From 66938be910a5642b50ddf28991649858b5c36580 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 6 Jun 2009 16:42:00 +0000
Subject: [PATCH] implementing status solution

git-svn-id: http://biopieces.googlecode.com/svn/trunk@488 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/add_ident               |  1 -
 bp_bin/align_pair_seq          |  1 -
 bp_bin/align_seq               | 15 +++++----------
 bp_bin/analyze_bed             | 15 +++++----------
 bp_bin/analyze_seq             | 15 +++++----------
 bp_bin/analyze_tags            | 15 +++++----------
 bp_bin/analyze_vals            | 15 ++++++---------
 bp_bin/assemble_tag_contigs    | 16 ++++++----------
 bp_bin/blast_seq               | 16 ++++++----------
 bp_bin/blat_seq                | 15 +++++----------
 bp_bin/calc_bit_scores         | 17 ++++++-----------
 bp_bin/calc_fixedstep          | 15 ++++++---------
 bp_bin/complement_seq          | 18 +++++++-----------
 bp_bin/compute                 | 15 ++++++---------
 bp_bin/count_records           | 15 ++++++---------
 bp_bin/count_vals              | 15 ++++++---------
 bp_bin/create_blast_db         | 16 ++++++----------
 bp_bin/create_vmatch_index     | 17 ++++++-----------
 bp_bin/create_weight_matrix    | 15 ++++++---------
 bp_bin/extract_seq             | 15 +++++----------
 bp_bin/flip_tab                | 15 ++++++---------
 bp_bin/fold_seq                | 15 ++++++---------
 bp_bin/format_genome           | 15 ++++++---------
 bp_bin/get_genome_align        |  1 -
 bp_bin/get_genome_phastcons    | 15 +++++----------
 bp_bin/get_genome_seq          | 15 +++++----------
 bp_bin/grab                    | 14 ++++----------
 bp_bin/head_records            | 15 +++++----------
 bp_bin/invert_align            | 15 +++++----------
 bp_bin/length_seq              | 15 +++++----------
 bp_bin/length_vals             | 15 +++++----------
 bp_bin/list_biopieces          | 11 +++--------
 bp_bin/list_genomes            | 11 +++--------
 bp_bin/match_seq               | 15 +++++----------
 bp_bin/max_vals                | 15 +++++----------
 bp_bin/mean_vals               | 15 +++++----------
 bp_bin/median_vals             | 15 +++++----------
 bp_bin/merge_records           | 15 +++++----------
 bp_bin/merge_vals              | 15 +++++----------
 bp_bin/min_vals                | 15 +++++----------
 bp_bin/oligo_freq              | 15 +++++----------
 bp_bin/patscan_seq             | 15 +++++----------
 bp_bin/plot_chrdist            | 15 +++++----------
 bp_bin/plot_histogram          | 15 +++++----------
 bp_bin/plot_karyogram          | 15 +++++----------
 bp_bin/plot_lendist            | 15 +++++----------
 bp_bin/plot_matches            | 15 +++++----------
 bp_bin/plot_phastcons_profiles | 15 +++++----------
 bp_bin/plot_seqlogo            | 15 +++++----------
 bp_bin/print_wiki              | 10 +++-------
 bp_bin/random_records          | 15 +++++----------
 bp_bin/read_2bit               | 15 ++++++---------
 bp_bin/read_bed                | 15 ++++++---------
 bp_bin/read_blast_tab          | 15 ++++++---------
 bp_bin/read_embl               | 15 ++++++---------
 bp_bin/read_fasta              |  1 -
 bp_bin/read_fixedstep          | 15 ++++++---------
 bp_bin/read_gff                | 15 ++++++---------
 bp_bin/read_mysql              | 15 ++++++---------
 bp_bin/read_psl                | 15 ++++++---------
 bp_bin/read_soft               | 15 ++++++---------
 bp_bin/read_solexa             | 15 ++++++---------
 bp_bin/read_solid              | 15 ++++++---------
 bp_bin/read_stockholm          | 14 +++++---------
 bp_bin/read_tab                | 19 ++++++-------------
 bp_bin/read_ucsc_config        | 15 ++++++---------
 bp_bin/remove_adaptor          | 15 +++++----------
 bp_bin/remove_indels           | 15 +++++----------
 bp_bin/remove_keys             | 15 +++++----------
 bp_bin/remove_mysql_tables     | 15 +++++----------
 bp_bin/remove_ucsc_tracks      | 15 +++++----------
 bp_bin/rename_keys             | 15 +++++----------
 bp_bin/reverse_seq             | 16 +++++++---------
 bp_bin/shuffle_seq             | 16 +++++++---------
 bp_bin/soap_seq                | 16 ++++++----------
 bp_bin/sort_records            | 15 +++++----------
 bp_bin/split_bed               | 15 +++++----------
 bp_bin/split_seq               | 15 +++++----------
 bp_bin/split_vals              |  1 -
 bp_bin/sum_vals                | 15 +++++----------
 bp_bin/tile_seq                | 15 +++++----------
 bp_bin/translate_seq           | 15 +++++----------
 bp_bin/transliterate_seq       | 15 +++++----------
 bp_bin/transliterate_vals      | 15 +++++----------
 bp_bin/uniq_vals               | 15 +++++----------
 bp_bin/upload_to_ucsc          | 15 +++++----------
 bp_bin/uppercase_seq           | 16 +++++++---------
 bp_bin/vmatch_seq              | 16 ++++++----------
 bp_bin/write_2bit              | 15 ++++++---------
 bp_bin/write_align             | 15 ++++++---------
 bp_bin/write_bed               | 15 ++++++---------
 bp_bin/write_blast             | 17 +++++++----------
 bp_bin/write_fasta             | 15 ++++++---------
 bp_bin/write_fixedstep         | 15 ++++++---------
 bp_bin/write_psl               | 15 ++++++---------
 bp_bin/write_solid             | 15 ++++++---------
 bp_bin/write_tab               | 15 ++++++---------
 bp_bin/write_ucsc_config       | 15 ++++++---------
 98 files changed, 506 insertions(+), 900 deletions(-)

