diff --git a/cmd/agent/main.go b/cmd/agent/main.go
index d425d1b59f8..32faf3ca882 100644
--- a/cmd/agent/main.go
+++ b/cmd/agent/main.go
@@ -15,6 +15,8 @@
 package main
 
 import (
+	"fmt"
+	"os"
 	"runtime"
 
 	"github.com/pkg/errors"
@@ -30,14 +32,22 @@ import (
 )
 
 func main() {
-	logger, _ := zap.NewProduction()
 	v := viper.New()
 	var command = &cobra.Command{
 		Use:   "jaeger-agent",
 		Short: "Jaeger agent is a local daemon program which collects tracing data.",
 		Long:  `Jaeger agent is a daemon program that runs on every host and receives tracing data submitted by Jaeger client libraries.`,
 		RunE: func(cmd *cobra.Command, args []string) error {
-			flags.TryLoadConfigFile(v, logger)
+			err := flags.TryLoadConfigFile(v)
+			if err != nil {
+				return err
+			}
+
+			sFlags := new(flags.SharedFlags).InitFromViper(v)
+			logger, err := sFlags.NewLogger(zap.NewProductionConfig())
+			if err != nil {
+				return err
+			}
 
 			builder := &app.Builder{}
 			builder.InitFromViper(v)
@@ -70,6 +80,7 @@ func main() {
 	)
 
 	if err := command.Execute(); err != nil {
-		logger.Fatal("agent command failed", zap.Error(err))
+		fmt.Println(err.Error())
+		os.Exit(1)
 	}
 }
diff --git a/cmd/collector/main.go b/cmd/collector/main.go
index fe8b200ecf1..f9011d7e75b 100644
--- a/cmd/collector/main.go
+++ b/cmd/collector/main.go
@@ -15,6 +15,7 @@
 package main
 
 import (
+	"fmt"
 	"net"
 	"net/http"
 	"os"
@@ -50,7 +51,6 @@ func main() {
 	var signalsChannel = make(chan os.Signal, 0)
 	signal.Notify(signalsChannel, os.Interrupt, syscall.SIGTERM)
 
-	logger, _ := zap.NewProduction()
 	serviceName := "jaeger-collector"
 	casOptions := casFlags.NewOptions("cassandra")
 	esOptions := esFlags.NewOptions("es")
@@ -61,10 +61,18 @@ func main() {
 		Short: "Jaeger collector receives and processes traces from Jaeger agents and clients",
 		Long: `Jaeger collector receives traces from Jaeger agents and agent and runs them through
 				a processing pipeline.`,
-		Run: func(cmd *cobra.Command, args []string) {
-			flags.TryLoadConfigFile(v, logger)
+		RunE: func(cmd *cobra.Command, args []string) error {
+			err := flags.TryLoadConfigFile(v)
+			if err != nil {
+				return err
+			}
 
 			sFlags := new(flags.SharedFlags).InitFromViper(v)
+			logger, err := sFlags.NewLogger(zap.NewProductionConfig())
+			if err != nil {
+				return err
+			}
+
 			casOptions.InitFromViper(v)
 			esOptions.InitFromViper(v)
 
@@ -127,6 +135,7 @@ func main() {
 			case <-signalsChannel:
 				logger.Info("Jaeger Collector is finishing")
 			}
+			return nil
 		},
 	}
 
@@ -143,7 +152,8 @@ func main() {
 	)
 
 	if error := command.Execute(); error != nil {
-		logger.Fatal(error.Error())
+		fmt.Println(error.Error())
+		os.Exit(1)
 	}
 }
 
diff --git a/cmd/flags/flags.go b/cmd/flags/flags.go
index c8184af6b33..f17cd1317a3 100644
--- a/cmd/flags/flags.go
+++ b/cmd/flags/flags.go
@@ -15,14 +15,14 @@
 package flags
 
 import (
-	"errors"
 	"flag"
 	"fmt"
-	"strings"
 	"time"
 
+	"github.com/pkg/errors"
 	"github.com/spf13/viper"
 	"go.uber.org/zap"
+	"go.uber.org/zap/zapcore"
 )
 
 const (
@@ -44,14 +44,26 @@ func AddConfigFileFlag(flagSet *flag.FlagSet) {
 }
 
 // TryLoadConfigFile initializes viper with config file specified as flag
-func TryLoadConfigFile(v *viper.Viper, logger *zap.Logger) {
+func TryLoadConfigFile(v *viper.Viper) error {
 	if file := v.GetString(configFile); file != "" {
 		v.SetConfigFile(file)
 		err := v.ReadInConfig()
 		if err != nil {
-			logger.Fatal("Error loading config file", zap.Error(err), zap.String(configFile, file))
+			return errors.Wrapf(err, "Error loading config file %s", file)
 		}
 	}
+	return nil
+}
+
+// NewLogger returns logger based on configuration in SharedFlags
+func (flags *SharedFlags) NewLogger(conf zap.Config, options ...zap.Option) (*zap.Logger, error) {
+	var level zapcore.Level
+	err := (&level).UnmarshalText([]byte(flags.Logging.Level))
+	if err != nil {
+		return nil, err
+	}
+	conf.Level = zap.NewAtomicLevelAt(level)
+	return conf.Build(options...)
 }
 
 // SharedFlags holds flags configuration
@@ -60,19 +72,22 @@ type SharedFlags struct {
 	SpanStorage spanStorage
 	// DependencyStorage defines common settings for Dependency Storage.
 	DependencyStorage dependencyStorage
+	// Logging holds logging configuration
+	Logging logging
 }
 
