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author dave
date Mon, 10 Jun 2019 16:04:10 -0400
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-1:000000000000 0:9a3a2e04f47a
1
2 [28 May 13:09:56] Pipelign started with sequence file <pipelign-in1.fasta>
3 ================================================================
4 Program: CD-HIT, V4.8.1 (+OpenMP), May 14 2019, 14:40:47
5 Command: cd-hit-est -c 0.8 -n 5 -i long.good.fas -o grp -d 0
6 -T 1
7
8 Started: Tue May 28 13:09:56 2019
9 ================================================================
10 Output
11 ----------------------------------------------------------------
12 total seq: 100
13 longest and shortest : 70 and 70
14 Total letters: 7000
15 Sequences have been sorted
16
17 Approximated minimal memory consumption:
18 Sequence : 0M
19 Buffer : 1 X 12M = 12M
20 Table : 1 X 0M = 0M
21 Miscellaneous : 0M
22 Total : 12M
23
24 Table limit with the given memory limit:
25 Max number of representatives: 4000000
26 Max number of word counting entries: 98487020
27
28
29 comparing sequences from 0 to 100
30
31 100 finished 84 clusters
32
33 Approximated maximum memory consumption: 12M
34 writing new database
35 writing clustering information
36 program completed !
37
38 Total CPU time 0.04
39 inputfile = orig
40 84 x 70 - 70 d
41 outputhat23=1
42 treein = 0
43 compacttree = 0
44 stacksize: 8192 kb
45 generating a scoring matrix for nucleotide (dist=200) ... done
46 All-to-all alignment.
47 0 / 84 (by thread 0)
48 10 / 84 (by thread 0)
49 20 / 84 (by thread 0)
50 30 / 84 (by thread 0)
51 40 / 84 (by thread 0)
52 50 / 84 (by thread 0)
53 60 / 84 (by thread 0)
54 70 / 84 (by thread 0)
55 80 / 84 (by thread 0)
56 tbfast-pair (nuc) Version 7.407
57 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
58 1 thread(s)
59
60 outputhat23=1
61 Loading 'hat3.seed' ...
62 done.
63 Writing hat3 for iterative refinement
64 generating a scoring matrix for nucleotide (dist=200) ... done
65 Gap Penalty = -1.53, +0.00, +0.00
66 tbutree = 1, compacttree = 0
67 Constructing a UPGMA tree ...
68
69 0 / 84
70 10 / 84
71 20 / 84
72 30 / 84
73 40 / 84
74 50 / 84
75 60 / 84
76 70 / 84
77 80 / 84
78 done.
79
80 Progressive alignment ...
81
82 STEP 1 /83 (thread 0)
83 STEP 2 /83 (thread 0)
84 STEP 3 /83 (thread 0)
85 STEP 4 /83 (thread 0)