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
index 16bde7a..bbf6623 100755
--- a/bp_bin/add_ident
+++ b/bp_bin/add_ident
@@ -82,4 +82,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq
index 817ac25..ebe340d 100755
--- a/bp_bin/align_pair_seq
+++ b/bp_bin/align_pair_seq
@@ -92,4 +92,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index 56a6e54..469a97a 100755
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -73,26 +73,22 @@ foreach $entry ( @entries )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -100,4 +96,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
index 8548fa6..544424f 100755
--- a/bp_bin/analyze_bed
+++ b/bp_bin/analyze_bed
@@ -48,26 +48,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -75,4 +71,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
index 6f76a94..952fc4a 100755
--- a/bp_bin/analyze_seq
+++ b/bp_bin/analyze_seq
@@ -54,26 +54,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -81,4 +77,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
index 68f97ac..cb24523 100755
--- a/bp_bin/analyze_tags
+++ b/bp_bin/analyze_tags
@@ -74,26 +74,22 @@ foreach $key ( sort { $a <=> $b } keys %len_hash )
     Maasha::Biopieces::put_record( $tag_record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index 86e50e6..d246ac7 100755
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -126,25 +126,22 @@ print "$maxs\n";
 print "$sums\n";
 print "$means\n";
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
index 898837e..9236586 100755
--- a/bp_bin/assemble_tag_contigs
+++ b/bp_bin/assemble_tag_contigs
@@ -93,25 +93,22 @@ foreach $chr ( sort keys %{ $file_hash } )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -119,4 +116,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index 1534c77..2d06389 100755
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -141,6 +141,9 @@ unlink $tmp_out;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -268,19 +271,13 @@ sub blast_tab2biopiece
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -288,4 +285,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
index 9c3ffa7..4f68e0e 100755
--- a/bp_bin/blat_seq
+++ b/bp_bin/blat_seq
@@ -105,26 +105,22 @@ unlink $result_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -132,4 +128,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index 6bb5374..a634701 100755
--- a/bp_bin/calc_bit_scores
+++ b/bp_bin/calc_bit_scores
@@ -85,25 +85,22 @@ for ( $i = 0; $i < keys %freq_hash; $i++ )
 
 Maasha::Biopieces::put_record( $record, $out );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -111,5 +108,3 @@ END
 
 
 __END__
-
-
diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
index cbb068a..27cae9f 100755
--- a/bp_bin/calc_fixedstep
+++ b/bp_bin/calc_fixedstep
@@ -95,25 +95,22 @@ foreach $chr ( sort keys %{ $file_hash } )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
index 38d1dae..6e7ba90 100755
--- a/bp_bin/complement_seq
+++ b/bp_bin/complement_seq
@@ -60,24 +60,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 }
 