 // InitFromViper initializes SharedFlags with properties from viper
 func (flags *SharedFlags) InitFromViper(v *viper.Viper) *SharedFlags {
 	flags.SpanStorage.Type = v.GetString(spanStorageType)
 	flags.DependencyStorage.DataFrequency = v.GetDuration(dependencyStorageDataFrequency)
+	flags.Logging.Level = v.GetString(logLevel)
 	return flags
 }
 
 // AddFlags adds flags for SharedFlags
 func AddFlags(flagSet *flag.FlagSet) {
 	flagSet.String(spanStorageType, CassandraStorageType, fmt.Sprintf("The type of span storage backend to use, options are currently [%v,%v,%v]", CassandraStorageType, ESStorageType, MemoryStorageType))
-	flagSet.String(logLevel, "info", "Minimal allowed log level")
+	flagSet.String(logLevel, "info", "Minimal allowed log Level. For more levels see https://github.com/uber-go/zap")
 	flagSet.Duration(dependencyStorageDataFrequency, time.Hour*24, "Frequency of service dependency calculations")
 }
 
@@ -88,19 +103,5 @@ type spanStorage struct {
 }
 
 type dependencyStorage struct {
-	Type          string
 	DataFrequency time.Duration
 }
-
-type cassandraOptions struct {
-	ConnectionsPerHost int
-	MaxRetryAttempts   int
-	QueryTimeout       time.Duration
-	Servers            string
-	Port               int
-	Keyspace           string
-}
-
-func (co cassandraOptions) ServerList() []string {
-	return strings.Split(co.Servers, ",")
-}
diff --git a/cmd/query/main.go b/cmd/query/main.go
index 6eb2fb15a04..6e76b3e1d51 100644
--- a/cmd/query/main.go
+++ b/cmd/query/main.go
@@ -15,6 +15,7 @@
 package main
 
 import (
+	"fmt"
 	"net/http"
 	"os"
 	"os/signal"
@@ -45,7 +46,6 @@ func main() {
 	var serverChannel = make(chan os.Signal, 0)
 	signal.Notify(serverChannel, os.Interrupt, syscall.SIGTERM)
 
-	logger, _ := zap.NewProduction()
 	casOptions := casFlags.NewOptions("cassandra", "cassandra.archive")
 	esOptions := esFlags.NewOptions("es", "es.archive")
 	v := viper.New()
@@ -54,10 +54,18 @@ func main() {
 		Use:   "jaeger-query",
 		Short: "Jaeger query is a service to access tracing data",
 		Long:  `Jaeger query is a service to access tracing data and host UI.`,
-		Run: func(cmd *cobra.Command, args []string) {
-			flags.TryLoadConfigFile(v, logger)
+		RunE: func(cmd *cobra.Command, args []string) error {
+			err := flags.TryLoadConfigFile(v)
+			if err != nil {
+				return err
+			}
 
 			sFlags := new(flags.SharedFlags).InitFromViper(v)
+			logger, err := sFlags.NewLogger(zap.NewProductionConfig())
+			if err != nil {
+				return err
+			}
+
 			casOptions.InitFromViper(v)
 			esOptions.InitFromViper(v)
 			queryOpts := new(builder.QueryOptions).InitFromViper(v)
@@ -119,6 +127,7 @@ func main() {
 			case <-serverChannel:
 				logger.Info("Jaeger Query is finishing")
 			}
+			return nil
 		},
 	}
 
@@ -135,7 +144,8 @@ func main() {
 	)
 
 	if error := command.Execute(); error != nil {
-		logger.Fatal(error.Error())
+		fmt.Println(error.Error())
+		os.Exit(1)
 	}
 }
 
diff --git a/cmd/standalone/main.go b/cmd/standalone/main.go
index 9e2376a1948..c125130476f 100644
--- a/cmd/standalone/main.go
+++ b/cmd/standalone/main.go
@@ -18,6 +18,7 @@ import (
 	"fmt"
 	"net"
 	"net/http"
+	"os"
 	"runtime"
 	"strconv"
 
@@ -51,19 +52,25 @@ import (
 
 // standalone/main is a standalone full-stack jaeger backend, backed by a memory store
 func main() {
-	logger, _ := zap.NewProduction()
 	v := viper.New()
-
 	command := &cobra.Command{
 		Use:   "jaeger-standalone",
 		Short: "Jaeger all-in-one distribution with agent, collector and query in one process.",
 		Long: `Jaeger all-in-one distribution with agent, collector and query. Use with caution this version
 		 uses only in-memory database.`,
 		RunE: func(cmd *cobra.Command, args []string) error {
-			flags.TryLoadConfigFile(v, logger)
+			err := flags.TryLoadConfigFile(v)
+			if err != nil {
+				return err
+			}
 
-			runtime.GOMAXPROCS(runtime.NumCPU())
 			sFlags := new(flags.SharedFlags).InitFromViper(v)
+			logger, err := sFlags.NewLogger(zap.NewProductionConfig())
+			if err != nil {
+				return err
+			}
+
+			runtime.GOMAXPROCS(runtime.NumCPU())
 			cOpts := new(collector.CollectorOptions).InitFromViper(v)
 			qOpts := new(query.QueryOptions).InitFromViper(v)
 
@@ -93,7 +100,8 @@ func main() {
 	)
 
 	if err := command.Execute(); err != nil {
-		logger.Fatal("standalone command failed", zap.Error(err))
+		fmt.Println(err.Error())
+		os.Exit(1)
 	}
 }