86 STEP 5 /83 (thread 0)
87 STEP 6 /83 (thread 0)
88 STEP 7 /83 (thread 0)
89 STEP 8 /83 (thread 0)
90 STEP 9 /83 (thread 0)
91 STEP 10 /83 (thread 0)
92 STEP 11 /83 (thread 0)
93 Reallocating (by thread 0) ..done. *alloclen = 1159
94
95 STEP 12 /83 (thread 0)
96 STEP 13 /83 (thread 0)
97 STEP 14 /83 (thread 0)
98 STEP 15 /83 (thread 0)
99 STEP 16 /83 (thread 0)
100 STEP 17 /83 (thread 0)
101 STEP 18 /83 (thread 0)
102 STEP 19 /83 (thread 0)
103 STEP 20 /83 (thread 0)
104 STEP 21 /83 (thread 0)
105 STEP 22 /83 (thread 0)
106 STEP 23 /83 (thread 0)
107 STEP 24 /83 (thread 0)
108 STEP 25 /83 (thread 0)
109 STEP 26 /83 (thread 0)
110 STEP 27 /83 (thread 0)
111 STEP 28 /83 (thread 0)
112 STEP 29 /83 (thread 0)
113 STEP 30 /83 (thread 0)
114 STEP 31 /83 (thread 0)
115 STEP 32 /83 (thread 0)
116 STEP 33 /83 (thread 0)
117 STEP 34 /83 (thread 0)
118 STEP 35 /83 (thread 0)
119 STEP 36 /83 (thread 0)
120 STEP 37 /83 (thread 0)
121 STEP 38 /83 (thread 0)
122 STEP 39 /83 (thread 0)
123 STEP 40 /83 (thread 0)
124 STEP 41 /83 (thread 0)
125 STEP 42 /83 (thread 0)
126 STEP 43 /83 (thread 0)
127 STEP 44 /83 (thread 0)
128 STEP 45 /83 (thread 0)
129 STEP 46 /83 (thread 0)
130 STEP 47 /83 (thread 0)
131 STEP 48 /83 (thread 0)
132 STEP 49 /83 (thread 0)
133 STEP 50 /83 (thread 0)
134 STEP 51 /83 (thread 0)
135 STEP 52 /83 (thread 0)
136 STEP 53 /83 (thread 0)
137 STEP 54 /83 (thread 0)
138 STEP 55 /83 (thread 0)
139 STEP 56 /83 (thread 0)
140 STEP 57 /83 (thread 0)
141 STEP 58 /83 (thread 0)
142 STEP 59 /83 (thread 0)
143 STEP 60 /83 (thread 0)
144 STEP 61 /83 (thread 0)
145 STEP 62 /83 (thread 0)
146 STEP 63 /83 (thread 0)
147 STEP 64 /83 (thread 0)
148 STEP 65 /83 (thread 0)
149 STEP 66 /83 (thread 0)
150 STEP 67 /83 (thread 0)
151 STEP 68 /83 (thread 0)
152 STEP 69 /83 (thread 0)
153 STEP 70 /83 (thread 0)
154 STEP 71 /83 (thread 0)
155 STEP 72 /83 (thread 0)
156 STEP 73 /83 (thread 0)
157 STEP 74 /83 (thread 0)
158 STEP 75 /83 (thread 0)
159 STEP 76 /83 (thread 0)
160 STEP 77 /83 (thread 0)
161 STEP 78 /83 (thread 0)
162 STEP 79 /83 (thread 0)
163 STEP 80 /83 (thread 0)
164 STEP 81 /83 (thread 0)
165 STEP 82 /83 (thread 0)
166 STEP 83 /83 (thread 0)
167 done.
168 tbfast (nuc) Version 7.407
169 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
170 1 thread(s)
171
172 minimumweight = 0.000010
173 autosubalignment = 0.000000
174 nthread = 1
175 randomseed = 0
176 blosum 62 / kimura 200
177 poffset = 0
178 niter = 1
179 sueff_global = 0.100000
180 nadd = 1
181 Loading 'hat3' ... done.
182 generating a scoring matrix for nucleotide (dist=200) ... done
183
184
185 0 / 84
186 10 / 84
187 20 / 84
188 30 / 84
189 40 / 84
190 50 / 84
191 60 / 84
192 70 / 84
193 80 / 84
194 Segment 1/ 1 1- 271
195 001-0000-0 (thread 1) identical
196 001-0000-0 (thread 1) worse
197
198 001-0001-1 (thread 1) identical
199 001-0001-1 (thread 1) worse
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201 001-0002-0 (thread 1) identical
202 001-0002-0 (thread 1) worse
203
204 001-0003-1 (thread 1) identical
205
206 001-0004-0 (thread 1) identical
207 001-0004-0 (thread 1) worse
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209 001-0005-1 (thread 1) identical
210 001-0005-1 (thread 1) better
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213 001-0006-0 (thread 1) better
214
215 001-0007-1 (thread 1) identical
216 001-0007-1 (thread 1) worse
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219 001-0008-0 (thread 1) worse
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221 001-0009-1 (thread 1) identical
222 001-0009-1 (thread 1) worse
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224 001-0010-0 (thread 1) identical
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227 001-0011-1 (thread 1) identical
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231 001-0013-1 (thread 1) identical
232 001-0013-1 (thread 1) better
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237 001-0015-1 (thread 1) worse
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239 001-0016-0 (thread 1) identical
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244 001-0018-0 (thread 1) worse
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247 001-0019-1 (thread 1) better
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250 001-0020-0 (thread 1) worse
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253 001-0021-1 (thread 1) better
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258 001-0023-1 (thread 1) better
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260 001-0024-0 (thread 1) identical
261 001-0024-0 (thread 1) worse
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264 001-0025-1 (thread 1) better
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266 001-0026-0 (thread 1) identical
267 001-0026-0 (thread 1) better
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269 001-0027-1 (thread 1) identical
270 001-0027-1 (thread 1) worse
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279 001-0030-0 (thread 1) better
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281 001-0031-1 (thread 1) identical
282 001-0031-1 (thread 1) better
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284 001-0032-0 (thread 1) identical
285 001-0032-0 (thread 1) worse
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288 001-0033-1 (thread 1) better
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290 001-0034-0 (thread 1) identical
291 001-0034-0 (thread 1) better
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293 001-0035-1 (thread 1) identical
294 001-0035-1 (thread 1) worse
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296 001-0036-0 (thread 1) identical
297 001-0036-0 (thread 1) worse
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299 001-0037-1 (thread 1) identical
300 001-0037-1 (thread 1) better
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302 001-0038-0 (thread 1) identical
303 001-0038-0 (thread 1) better
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305 001-0039-1 (thread 1) identical
306 001-0039-1 (thread 1) better
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308 001-0040-0 (thread 1) identical
309 001-0040-0 (thread 1) worse
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311 001-0041-1 (thread 1) identical
312 001-0041-1 (thread 1) better
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314 001-0042-0 (thread 1) identical
315 001-0042-0 (thread 1) worse
316
317 001-0043-1 (thread 1) identical
318 001-0043-1 (thread 1) better
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320 001-0044-0 (thread 1) identical
321 001-0044-0 (thread 1) worse
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323 001-0045-1 (thread 1) identical
324 001-0045-1 (thread 1) better
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326 001-0046-0 (thread 1) identical
327 001-0046-0 (thread 1) worse
328
329 001-0047-1 (thread 1) identical
330 001-0047-1 (thread 1) worse
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332 001-0048-0 (thread 1) identical
333 001-0048-0 (thread 1) worse
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335 001-0049-1 (thread 1) identical
336 001-0049-1 (thread 1) worse
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338 001-0050-0 (thread 1) identical
339 001-0050-0 (thread 1) worse
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341 001-0051-1 (thread 1) identical
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343 001-0052-0 (thread 1) identical
344 001-0052-0 (thread 1) worse
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346 001-0053-1 (thread 1) identical
347 001-0053-1 (thread 1) worse
348
349 001-0054-0 (thread 1) identical
350 001-0054-0 (thread 1) better
351
352 001-0055-1 (thread 1) identical
353 001-0055-1 (thread 1) better
354
355 001-0056-0 (thread 1) identical
356 001-0056-0 (thread 1) worse
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358 001-0057-1 (thread 1) identical
359 001-0057-1 (thread 1) worse
360
361 001-0058-0 (thread 1) identical
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363 001-0059-1 (thread 1) identical
364 001-0059-1 (thread 1) better
365
366 001-0060-0 (thread 1) identical
367 001-0060-0 (thread 1) worse
368
369 001-0061-1 (thread 1) identical
370 001-0061-1 (thread 1) worse
371
372 001-0062-0 (thread 1) identical
373 001-0062-0 (thread 1) better
374
375 001-0063-1 (thread 1) identical
376 001-0063-1 (thread 1) worse
377
378 001-0064-0 (thread 1) identical
379 001-0064-0 (thread 1) worse
380
381 001-0065-1 (thread 1) identical
382 001-0065-1 (thread 1) better
383
384 001-0066-0 (thread 1) identical
385 001-0066-0 (thread 1) better
386
387 001-0067-1 (thread 1) identical
388 001-0067-1 (thread 1) better
389
