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comparison test-data/last_train.txt @ 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 9a7e91fc6562
children 8705e0d74a0f
comparison
equal deleted inserted replaced
2:bf30030e5265 3:3de2195f32c0
1 # lastal version: 1021 1 # lastal version: 1021
2 # maximum percent identity: 100 2 # maximum percent identity: 100
3 # scale of score parameters: 4.5512 3 # scale of score parameters: 4.5512
4 # scale used while training: 91.024 4 # scale used while training: 91.024
5 5
6 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 6 # 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
7 7
8 # aligned letter pairs: 14901 8 # aligned letter pairs: 14938.3
9 # deletes: 694 9 # deletes: 664.27
10 # inserts: 834 10 # inserts: 839.49
11 # delOpens: 350 11 # delOpens: 344.82
12 # insOpens: 402 12 # insOpens: 404.93
13 # alignments: 1 13 # alignments: 3
14 # mean delete size: 1.98286 14 # mean delete size: 1.92643
15 # mean insert size: 2.07463 15 # mean insert size: 2.07317
16 # matchProb: 0.951836 16 # matchProb: 0.951966
17 # delOpenProb: 0.0223571 17 # delOpenProb: 0.0219742
18 # insOpenProb: 0.0256787 18 # insOpenProb: 0.0258048
19 # delExtendProb: 0.495677 19 # delExtendProb: 0.480904
20 # insExtendProb: 0.517986 20 # insExtendProb: 0.517648
21 21
22 # substitution percent identity: 71.9408 22 # substitution percent identity: 71.9318
23 23
24 # count matrix (query letters = columns, reference letters = rows): 24 # count matrix (query letters = columns, reference letters = rows):
25 # A C G T 25 # A C G T
26 # A 3291 532 387 390 26 # A 3296.3 533.237 387.81 392.24
27 # C 552 3221 180 685 27 # C 553.59 3241.5 182.39 686.22
28 # G 235 102 1561 84.7 28 # G 232.54 102.399 1565.4 84.91
29 # T 335 554 146 2651 29 # T 335.173 558.68 147.16 2651
30 30
31 # probability matrix (query letters = columns, reference letters = rows): 31 # probability matrix (query letters = columns, reference letters = rows):
32 # A C G T 32 # A C G T
33 # A 0.220773 0.0356887 0.0259615 0.0261627 33 # A 0.22048 0.0356667 0.0259395 0.0262358
34 # C 0.0370303 0.216077 0.0120751 0.0459525 34 # C 0.0370281 0.216815 0.0121996 0.0458993
35 # G 0.0157647 0.00684256 0.104718 0.00568201 35 # G 0.0155539 0.00684918 0.104705 0.00567939
36 # T 0.0224731 0.0371645 0.00979425 0.177839 36 # T 0.0224188 0.0373685 0.00984312 0.177318
37 37
38 # delExistCost: 346 38 # delExistCost: 343
39 # insExistCost: 342 39 # insExistCost: 341
40 # delExtendCost: 62 40 # delExtendCost: 64
41 # insExtendCost: 58 41 # insExtendCost: 58
42 42
43 # score matrix (query letters = columns, reference letters = rows): 43 # score matrix (query letters = columns, reference letters = rows):
44 # A C G T 44 # A C G T
45 # A 76 -90 -59 -105 45 # A 76 -90 -59 -104
46 # C -87 73 -129 -54 46 # C -87 73 -128 -55
47 # G -88 -164 145 -167 47 # G -89 -164 145 -167
48 # T -112 -66 -127 90 48 # T -112 -66 -127 90
49 49
50 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 50 # 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
51 51
52 # aligned letter pairs: 14771 52 # aligned letter pairs: 14338.3
53 # deletes: 379.3 53 # deletes: 327.44
54 # inserts: 567.1 54 # inserts: 474.13
55 # delOpens: 185.2 55 # delOpens: 166.73
56 # insOpens: 246.1 56 # insOpens: 216.45
57 # alignments: 2 57 # alignments: 10
58 # mean delete size: 2.04806 58 # mean delete size: 1.96389
59 # mean insert size: 2.30435 59 # mean insert size: 2.19048
60 # matchProb: 0.971438 60 # matchProb: 0.973244
61 # delOpenProb: 0.01218 61 # delOpenProb: 0.0113172
62 # insOpenProb: 0.0161851 62 # insOpenProb: 0.014692
63 # delExtendProb: 0.511732 63 # delExtendProb: 0.490807
64 # insExtendProb: 0.566038 64 # insExtendProb: 0.54348
65 65
66 # substitution percent identity: 70.0105 66 # substitution percent identity: 70.6019
67 67
68 # count matrix (query letters = columns, reference letters = rows): 68 # count matrix (query letters = columns, reference letters = rows):
69 # A C G T 69 # A C G T
70 # A 3158 583.4 429.9 391.6 70 # A 3076.4 546.106 412.41 369.93
71 # C 589 3065 156.8 774 71 # C 561.42 2983.2 149.401 735.35
72 # G 252.2 88.64 1571 68.46 72 # G 245.82 80.868 1562.07 66.655
73 # T 342.6 630.1 131.09 2566 73 # T 326.724 603.44 120.838 2510.5
74 74
75 # probability matrix (query letters = columns, reference letters = rows): 75 # probability matrix (query letters = columns, reference letters = rows):
76 # A C G T 76 # A C G T
77 # A 0.21341 0.0394248 0.0290516 0.0264634 77 # A 0.214366 0.0380532 0.0287371 0.0257771
78 # C 0.0398032 0.207126 0.0105962 0.0523051 78 # C 0.0391203 0.207872 0.0104104 0.0512399
79 # G 0.0170431 0.00599008 0.106165 0.00462637 79 # G 0.017129 0.00563496 0.108846 0.00464458
80 # T 0.0231521 0.0425807 0.00885876 0.173404 80 # T 0.0227664 0.0420483 0.0084201 0.174934
81 81
82 # delExistCost: 406 82 # delExistCost: 405
83 # insExistCost: 400 83 # insExistCost: 402
84 # delExtendCost: 60 84 # delExtendCost: 64
85 # insExtendCost: 51 85 # insExtendCost: 54
86 86
87 # score matrix (query letters = columns, reference letters = rows): 87 # score matrix (query letters = columns, reference letters = rows):
88 # A C G T 88 # A C G T
89 # A 75 -79 -48 -102 89 # A 77 -81 -49 -104
90 # C -78 72 -140 -41 90 # C -79 73 -142 -42
91 # G -79 -174 146 -185 91 # G -80 -181 146 -186
92 # T -107 -52 -136 89 92 # T -108 -52 -142 90
93 93
94 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 94 # 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
95 95
96 # aligned letter pairs: 14881 96 # aligned letter pairs: 14657.7
97 # deletes: 258.8 97 # deletes: 218.21
98 # inserts: 446.1 98 # inserts: 385.36
99 # delOpens: 112.91 99 # delOpens: 102.2
100 # insOpens: 168 100 # insOpens: 152.161
101 # alignments: 2 101 # alignments: 10
102 # mean delete size: 2.29209 102 # mean delete size: 2.13513
103 # mean insert size: 2.65536 103 # mean insert size: 2.53258
104 # matchProb: 0.981278 104 # matchProb: 0.982218
105 # delOpenProb: 0.00744548 105 # delOpenProb: 0.00684846
106 # insOpenProb: 0.0110782 106 # insOpenProb: 0.0101964
107 # delExtendProb: 0.563717 107 # delExtendProb: 0.531644
108 # insExtendProb: 0.623403 108 # insExtendProb: 0.605146
109 109
110 # substitution percent identity: 68.9366 110 # substitution percent identity: 69.4007
111 111
112 # count matrix (query letters = columns, reference letters = rows): 112 # count matrix (query letters = columns, reference letters = rows):
113 # A C G T 113 # A C G T
114 # A 3126 618.3 445 406.6 114 # A 3091.6 591.394 434.35 391.72
115 # C 622.8 3041 159.4 805.4 115 # C 605.8 2996.8 154.6091 779.75
116 # G 265.2 91.16 1560 68.22 116 # G 260.46 83.802 1568.22 67.9713
117 # T 357.3 660 133.33 2554 117 # T 351.852 646.07 124.676 2532.5
118 118
119 # probability matrix (query letters = columns, reference letters = rows): 119 # probability matrix (query letters = columns, reference letters = rows):
120 # A C G T 120 # A C G T
121 # A 0.209606 0.0414585 0.0298383 0.0272635 121 # A 0.210577 0.0402814 0.0295847 0.0266811
122 # C 0.0417602 0.203906 0.0106882 0.054004 122 # C 0.0412626 0.20412 0.0105308 0.0531108
123 # G 0.0177823 0.0061125 0.104602 0.00457431 123 # G 0.0177406 0.00570797 0.106816 0.0046297
124 # T 0.0239578 0.0442546 0.0089401 0.171252 124 # T 0.0239655 0.0440055 0.008492 0.172495
125 125
126 # delExistCost: 470 126 # delExistCost: 466
127 # insExistCost: 457 127 # insExistCost: 457
128 # delExtendCost: 52 128 # delExtendCost: 57
129 # insExtendCost: 42 129 # insExtendCost: 45
130 130
131 # score matrix (query letters = columns, reference letters = rows): 131 # score matrix (query letters = columns, reference letters = rows):
132 # A C G T 132 # A C G T
133 # A 75 -73 -44 -99 133 # A 76 -75 -45 -100
134 # C -73 71 -138 -37 134 # C -73 72 -140 -38
135 # G -73 -171 147 -185 135 # G -75 -178 147 -185
136 # T -103 -48 -134 88 136 # T -103 -48 -140 89
137 137
138 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 138 # 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
139 139
140 # aligned letter pairs: 14981 140 # aligned letter pairs: 14615.5
141 # deletes: 214.8 141 # deletes: 176.132
142 # inserts: 402.9 142 # inserts: 337.667
143 # delOpens: 82.32 143 # delOpens: 73.361
144 # insOpens: 131.98 144 # insOpens: 117.993
145 # alignments: 2 145 # alignments: 8
146 # mean delete size: 2.60933 146 # mean delete size: 2.40089
147 # mean insert size: 3.05274 147 # mean insert size: 2.86175
148 # matchProb: 0.985702 148 # matchProb: 0.986477
149 # delOpenProb: 0.0054164 149 # delOpenProb: 0.00495152
150 # insOpenProb: 0.00868387 150 # insOpenProb: 0.00796397
151 # delExtendProb: 0.61676 151 # delExtendProb: 0.583489
152 # insExtendProb: 0.672425 152 # insExtendProb: 0.650564
153 153
154 # substitution percent identity: 68.4035 154 # substitution percent identity: 68.8798
155 155
156 # count matrix (query letters = columns, reference letters = rows): 156 # count matrix (query letters = columns, reference letters = rows):
157 # A C G T 157 # A C G T
158 # A 3114 635.9 450 416.3 158 # A 3057.2 603.516 434.56 399.47
159 # C 640.1 3019 164.9 816.3 159 # C 620.42 2962.4 159.336 789.74
160 # G 270.6 93.43 1560 69.38 160 # G 264.31 86.899 1557.17 68.449
161 # T 365.7 670 135.53 2543 161 # T 353.847 650 125.897 2508.2
162 162
163 # probability matrix (query letters = columns, reference letters = rows): 163 # probability matrix (query letters = columns, reference letters = rows):
164 # A C G T 164 # A C G T
165 # A 0.208097 0.0424949 0.0300719 0.0278198 165 # A 0.208805 0.0412198 0.0296802 0.0272836
166 # C 0.0427756 0.201749 0.0110197 0.0545504 166 # C 0.0423743 0.20233 0.0108826 0.0539388
167 # G 0.0180832 0.00624359 0.104249 0.00463642 167 # G 0.0180522 0.00593515 0.106354 0.00467503
168 # T 0.0244384 0.0447737 0.00905699 0.16994 168 # T 0.0241675 0.0443946 0.00859869 0.171309
169 169
170 # delExistCost: 518 170 # delExistCost: 514
171 # insExistCost: 498 171 # insExistCost: 497
172 # delExtendCost: 44 172 # delExtendCost: 49
173 # insExtendCost: 36 173 # insExtendCost: 39
174 174
175 # score matrix (query letters = columns, reference letters = rows): 175 # score matrix (query letters = columns, reference letters = rows):
176 # A C G T 176 # A C G T
177 # A 74 -71 -43 -97 177 # A 75 -72 -44 -98
178 # C -70 71 -135 -36 178 # C -71 72 -137 -37
179 # G -73 -174 146 -184
180 # T -102 -46 -138 89
181
182 # 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
183
184 # aligned letter pairs: 14806.2
185 # deletes: 167.925
186 # inserts: 326.866
187 # delOpens: 62.871
188 # insOpens: 105.559
189 # alignments: 7
190 # mean delete size: 2.67095
191 # mean insert size: 3.09652
192 # matchProb: 0.988224
193 # delOpenProb: 0.00419626
194 # insOpenProb: 0.00704543
195 # delExtendProb: 0.625601
