this file.
; *Any* user with PHP access can run 'echo get_cfg_var("mysqli.default_pw")
; and reveal this password!  And of course, any users with read access to this
; file will be able to reveal the password as well.
; http://php.net/mysqli.default-pw
mysqli.default_pw =
; Allow or prevent reconnect
mysqli.reconnect = Off

MARIADB

/etc/mysql/my.cnf

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html
# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port		= 3306
socket		= /var/run/mysqld/mysqld.sock
# Here is entries for some specific programs
# The following values assume you have at least 32M ram
# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket		= /var/run/mysqld/mysqld.sock
nice		= 0
[mysqld]
#
# * Basic Settings
#
user		= mysql
pid-file	= /var/run/mysqld/mysqld.pid
socket		= /var/run/mysqld/mysqld.sock
port		= 3306
basedir		= /usr
datadir		= /var/lib/mysql
tmpdir		= /tmp
lc-messages-dir	= /usr/share/mysql
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address		= 127.0.0.1
#
# * Fine Tuning
#
key_buffer		= 128M
max_allowed_packet	= 128M
thread_stack		= 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit	= 16M
query_cache_size        = 256M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#slow_query_log_file = /var/log/mysql/mysql-slow.log
#slow_query_log      = 1
#long_query_time = 2
#log_queries_not_using_indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id		= 1
#log_bin			= /var/log/mysql/mysql-bin.log
expire_logs_days	= 10
max_binlog_size         = 100M
#binlog_do_db		= include_database_name
#binlog_ignore_db	= include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem
[mysqldump]
quick
quote-names
max_allowed_packet	= 256M
[mysql]
#no-auto-rehash	# faster start of mysql but no tab completition
[isamchk]
key_buffer		= 256M
#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

OWNCLOUD

/var/www/owncloud/.user.ini

upload_max_filesize=200G
post_max_size=200G
memory_limit=2G
mbstring.func_overload=0
always_populate_raw_post_data=-1
default_charset='UTF-8'
output_buffering=0
upload_tmp_dir = /home/cloud/tmp
max_file_upload = 600000

Unfortunately it will be hard to debug or help here from remote. You most likely need to work your way through the already known resources at [1] and [2].

As an alternative just wait for the upcoming ownCloud 10.0 which uses WebDAV PUT for WebGUI uploads which mostly works around environmental (webserver config, php) issues which are most likely the reason for such issues like seen here.

[1] https://doc.owncloud.org/server/latest/admin_manual/configuration_files/big_file_upload_configuration.html

[2]

Is it possible to download the beta of owncloud 10.0.0? https://central.owncloud.org/t/owncloud-server-10-0-0-beta-2/6929 the link is not found

Seems the RC1 is now more current, the links here should work: