annotate test-data/last_train.txt @ 7:eca7ac1eb423 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit ddb5e058a7877e627ed24ef8cb9a046ccb450cb4

# lastal version: 1205
# 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/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14938.4
# deletes: 664.28
# inserts: 839.52
# delOpens: 344.93
# insOpens: 404.94
# alignments: 3
# mean delete size: 1.92584
# mean insert size: 2.0732
# matchProb: 0.951959
# delOpenProb: 0.0219809
# insOpenProb: 0.0258051
# delExtendProb: 0.480746
# insExtendProb: 0.517653

# substitution percent identity: 71.9301

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3296.3         533.242        387.82         392.35        
# C 553.59         3241.5         182.39         686.23        
# G 232.64         102.401        1565.4         84.91         
# T 335.174        558.781        147.17         2651          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.220475       0.0356662      0.0259396      0.0262426     
# C 0.0370272      0.21681        0.0121993      0.0458989     
# G 0.0155603      0.00684915     0.104703       0.00567926    
# T 0.0224183      0.0373744      0.00984356     0.177314      

# delExistCost: 342
# insExistCost: 341
# delExtendCost: 65
# 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 -t91.1872 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14397.9
# deletes: 322.93
# inserts: 481.67
# delOpens: 166.26
# insOpens: 218.88
# alignments: 10
# mean delete size: 1.94232
# mean insert size: 2.20061
# matchProb: 0.973223
# delOpenProb: 0.0112383
# insOpenProb: 0.0147951
# delExtendProb: 0.485152
# insExtendProb: 0.545581

# substitution percent identity: 70.5263

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3087.2         550.976        415.27         370.69        
# C 567.6          2996           150.293        740.47        
# G 246.31         81.558         1563.06        66.884        
# T 329.603        608.12         121.409        2521.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.214138       0.0382175      0.0288045      0.0257123     
# C 0.0393706      0.207812       0.0104248      0.0513615     
# G 0.0170849      0.00565713     0.108419       0.0046393     
# T 0.0228624      0.0421812      0.00842133     0.174893      

# delExistCost: 404
# insExistCost: 401
# delExtendCost: 65
# insExtendCost: 54

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -81    -49   -104
# C    -78     73   -142    -42
# G    -79   -180    146   -186
# T   -108    -52   -141     89

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.4093 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14586.1
# deletes: 207.97
# inserts: 370.61
# delOpens: 97.51
# insOpens: 146.118
# alignments: 10
# mean delete size: 2.13281
# mean insert size: 2.53637
# matchProb: 0.982843
# delOpenProb: 0.00657043
# insOpenProb: 0.00984574
# delExtendProb: 0.531134
# insExtendProb: 0.605736

# substitution percent identity: 69.4001

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3071.2         586.39         432.58         390.03        
# C 602.06         2979.4         154.2015       775.84        
# G 260.13         83.439         1563.17        67.5164       
# T 349.003        643.71         124.293        2522.3        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.21028        0.0401492      0.0296181      0.0267048     
# C 0.0412221      0.203995       0.0105579      0.0531206     
# G 0.0178107      0.00571294     0.107028       0.00462274    
# T 0.0238957      0.0440738      0.00851015     0.172698      

# delExistCost: 469
# insExistCost: 460
# 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    -74   -178    147   -185
# T   -103    -48   -140     89

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4064 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14614.3
# deletes: 173.005
# inserts: 333.783
# delOpens: 71.881
# insOpens: 116.037
# alignments: 8
# mean delete size: 2.40683
# mean insert size: 2.87652
# matchProb: 0.986705
# delOpenProb: 0.00485315
# insOpenProb: 0.0078344
# delExtendProb: 0.584515
# insExtendProb: 0.652358

# substitution percent identity: 68.8464

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3054           603.416        435.41         400.71        
# C 620.59         2961.2         159.53         789.72        
# G 265.6          86.864         1557.13        68.4163       
# T 354.125        649.76         125.994        2505.1        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.208641       0.0412238      0.0297461      0.0273755     
# C 0.0423971      0.202301       0.0108987      0.0539516     
# G 0.0181451      0.00593432     0.106379       0.00467402    
# T 0.0241929      0.0443899      0.00860758     0.171142      

# delExistCost: 516
# insExistCost: 500
# delExtendCost: 49
# insExtendCost: 38

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -72    -44    -98
# C    -70     72   -136    -37
# G    -72   -174    146   -184
# T   -102    -46   -138     89

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2552 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14846.5
# deletes: 168.42
# inserts: 340.671
# delOpens: 63.085
# insOpens: 107.237
# alignments: 7
# mean delete size: 2.66973
# mean insert size: 3.1768
# matchProb: 0.988132
# delOpenProb: 0.00419872
# insOpenProb: 0.00713732
# delExtendProb: 0.62543
# insExtendProb: 0.685218