196 # insExtendProb: 0.677057
197
198 # substitution percent identity: 68.3956
199
200 # count matrix (query letters = columns, reference letters = rows):
201 # A C G T
202 # A 3074.6 626.457 444.21 418.05
203 # C 637.55 2977.3 164.69 809.88
204 # G 269.41 92.415 1559.3 69.29
205 # T 359.136 664.2 129.482 2527.2
206
207 # probability matrix (query letters = columns, reference letters = rows):
208 # A C G T
209 # A 0.207419 0.042262 0.0299673 0.0282025
210 # C 0.0430104 0.200854 0.0111103 0.0546361
211 # G 0.0181749 0.0062345 0.105193 0.00467444
212 # T 0.024228 0.0448082 0.00873511 0.17049
213
214 # delExistCost: 546
215 # insExistCost: 519
216 # delExtendCost: 42
217 # insExtendCost: 35
218
219 # score matrix (query letters = columns, reference letters = rows):
220 # A C G T
221 # A 75 -70 -43 -95
222 # C -69 71 -134 -36
179 # G -71 -169 146 -183 223 # G -71 -169 146 -183
180 # T -101 -46 -133 88 224 # T -101 -45 -136 88
181 225
182 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 226 # 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
183 227
184 # aligned letter pairs: 14981 228 # aligned letter pairs: 14896.9
185 # deletes: 197.5 229 # deletes: 177.451
186 # inserts: 386.4 230 # inserts: 344.879
187 # delOpens: 68.51 231 # delOpens: 59.29
188 # insOpens: 115.71 232 # insOpens: 103.311
189 # alignments: 2 233 # alignments: 5
190 # mean delete size: 2.88279 234 # mean delete size: 2.99293
191 # mean insert size: 3.33938 235 # mean insert size: 3.33826
192 # matchProb: 0.987657 236 # matchProb: 0.988809
193 # delOpenProb: 0.00451668 237 # delOpenProb: 0.00393548
194 # insOpenProb: 0.00762845 238 # insOpenProb: 0.00685746
195 # delExtendProb: 0.653114 239 # delExtendProb: 0.66588
196 # insExtendProb: 0.700543 240 # insExtendProb: 0.700443
197 241
198 # substitution percent identity: 68.1501 242 # substitution percent identity: 68.1858
199 243
200 # count matrix (query letters = columns, reference letters = rows): 244 # count matrix (query letters = columns, reference letters = rows):
201 # A C G T 245 # A C G T
202 # A 3103 643.6 451.1 422.5 246 # A 3084.6 635.337 445.51 422.24
203 # C 649.8 3008 167 819.5 247 # C 649.18 2997.2 169.11 816.24
204 # G 272.7 94.59 1560 70.43 248 # G 273.53 93.848 1562.4 71.64
205 # T 369.8 675.4 136.61 2542 249 # T 365.354 674.15 132.032 2532.3
206 250
207 # probability matrix (query letters = columns, reference letters = rows): 251 # probability matrix (query letters = columns, reference letters = rows):
208 # A C G T 252 # A C G T
209 # A 0.20706 0.0429467 0.0301014 0.0281929 253 # A 0.206678 0.0425696 0.0298506 0.0282914
210 # C 0.0433604 0.20072 0.0111437 0.0546843 254 # C 0.0434971 0.200822 0.0113309 0.0546907
211 # G 0.0181969 0.00631188 0.104097 0.00469971 255 # G 0.0183274 0.00628811 0.104686 0.00480011
212 # T 0.0246763 0.0450686 0.00911582 0.169625 256 # T 0.0244799 0.0451702 0.00884656 0.169672
213 257
214 # delExistCost: 549 258 # delExistCost: 567
215 # insExistCost: 522 259 # insExistCost: 531
216 # delExtendCost: 39 260 # delExtendCost: 37
217 # insExtendCost: 32 261 # insExtendCost: 32
218 262
219 # score matrix (query letters = columns, reference letters = rows): 263 # score matrix (query letters = columns, reference letters = rows):
220 # A C G T 264 # A C G T
221 # A 74 -69 -43 -95 265 # A 75 -70 -43 -95
222 # C -68 70 -134 -35 266 # C -68 71 -132 -35
223 # G -71 -168 146 -182 267 # G -70 -168 146 -181
224 # T -100 -45 -132 88 268 # T -100 -45 -135 88
225 269
226 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 270 # 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
227 271
228 # aligned letter pairs: 14981 272 # aligned letter pairs: 14897.4
229 # deletes: 192.1 273 # deletes: 183.45
230 # inserts: 380.9 274 # inserts: 350.682
231 # delOpens: 62.34 275 # delOpens: 57.728
232 # insOpens: 108.21 276 # insOpens: 101.786
233 # alignments: 2 277 # alignments: 5
234 # mean delete size: 3.08149 278 # mean delete size: 3.17783
235 # mean insert size: 3.52001 279 # mean insert size: 3.44529
236 # matchProb: 0.988548 280 # matchProb: 0.989012
237 # delOpenProb: 0.00411362 281 # delOpenProb: 0.00383246
238 # insOpenProb: 0.00714043 282 # insOpenProb: 0.00675739
239 # delExtendProb: 0.675482 283 # delExtendProb: 0.68532
240 # insExtendProb: 0.71591 284 # insExtendProb: 0.709748
241 285
242 # substitution percent identity: 67.9883 286 # substitution percent identity: 68.1676
243 287
244 # count matrix (query letters = columns, reference letters = rows): 288 # count matrix (query letters = columns, reference letters = rows):
245 # A C G T 289 # A C G T
246 # A 3093 648 451.1 425.7 290 # A 3083.6 635.04 445.71 423.87
247 # C 654.2 3008 169 821.5 291 # C 650.27 2996.2 169.49 816.21
248 # G 272.8 95.26 1550 71.05 292 # G 272.96 94.054 1562.4 71.81
249 # T 371.8 677.5 136.66 2532 293 # T 365.777 674.06 132.018 2532.4
250 294
251 # probability matrix (query letters = columns, reference letters = rows): 295 # probability matrix (query letters = columns, reference letters = rows):
252 # A C G T 296 # A C G T
253 # A 0.206509 0.0432647 0.0301184 0.0284225 297 # A 0.206594 0.0425463 0.0298616 0.0283983
254 # C 0.0436786 0.200834 0.0112835 0.0548487 298 # C 0.0435666 0.200739 0.0113555 0.0546843
255 # G 0.0182139 0.00636018 0.103488 0.00474376 299 # G 0.0182877 0.00630141 0.104677 0.00481111
256 # T 0.0248238 0.0452343 0.00912431 0.169053 300 # T 0.0245062 0.0451605 0.00884491 0.169665
257 301
258 # delExistCost: 566 302 # delExistCost: 578
259 # insExistCost: 534 303 # insExistCost: 536
260 # delExtendCost: 36 304 # delExtendCost: 34
305 # insExtendCost: 31
306
307 # score matrix (query letters = columns, reference letters = rows):
308 # A C G T
309 # A 75 -70 -43 -94
310 # C -68 71 -132 -36
311 # G -71 -168 146 -180
312 # T -100 -45 -135 88
313
314 # 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
315
316 # aligned letter pairs: 14897.3
317 # deletes: 186.949
318 # inserts: 354.265
319 # delOpens: 56.756
320 # insOpens: 101.214
321 # alignments: 5
322 # mean delete size: 3.29391
323 # mean insert size: 3.50016
324 # matchProb: 0.989113
325 # delOpenProb: 0.00376834
326 # insOpenProb: 0.00672015
327 # delExtendProb: 0.696409
328 # insExtendProb: 0.714299
329
330 # substitution percent identity: 68.1476
331
332 # count matrix (query letters = columns, reference letters = rows):
333 # A C G T
334 # A 3081.6 633.831 445.71 424.07
335 # C 650.26 2986.2 169.38 816.09
336 # G 272.84 94.051 1561.4 71.9
337 # T 365.569 674.07 131.791 2532.4
338
339 # probability matrix (query letters = columns, reference letters = rows):
340 # A C G T
341 # A 0.206664 0.0425072 0.029891 0.0284398
342 # C 0.0436089 0.200266 0.0113593 0.0547301
343 # G 0.0182977 0.00630742 0.104714 0.00482189
344 # T 0.0245165 0.0452057 0.00883841 0.169833
345
346 # delExistCost: 584
347 # insExistCost: 539
348 # delExtendCost: 33
261 # insExtendCost: 30 349 # insExtendCost: 30
262 350
263 # score matrix (query letters = columns, reference letters = rows): 351 # score matrix (query letters = columns, reference letters = rows):
264 # A C G T 352 # A C G T
265 # A 74 -69 -42 -94 353 # A 75 -70 -43 -94
266 # C -68 70 -133 -35 354 # C -68 71 -132 -35