390 001-0068-0 (thread 1) identical
391 001-0068-0 (thread 1) worse
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393 001-0069-1 (thread 1) identical
394 001-0069-1 (thread 1) worse
395
396 001-0070-0 (thread 1) identical
397 001-0070-0 (thread 1) worse
398
399 001-0071-1 (thread 1) identical
400 001-0071-1 (thread 1) better
401
402 001-0072-0 (thread 1) identical
403
404 001-0073-1 (thread 1) identical
405 001-0073-1 (thread 1) better
406
407 001-0074-0 (thread 1) identical
408 001-0074-0 (thread 1) worse
409
410 001-0075-1 (thread 1) identical
411 001-0075-1 (thread 1) better
412
413 001-0076-0 (thread 1) identical
414 001-0076-0 (thread 1) better
415
416 001-0077-1 (thread 1) identical
417 001-0077-1 (thread 1) better
418
419 001-0078-0 (thread 1) identical
420 001-0078-0 (thread 1) worse
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423 001-0079-1 (thread 1) worse
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429 001-0081-1 (thread 1) worse
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434 001-0083-1 (thread 1) better
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437 001-0084-0 (thread 1) worse
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439 001-0085-1 (thread 1) identical
440 001-0085-1 (thread 1) worse
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448 001-0088-0 (thread 1) worse
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454 001-0090-0 (thread 1) better
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456 001-0091-1 (thread 1) identical
457 001-0091-1 (thread 1) better
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460 001-0092-0 (thread 1) worse
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463 001-0093-1 (thread 1) better
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466 001-0094-0 (thread 1) better
467
468 001-0095-1 (thread 1) identical
469 001-0095-1 (thread 1) better
470
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478 001-0098-0 (thread 1) worse
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481 001-0099-1 (thread 1) worse
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486 001-0101-1 (thread 1) identical
487 001-0101-1 (thread 1) worse
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489 001-0102-0 (thread 1) identical
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494 001-0104-0 (thread 1) worse
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497 001-0105-1 (thread 1) better
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503 001-0108-0 (thread 1) identical
504 001-0108-0 (thread 1) worse
505
506 001-0109-1 (thread 1) identical
507 001-0109-1 (thread 1) better
508
509 001-0110-0 (thread 1) identical
510 001-0110-0 (thread 1) better
511
512 001-0111-1 (thread 1) identical
513 001-0111-1 (thread 1) better
514
515 001-0112-0 (thread 1) identical
516
517 001-0113-1 (thread 1) identical
518 001-0113-1 (thread 1) better
519
520 001-0114-0 (thread 1) identical
521 001-0114-0 (thread 1) worse
522
523 001-0115-1 (thread 1) identical
524 001-0115-1 (thread 1) better
525
526 001-0116-0 (thread 1) identical
527 001-0116-0 (thread 1) worse
528
529 001-0117-1 (thread 1) identical
530 001-0117-1 (thread 1) worse
531
532 001-0118-0 (thread 1) identical
533 001-0118-0 (thread 1) better
534
535 001-0119-1 (thread 1) identical
536
537 001-0120-0 (thread 1) identical
538 001-0120-0 (thread 1) worse
539
540 001-0121-1 (thread 1) identical
541 001-0121-1 (thread 1) worse
542
543 001-0122-0 (thread 1) identical
544 001-0122-0 (thread 1) better
545
546 001-0123-1 (thread 1) identical
547
548 001-0124-0 (thread 1) identical
549 001-0124-0 (thread 1) better
550
551 001-0125-1 (thread 1) identical
552 001-0125-1 (thread 1) better
553
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557 001-0127-1 (thread 1) worse
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563 001-0129-1 (thread 1) worse
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566 001-0130-0 (thread 1) better
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568 001-0131-1 (thread 1) identical
569 001-0131-1 (thread 1) better
570
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572 001-0132-0 (thread 1) better
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577 001-0134-0 (thread 1) worse
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579 001-0135-1 (thread 1) identical
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582
583 001-0137-1 (thread 1) identical
584 001-0137-1 (thread 1) worse
585
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590 001-0139-1 (thread 1) better
591
592 001-0140-0 (thread 1) identical
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594 001-0141-1 (thread 1) identical
595 001-0141-1 (thread 1) better
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600 001-0143-1 (thread 1) worse
601
602 001-0144-0 (thread 1) identical
603 001-0144-0 (thread 1) worse
604
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606 001-0145-1 (thread 1) better
607
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609 001-0146-0 (thread 1) better
610
611 001-0147-1 (thread 1) identical
612 001-0147-1 (thread 1) worse
613
614 001-0148-0 (thread 1) identical
615
616 001-0149-1 (thread 1) identical
617 001-0149-1 (thread 1) better
618
619 001-0150-0 (thread 1) identical
620
621 001-0151-1 (thread 1) identical
622
623 001-0152-0 (thread 1) identical
624
625 001-0153-1 (thread 1) identical
626
627 001-0154-0 (thread 1) identical
628
629 001-0155-1 (thread 1) identical
630
631 001-0156-0 (thread 1) identical
632
633 001-0157-1 (thread 1) identical
634 001-0157-1 (thread 1) worse
635
636 001-0158-0 (thread 1) identical
637
638 001-0159-1 (thread 1) identical
639 001-0159-1 (thread 1) worse
640
641 001-0160-0 (thread 1) identical
642 001-0160-0 (thread 1) worse
643
644 001-0161-1 (thread 1) identical
645 001-0161-1 (thread 1) worse
646
647 001-0162-0 (thread 1) identical
648 001-0162-0 (thread 1) worse
649
650 001-0163-1 (thread 1) identical
651 001-0163-1 (thread 1) worse
652
653 001-0164-1 (thread 1) identical
654 001-0164-1 (thread 1) worse
655
656 Reached 1
657 done
658 dvtditr (nuc) Version 7.407
659 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
660 1 thread(s)
661
662
663 Strategy:
664 L-INS-i (Probably most accurate, very slow)
665 Iterative refinement method (<1) with LOCAL pairwise alignment information
666
667 If unsure which option to use, try 'mafft --auto input > output'.