# substitution percent identity: 68.3619

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3085.6         630.559        444.71         420.06        
# C 641.49         2985.3         165.39         812.21        
# G 270.72         92.7           1563.4         69.63         
# T 360.446        667.21         130.014        2532.3        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.207481       0.0423998      0.029903       0.0282455     
# C 0.0431348      0.200736       0.0111211      0.0546143     
# G 0.0182037      0.0062333      0.105126       0.00468203    
# T 0.024237       0.0448643      0.00874235     0.170276      

# delExistCost: 546
# insExistCost: 521
# delExtendCost: 42
# insExtendCost: 34

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -44    -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 -t91.0533 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14896.8
# deletes: 179.049
# inserts: 347.285
# delOpens: 59.728
# insOpens: 103.021
# alignments: 5
# mean delete size: 2.99774
# mean insert size: 3.37101
# matchProb: 0.988799
# delOpenProb: 0.00396454
# insOpenProb: 0.00683818
# delExtendProb: 0.666415
# insExtendProb: 0.703353

# substitution percent identity: 68.1898

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3083.6         634.137        445.41         422.54        
# C 648.98         2997.2         169.11         816.24        
# G 273.63         93.839         1562.4         71.58         
# T 365.254        674.05         132.042        2532.3        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206644       0.0424959      0.0298486      0.028316      
# C 0.0434906      0.200854       0.0113327      0.0546993     
# G 0.018337       0.0062885      0.104702       0.00479684    
# T 0.024477       0.0451706      0.00884863     0.169699      

# delExistCost: 566
# insExistCost: 532
# 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    -36
# G    -70   -168    146   -181
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3763 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14897.3
# deletes: 182.446
# inserts: 350.271
# delOpens: 57.786
# insOpens: 101.442
# alignments: 5
# mean delete size: 3.15727
# mean insert size: 3.45292
# matchProb: 0.989031
# delOpenProb: 0.00383641
# insOpenProb: 0.00673473
# delExtendProb: 0.683271
# insExtendProb: 0.71039

# substitution percent identity: 68.1657

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3083.6         635.136        445.71         423.86        
# C 650.36         2996.2         169.48         816.19        
# G 272.95         94.064         1561.4         71.9          
# T 365.571        674.06         131.918        2532.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206609       0.0425557      0.0298637      0.0283997     
# C 0.0435758      0.200753       0.0113556      0.0546868     
# G 0.0182884      0.00630253     0.104618       0.00481749    
# T 0.0244942      0.0451638      0.00883885     0.169677      

# delExistCost: 577
# insExistCost: 537
# 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 -t91.3676 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14897.3
# deletes: 186.95
# inserts: 354.262
# delOpens: 56.767
# insOpens: 100.893
# alignments: 5
# mean delete size: 3.29329
# mean insert size: 3.51126
# matchProb: 0.989133
# delOpenProb: 0.00376915
# insOpenProb: 0.00669898
# delExtendProb: 0.696352
# insExtendProb: 0.715202

# substitution percent identity: 68.1477

# 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         816.08        
# G 272.84         94.051         1561.4         71.9          
# T 365.569        674.17         131.691        2532.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206664       0.0425072      0.0298911      0.0284398     
# C 0.043609       0.200266       0.0113593      0.0547295     
# G 0.0182977      0.00630743     0.104714       0.00482189    
# T 0.0245165      0.0452125      0.00883171     0.169833      

# delExistCost: 583
# insExistCost: 540
# 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 -t91.511 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14897.4
# deletes: 188.952
# inserts: 357.073
# delOpens: 56.483
# insOpens: 100.742
# alignments: 5
# mean delete size: 3.34529
# mean insert size: 3.54443
# matchProb: 0.989162
# delOpenProb: 0.00375038
# insOpenProb: 0.0066891
# delExtendProb: 0.701072
# insExtendProb: 0.717867

# substitution percent identity: 68.1444

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         633.732        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        674.17         131.782        2531.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206675       0.0425027      0.0298993      0.0284352     
# C 0.0436058      0.200276       0.0113605      0.0547336     
# G 0.0183127      0.00631331     0.104719       0.00482214    
# T 0.0245181      0.0452147      0.00883826     0.169774      

# delExistCost: 586
# 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 -t91.494 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# aligned letter pairs: 14897.4
# deletes: 190.558
# inserts: 358.367
# delOpens: 56.231
# insOpens: 100.769
# alignments: 5
# mean delete size: 3.38884
# mean insert size: 3.55632
# matchProb: 0.989177
# delOpenProb: 0.0037337
# insOpenProb: 0.00669099
# delExtendProb: 0.704914
# insExtendProb: 0.718811

# substitution percent identity: 68.1458

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         633.732        445.81         423.98        
# C 650.08         2986.2         169.39         816.1         
# G 273.05         94.125         1561.4         71.9          
# T 365.574        674.07         131.672        2531.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206679       0.0425036      0.0298999      0.0284358     
# C 0.0436         0.200281       0.0113608      0.0547348     
# G 0.0183131      0.00631284     0.104721       0.00482224    
# T 0.0245186      0.045209       0.00883107     0.169778      

# 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/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco

# 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