Fixed a bug in perl scripts for printing error messages

[rsem.git] / convert-sam-for-rsem

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 13b9b13b209786d0e90d445d2a108834d8d460c8..decf86195f25d65a9cdacddb98d272d25c160df3 100755 (executable)
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -82,16 +82,16 @@ $command = $dir."rsem-sam-validator $out_file";
 
 # command, {err_msg}
 sub runCommand {
-    print STDERR $_[0]."\n";
+    print $_[0]."\n";
     my $status = system($_[0]);
     if ($status != 0) { 
        my $errmsg;
        if (scalar(@_) > 1) { $errmsg = $_[1]; }
-       else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the script!"; }
-       print STDERR $errmsg."\n";
+       else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
+       print $errmsg."\n";
        exit(-1);
     }
-    print STDERR "\n";
+    print "\n";
 }
 
 __END__