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -85,5 +83,3 @@ END
 
 
 __END__
-
-
diff --git a/bp_bin/compute b/bp_bin/compute
index 299b787..6fbcdbb 100755
--- a/bp_bin/compute
+++ b/bp_bin/compute
@@ -72,25 +72,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/count_records b/bp_bin/count_records
index 3907e4f..6f97188 100755
--- a/bp_bin/count_records
+++ b/bp_bin/count_records
@@ -75,25 +75,22 @@ Maasha::Biopieces::put_record( $result, $data_out );
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/count_vals b/bp_bin/count_vals
index 449fe81..7f0fe50 100755
--- a/bp_bin/count_vals
+++ b/bp_bin/count_vals
@@ -107,25 +107,22 @@ unlink $tmp_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
index 9273af6..5882469 100755
--- a/bp_bin/create_blast_db
+++ b/bp_bin/create_blast_db
@@ -73,25 +73,22 @@ if ( $seq_type eq "protein" ) {
 
 unlink $path;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -99,4 +96,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
index e6dc983..0dc28c0 100755
--- a/bp_bin/create_vmatch_index
+++ b/bp_bin/create_vmatch_index
@@ -75,25 +75,22 @@ if ( $type eq "protein" ) {
 
 unlink $file_tmp;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -101,5 +98,3 @@ END
 
 
 __END__
-
-
diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
index 8adffcf..fa3cd77 100755
--- a/bp_bin/create_weight_matrix
+++ b/bp_bin/create_weight_matrix
@@ -87,25 +87,22 @@ foreach $res ( sort keys %res_hash )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index c900bc7..1588042 100755
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -93,26 +93,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -120,4 +116,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
index 605b277..c24cf0f 100755
--- a/bp_bin/flip_tab
+++ b/bp_bin/flip_tab
@@ -67,25 +67,22 @@ foreach $row ( @matrix )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
index 701f900..c8eba69 100755
--- a/bp_bin/fold_seq
+++ b/bp_bin/fold_seq
@@ -62,25 +62,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 6ffa92d..d5058ca 100755
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -114,25 +114,22 @@ foreach $format ( @{ $options->{ 'formats' } } )
 
 close $fh_out if $fh_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
index 3b8bf43..b1e5c1d 100755
--- a/bp_bin/get_genome_align
+++ b/bp_bin/get_genome_align
@@ -181,4 +181,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
index 337c019..24994ab 100755
--- a/bp_bin/get_genome_phastcons
+++ b/bp_bin/get_genome_phastcons
@@ -101,26 +101,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh_phastcons if $fh_phastcons;                                                                                                                                          
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -128,4 +124,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index bf0f787..b5ea5a7 100755
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -191,26 +191,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -218,4 +214,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/grab b/bp_bin/grab
index 1fecf43..806ae1c 100755
--- a/bp_bin/grab
+++ b/bp_bin/grab
@@ -120,6 +120,8 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -274,20 +276,13 @@ sub grab_eval
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -295,4 +290,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/head_records b/bp_bin/head_records
index 631973c..d537501 100755
--- a/bp_bin/head_records
+++ b/bp_bin/head_records
@@ -55,26 +55,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     last if $count == $options->{ "num" };
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -82,4 +78,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/invert_align b/bp_bin/invert_align
index f8b330a..84f17d3 100755
--- a/bp_bin/invert_align
+++ b/bp_bin/invert_align
@@ -66,26 +66,22 @@ Maasha::Align::align_invert( \@entries, $options->{ "soft" } );
 
 map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -93,4 +89,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/length_seq b/bp_bin/length_seq
index b00eb3e..f7c3d95 100755
--- a/bp_bin/length_seq
+++ b/bp_bin/length_seq
@@ -58,26 +58,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 Maasha::Biopieces::put_record( { TOTAL_SEQ_LEN => $total }, $out );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -85,4 +81,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/length_vals b/bp_bin/length_vals
index f9f1616..99a3c2b 100755
--- a/bp_bin/length_vals
+++ b/bp_bin/length_vals
@@ -56,26 +56,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -83,4 +79,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
index f58f2e8..a51a2ad 100755
--- a/bp_bin/list_biopieces
+++ b/bp_bin/list_biopieces
@@ -62,16 +62,13 @@ foreach $file ( sort @files )
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -79,5 +76,3 @@ END
 
 
 __END__
-
-
diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
index 147d5c1..7a4f457 100755
--- a/bp_bin/list_genomes
+++ b/bp_bin/list_genomes
@@ -85,16 +85,13 @@ foreach $genome ( sort keys %hash )
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -102,5 +99,3 @@ END
 
