You should try the -t flag along with the debug log level. This is the config test and exit
In the DEBUG level logging output, if the config file was read correctly, you will see lots of references to the inputs and outputs being setup. in the example below, the lines containing ] config is the config being read, parsed and checked.
As none of this appears, I would say that you have a permissions problem.
Example:
$ bin/logstash -t
Sending Logstash's logs to /tmp/logstash-6.0.0-beta1/logs which is now configured via log4j2.properties
[2017-09-07T17:49:12,863][DEBUG][logstash.plugins.registry] Adding plugin to the registry {:name=>"fb_apache", :type=>:modules, :class=>#<LogStash::Modules::Scaffold:0xedcaecc @module_name="fb_apache", @directory="/tmp/logstash-6.0.0-beta1/modules/fb_apache/configuration", @kibana_version_parts=["6", "0", "0"]>}
[2017-09-07T17:49:12,866][DEBUG][logstash.plugins.registry] Adding plugin to the registry {:name=>"netflow", :type=>:modules, :class=>#<LogStash::Modules::Scaffold:0x4a34840a @module_name="netflow", @directory="/tmp/logstash-6.0.0-beta1/modules/netflow/configuration", @kibana_version_parts=["6", "0", "0"]>}
[2017-09-07T17:49:12,885][DEBUG][logstash.runner ] -------- Logstash Settings (* means modified) ---------
.... removed ....
[2017-09-07T17:49:12,890][DEBUG][logstash.runner ] --------------- Logstash Settings -------------------
[2017-09-07T17:49:12,896][DEBUG][logstash.config.source.multilocal] Reading pipeline configurations from YAML {:location=>"/tmp/logstash-6.0.0-beta1/config/pipelines.yml"}
[2017-09-07T17:49:12,905][DEBUG][logstash.config.source.multilocal] Reading pipeline configurations from YAML {:location=>"/tmp/logstash-6.0.0-beta1/config/pipelines.yml"}
[2017-09-07T17:49:13,040][DEBUG][logstash.config.source.local.configpathloader] Skipping the following files while reading config since they don't match the specified glob pattern {:files=>[]}
[2017-09-07T17:49:13,041][DEBUG][logstash.config.source.local.configpathloader] Reading config file {:config_file=>"/tmp/testing/confs/test.conf"}
[2017-09-07T17:49:13,536][DEBUG][logstash.plugins.registry] On demand adding plugin to the registry {:name=>"generator", :type=>"input", :class=>LogStash::Inputs::Generator}
[2017-09-07T17:49:13,578][DEBUG][logstash.plugins.registry] On demand adding plugin to the registry {:name=>"plain", :type=>"codec", :class=>LogStash::Codecs::Plain}
[2017-09-07T17:49:13,582][DEBUG][logstash.codecs.plain ] config LogStash::Codecs::Plain/@id = "plain_4619c713-2323-4648-9edc-3a890bddd58c"
[2017-09-07T17:49:13,582][DEBUG][logstash.codecs.plain ] config LogStash::Codecs::Plain/@enable_metric = true
[2017-09-07T17:49:13,582][DEBUG][logstash.codecs.plain ] config LogStash::Codecs::Plain/@charset = "UTF-8"
[2017-09-07T17:49:13,584][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@lines = ["<1>Oct 16 20:21:22 wonker 1,2016/10/16 20:21:20,3,THREAT,SCAN,6,2016/10/16 20:21:20,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54"]
[2017-09-07T17:49:13,584][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@count = 10
[2017-09-07T17:49:13,584][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@id = "3e3c03b67a3fd567f9ef9361e0ced345840e0cf1-1"
[2017-09-07T17:49:13,584][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@enable_metric = true
[2017-09-07T17:49:13,585][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@codec = <LogStash::Codecs::Plain id=>"plain_4619c713-2323-4648-9edc-3a890bddd58c", enable_metric=>true, charset=>"UTF-8">
[2017-09-07T17:49:13,585][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@add_field = {}
[2017-09-07T17:49:13,585][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@threads = 1
[2017-09-07T17:49:13,586][DEBUG][logstash.inputs.generator] config LogStash::Inputs::Generator/@message = "Hello world!"
[2017-09-07T17:49:13,613][DEBUG][logstash.plugins.registry] On demand adding plugin to the registry {:name=>"stdout", :type=>"output", :class=>LogStash::Outputs::Stdout}
[2017-09-07T17:49:13,621][DEBUG][logstash.plugins.registry] On demand adding plugin to the registry {:name=>"rubydebug", :type=>"codec", :class=>LogStash::Codecs::RubyDebug}
[2017-09-07T17:49:13,625][DEBUG][logstash.codecs.rubydebug] config LogStash::Codecs::RubyDebug/@id = "rubydebug_752f09ec-e718-4c7f-b715-2a1c72aeb530"
[2017-09-07T17:49:13,625][DEBUG][logstash.codecs.rubydebug] config LogStash::Codecs::RubyDebug/@enable_metric = true
[2017-09-07T17:49:13,625][DEBUG][logstash.codecs.rubydebug] config LogStash::Codecs::RubyDebug/@metadata = false
[2017-09-07T17:49:14,785][DEBUG][logstash.outputs.stdout ] config LogStash::Outputs::Stdout/@codec = <LogStash::Codecs::RubyDebug id=>"rubydebug_752f09ec-e718-4c7f-b715-2a1c72aeb530", enable_metric=>true, metadata=>false>
[2017-09-07T17:49:14,785][DEBUG][logstash.outputs.stdout ] config LogStash::Outputs::Stdout/@id = "3e3c03b67a3fd567f9ef9361e0ced345840e0cf1-3"
[2017-09-07T17:49:14,786][DEBUG][logstash.outputs.stdout ] config LogStash::Outputs::Stdout/@enable_metric = true
[2017-09-07T17:49:14,786][DEBUG][logstash.outputs.stdout ] config LogStash::Outputs::Stdout/@workers = 1
Configuration OK
[2017-09-07T17:49:14,787][INFO ][logstash.runner ] Using config.test_and_exit mode. Config Validation Result: OK. Exiting Logstash