267 # G -70 -167 147 -181 355 # G -71 -168 146 -180
268 # T -99 -45 -131 88 356 # T -100 -45 -135 88
269 357
270 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 358 # 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
271 359
272 # aligned letter pairs: 14981 360 # aligned letter pairs: 14897.4
273 # deletes: 194.5 361 # deletes: 188.951
274 # inserts: 383.3 362 # inserts: 357.176
275 # delOpens: 60.42 363 # delOpens: 56.362
276 # insOpens: 106.36 364 # insOpens: 100.973
277 # alignments: 2 365 # alignments: 5
278 # mean delete size: 3.21913 366 # mean delete size: 3.35245
279 # mean insert size: 3.6038 367 # mean insert size: 3.53734
280 # matchProb: 0.988794 368 # matchProb: 0.989155
281 # delOpenProb: 0.00398791 369 # delOpenProb: 0.00374231
282 # insOpenProb: 0.0070201 370 # insOpenProb: 0.00670439
283 # delExtendProb: 0.689357 371 # delExtendProb: 0.701711
284 # insExtendProb: 0.722515 372 # insExtendProb: 0.717302
285 373
286 # substitution percent identity: 67.9593 374 # substitution percent identity: 68.1403
287 375
288 # count matrix (query letters = columns, reference letters = rows): 376 # count matrix (query letters = columns, reference letters = rows):
289 # A C G T 377 # A C G T
290 # A 3093 648.9 451.2 426.7 378 # A 3081.6 634.732 445.81 423.98
291 # C 655.2 3008 169 821.4 379 # C 650.18 2986.2 169.39 816.1
292 # G 273.8 95.46 1550 71.26 380 # G 273.05 94.134 1561.4 71.9
293 # T 372.8 678.6 136.64 2532 381 # T 365.574 674.07 131.782 2531.4
294 382
295 # probability matrix (query letters = columns, reference letters = rows): 383 # probability matrix (query letters = columns, reference letters = rows):
296 # A C G T 384 # A C G T
297 # A 0.206421 0.0433063 0.0301122 0.0284771 385 # A 0.206662 0.0425672 0.0298975 0.0284335
298 # C 0.0437268 0.200748 0.0112787 0.0548186 386 # C 0.0436032 0.200264 0.0113598 0.0547303
299 # G 0.0182729 0.00637081 0.103444 0.00475575 387 # G 0.0183116 0.00631293 0.104713 0.00482185
300 # T 0.0248799 0.0452884 0.00911908 0.168981 388 # T 0.0245166 0.0452053 0.00883773 0.169764
301 389
302 # delExistCost: 575 390 # delExistCost: 587
303 # insExistCost: 539
304 # delExtendCost: 34
305 # insExtendCost: 29
306
307 # score matrix (query letters = columns, reference letters = rows):
308 # A C G T
309 # A 74 -69 -42 -94
310 # C -68 70 -132 -35
311 # G -70 -167 147 -180
312 # T -99 -45 -131 88
313
314 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
315
316 # aligned letter pairs: 14981
317 # deletes: 196.9
318 # inserts: 385.7
319 # delOpens: 59.47
320 # insOpens: 105.68
321 # alignments: 2
322 # mean delete size: 3.31091
323 # mean insert size: 3.6497
324 # matchProb: 0.9889
325 # delOpenProb: 0.00392563
326 # insOpenProb: 0.00697597
327 # delExtendProb: 0.697969
328 # insExtendProb: 0.726005
329
330 # substitution percent identity: 67.9572
331
332 # count matrix (query letters = columns, reference letters = rows):
333 # A C G T
334 # A 3093 648.8 451.2 426.6
335 # C 655.1 3008 169.9 821.4
336 # G 273.8 95.45 1550 71.26
337 # T 372.7 678.6 136.63 2532
338
339 # probability matrix (query letters = columns, reference letters = rows):
340 # A C G T
341 # A 0.206414 0.0432982 0.0301112 0.0284695
342 # C 0.0437187 0.200742 0.0113384 0.0548169
343 # G 0.0182723 0.00636994 0.103441 0.0047556
344 # T 0.0248725 0.045287 0.00911813 0.168975
345
346 # delExistCost: 580
347 # insExistCost: 541 391 # insExistCost: 541
348 # delExtendCost: 33
349 # insExtendCost: 29
350
351 # score matrix (query letters = columns, reference letters = rows):
352 # A C G T
353 # A 74 -69 -42 -94
354 # C -68 70 -132 -35