668 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
669
670 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
671 It tends to insert more gaps into gap-rich regions than previous versions.
672 To disable this change, add the --leavegappyregion option.
673
674 IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019
675 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
676 Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
677
678 Host: gaius (AVX2, FMA3, 15 GB RAM)
679 Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1
680 Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator)
681 Time: Tue May 28 13:09:57 2019
682 Kernel: AVX+FMA - 1 threads (8 CPU cores detected)
683
684 HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
685 HINT: -nt AUTO will automatically determine the best number of threads to use.
686
687 Reading alignment file clsReps.aln ... Fasta format detected
688 Alignment most likely contains DNA/RNA sequences
689 Alignment has 84 sequences with 305 columns, 301 distinct patterns
690 238 parsimony-informative, 52 singleton sites, 15 constant sites
691 WARNING: Some sequence names are changed as follows:
692 K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0
693 K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1
694 K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2
695 K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3
696 K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4
697 K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5
698 K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6
699 K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7
700 K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8
701 K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9
702 K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10
703 K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11
704 K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12
705 K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13
706 K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14
707 K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15
708 K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16
709 K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17
710 K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18
711 K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19
712 K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20
713 K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21
714 K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22
715 K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23
716 K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24
717 K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25
718 K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26
719 K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27
720 K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28
721 K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29
722 K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30
723 K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31
724 K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32
725 K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33
726 K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34
727 K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35
728 K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36
729 K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37
730 K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38
731 K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39
732 K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40
733 K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41
734 K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42
735 K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43
736 K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44
737 K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45
738 K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46
739 K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47
740 K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48
741 K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49
742 K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50
743 K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51
744 K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52
745 K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53
746 K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54
747 K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55
748 K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56
749 K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57
750 K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58
751 K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59
752 K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60
753 K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61
754 K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62
755 K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63
756 K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64
757 K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65
758 K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66
759 K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67
760 K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68
761 K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69
762 K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70
763 K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71
764 K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72
765 K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73
766 K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74
767 K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75
768 K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76
769 K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77
770 K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78
771 K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79
772 K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80
773 K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81
774 K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82
775 K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83
776
777 Gap/Ambiguity Composition p-value
778 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90%
779 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53%
