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changeset 3:3de2195f32c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
author iuc
date Fri, 13 Nov 2020 09:05:49 +0000
parents bf30030e5265
children 8705e0d74a0f
files lasttrain.xml test-data/last_train.txt test-data/last_train_E.txt
diffstat 3 files changed, 884 insertions(+), 368 deletions(-) [+]
line wrap: on
line diff
--- a/lasttrain.xml	Thu Sep 10 16:08:15 2020 +0000
+++ b/lasttrain.xml	Fri Nov 13 09:05:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
+<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01">
 
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
 
@@ -18,17 +18,16 @@
         last-train
 
         -Q $init_options.Q
-
         -r $init_options.r
         -q $init_options.q
-
         -a $init_options.cost_opt.a
         -b $init_options.cost_opt.b
         -A $init_options.cost_opt.A
         -B $init_options.cost_opt.B
-
         -D $last_train_opt.align_opt.D
-        -E $last_train_opt.align_opt.E
+        #if $last_train_opt.align_opt.E != ""
+            -E $last_train_opt.align_opt.E
+        #end if
         -s $last_train_opt.align_opt.s
         -S $last_train_opt.align_opt.S
         -T $last_train_opt.align_opt.T
@@ -74,7 +73,7 @@
             <!-- Training options missing  -->
             <section name="align_opt" title="Alignment options" expanded="true">
                 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
-                <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/>
+                <param argument="-E" type="integer" value="" optional="true" label="Maximum expected alignments per square giga"/>
                 <param argument="-s" type="select" multiple="false" label="Query strand to use">
                     <option value="0">Reverse</option>
                     <option value="1" selected="true">Forward</option>
@@ -111,6 +110,19 @@
                 <param name="db_opts_input" value="db"/>
                 <param name="database" value="humdb"/>
             </conditional>
+            <section name="last_train_opt">
+                <section name="align_opt">
+                    <param name="E" value="10"/>
+                </section>
+            </section>
+            <param name="query_fasta" value="fuguMito.fa"/>
+            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/>
+        </test>
+        <test>
+            <conditional name="db_opts">
+                <param name="db_opts_input" value="db"/>
+                <param name="database" value="humdb"/>
+            </conditional>
             <param name="query_fasta" value="fuguMito.fa"/>
             <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
         </test>
--- a/test-data/last_train.txt	Thu Sep 10 16:08:15 2020 +0000
+++ b/test-data/last_train.txt	Fri Nov 13 09:05:49 2020 +0000
@@ -3,493 +3,493 @@
 # scale of score parameters: 4.5512
 # scale used while training: 91.024
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14901
-# deletes: 694
-# inserts: 834
-# delOpens: 350
-# insOpens: 402
-# alignments: 1
-# mean delete size: 1.98286
-# mean insert size: 2.07463
-# matchProb: 0.951836
-# delOpenProb: 0.0223571
-# insOpenProb: 0.0256787
-# delExtendProb: 0.495677
-# insExtendProb: 0.517986
+# aligned letter pairs: 14938.3
+# deletes: 664.27
+# inserts: 839.49
+# delOpens: 344.82
+# insOpens: 404.93
+# alignments: 3
+# mean delete size: 1.92643
+# mean insert size: 2.07317
+# matchProb: 0.951966
+# delOpenProb: 0.0219742
+# insOpenProb: 0.0258048
+# delExtendProb: 0.480904
+# insExtendProb: 0.517648
 
-# substitution percent identity: 71.9408
+# substitution percent identity: 71.9318
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3291           532            387            390           
-# C 552            3221           180            685           
-# G 235            102            1561           84.7          
-# T 335            554            146            2651          
+# A 3296.3         533.237        387.81         392.24        
+# C 553.59         3241.5         182.39         686.22        
+# G 232.54         102.399        1565.4         84.91         
+# T 335.173        558.68         147.16         2651          
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.220773       0.0356887      0.0259615      0.0261627     
-# C 0.0370303      0.216077       0.0120751      0.0459525     
-# G 0.0157647      0.00684256     0.104718       0.00568201    
-# T 0.0224731      0.0371645      0.00979425     0.177839      
+# A 0.22048        0.0356667      0.0259395      0.0262358     
+# C 0.0370281      0.216815       0.0121996      0.0458993     
+# G 0.0155539      0.00684918     0.104705       0.00567939    
+# T 0.0224188      0.0373685      0.00984312     0.177318      
 
-# delExistCost: 346
-# insExistCost: 342
-# delExtendCost: 62
+# delExistCost: 343
+# insExistCost: 341
+# delExtendCost: 64
 # insExtendCost: 58
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     76    -90    -59   -105
-# C    -87     73   -129    -54
-# G    -88   -164    145   -167
+# A     76    -90    -59   -104
+# C    -87     73   -128    -55
+# G    -89   -164    145   -167
 # T   -112    -66   -127     90
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3148 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14771
-# deletes: 379.3
-# inserts: 567.1
-# delOpens: 185.2
-# insOpens: 246.1
-# alignments: 2
-# mean delete size: 2.04806
-# mean insert size: 2.30435
-# matchProb: 0.971438
-# delOpenProb: 0.01218
-# insOpenProb: 0.0161851
-# delExtendProb: 0.511732
-# insExtendProb: 0.566038
+# aligned letter pairs: 14338.3
+# deletes: 327.44
+# inserts: 474.13
+# delOpens: 166.73
+# insOpens: 216.45
+# alignments: 10
+# mean delete size: 1.96389
+# mean insert size: 2.19048
+# matchProb: 0.973244
+# delOpenProb: 0.0113172
+# insOpenProb: 0.014692
+# delExtendProb: 0.490807
+# insExtendProb: 0.54348
 
-# substitution percent identity: 70.0105
+# substitution percent identity: 70.6019
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3158           583.4          429.9          391.6         
-# C 589            3065           156.8          774           
-# G 252.2          88.64          1571           68.46         
-# T 342.6          630.1          131.09         2566          
+# A 3076.4         546.106        412.41         369.93        
+# C 561.42         2983.2         149.401        735.35        
+# G 245.82         80.868         1562.07        66.655        
+# T 326.724        603.44         120.838        2510.5        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.21341        0.0394248      0.0290516      0.0264634     
-# C 0.0398032      0.207126       0.0105962      0.0523051     
-# G 0.0170431      0.00599008     0.106165       0.00462637    
-# T 0.0231521      0.0425807      0.00885876     0.173404      
+# A 0.214366       0.0380532      0.0287371      0.0257771     
+# C 0.0391203      0.207872       0.0104104      0.0512399     
+# G 0.017129       0.00563496     0.108846       0.00464458    
+# T 0.0227664      0.0420483      0.0084201      0.174934      
 
-# delExistCost: 406
-# insExistCost: 400
-# delExtendCost: 60
-# insExtendCost: 51
+# delExistCost: 405
+# insExistCost: 402
+# delExtendCost: 64
+# insExtendCost: 54
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     75    -79    -48   -102
-# C    -78     72   -140    -41
-# G    -79   -174    146   -185
-# T   -107    -52   -136     89
+# A     77    -81    -49   -104
+# C    -79     73   -142    -42
+# G    -80   -181    146   -186
+# T   -108    -52   -142     90
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4973 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14881
-# deletes: 258.8
-# inserts: 446.1
-# delOpens: 112.91
-# insOpens: 168
-# alignments: 2
-# mean delete size: 2.29209
-# mean insert size: 2.65536
-# matchProb: 0.981278
-# delOpenProb: 0.00744548
-# insOpenProb: 0.0110782
-# delExtendProb: 0.563717
-# insExtendProb: 0.623403
+# aligned letter pairs: 14657.7
+# deletes: 218.21
+# inserts: 385.36
+# delOpens: 102.2
+# insOpens: 152.161
+# alignments: 10
+# mean delete size: 2.13513
+# mean insert size: 2.53258
+# matchProb: 0.982218
+# delOpenProb: 0.00684846
+# insOpenProb: 0.0101964
+# delExtendProb: 0.531644
+# insExtendProb: 0.605146
 
-# substitution percent identity: 68.9366
+# substitution percent identity: 69.4007
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3126           618.3          445            406.6         
-# C 622.8          3041           159.4          805.4         
-# G 265.2          91.16          1560           68.22         
-# T 357.3          660            133.33         2554          
+# A 3091.6         591.394        434.35         391.72        
+# C 605.8          2996.8         154.6091       779.75        
+# G 260.46         83.802         1568.22        67.9713       
+# T 351.852        646.07         124.676        2532.5        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.209606       0.0414585      0.0298383      0.0272635     
-# C 0.0417602      0.203906       0.0106882      0.054004      
-# G 0.0177823      0.0061125      0.104602       0.00457431    
-# T 0.0239578      0.0442546      0.0089401      0.171252      
+# A 0.210577       0.0402814      0.0295847      0.0266811     
+# C 0.0412626      0.20412        0.0105308      0.0531108     
+# G 0.0177406      0.00570797     0.106816       0.0046297     
+# T 0.0239655      0.0440055      0.008492       0.172495      
 
-# delExistCost: 470
+# delExistCost: 466
 # insExistCost: 457
-# delExtendCost: 52
-# insExtendCost: 42
+# delExtendCost: 57
+# insExtendCost: 45
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     75    -73    -44    -99
-# C    -73     71   -138    -37
-# G    -73   -171    147   -185
-# T   -103    -48   -134     88
+# A     76    -75    -45   -100
+# C    -73     72   -140    -38
+# G    -75   -178    147   -185
+# T   -103    -48   -140     89
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5154 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14981
-# deletes: 214.8
-# inserts: 402.9
-# delOpens: 82.32
-# insOpens: 131.98
-# alignments: 2
-# mean delete size: 2.60933
-# mean insert size: 3.05274
-# matchProb: 0.985702
-# delOpenProb: 0.0054164
-# insOpenProb: 0.00868387
-# delExtendProb: 0.61676
-# insExtendProb: 0.672425
+# aligned letter pairs: 14615.5
+# deletes: 176.132
+# inserts: 337.667
+# delOpens: 73.361
+# insOpens: 117.993
+# alignments: 8
+# mean delete size: 2.40089
+# mean insert size: 2.86175
+# matchProb: 0.986477
+# delOpenProb: 0.00495152
+# insOpenProb: 0.00796397
+# delExtendProb: 0.583489
+# insExtendProb: 0.650564
 
