capture all "dies" during worker->run() and try to record them in log_message

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -302,9 +302,9 @@ sub register_worker_death {
 
     if( $current_role and !$current_role->when_finished() ) {
         # List of cause_of_death:
-        # only happen before or after a batch: 'NO_ROLE','NO_WORK','JOB_LIMIT','HIVE_OVERLOAD','LIFESPAN', 'SEE_MSG'
-        # can happen whilst the worker is running a batch: 'CONTAMINATED','RELOCATED','KILLED_BY_USER','MEMLIMIT','RUNLIMIT','UNKNOWN'
-        my $release_undone_jobs = ($cause_of_death =~ /^(CONTAMINATED|RELOCATED|KILLED_BY_USER|MEMLIMIT|RUNLIMIT|UNKNOWN)$/);
+        # only happen before or after a batch: 'NO_ROLE','NO_WORK','JOB_LIMIT','HIVE_OVERLOAD','LIFESPAN','SEE_MSG'
+        # can happen whilst the worker is running a batch: 'CONTAMINATED','RELOCATED','KILLED_BY_USER','MEMLIMIT','RUNLIMIT','SEE_MSG','UNKNOWN'
+        my $release_undone_jobs = ($cause_of_death =~ /^(CONTAMINATED|RELOCATED|KILLED_BY_USER|MEMLIMIT|RUNLIMIT|SEE_MSG|UNKNOWN)$/);
         $current_role->worker($worker); # So that release_undone_jobs_from_role() has the correct cause_of_death and work_done
         $current_role->when_finished( $worker_died );
         $self->db->get_RoleAdaptor->finalize_role( $current_role, $release_undone_jobs );

scripts/runWorker.pl

@@ -138,11 +138,24 @@ sub main {
         $analyses_pattern = $analysis_id;
     }
 
-    $worker->run( {
-         -analyses_pattern      => $analyses_pattern,
-         -job_id                => $job_id,
-         -force                 => $force,
-    } );
+    eval {
+        $worker->run( {
+             -analyses_pattern      => $analyses_pattern,
+             -job_id                => $job_id,
+             -force                 => $force,
+        } );
+
+        1;
+    } or do {
+        my $msg = $@;
+
+        $hive_dba->get_LogMessageAdaptor()->store_worker_message($worker, $msg, 1 );
+
+        $worker->cause_of_death( 'SEE_MSG' );
+        $queen->register_worker_death($worker, 1);
+
+        die $msg;
+    };
 }