PerlLib/Thread_helper.pm

@@ -202,7 +202,10 @@ sub wait_for_all_threads_to_complete {
             $self->_add_error_thread($thread);
             $status = "ERROR";
         }
-        $self->report_thread_info($thread_id, $status);
+        $self->{thread_id_timing}->{end}->{$thread_id} = time();
+        if ($THREAD_MONITORING) { 
+            $self->report_thread_info($thread_id, $status);
+        }
     }
     
     @{$self->{current_threads}} = (); # clear them out.

scripts/cDNA_annotation_comparer.dbi

@@ -34,6 +34,9 @@ use vars qw ($opt_h $opt_p $DEBUG $opt_M $opt_G $MIN_PERCENT_OVERLAP $MIN_PERCEN
              $STOMP_HIGH_PERCENTAGE_OVERLAPPING_GENE $MIN_PERCENT_ALIGN_LENGTH 
              $MIN_PERCENT_LENGTH_FL_COMPARE $TRUST_FL_STATUS $CLUSTER_ID_ONLY);
 
+
+my $RESTRICT_SINGLE_CONTIG = undef;
+
 my $CPU = 2;
 
 &GetOptions ('M=s' => \$opt_M,
@@ -62,6 +65,8 @@ my $CPU = 2;
              ## hidden opts for debugging purposes
              'CLUSTER_ID_ONLY=i' => \$CLUSTER_ID_ONLY,  # the only cluster ID to process.
 
+             'RESTRICT_SINGLE_CONTIG=s' => \$RESTRICT_SINGLE_CONTIG,
+             
 );
 
 
@@ -140,6 +145,12 @@ _EOH_
     
     ;
 
+###  Hidden options
+###
+## --RESTRICT_SINGLE_CONTIG <string>        genomic contig to restrict analysis to
+###
+
+
 if ($opt_h) {die $usage;}
 
 
@@ -291,7 +302,9 @@ main: {
     print "### There are $num_contigs genomic contigs which will be examined.\n";
     foreach my $result (@results) {
         my $asmbl_id = $result->[0];
-        
+
+        if ($RESTRICT_SINGLE_CONTIG && $asmbl_id ne $RESTRICT_SINGLE_CONTIG) { next; }
+                
         $thread_helper->wait_for_open_thread();
         my $thread = threads->create('process_contig', $asmbl_id);
 
@@ -308,7 +321,17 @@ main: {
     if (@failures) {
         ## examine them...   these are the same threads created above, use use the threads api to access info about them
         ## such as error messages
-        die "Error, there were " . scalar(@failures) . " threads (contig jobs) that failed...  See error messages above in order to troubleshoot further";
+        
+        print STDERR "Error, there were " . scalar(@failures) . " threads (contig jobs) that failed...  See error messages above in order to troubleshoot further";
+
+        foreach my $failed_thread (@failures) {
+            my $thread_id = $failed_thread->tid;
+            print STDERR "Failed thread ($thread_id) info:\n"; 
+            $thread_helper->report_thread_info($thread_id, "FAILED");
+        }
+        
+        exit(1);
+        
     }
     else {
         ## all good!

scripts/create_mysql_cdnaassembly_db.dbi

@@ -14,7 +14,7 @@ use ConfigFileReader;
 
 use vars qw ($opt_c $opt_p $opt_d $opt_h $opt_S $opt_r);
 
-&getopts ('c:p:S:r');
+&getopts ('c:p:S:rd');
 
 
 $|=1;
@@ -88,6 +88,7 @@ if (index($mysql_server, "mysql_socket") != -1) {
 
 ## Populate the database structure and static data.
 my $cmd = "$mysql_exec $mysql_options -D$mysql_db -e 'source $schemafile'";
+print STDERR "CMD: $cmd\n" if $DEBUG;
 my $result = system ($cmd);
 
 die "CMD: $cmd failed.\n" if $result;