355 # G -70 -167 147 -180
356 # T -99 -45 -131 88
357
358 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB
359
360 # aligned letter pairs: 14981
361 # deletes: 197
362 # inserts: 385.7
363 # delOpens: 58.72
364 # insOpens: 105.14
365 # alignments: 2
366 # mean delete size: 3.3549
367 # mean insert size: 3.66844
368 # matchProb: 0.988985
369 # delOpenProb: 0.00387646
370 # insOpenProb: 0.00694091
371 # delExtendProb: 0.701929
372 # insExtendProb: 0.727405
373
374 # substitution percent identity: 67.9308
375
376 # count matrix (query letters = columns, reference letters = rows):
377 # A C G T
378 # A 3093 648.8 451.2 426.6
379 # C 656 2998 169.9 821.4
380 # G 273.8 95.55 1550 71.36
381 # T 372.7 678.6 136.62 2532
382
383 # probability matrix (query letters = columns, reference letters = rows):
384 # A C G T
385 # A 0.206537 0.043324 0.0301292 0.0284865
386 # C 0.0438048 0.200193 0.0113452 0.0548495
387 # G 0.0182832 0.00638041 0.103502 0.00476511
388 # T 0.0248873 0.0453139 0.00912288 0.169076
389
390 # delExistCost: 584
391 # insExistCost: 542
392 # delExtendCost: 32 392 # delExtendCost: 32
393 # insExtendCost: 29 393 # insExtendCost: 30
394 394
395 # score matrix (query letters = columns, reference letters = rows): 395 # score matrix (query letters = columns, reference letters = rows):
396 # A C G T 396 # A C G T
397 # A 74 -69 -42 -94 397 # A 75 -70 -43 -94
398 # C -68 70 -132 -35 398 # C -68 71 -132 -35
399 # G -70 -166 146 -180 399 # G -71 -168 146 -180
400 # T -99 -45 -132 88 400 # T -100 -45 -135 88
401 401
402 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 402 # 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
403 403
404 # aligned letter pairs: 14981 404 # aligned letter pairs: 14897.4
405 # deletes: 197 405 # deletes: 189.355
406 # inserts: 384.7 406 # inserts: 357.265
407 # delOpens: 57.97 407 # delOpens: 56.08
408 # insOpens: 104.51 408 # insOpens: 100.658
409 # alignments: 2 409 # alignments: 5
410 # mean delete size: 3.39831 410 # mean delete size: 3.37652
411 # mean insert size: 3.68099 411 # mean insert size: 3.5493
412 # matchProb: 0.989075 412 # matchProb: 0.989194
413 # delOpenProb: 0.00382729 413 # delOpenProb: 0.00372374
414 # insOpenProb: 0.00689995 414 # insOpenProb: 0.00668374
415 # delExtendProb: 0.705736 415 # delExtendProb: 0.703837
416 # insExtendProb: 0.728334 416 # insExtendProb: 0.718254
417 417
418 # substitution percent identity: 67.93 418 # substitution percent identity: 68.1453
419 419
420 # count matrix (query letters = columns, reference letters = rows): 420 # count matrix (query letters = columns, reference letters = rows):
421 # A C G T 421 # A C G T
422 # A 3093 648.8 451.2 427.6 422 # A 3081.6 633.731 445.81 423.98
423 # C 656 2998 169.9 821.4 423 # C 650.08 2986.2 169.39 816.1
424 # G 273.8 95.75 1550 71.36 424 # G 273.05 94.136 1561.4 71.9
425 # T 372.7 678.6 135.61 2532 425 # T 365.674 674.07 131.672 2531.4
426 426
427 # probability matrix (query letters = columns, reference letters = rows): 427 # probability matrix (query letters = columns, reference letters = rows):
428 # A C G T 428 # A C G T
429 # A 0.206534 0.0433235 0.0301288 0.0285529 429 # A 0.206677 0.0425032 0.0298997 0.0284356
430 # C 0.0438042 0.200191 0.011345 0.0548488 430 # C 0.0435997 0.200279 0.0113607 0.0547344
431 # G 0.0182829 0.00639368 0.103501 0.00476505 431 # G 0.018313 0.00631353 0.10472 0.0048222
432 # T 0.024887 0.0453133 0.00905532 0.169074 432 # T 0.0245251 0.0452087 0.00883101 0.169776
433 433
434 # delExistCost: 586 434 # delExistCost: 588
435 # insExistCost: 543 435 # insExistCost: 541