780 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21%
781 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36%
782 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86%
783 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72%
784 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71%
785 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58%
786 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28%
787 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71%
788 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76%
789 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06%
790 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72%
791 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74%
792 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54%
793 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66%
794 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47%
795 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11%
796 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61%
797 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18%
798 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00%
799 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75%
800 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23%
801 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67%
802 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02%
803 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52%
804 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05%
805 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57%
806 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98%
807 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02%
808 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08%
809 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03%
810 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47%
811 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89%
812 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36%
813 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48%
814 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92%
815 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51%
816 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24%
817 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06%
818 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06%
819 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00%
820 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90%
821 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68%
822 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88%
823 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28%
824 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89%
825 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69%
826 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81%
827 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95%
828 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20%
829 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44%
830 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71%
831 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60%
832 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49%
833 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92%
834 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75%
835 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72%
836 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57%
837 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40%
838 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77%
839 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83%
840 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48%
841 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69%
842 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64%
843 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23%
844 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65%
845 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90%
846 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19%
847 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60%
848 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10%
849 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03%
850 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28%
851 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17%
852 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26%
853 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77%
854 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37%
855 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04%
856 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16%
857 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98%
858 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70%
859 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88%
860 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25%
861 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89%
862 WARNING: 84 sequences contain more than 50% gaps/ambiguity
863 **** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3)
864
865 Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds
866
867 NOTE: 3 MB RAM (0 GB) is required!
868 Estimate model parameters (epsilon = 0.100)
869 1. Initial log-likelihood: -7393.152
870 2. Current log-likelihood: -6850.590
871 3. Current log-likelihood: -6814.795
872 4. Current log-likelihood: -6812.204
873 5. Current log-likelihood: -6811.732
874 6. Current log-likelihood: -6811.618
875 Optimal log-likelihood: -6811.491
876 Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000
877 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
878 Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200)
879 Parameters optimization took 6 rounds (0.508 sec)
880 Computing ML distances based on estimated model parameters... 0.032 sec
881 WARNING: Some pairwise ML distances are too long (saturated)
882 Computing BIONJ tree...
883 0.003 seconds
884 Log-likelihood of BIONJ tree: -6859.680
885 --------------------------------------------------------------------
886 | INITIALIZING CANDIDATE TREE SET |
887 --------------------------------------------------------------------
888 Generating 98 parsimony trees... 1.076 second
889 Computing log-likelihood of 98 initial trees ... 1.196 seconds
890 Current best score: -6803.399
891
892 Do NNI search on 20 best initial trees
893 Estimate model parameters (epsilon = 0.100)
