log filename format change

misc-scripts/id_mapping/synteny_rescore.pl

@@ -73,7 +73,7 @@ $conf->parse_options(
 
 # append job index to logfile name
 my $index = $conf->param('index');
-my $logautobase = ($conf->param('logautobase') || 'synteny_rescore_') . $index;
+my $logautobase = $conf->param('logautobase') || 'synteny_rescore';
 
 # get log filehandle and print heading and parameters to logfile
 my $logger = new Bio::EnsEMBL::Utils::Logger(
@@ -117,7 +117,7 @@ $gene_scores = $sf->rescore_gene_matrix($gene_scores);
 $gene_scores->write_to_file;
 
 # set flag to indicate everything went fine
-my $success_file = $conf->param('logpath')."/synteny_rescore_$index.success";
+my $success_file = $conf->param('logpath')."/synteny_rescore.$index.success";
 open(TMPFILE, '>', $success_file) and close TMPFILE
   or die "Can't open $success_file for writing: $!";
 

modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm

@@ -380,7 +380,7 @@ sub run_exonerate {
   }
 
   # create an empty lsf log directory
-  my $logpath = path_append($self->logger->logpath, 'lsf_exonerate');
+  my $logpath = path_append($self->logger->logpath, 'exonerate');
   system("rm -rf $logpath") == 0 or
     $self->logger->error("Unable to delete lsf log dir $logpath: $!\n");
   system("mkdir -p $logpath") == 0 or

modules/Bio/EnsEMBL/IdMapping/SyntenyFramework.pm

@@ -231,7 +231,7 @@ sub rescore_gene_matrix_lsf {
   $self->logger->debug("Done.\n", 0, 'stamped');
 
   # create an empty lsf log directory
-  my $logpath = path_append($self->logger->logpath, 'lsf_synteny_rescore');
+  my $logpath = path_append($self->logger->logpath, 'synteny_rescore');
   system("rm -rf $logpath") == 0 or
     $self->logger->error("Unable to delete lsf log dir $logpath: $!\n");
   system("mkdir -p $logpath") == 0 or
@@ -242,7 +242,7 @@ sub rescore_gene_matrix_lsf {
 
   my $options = $self->conf->create_commandline_options(
       logauto       => 1,
-      logautobase   => "synteny_rescore_",
+      logautobase   => "synteny_rescore",
       logpath       => $logpath,
       interactive   => 0,
       is_component  => 1,
@@ -283,7 +283,7 @@ sub rescore_gene_matrix_lsf {
   sleep(5);
   my $err;
   foreach my $i (1..$num_jobs) {
-    $err++ unless (-e "$logpath/synteny_rescore_$i.success");
+    $err++ unless (-e "$logpath/synteny_rescore.$i.success");
   }
 
   if ($err) {