-# substitution percent identity: 68.4035
+# substitution percent identity: 68.8798
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3114           635.9          450            416.3         
-# C 640.1          3019           164.9          816.3         
-# G 270.6          93.43          1560           69.38         
-# T 365.7          670            135.53         2543          
+# A 3057.2         603.516        434.56         399.47        
+# C 620.42         2962.4         159.336        789.74        
+# G 264.31         86.899         1557.17        68.449        
+# T 353.847        650            125.897        2508.2        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.208097       0.0424949      0.0300719      0.0278198     
-# C 0.0427756      0.201749       0.0110197      0.0545504     
-# G 0.0180832      0.00624359     0.104249       0.00463642    
-# T 0.0244384      0.0447737      0.00905699     0.16994       
+# A 0.208805       0.0412198      0.0296802      0.0272836     
+# C 0.0423743      0.20233        0.0108826      0.0539388     
+# G 0.0180522      0.00593515     0.106354       0.00467503    
+# T 0.0241675      0.0443946      0.00859869     0.171309      
 
-# delExistCost: 518
-# insExistCost: 498
-# delExtendCost: 44
-# insExtendCost: 36
+# delExistCost: 514
+# insExistCost: 497
+# delExtendCost: 49
+# insExtendCost: 39
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -71    -43    -97
-# C    -70     71   -135    -36
-# G    -71   -169    146   -183
-# T   -101    -46   -133     88
+# A     75    -72    -44    -98
+# C    -71     72   -137    -37
+# G    -73   -174    146   -184
+# T   -102    -46   -138     89
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0742 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14981
-# deletes: 197.5
-# inserts: 386.4
-# delOpens: 68.51
-# insOpens: 115.71
-# alignments: 2
-# mean delete size: 2.88279
-# mean insert size: 3.33938
-# matchProb: 0.987657
-# delOpenProb: 0.00451668
-# insOpenProb: 0.00762845
-# delExtendProb: 0.653114
-# insExtendProb: 0.700543
+# aligned letter pairs: 14806.2
+# deletes: 167.925
+# inserts: 326.866
+# delOpens: 62.871
+# insOpens: 105.559
+# alignments: 7
+# mean delete size: 2.67095
+# mean insert size: 3.09652
+# matchProb: 0.988224
+# delOpenProb: 0.00419626
+# insOpenProb: 0.00704543
+# delExtendProb: 0.625601
+# insExtendProb: 0.677057
 
-# substitution percent identity: 68.1501
+# substitution percent identity: 68.3956
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3103           643.6          451.1          422.5         
-# C 649.8          3008           167            819.5         
-# G 272.7          94.59          1560           70.43         
-# T 369.8          675.4          136.61         2542          
+# A 3074.6         626.457        444.21         418.05        
+# C 637.55         2977.3         164.69         809.88        
+# G 269.41         92.415         1559.3         69.29         
+# T 359.136        664.2          129.482        2527.2        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.20706        0.0429467      0.0301014      0.0281929     
-# C 0.0433604      0.20072        0.0111437      0.0546843     
-# G 0.0181969      0.00631188     0.104097       0.00469971    
-# T 0.0246763      0.0450686      0.00911582     0.169625      
+# A 0.207419       0.042262       0.0299673      0.0282025     
+# C 0.0430104      0.200854       0.0111103      0.0546361     
+# G 0.0181749      0.0062345      0.105193       0.00467444    
+# T 0.024228       0.0448082      0.00873511     0.17049       
+
+# delExistCost: 546
+# insExistCost: 519
+# delExtendCost: 42
+# insExtendCost: 35
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -70    -43    -95
+# C    -69     71   -134    -36
+# G    -71   -169    146   -183
+# T   -101    -45   -136     88
+
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1177 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# delExistCost: 549
-# insExistCost: 522
-# delExtendCost: 39
+# aligned letter pairs: 14896.9
+# deletes: 177.451
+# inserts: 344.879
+# delOpens: 59.29
+# insOpens: 103.311
+# alignments: 5
+# mean delete size: 2.99293
+# mean insert size: 3.33826
+# matchProb: 0.988809
+# delOpenProb: 0.00393548
+# insOpenProb: 0.00685746
+# delExtendProb: 0.66588
+# insExtendProb: 0.700443
+
+# substitution percent identity: 68.1858
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3084.6         635.337        445.51         422.24        
+# C 649.18         2997.2         169.11         816.24        
+# G 273.53         93.848         1562.4         71.64         
+# T 365.354        674.15         132.032        2532.3        
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206678       0.0425696      0.0298506      0.0282914     
+# C 0.0434971      0.200822       0.0113309      0.0546907     
+# G 0.0183274      0.00628811     0.104686       0.00480011    
+# T 0.0244799      0.0451702      0.00884656     0.169672      
+
+# delExistCost: 567
+# insExistCost: 531
+# delExtendCost: 37
 # insExtendCost: 32
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -69    -43    -95
-# C    -68     70   -134    -35
-# G    -71   -168    146   -182
-# T   -100    -45   -132     88
+# A     75    -70    -43    -95
+# C    -68     71   -132    -35
+# G    -70   -168    146   -181
+# T   -100    -45   -135     88
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5512 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14981
-# deletes: 192.1
-# inserts: 380.9
-# delOpens: 62.34
-# insOpens: 108.21
-# alignments: 2
-# mean delete size: 3.08149
-# mean insert size: 3.52001
-# matchProb: 0.988548
-# delOpenProb: 0.00411362
-# insOpenProb: 0.00714043
-# delExtendProb: 0.675482
-# insExtendProb: 0.71591
+# aligned letter pairs: 14897.4
+# deletes: 183.45
+# inserts: 350.682
+# delOpens: 57.728
+# insOpens: 101.786
+# alignments: 5
+# mean delete size: 3.17783
+# mean insert size: 3.44529
+# matchProb: 0.989012
+# delOpenProb: 0.00383246
+# insOpenProb: 0.00675739
+# delExtendProb: 0.68532
+# insExtendProb: 0.709748
 
