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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 9a7e91fc6562
children 8705e0d74a0f
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# lastal version: 1021
# maximum percent identity: 100
# scale of score parameters: 4.5512
# scale used while training: 91.024

# 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: 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: 71.9318

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.22048        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: 343
# insExistCost: 341
# delExtendCost: 64
# insExtendCost: 58

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -90    -59   -104
# C    -87     73   -128    -55
# G    -89   -164    145   -167
# T   -112    -66   -127     90

# 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: 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: 70.6019

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.214366       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: 405
# insExistCost: 402
# delExtendCost: 64
# insExtendCost: 54

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     77    -81    -49   -104
# C    -79     73   -142    -42
# G    -80   -181    146   -186
# T   -108    -52   -142     90

# 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: 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: 69.4007

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.210577       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: 466
# insExistCost: 457
# delExtendCost: 57
# insExtendCost: 45

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -75    -45   -100
# C    -73     72   -140    -38
# G    -75   -178    147   -185
# T   -103    -48   -140     89

# 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: 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: 68.8798

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.208805       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: 514
# insExistCost: 497
# delExtendCost: 49
# insExtendCost: 39

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -72    -44    -98
# C    -71     72   -137    -37
# G    -73   -174    146   -184
# T   -102    -46   -138     89

# 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: 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: 68.3956

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.207419       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

# 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     75    -70    -43    -95
# C    -68     71   -132    -35
# G    -70   -168    146   -181
# T   -100    -45   -135     88

# 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: 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: 68.1676

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.206594       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

# 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     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# 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: 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: 68.1403

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.206662       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: 587
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# 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

# 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

# substitution percent identity: 68.1453

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.206677       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: 588
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# 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: 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: 68.1409

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# 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 0.206684       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: 588
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# 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 -t4.72795
#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     -4     -8      7     -9
T     -5     -2     -7      4