diff --git a/src/pipeline/Plgd/GridLsf.pm b/src/pipeline/Plgd/GridLsf.pm
index 2072b46..e50eeba 100644
--- a/src/pipeline/Plgd/GridLsf.pm
+++ b/src/pipeline/Plgd/GridLsf.pm
@@ -36,7 +36,7 @@ sub submitScriptLsf($$$$) {
     $cmd = $cmd . " -e $script.log";                                        # output
     $cmd = $cmd . " $options";                                              # other options
     $cmd = $cmd . " $script";                                               # script
-    plgdInfo("Sumbit command: $cmd");    
+    plgdInfo("Submit command: $cmd");    
     my $result = `$cmd`;
 
     my @items = split(" ", $result);
diff --git a/src/pipeline/Plgd/GridPbs.pm b/src/pipeline/Plgd/GridPbs.pm
index 5b55fe3..5a75d7d 100644
--- a/src/pipeline/Plgd/GridPbs.pm
+++ b/src/pipeline/Plgd/GridPbs.pm
@@ -61,7 +61,7 @@ sub submitScriptPbs($$$$) {
     $cmd = $cmd . " -o $script.log";                            # output
     $cmd = $cmd . " $options";                                  # other options
     $cmd = $cmd . " $script";                                   # script
-    plgdInfo("Sumbit command: $cmd");    
+    plgdInfo("Submit command: $cmd");    
     my $result = `$cmd`;
 
     if (not $result eq "") {
@@ -86,7 +86,7 @@ sub checkScriptPbs($$) {
         my @items = split(" ", $_);
         if (scalar @items >= 6 and $jobid =~ /$items[0]/) {
             $state = $items[4];
-            break;
+            last;
         }
         
     }
diff --git a/src/pipeline/Plgd/GridSge.pm b/src/pipeline/Plgd/GridSge.pm
index bb23894..1b0cb5d 100644
--- a/src/pipeline/Plgd/GridSge.pm
+++ b/src/pipeline/Plgd/GridSge.pm
@@ -35,7 +35,7 @@ sub submitScriptSge($$$$) {
     $cmd = $cmd . " -o $script.log -j yes";                 # output
     $cmd = $cmd . " $options";                              # other options
     $cmd = $cmd . " $script";                               # script
-    plgdInfo("Sumbit command: $cmd");    
+    plgdInfo("Submit command: $cmd");    
     my $result = `$cmd`;
     my @items = split(" ", $result);
     if (scalar @items >= 3) {
diff --git a/src/pipeline/Plgd/GridSlurm.pm b/src/pipeline/Plgd/GridSlurm.pm
index 127e2ae..7fb496c 100644
--- a/src/pipeline/Plgd/GridSlurm.pm
+++ b/src/pipeline/Plgd/GridSlurm.pm
@@ -37,7 +37,7 @@ sub submitScriptSlurm ($$$$) {
     $cmd = $cmd . " -o $script.log";                                        # output
     $cmd = $cmd . " $options";                                              # other options
     $cmd = $cmd . " $script";                                               # script
-    plgdInfo("Sumbit command: $cmd");    
+    plgdInfo("Submit command: $cmd");    
     my $result = `$cmd`;
 
     my @items = split(" ", $result);
diff --git a/src/pipeline/Plgd/Project.pm b/src/pipeline/Plgd/Project.pm
index 105de2e..209a9d3 100644
--- a/src/pipeline/Plgd/Project.pm
+++ b/src/pipeline/Plgd/Project.pm
@@ -153,7 +153,7 @@ sub runJob ($$$) {
             echoFile("$script.done", "0");
         } elsif (scalar @{$job->jobs} > 0) {
             foreach my $j (@{$job->jobs}) {
-                runJob($env, $cfg, $j);
+                &runJob($env, $cfg, $j);
             }
             echoFile("$script.done", "0");
         } elsif (scalar @{$job->pjobs} > 0) {
diff --git a/src/pipeline/Plgd/Utils.pm b/src/pipeline/Plgd/Utils.pm
index a876c5a..ee874a8 100644
--- a/src/pipeline/Plgd/Utils.pm
+++ b/src/pipeline/Plgd/Utils.pm
@@ -190,7 +190,7 @@ sub plgdLogLevel($) {
 }
 
 sub plgdDebug($) {
-    plgdLog("Debug", @_[0]) if $logLevel <= 0;
+    plgdLog("Debug", $_[0]) if $logLevel <= 0;
 }
 