-# substitution percent identity: 67.9883
+# substitution percent identity: 68.1676
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3093           648            451.1          425.7         
-# C 654.2          3008           169            821.5         
-# G 272.8          95.26          1550           71.05         
-# T 371.8          677.5          136.66         2532          
+# A 3083.6         635.04         445.71         423.87        
+# C 650.27         2996.2         169.49         816.21        
+# G 272.96         94.054         1562.4         71.81         
+# T 365.777        674.06         132.018        2532.4        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.206509       0.0432647      0.0301184      0.0284225     
-# C 0.0436786      0.200834       0.0112835      0.0548487     
-# G 0.0182139      0.00636018     0.103488       0.00474376    
-# T 0.0248238      0.0452343      0.00912431     0.169053      
+# A 0.206594       0.0425463      0.0298616      0.0283983     
+# C 0.0435666      0.200739       0.0113555      0.0546843     
+# G 0.0182877      0.00630141     0.104677       0.00481111    
+# T 0.0245062      0.0451605      0.00884491     0.169665      
+
+# delExistCost: 578
+# insExistCost: 536
+# delExtendCost: 34
+# insExtendCost: 31
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -70    -43    -94
+# C    -68     71   -132    -36
+# G    -71   -168    146   -180
+# T   -100    -45   -135     88
+
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3765 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# delExistCost: 566
-# insExistCost: 534
-# delExtendCost: 36
+# aligned letter pairs: 14897.3
+# deletes: 186.949
+# inserts: 354.265
+# delOpens: 56.756
+# insOpens: 101.214
+# alignments: 5
+# mean delete size: 3.29391
+# mean insert size: 3.50016
+# matchProb: 0.989113
+# delOpenProb: 0.00376834
+# insOpenProb: 0.00672015
+# delExtendProb: 0.696409
+# insExtendProb: 0.714299
+
+# substitution percent identity: 68.1476
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3081.6         633.831        445.71         424.07        
+# C 650.26         2986.2         169.38         816.09        
+# G 272.84         94.051         1561.4         71.9          
+# T 365.569        674.07         131.791        2532.4        
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206664       0.0425072      0.029891       0.0284398     
+# C 0.0436089      0.200266       0.0113593      0.0547301     
+# G 0.0182977      0.00630742     0.104714       0.00482189    
+# T 0.0245165      0.0452057      0.00883841     0.169833      
+
+# delExistCost: 584
+# insExistCost: 539
+# delExtendCost: 33
 # insExtendCost: 30
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -133    -35
-# G    -70   -167    147   -181
-# T    -99    -45   -131     88
+# A     75    -70    -43    -94
+# C    -68     71   -132    -35
+# G    -71   -168    146   -180
+# T   -100    -45   -135     88
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5205 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14981
-# deletes: 194.5
-# inserts: 383.3
-# delOpens: 60.42
-# insOpens: 106.36
-# alignments: 2
-# mean delete size: 3.21913
-# mean insert size: 3.6038
-# matchProb: 0.988794
-# delOpenProb: 0.00398791
-# insOpenProb: 0.0070201
-# delExtendProb: 0.689357
-# insExtendProb: 0.722515
+# aligned letter pairs: 14897.4
+# deletes: 188.951
+# inserts: 357.176
+# delOpens: 56.362
+# insOpens: 100.973
+# alignments: 5
+# mean delete size: 3.35245
+# mean insert size: 3.53734
+# matchProb: 0.989155
+# delOpenProb: 0.00374231
+# insOpenProb: 0.00670439
+# delExtendProb: 0.701711
+# insExtendProb: 0.717302
 
-# substitution percent identity: 67.9593
+# substitution percent identity: 68.1403
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3093           648.9          451.2          426.7         
-# C 655.2          3008           169            821.4         
-# G 273.8          95.46          1550           71.26         
-# T 372.8          678.6          136.64         2532          
+# A 3081.6         634.732        445.81         423.98        
+# C 650.18         2986.2         169.39         816.1         
+# G 273.05         94.134         1561.4         71.9          
+# T 365.574        674.07         131.782        2531.4        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.206421       0.0433063      0.0301122      0.0284771     
-# C 0.0437268      0.200748       0.0112787      0.0548186     
-# G 0.0182729      0.00637081     0.103444       0.00475575    
-# T 0.0248799      0.0452884      0.00911908     0.168981      
+# A 0.206662       0.0425672      0.0298975      0.0284335     
+# C 0.0436032      0.200264       0.0113598      0.0547303     
+# G 0.0183116      0.00631293     0.104713       0.00482185    
+# T 0.0245166      0.0452053      0.00883773     0.169764      
 