 
 __END__
-
-
diff --git a/bp_bin/match_seq b/bp_bin/match_seq
index 0ce31eb..b418f3c 100755
--- a/bp_bin/match_seq
+++ b/bp_bin/match_seq
@@ -73,26 +73,22 @@ elsif ( @entries == 2 )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -100,4 +96,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/max_vals b/bp_bin/max_vals
index 7c760a5..49e6fed 100755
--- a/bp_bin/max_vals
+++ b/bp_bin/max_vals
@@ -74,26 +74,22 @@ Maasha::Biopieces::put_record( $max_record, $fh );
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index fb073cd..654c4fe 100755
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -75,26 +75,22 @@ foreach $key ( @{ $options->{ "keys" } } )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -102,4 +98,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 9428f9a..c1b8013 100755
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -71,26 +71,22 @@ foreach $key ( @{ $options->{ "keys" } } )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/merge_records b/bp_bin/merge_records
index 39f09e2..ad0d06e 100755
--- a/bp_bin/merge_records
+++ b/bp_bin/merge_records
@@ -203,26 +203,22 @@ if ( $num2 > 0 and $options->{ 'merge' } =~ /^(BorA|BnotA)$/ )
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -230,4 +226,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
index c751a4d..9979d07 100755
--- a/bp_bin/merge_vals
+++ b/bp_bin/merge_vals
@@ -61,26 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -88,4 +84,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/min_vals b/bp_bin/min_vals
index 34024b1..7eeb7a6 100755
--- a/bp_bin/min_vals
+++ b/bp_bin/min_vals
@@ -74,26 +74,22 @@ Maasha::Biopieces::put_record( $min_record, $fh );
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -101,4 +97,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index e179d8d..d660610 100755
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -71,26 +71,22 @@ if ( defined $options->{ "all" } )
     map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 60a5cae..d6b9c1b 100755
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -139,6 +139,9 @@ unlink $seq_file if not $options->{ 'genome' };
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -219,20 +222,13 @@ sub pat_write
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -240,4 +236,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
index df4db5a..16b86a6 100755
--- a/bp_bin/plot_chrdist
+++ b/bp_bin/plot_chrdist
@@ -97,26 +97,22 @@ print $fh "$_\n" foreach @{ $result };
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -124,4 +120,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
index 9eccb68..74ba748 100755
--- a/bp_bin/plot_histogram
+++ b/bp_bin/plot_histogram
@@ -76,26 +76,22 @@ print $fh "$_\n" foreach @{ $result };
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -103,4 +99,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
index 9adf2f8..e9542ca 100755
--- a/bp_bin/plot_karyogram
+++ b/bp_bin/plot_karyogram
@@ -69,26 +69,22 @@ print $fh $result;
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -96,4 +92,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
index a2fb9cc..a515f5c 100755
--- a/bp_bin/plot_lendist
+++ b/bp_bin/plot_lendist
@@ -76,26 +76,22 @@ print $fh "$_\n" foreach @{ $result };
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -103,4 +99,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
index f383da8..9bdb087 100755
--- a/bp_bin/plot_matches
+++ b/bp_bin/plot_matches
@@ -80,6 +80,9 @@ close $fh;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -189,20 +192,13 @@ sub dotplot_matches
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -210,4 +206,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index caf444f..b1af87b 100755
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -101,26 +101,22 @@ close $fh;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -128,4 +124,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
index e9be5a6..34a533f 100755
--- a/bp_bin/plot_seqlogo
+++ b/bp_bin/plot_seqlogo
@@ -63,26 +63,22 @@ print $fh $logo;
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -90,4 +86,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/print_wiki b/bp_bin/print_wiki
index b13d514..1c36c10 100755
--- a/bp_bin/print_wiki
+++ b/bp_bin/print_wiki
@@ -62,21 +62,17 @@ print STDERR "$_\n" foreach @{ $lines };
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 __END__
-
diff --git a/bp_bin/random_records b/bp_bin/random_records
index 5c4595c..83ac80d 100755
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -98,26 +98,22 @@ close $fh_in;
 unlink $tmp_file;
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -125,4 +121,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
index 63bb7e1..ab2816a 100755
--- a/bp_bin/read_2bit
+++ b/bp_bin/read_2bit
@@ -82,25 +82,22 @@ NUM:
 