 sub plgdInfo($) {
@@ -199,11 +199,11 @@ sub plgdInfo($) {
 }
 
 sub plgdWarn($) {
-    plgdLog("Warning", @_[0]) if $logLevel <= 2;
+    plgdLog("Warning", $_[0]) if $logLevel <= 2;
 }
 
 sub plgdError($) {
-    plgdLog("Error", @_[0]);    # 
+    plgdLog("Error", $_[0]);    # 
     exit(1);
 }
  
diff --git a/src/pipeline/necat.pl b/src/pipeline/necat.pl
old mode 100644
new mode 100755
index 67ba178..1a6057e
--- a/src/pipeline/necat.pl
+++ b/src/pipeline/necat.pl
@@ -719,7 +719,6 @@ ($$)
     my $u2uVolDir = "$workDir/uu_ovlps";
     my $c2uVolDir = "$workDir/cu_ovlps";
 
-    my $trimReads = "$prjDir/trimReads.fasta";
     my $pmm4 = "$prjDir/3-assembly/pm.m4";
     my $trimPmm4 = "$workDir/pm.m4";
     my $tmpTrimReads = "$workDir/tmp_trimReads.fasta";
@@ -1507,8 +1506,8 @@ ($)
     %env = loadNecatEnv(\%cfg);
     initializeNecatProject(\%cfg);
 
-    my $prjDir = %env{"WorkPath"} . "/" .%cfg{"PROJECT"};
-    my $isGz = %cfg{"COMPRESS"};
+    my $prjDir = $env{"WorkPath"} . "/" .$cfg{"PROJECT"};
+    my $isGz = $cfg{"COMPRESS"};
     my $finalCnsReads = $isGz ? "1-consensus/cns_final.fasta.gz" : "1-consensus/cns_final.fasta";
 
     runConsensus(\%env, \%cfg);
@@ -1524,7 +1523,7 @@ ($)
     %env = loadNecatEnv(\%cfg);
     initializeNecatProject(\%cfg);
 
-    my $prjDir = %env{"WorkPath"} . "/" .%cfg{"PROJECT"};
+    my $prjDir = $env{"WorkPath"} . "/" .$cfg{"PROJECT"};
 
     runConsensus(\%env, \%cfg);
 
@@ -1532,7 +1531,7 @@ ($)
 
     runAssemble(\%env, \%cfg);
 
-    if (%cfg{"POLISH_CONTIGS"} == 1 or %cfg{"POLISH_CONTIGS"} eq "true") {
+    if ($cfg{"POLISH_CONTIGS"} == 1 or $cfg{"POLISH_CONTIGS"} eq "true") {
         runPolishContigs(\%env, \%cfg, "plctg0", "$prjDir/4-fsa/contigs.fasta", 
                      "$prjDir/4-fsa/contig_tiles", "$prjDir/trimReads.fasta.gz", "4-fsa");
         
@@ -1550,7 +1549,7 @@ ($)
     %env = loadNecatEnv(\%cfg);
     initializeNecatProject(\%cfg);
 
-    my $prjDir = %env{"WorkPath"} . "/" .%cfg{"PROJECT"};
+    my $prjDir = $env{"WorkPath"} . "/" .$cfg{"PROJECT"};
 
     runConsensus(\%env, \%cfg);
 
@@ -1561,7 +1560,7 @@ ($)
     runAlignContigs(\%env, \%cfg);
     runBridgeContigs(\%env, \%cfg);
     
-    if (%cfg{"POLISH_CONTIGS"} == 1 or %cfg{"POLISH_CONTIGS"} eq "true") {
+    if ($cfg{"POLISH_CONTIGS"} == 1 or $cfg{"POLISH_CONTIGS"} eq "true") {
         runPolishContigs(\%env, \%cfg, "plctg1", "$prjDir/6-bridge_contigs/bridged_contigs.fasta", 
                      "$prjDir/4-fsa/contig_tiles", "$prjDir/trimReads.fasta.gz", "6-bridge_contigs");
     
@@ -1597,8 +1596,7 @@ ()
 
 sub main() {
     if (scalar @ARGV >= 2) {
-        my $cmd = @ARGV[0];
-        my $cfgfname = @ARGV[1];
+        my ($cmd,$cfgfname) = @ARGV;
 
         if ($cmd eq "correct") {
             cmdCorrect($cfgfname);