-# delExistCost: 575
-# insExistCost: 539
-# delExtendCost: 34
-# insExtendCost: 29
+# delExistCost: 587
+# insExistCost: 541
+# delExtendCost: 32
+# insExtendCost: 30
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -132    -35
-# G    -70   -167    147   -180
-# T    -99    -45   -131     88
-
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# A     75    -70    -43    -94
+# C    -68     71   -132    -35
+# G    -71   -168    146   -180
+# T   -100    -45   -135     88
 
-# aligned letter pairs: 14981
-# deletes: 196.9
-# inserts: 385.7
-# delOpens: 59.47
-# insOpens: 105.68
-# alignments: 2
-# mean delete size: 3.31091
-# mean insert size: 3.6497
-# matchProb: 0.9889
-# delOpenProb: 0.00392563
-# insOpenProb: 0.00697597
-# delExtendProb: 0.697969
-# insExtendProb: 0.726005
-
-# substitution percent identity: 67.9572
-
-# count matrix (query letters = columns, reference letters = rows):
-#   A              C              G              T             
-# A 3093           648.8          451.2          426.6         
-# C 655.1          3008           169.9          821.4         
-# G 273.8          95.45          1550           71.26         
-# T 372.7          678.6          136.63         2532          
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4821 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# probability matrix (query letters = columns, reference letters = rows):
-#   A              C              G              T             
-# A 0.206414       0.0432982      0.0301112      0.0284695     
-# C 0.0437187      0.200742       0.0113384      0.0548169     
-# G 0.0182723      0.00636994     0.103441       0.0047556     
-# T 0.0248725      0.045287       0.00911813     0.168975      
-
-# delExistCost: 580
-# insExistCost: 541
-# delExtendCost: 33
-# insExtendCost: 29
+# aligned letter pairs: 14897.4
+# deletes: 189.355
+# inserts: 357.265
+# delOpens: 56.08
+# insOpens: 100.658
+# alignments: 5
+# mean delete size: 3.37652
+# mean insert size: 3.5493
+# matchProb: 0.989194
+# delOpenProb: 0.00372374
+# insOpenProb: 0.00668374
+# delExtendProb: 0.703837
+# insExtendProb: 0.718254
 
-# score matrix (query letters = columns, reference letters = rows):
-#        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -132    -35
-# G    -70   -167    147   -180
-# T    -99    -45   -131     88
-
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
-
-# aligned letter pairs: 14981
-# deletes: 197
-# inserts: 385.7
-# delOpens: 58.72
-# insOpens: 105.14
-# alignments: 2
-# mean delete size: 3.3549
-# mean insert size: 3.66844
-# matchProb: 0.988985
-# delOpenProb: 0.00387646
-# insOpenProb: 0.00694091
-# delExtendProb: 0.701929
-# insExtendProb: 0.727405
-
-# substitution percent identity: 67.9308
+# substitution percent identity: 68.1453
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3093           648.8          451.2          426.6         
-# C 656            2998           169.9          821.4         
-# G 273.8          95.55          1550           71.36         
-# T 372.7          678.6          136.62         2532          
-
-# probability matrix (query letters = columns, reference letters = rows):
-#   A              C              G              T             
-# A 0.206537       0.043324       0.0301292      0.0284865     
-# C 0.0438048      0.200193       0.0113452      0.0548495     
-# G 0.0182832      0.00638041     0.103502       0.00476511    
-# T 0.0248873      0.0453139      0.00912288     0.169076      
-
-# delExistCost: 584
-# insExistCost: 542
-# delExtendCost: 32
-# insExtendCost: 29
-
-# score matrix (query letters = columns, reference letters = rows):
-#        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -132    -35
-# G    -70   -166    146   -180
-# T    -99    -45   -132     88
-
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
-
-# aligned letter pairs: 14981
-# deletes: 197
-# inserts: 384.7
-# delOpens: 57.97
-# insOpens: 104.51
-# alignments: 2
-# mean delete size: 3.39831
-# mean insert size: 3.68099
-# matchProb: 0.989075
-# delOpenProb: 0.00382729
-# insOpenProb: 0.00689995
-# delExtendProb: 0.705736
-# insExtendProb: 0.728334
-
-# substitution percent identity: 67.93
-
-# count matrix (query letters = columns, reference letters = rows):
-#   A              C              G              T             
-# A 3093           648.8          451.2          427.6         
-# C 656            2998           169.9          821.4         
-# G 273.8          95.75          1550           71.36         
-# T 372.7          678.6          135.61         2532          
+# A 3081.6         633.731        445.81         423.98        
+# C 650.08         2986.2         169.39         816.1         
+# G 273.05         94.136         1561.4         71.9          
+# T 365.674        674.07         131.672        2531.4        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.206534       0.0433235      0.0301288      0.0285529     
-# C 0.0438042      0.200191       0.011345       0.0548488     
-# G 0.0182829      0.00639368     0.103501       0.00476505    
-# T 0.024887       0.0453133      0.00905532     0.169074      
+# A 0.206677       0.0425032      0.0298997      0.0284356     
+# C 0.0435997      0.200279       0.0113607      0.0547344     
+# G 0.018313       0.00631353     0.10472        0.0048222     
+# T 0.0245251      0.0452087      0.00883101     0.169776      
 