436 # delExtendCost: 32 436 # delExtendCost: 32
437 # insExtendCost: 29 437 # insExtendCost: 30
438 438
439 # score matrix (query letters = columns, reference letters = rows): 439 # score matrix (query letters = columns, reference letters = rows):
440 # A C G T 440 # A C G T
441 # A 74 -69 -42 -94 441 # A 75 -70 -43 -94
442 # C -68 70 -132 -35 442 # C -68 71 -132 -35
443 # G -70 -166 147 -180 443 # G -71 -168 146 -180
444 # T -99 -45 -132 88 444 # T -100 -45 -135 88
445 445
446 # lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB 446 # 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
447 447
448 # aligned letter pairs: 14981 448 # aligned letter pairs: 14897.4
449 # deletes: 196 449 # deletes: 188.951
450 # inserts: 384.7 450 # inserts: 356.964
451 # delOpens: 57.87 451 # delOpens: 55.8286
452 # insOpens: 104.51 452 # insOpens: 100.647
453 # alignments: 2 453 # alignments: 5
454 # mean delete size: 3.3869 454 # mean delete size: 3.38448
455 # mean insert size: 3.68099 455 # mean insert size: 3.54669
456 # matchProb: 0.989081 456 # matchProb: 0.989211
457 # delOpenProb: 0.00382071 457 # delOpenProb: 0.00370711
458 # insOpenProb: 0.0069 458 # insOpenProb: 0.00668312
459 # delExtendProb: 0.704745 459 # delExtendProb: 0.704534
460 # insExtendProb: 0.728334 460 # insExtendProb: 0.718047
461 461
462 # substitution percent identity: 67.93 462 # substitution percent identity: 68.1409
463 463
464 # count matrix (query letters = columns, reference letters = rows): 464 # count matrix (query letters = columns, reference letters = rows):
465 # A C G T 465 # A C G T
466 # A 3093 648.8 451.2 427.6 466 # A 3081.6 633.731 445.81 424.08
467 # C 656 2998 169.9 821.4 467 # C 650.28 2986.2 169.49 816.1
468 # G 273.8 95.75 1550 71.36 468 # G 273.05 94.136 1561.4 71.9
469 # T 372.7 678.6 135.61 2532 469 # T 365.673 674.17 131.672 2530.4
470 470
471 # probability matrix (query letters = columns, reference letters = rows): 471 # probability matrix (query letters = columns, reference letters = rows):
472 # A C G T 472 # A C G T
473 # A 0.206534 0.0433235 0.0301288 0.0285529 473 # A 0.206684 0.0425046 0.0299007 0.0284432
474 # C 0.0438042 0.200191 0.011345 0.0548488 474 # C 0.0436146 0.200286 0.0113678 0.0547362
475 # G 0.0182829 0.00639368 0.103501 0.00476505 475 # G 0.0183136 0.00631375 0.104724 0.00482237
476 # T 0.024887 0.0453133 0.00905532 0.169074 476 # T 0.0245259 0.0452169 0.0088313 0.169715
477 477
478 # delExistCost: 586 478 # delExistCost: 588
479 # insExistCost: 543 479 # insExistCost: 541
480 # delExtendCost: 32 480 # delExtendCost: 32
481 # insExtendCost: 29 481 # insExtendCost: 30
482 482
483 # score matrix (query letters = columns, reference letters = rows): 483 # score matrix (query letters = columns, reference letters = rows):
484 # A C G T 484 # A C G T
485 # A 74 -69 -42 -94 485 # A 75 -70 -43 -94
486 # C -68 70 -132 -35 486 # C -68 71 -132 -35
487 # G -70 -166 147 -180 487 # G -71 -168 146 -180
488 # T -99 -45 -132 88 488 # T -100 -45 -135 88
489 489
490 #last -X 0 490 #last -X 0
491 #last -Q 0 491 #last -Q 0
492 #last -t4.80115 492 #last -t4.72795
493 #last -a 29 493 #last -a 29
494 #last -A 28 494 #last -A 28
495 #last -b 2 495 #last -b 2
496 #last -B 1 496 #last -B 1
497 #last -s 1 497 #last -s 1
498 #last -S 1 498 #last -S 1
499 # score matrix (query letters = columns, reference letters = rows): 499 # score matrix (query letters = columns, reference letters = rows):
500 A C G T 500 A C G T
501 A 4 -3 -2 -5 501 A 4 -3 -2 -5
502 C -3 4 -7 -2 502 C -3 4 -7 -2
503 G -3 -8 7 -9 503 G -4 -8 7 -9
504 T -5 -2 -7 4 504 T -5 -2 -7 4