diff --git a/flowsim.cabal b/flowsim.cabal
--- a/flowsim.cabal
+++ b/flowsim.cabal
@@ -1,5 +1,5 @@
 Name:           flowsim
-Version:        0.2.6
+Version:        0.2.7
 License:        GPL
 
 Author:         Ketil Malde
@@ -13,7 +13,7 @@
                 The Darcs repository is at <http://malde.org/~ketil/biohaskell/pyrosim>.
 
 HomePage:       http://bhlog.malde.org/
-Build-Depends:  bio >= 0.4.4, base >= 4 && <= 5, array >= 0.1, bytestring >= 0.9.1, random, MonadRandom, cmdargs, containers, directory
+Build-Depends:  bio >= 0.4.4, base >= 4 && <= 5, array >= 0.1, bytestring >= 0.9.1, random, MonadRandom, cmdargs <= 0.1.1, containers, directory
 Build-Type:     Simple
 Tested-with:    GHC==6.8.2
 
diff --git a/src/CloneSim.hs b/src/CloneSim.hs
--- a/src/CloneSim.hs
+++ b/src/CloneSim.hs
@@ -11,7 +11,7 @@
 import Statistics
 
 import System.IO (stdin,stdout,stderr,hPutStrLn)
-import Control.Monad (forM)
+import Control.Monad (forM,when)
 import qualified Data.ByteString.Lazy as B
 import Data.Int (Int64)
 import System.Console.CmdArgs
@@ -35,7 +35,7 @@
                  ,"    Uniform a b, Normal mu sigma, LogNormal mu sigma"]
 
 version :: String
-version = "clonesim v0.2.6, copyright 2010 Ketil Malde" 
+version = "clonesim v0.2.7, copyright 2010 Ketil Malde" 
 
 data Dir   = Fwd | Rev deriving (Eq,Enum,Bounded)
 
@@ -51,7 +51,9 @@
         []  -> hPutStrLn stderr "clonesim: reading from stdin" >> hReadFasta stdin
         [x] -> readFasta x
         _   -> error "Please specify only a single input file"
+  seq inf $ return () -- force the above warning
   ss <- map (defragSeq . castToNuc) `fmap` inf
+  when (null ss) $ error  "No sequences in input, exiting!"
   let sa = listArray (0,length ss-1) ss
   hWriteFasta stdout =<< evalRandIO (simulate conf sa)
   
diff --git a/src/Config.hs b/src/Config.hs
--- a/src/Config.hs
+++ b/src/Config.hs
@@ -20,7 +20,7 @@
 import Generations.Empirical
 
 version :: String
-version = "flowsim v0.2.6, copyright 2010 Ketil Malde"
+version = "flowsim v0.2.7, copyright 2010 Ketil Malde"
 
 -- data GenName = Titanium | FLX | GS20 deriving (Typeable, Data, Show, Eq)
 type GenName = String