-# delExistCost: 586
-# insExistCost: 543
+# delExistCost: 588
+# insExistCost: 541
 # delExtendCost: 32
-# insExtendCost: 29
+# insExtendCost: 30
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -132    -35
-# G    -70   -166    147   -180
-# T    -99    -45   -132     88
+# A     75    -70    -43    -94
+# C    -68     71   -132    -35
+# G    -71   -168    146   -180
+# T   -100    -45   -135     88
 
-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84
 
-# aligned letter pairs: 14981
-# deletes: 196
-# inserts: 384.7
-# delOpens: 57.87
-# insOpens: 104.51
-# alignments: 2
-# mean delete size: 3.3869
-# mean insert size: 3.68099
-# matchProb: 0.989081
-# delOpenProb: 0.00382071
-# insOpenProb: 0.0069
-# delExtendProb: 0.704745
-# insExtendProb: 0.728334
+# aligned letter pairs: 14897.4
+# deletes: 188.951
+# inserts: 356.964
+# delOpens: 55.8286
+# insOpens: 100.647
+# alignments: 5
+# mean delete size: 3.38448
+# mean insert size: 3.54669
+# matchProb: 0.989211
+# delOpenProb: 0.00370711
+# insOpenProb: 0.00668312
+# delExtendProb: 0.704534
+# insExtendProb: 0.718047
 
-# substitution percent identity: 67.93
+# substitution percent identity: 68.1409
 
 # count matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 3093           648.8          451.2          427.6         
-# C 656            2998           169.9          821.4         
-# G 273.8          95.75          1550           71.36         
-# T 372.7          678.6          135.61         2532          
+# A 3081.6         633.731        445.81         424.08        
+# C 650.28         2986.2         169.49         816.1         
+# G 273.05         94.136         1561.4         71.9          
+# T 365.673        674.17         131.672        2530.4        
 
 # probability matrix (query letters = columns, reference letters = rows):
 #   A              C              G              T             
-# A 0.206534       0.0433235      0.0301288      0.0285529     
-# C 0.0438042      0.200191       0.011345       0.0548488     
-# G 0.0182829      0.00639368     0.103501       0.00476505    
-# T 0.024887       0.0453133      0.00905532     0.169074      
+# A 0.206684       0.0425046      0.0299007      0.0284432     
+# C 0.0436146      0.200286       0.0113678      0.0547362     
+# G 0.0183136      0.00631375     0.104724       0.00482237    
+# T 0.0245259      0.0452169      0.0088313      0.169715      
 
-# delExistCost: 586
-# insExistCost: 543
+# delExistCost: 588
+# insExistCost: 541
 # delExtendCost: 32
-# insExtendCost: 29
+# insExtendCost: 30
 
 # score matrix (query letters = columns, reference letters = rows):
 #        A      C      G      T
-# A     74    -69    -42    -94
-# C    -68     70   -132    -35
-# G    -70   -166    147   -180
-# T    -99    -45   -132     88
+# A     75    -70    -43    -94
+# C    -68     71   -132    -35
+# G    -71   -168    146   -180
+# T   -100    -45   -135     88
 