 close $data_in if $data_in;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_bed b/bp_bin/read_bed
index 551d86e..177d1c7 100755
--- a/bp_bin/read_bed
+++ b/bp_bin/read_bed
@@ -73,25 +73,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
index fcf53ae..d5aaf8a 100755
--- a/bp_bin/read_blast_tab
+++ b/bp_bin/read_blast_tab
@@ -99,25 +99,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_embl b/bp_bin/read_embl
index 80cc39a..7197794 100755
--- a/bp_bin/read_embl
+++ b/bp_bin/read_embl
@@ -106,25 +106,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index 17a26df..1c35069 100755
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -94,4 +94,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
index 794599b..16ad12f 100755
--- a/bp_bin/read_fixedstep
+++ b/bp_bin/read_fixedstep
@@ -71,25 +71,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_gff b/bp_bin/read_gff
index f7162a1..3901757 100755
--- a/bp_bin/read_gff
+++ b/bp_bin/read_gff
@@ -69,25 +69,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index b79458b..f0ce4de 100755
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -64,25 +64,22 @@ Maasha::SQL::disconnect( $dbh );
 
 map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_psl b/bp_bin/read_psl
index c7183ee..866b99b 100755
--- a/bp_bin/read_psl
+++ b/bp_bin/read_psl
@@ -69,25 +69,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_soft b/bp_bin/read_soft
index c51ba90..dfbf9f3 100755
--- a/bp_bin/read_soft
+++ b/bp_bin/read_soft
@@ -103,25 +103,22 @@ NUM:
 close $data_in if $data_in;
 close $fh if $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index b35c21c..f509aa4 100755
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -89,25 +89,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_solid b/bp_bin/read_solid
index b39e596..cfcd4e6 100755
--- a/bp_bin/read_solid
+++ b/bp_bin/read_solid
@@ -93,25 +93,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
index f883d41..177ded5 100755
--- a/bp_bin/read_stockholm
+++ b/bp_bin/read_stockholm
@@ -91,6 +91,8 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -98,19 +100,13 @@ if ( $options->{ 'data_in' } )
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/read_tab b/bp_bin/read_tab
index 152c0d5..0fda36b 100755
--- a/bp_bin/read_tab
+++ b/bp_bin/read_tab
@@ -104,25 +104,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -130,7 +127,3 @@ END
 
 
 __END__
-
-
-
-
diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
index a62000b..a07a99f 100755
--- a/bp_bin/read_ucsc_config
+++ b/bp_bin/read_ucsc_config
@@ -71,25 +71,22 @@ if ( $options->{ 'data_in' } )
     close $data_in;
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
index d989829..a07a719 100755
--- a/bp_bin/remove_adaptor
+++ b/bp_bin/remove_adaptor
@@ -94,26 +94,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -121,4 +117,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
index e476694..5d350e0 100755
--- a/bp_bin/remove_indels
+++ b/bp_bin/remove_indels
@@ -47,26 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -74,4 +70,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
index 0683dce..03c6bcb 100755
--- a/bp_bin/remove_keys
+++ b/bp_bin/remove_keys
@@ -61,26 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out ) if keys %{ $record };
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -88,4 +84,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
index 2875169..64450f4 100755
--- a/bp_bin/remove_mysql_tables
+++ b/bp_bin/remove_mysql_tables
@@ -84,26 +84,22 @@ foreach $table ( sort keys %table_hash )
 
 Maasha::SQL::disconnect( $dbh );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -111,4 +107,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
index ca56575..e400502 100755
--- a/bp_bin/remove_ucsc_tracks
+++ b/bp_bin/remove_ucsc_tracks
@@ -116,26 +116,22 @@ Maasha::SQL::disconnect( $dbh );
 
 Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -143,4 +139,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
index 4a804d4..a792544 100755
--- a/bp_bin/rename_keys
+++ b/bp_bin/rename_keys
@@ -56,26 +56,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -83,4 +79,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
index 7d2052d..1b331c9 100755
--- a/bp_bin/reverse_seq
+++ b/bp_bin/reverse_seq
@@ -47,24 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
index 05932c4..e791397 100755
--- a/bp_bin/shuffle_seq
+++ b/bp_bin/shuffle_seq
@@ -48,24 +48,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
index f99bbb3..7adb6a9 100755
--- a/bp_bin/soap_seq
+++ b/bp_bin/soap_seq
@@ -126,25 +126,22 @@ unlink $tmp_out;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -152,4 +149,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/sort_records b/bp_bin/sort_records
index 13bd4eb..c9b3085 100755
--- a/bp_bin/sort_records
+++ b/bp_bin/sort_records
@@ -87,26 +87,22 @@ else
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -114,4 +110,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/split_bed b/bp_bin/split_bed
index 97cbaf6..d344a3c 100755
--- a/bp_bin/split_bed
+++ b/bp_bin/split_bed
@@ -71,26 +71,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -98,4 +94,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/split_seq b/bp_bin/split_seq
index 776a79b..7c4c598 100755
--- a/bp_bin/split_seq
+++ b/bp_bin/split_seq
@@ -77,26 +77,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -104,4 +100,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/split_vals b/bp_bin/split_vals
index f7249f8..77194a3 100755
--- a/bp_bin/split_vals
+++ b/bp_bin/split_vals
@@ -91,4 +91,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
index 1da7130..b0b150a 100755
--- a/bp_bin/sum_vals
+++ b/bp_bin/sum_vals
@@ -66,26 +66,22 @@ foreach $key ( @{ $options->{ "keys" } } ) {
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -93,4 +89,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
index a90f1e4..139a6f2 100755
--- a/bp_bin/tile_seq
+++ b/bp_bin/tile_seq
@@ -78,26 +78,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -105,4 +101,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index 21452b9..9627c9d 100755
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -69,26 +69,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -96,4 +92,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
index 44c60ff..2908163 100755
--- a/bp_bin/transliterate_seq
+++ b/bp_bin/transliterate_seq
@@ -64,26 +64,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -91,4 +87,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
index 091aa9d..546652c 100755
--- a/bp_bin/transliterate_vals
+++ b/bp_bin/transliterate_vals
@@ -68,26 +68,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -95,4 +91,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
index 93fd3be..f01be81 100755
--- a/bp_bin/uniq_vals
+++ b/bp_bin/uniq_vals
@@ -70,26 +70,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -97,4 +93,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
index 5fa6c3e..25c3103 100755
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -228,26 +228,22 @@ Maasha::UCSC::ucsc_update_config( $options, $type );
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -255,4 +251,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
index 3a9c89b..5e1ec7b 100755
--- a/bp_bin/uppercase_seq
+++ b/bp_bin/uppercase_seq
@@ -47,24 +47,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
index 0cddbe0..4d54dc9 100755
--- a/bp_bin/vmatch_seq
+++ b/bp_bin/vmatch_seq
@@ -268,25 +268,22 @@ sub vmatch_get_entry
     }
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -294,4 +291,3 @@ END
 
 
 __END__
-
diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
index 459f852..3929bba 100755
--- a/bp_bin/write_2bit
+++ b/bp_bin/write_2bit
@@ -84,25 +84,22 @@ unlink $tmp_file;
 
 Maasha::Filesys::dir_remove( $tmp_dir );
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_align b/bp_bin/write_align
index d978bd4..3963d94 100755
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -68,25 +68,22 @@ if ( scalar( @entries ) == 2 ) {
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_bed b/bp_bin/write_bed
index 38b8704..34f8810 100755
--- a/bp_bin/write_bed
+++ b/bp_bin/write_bed
@@ -64,25 +64,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_blast b/bp_bin/write_blast
index 27f164a..ecf0862 100755
--- a/bp_bin/write_blast
+++ b/bp_bin/write_blast
@@ -70,8 +70,11 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 sub biopiece2blast_tab
@@ -123,19 +126,13 @@ sub biopiece2blast_tab
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
index f71aa26..a2f68c6 100755
--- a/bp_bin/write_fasta
+++ b/bp_bin/write_fasta
@@ -61,25 +61,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index 5de9a6b..7fbd8f9 100755
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -60,25 +60,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_psl b/bp_bin/write_psl
index 43c85d4..404e21a 100755
--- a/bp_bin/write_psl
+++ b/bp_bin/write_psl
@@ -65,25 +65,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_solid b/bp_bin/write_solid
index b467e55..f999c8b 100755
--- a/bp_bin/write_solid
+++ b/bp_bin/write_solid
@@ -65,25 +65,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_tab b/bp_bin/write_tab
index e20794d..eab15ff 100755
--- a/bp_bin/write_tab
+++ b/bp_bin/write_tab
@@ -123,25 +123,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $data_out;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
index efd4dd0..c8d2df3 100755
--- a/bp_bin/write_ucsc_config
+++ b/bp_bin/write_ucsc_config
@@ -58,25 +58,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 close $fh;
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
+
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
-- 
2.39.5