 #last -X 0
 #last -Q 0
-#last -t4.80115
+#last -t4.72795
 #last -a 29
 #last -A 28
 #last -b 2
@@ -500,5 +500,5 @@
        A      C      G      T
 A      4     -3     -2     -5
 C     -3      4     -7     -2
-G     -3     -8      7     -9
+G     -4     -8      7     -9
 T     -5     -2     -7      4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/last_train_E.txt	Fri Nov 13 09:05:49 2020 +0000
@@ -0,0 +1,504 @@
+# lastal version: 1021
+# maximum percent identity: 100
+# scale of score parameters: 4.5512
+# scale used while training: 91.024
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14901
+# deletes: 694
+# inserts: 834
+# delOpens: 350
+# insOpens: 402
+# alignments: 1
+# mean delete size: 1.98286
+# mean insert size: 2.07463
+# matchProb: 0.951836
+# delOpenProb: 0.0223571
+# insOpenProb: 0.0256787
+# delExtendProb: 0.495677
+# insExtendProb: 0.517986
+
+# substitution percent identity: 71.9408
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3291           532            387            390           
+# C 552            3221           180            685           
+# G 235            102            1561           84.7          
+# T 335            554            146            2651          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.220773       0.0356887      0.0259615      0.0261627     
+# C 0.0370303      0.216077       0.0120751      0.0459525     
+# G 0.0157647      0.00684256     0.104718       0.00568201    
+# T 0.0224731      0.0371645      0.00979425     0.177839      
+
+# delExistCost: 346
+# insExistCost: 342
+# delExtendCost: 62
+# insExtendCost: 58
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     76    -90    -59   -105
+# C    -87     73   -129    -54
+# G    -88   -164    145   -167
+# T   -112    -66   -127     90
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14771
+# deletes: 379.3
+# inserts: 567.1
+# delOpens: 185.2
+# insOpens: 246.1
+# alignments: 2
+# mean delete size: 2.04806
+# mean insert size: 2.30435
+# matchProb: 0.971438
+# delOpenProb: 0.01218
+# insOpenProb: 0.0161851
+# delExtendProb: 0.511732
+# insExtendProb: 0.566038
+
+# substitution percent identity: 70.0105
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3158           583.4          429.9          391.6         
+# C 589            3065           156.8          774           
+# G 252.2          88.64          1571           68.46         
+# T 342.6          630.1          131.09         2566          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.21341        0.0394248      0.0290516      0.0264634     
+# C 0.0398032      0.207126       0.0105962      0.0523051     
+# G 0.0170431      0.00599008     0.106165       0.00462637    
+# T 0.0231521      0.0425807      0.00885876     0.173404      
+
+# delExistCost: 406
+# insExistCost: 400
+# delExtendCost: 60
+# insExtendCost: 51
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -79    -48   -102
+# C    -78     72   -140    -41
+# G    -79   -174    146   -185
+# T   -107    -52   -136     89
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14881
+# deletes: 258.8
+# inserts: 446.1
+# delOpens: 112.91
+# insOpens: 168
+# alignments: 2
+# mean delete size: 2.29209
+# mean insert size: 2.65536
+# matchProb: 0.981278
+# delOpenProb: 0.00744548
+# insOpenProb: 0.0110782
+# delExtendProb: 0.563717
+# insExtendProb: 0.623403
+
+# substitution percent identity: 68.9366
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3126           618.3          445            406.6         
+# C 622.8          3041           159.4          805.4         
+# G 265.2          91.16          1560           68.22         
+# T 357.3          660            133.33         2554          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.209606       0.0414585      0.0298383      0.0272635     
+# C 0.0417602      0.203906       0.0106882      0.054004      
+# G 0.0177823      0.0061125      0.104602       0.00457431    
+# T 0.0239578      0.0442546      0.0089401      0.171252      
+
+# delExistCost: 470
+# insExistCost: 457
+# delExtendCost: 52
+# insExtendCost: 42
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     75    -73    -44    -99
+# C    -73     71   -138    -37
+# G    -73   -171    147   -185
+# T   -103    -48   -134     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 214.8
+# inserts: 402.9
+# delOpens: 82.32
+# insOpens: 131.98
+# alignments: 2
+# mean delete size: 2.60933
+# mean insert size: 3.05274
+# matchProb: 0.985702
+# delOpenProb: 0.0054164
+# insOpenProb: 0.00868387
+# delExtendProb: 0.61676
+# insExtendProb: 0.672425
+
+# substitution percent identity: 68.4035
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3114           635.9          450            416.3         
+# C 640.1          3019           164.9          816.3         
+# G 270.6          93.43          1560           69.38         
+# T 365.7          670            135.53         2543          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.208097       0.0424949      0.0300719      0.0278198     
+# C 0.0427756      0.201749       0.0110197      0.0545504     
+# G 0.0180832      0.00624359     0.104249       0.00463642    
+# T 0.0244384      0.0447737      0.00905699     0.16994       
+
+# delExistCost: 518
+# insExistCost: 498
+# delExtendCost: 44
+# insExtendCost: 36
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -71    -43    -97
+# C    -70     71   -135    -36
+# G    -71   -169    146   -183
+# T   -101    -46   -133     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197.5
+# inserts: 386.4
+# delOpens: 68.51
+# insOpens: 115.71
+# alignments: 2
+# mean delete size: 2.88279
+# mean insert size: 3.33938
+# matchProb: 0.987657
+# delOpenProb: 0.00451668
+# insOpenProb: 0.00762845
+# delExtendProb: 0.653114
+# insExtendProb: 0.700543
+
+# substitution percent identity: 68.1501
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3103           643.6          451.1          422.5         
+# C 649.8          3008           167            819.5         
+# G 272.7          94.59          1560           70.43         
+# T 369.8          675.4          136.61         2542          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.20706        0.0429467      0.0301014      0.0281929     
+# C 0.0433604      0.20072        0.0111437      0.0546843     
+# G 0.0181969      0.00631188     0.104097       0.00469971    
+# T 0.0246763      0.0450686      0.00911582     0.169625      
+
+# delExistCost: 549
+# insExistCost: 522
+# delExtendCost: 39
+# insExtendCost: 32
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -43    -95
+# C    -68     70   -134    -35
+# G    -71   -168    146   -182
+# T   -100    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 192.1
+# inserts: 380.9
+# delOpens: 62.34
+# insOpens: 108.21
+# alignments: 2
+# mean delete size: 3.08149
+# mean insert size: 3.52001
+# matchProb: 0.988548
+# delOpenProb: 0.00411362
+# insOpenProb: 0.00714043
+# delExtendProb: 0.675482
+# insExtendProb: 0.71591
+
+# substitution percent identity: 67.9883
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648            451.1          425.7         
+# C 654.2          3008           169            821.5         
+# G 272.8          95.26          1550           71.05         
+# T 371.8          677.5          136.66         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206509       0.0432647      0.0301184      0.0284225     
+# C 0.0436786      0.200834       0.0112835      0.0548487     
+# G 0.0182139      0.00636018     0.103488       0.00474376    
+# T 0.0248238      0.0452343      0.00912431     0.169053      
+
+# delExistCost: 566
+# insExistCost: 534
+# delExtendCost: 36
+# insExtendCost: 30
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -133    -35
+# G    -70   -167    147   -181
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 194.5
+# inserts: 383.3
+# delOpens: 60.42
+# insOpens: 106.36
+# alignments: 2
+# mean delete size: 3.21913
+# mean insert size: 3.6038
+# matchProb: 0.988794
+# delOpenProb: 0.00398791
+# insOpenProb: 0.0070201
+# delExtendProb: 0.689357
+# insExtendProb: 0.722515
+
+# substitution percent identity: 67.9593
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.9          451.2          426.7         
+# C 655.2          3008           169            821.4         
+# G 273.8          95.46          1550           71.26         
+# T 372.8          678.6          136.64         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206421       0.0433063      0.0301122      0.0284771     
+# C 0.0437268      0.200748       0.0112787      0.0548186     
+# G 0.0182729      0.00637081     0.103444       0.00475575    
+# T 0.0248799      0.0452884      0.00911908     0.168981      
+
+# delExistCost: 575
+# insExistCost: 539
+# delExtendCost: 34
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -167    147   -180
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 196.9
+# inserts: 385.7
+# delOpens: 59.47
+# insOpens: 105.68
+# alignments: 2
+# mean delete size: 3.31091
+# mean insert size: 3.6497
+# matchProb: 0.9889
+# delOpenProb: 0.00392563
+# insOpenProb: 0.00697597
+# delExtendProb: 0.697969
+# insExtendProb: 0.726005
+
+# substitution percent identity: 67.9572
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          426.6         
+# C 655.1          3008           169.9          821.4         
+# G 273.8          95.45          1550           71.26         
+# T 372.7          678.6          136.63         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206414       0.0432982      0.0301112      0.0284695     
+# C 0.0437187      0.200742       0.0113384      0.0548169     
+# G 0.0182723      0.00636994     0.103441       0.0047556     
+# T 0.0248725      0.045287       0.00911813     0.168975      
+
+# delExistCost: 580
+# insExistCost: 541
+# delExtendCost: 33
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -167    147   -180
+# T    -99    -45   -131     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197
+# inserts: 385.7
+# delOpens: 58.72
+# insOpens: 105.14
+# alignments: 2
+# mean delete size: 3.3549
+# mean insert size: 3.66844
+# matchProb: 0.988985
+# delOpenProb: 0.00387646
+# insOpenProb: 0.00694091
+# delExtendProb: 0.701929
+# insExtendProb: 0.727405
+
+# substitution percent identity: 67.9308
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          426.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.55          1550           71.36         
+# T 372.7          678.6          136.62         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206537       0.043324       0.0301292      0.0284865     
+# C 0.0438048      0.200193       0.0113452      0.0548495     
+# G 0.0182832      0.00638041     0.103502       0.00476511    
+# T 0.0248873      0.0453139      0.00912288     0.169076      
+
+# delExistCost: 584
+# insExistCost: 542
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    146   -180
+# T    -99    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 197
+# inserts: 384.7
+# delOpens: 57.97
+# insOpens: 104.51
+# alignments: 2
+# mean delete size: 3.39831
+# mean insert size: 3.68099
+# matchProb: 0.989075
+# delOpenProb: 0.00382729
+# insOpenProb: 0.00689995
+# delExtendProb: 0.705736
+# insExtendProb: 0.728334
+
+# substitution percent identity: 67.93
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          427.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.75          1550           71.36         
+# T 372.7          678.6          135.61         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206534       0.0433235      0.0301288      0.0285529     
+# C 0.0438042      0.200191       0.011345       0.0548488     
+# G 0.0182829      0.00639368     0.103501       0.00476505    
+# T 0.024887       0.0453133      0.00905532     0.169074      
+
+# delExistCost: 586
+# insExistCost: 543
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    147   -180
+# T    -99    -45   -132     88
+
+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
+
+# aligned letter pairs: 14981
+# deletes: 196
+# inserts: 384.7
+# delOpens: 57.87
+# insOpens: 104.51
+# alignments: 2
+# mean delete size: 3.3869
+# mean insert size: 3.68099
+# matchProb: 0.989081
+# delOpenProb: 0.00382071
+# insOpenProb: 0.0069
+# delExtendProb: 0.704745
+# insExtendProb: 0.728334
+
+# substitution percent identity: 67.93
+
+# count matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 3093           648.8          451.2          427.6         
+# C 656            2998           169.9          821.4         
+# G 273.8          95.75          1550           71.36         
+# T 372.7          678.6          135.61         2532          
+
+# probability matrix (query letters = columns, reference letters = rows):
+#   A              C              G              T             
+# A 0.206534       0.0433235      0.0301288      0.0285529     
+# C 0.0438042      0.200191       0.011345       0.0548488     
+# G 0.0182829      0.00639368     0.103501       0.00476505    
+# T 0.024887       0.0453133      0.00905532     0.169074      
+
+# delExistCost: 586
+# insExistCost: 543
+# delExtendCost: 32
+# insExtendCost: 29
+
+# score matrix (query letters = columns, reference letters = rows):
+#        A      C      G      T
+# A     74    -69    -42    -94
+# C    -68     70   -132    -35
+# G    -70   -166    147   -180
+# T    -99    -45   -132     88
+
+#last -X 0
+#last -Q 0
+#last -t4.80115
+#last -a 29
+#last -A 28
+#last -b 2
+#last -B 1
+#last -s 1
+#last -S 1
+# score matrix (query letters = columns, reference letters = rows):
+       A      C      G      T
+A      4     -3     -2     -5
+C     -3      4     -7     -2
+G     -3     -8      7     -9
+T     -5     -2     -7      4