894 BETTER TREE FOUND at iteration 1: -6746.667
895 Estimate model parameters (epsilon = 0.100)
896 BETTER TREE FOUND at iteration 4: -6743.453
897 Estimate model parameters (epsilon = 0.100)
898 BETTER TREE FOUND at iteration 8: -6739.399
899 Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s
900 Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s
901 Finish initializing candidate tree set (20)
902 Current best tree score: -6739.399 / CPU time: 11.455
903 Number of iterations: 20
904 --------------------------------------------------------------------
905 | OPTIMIZING CANDIDATE TREE SET |
906 --------------------------------------------------------------------
907 Estimate model parameters (epsilon = 0.100)
908 BETTER TREE FOUND at iteration 24: -6738.697
909 Estimate model parameters (epsilon = 0.100)
910 BETTER TREE FOUND at iteration 25: -6730.006
911 Estimate model parameters (epsilon = 0.100)
912 BETTER TREE FOUND at iteration 27: -6728.392
913 Estimate model parameters (epsilon = 0.100)
914 BETTER TREE FOUND at iteration 29: -6725.172
915 Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left)
916 Estimate model parameters (epsilon = 0.100)
917 BETTER TREE FOUND at iteration 31: -6723.283
918 Estimate model parameters (epsilon = 0.100)
919 BETTER TREE FOUND at iteration 37: -6720.321
920 Estimate model parameters (epsilon = 0.100)
921 BETTER TREE FOUND at iteration 39: -6717.689
922 Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left)
923 Estimate model parameters (epsilon = 0.100)
924 BETTER TREE FOUND at iteration 41: -6717.333
925 Estimate model parameters (epsilon = 0.100)
926 BETTER TREE FOUND at iteration 44: -6715.754
927 Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left)
928 Estimate model parameters (epsilon = 0.100)
929 BETTER TREE FOUND at iteration 56: -6714.598
930 Estimate model parameters (epsilon = 0.100)
931 BETTER TREE FOUND at iteration 59: -6714.257
932 Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left)
933 Estimate model parameters (epsilon = 0.100)
934 BETTER TREE FOUND at iteration 66: -6713.872
935 Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left)
936 Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left)
937 Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left)
938 Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left)
939 BETTER TREE FOUND at iteration 105: -6713.864
940 Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left)
941 Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left)
942 Estimate model parameters (epsilon = 0.100)
943 BETTER TREE FOUND at iteration 123: -6712.300
944 Estimate model parameters (epsilon = 0.100)
945 BETTER TREE FOUND at iteration 126: -6710.985
946 Estimate model parameters (epsilon = 0.100)
947 BETTER TREE FOUND at iteration 127: -6710.445
948 Estimate model parameters (epsilon = 0.100)
949 BETTER TREE FOUND at iteration 130: -6709.739
950 Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left)
951 Estimate model parameters (epsilon = 0.100)
952 BETTER TREE FOUND at iteration 136: -6709.364
953 Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left)
954 Estimate model parameters (epsilon = 0.100)
955 BETTER TREE FOUND at iteration 142: -6709.294
956 Estimate model parameters (epsilon = 0.100)
957 BETTER TREE FOUND at iteration 147: -6708.895
958 Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left)
959 Estimate model parameters (epsilon = 0.100)
960 BETTER TREE FOUND at iteration 160: -6708.749
961 Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left)
962 Estimate model parameters (epsilon = 0.100)
963 BETTER TREE FOUND at iteration 163: -6708.686
964 Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left)
965 Estimate model parameters (epsilon = 0.100)
966 BETTER TREE FOUND at iteration 173: -6708.554
967 Estimate model parameters (epsilon = 0.100)
968 BETTER TREE FOUND at iteration 180: -6708.518
969 Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left)
970 Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left)
971 Estimate model parameters (epsilon = 0.100)
972 BETTER TREE FOUND at iteration 193: -6705.296
973 BETTER TREE FOUND at iteration 200: -6705.295
974 Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left)
975 Estimate model parameters (epsilon = 0.100)
976 BETTER TREE FOUND at iteration 202: -6705.270
977 Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left)
978 Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left)
979 Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left)
980 Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left)
981 Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left)
982 Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left)
983 Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left)
984 Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left)
985 Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left)
986 BETTER TREE FOUND at iteration 293: -6705.270
987 BETTER TREE FOUND at iteration 295: -6705.269
988 Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left)
989 Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left)
990 Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left)
991 UPDATE BEST LOG-LIKELIHOOD: -6705.269
992 Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left)
993 Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left)
994 Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left)
995 Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left)
996 Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left)
997 Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left)
998 Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left)
999 TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s
1000
1001 --------------------------------------------------------------------
1002 | FINALIZING TREE SEARCH |
1003 --------------------------------------------------------------------
1004 Performs final model parameters optimization
1005 Estimate model parameters (epsilon = 0.010)
1006 1. Initial log-likelihood: -6705.269
1007 Optimal log-likelihood: -6705.266
1008 Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000
1009 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
1010 Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143)
1011 Parameters optimization took 1 rounds (0.062 sec)
1012 BEST SCORE FOUND : -6705.266
1013 Total tree length: 81.560
1014
1015 Total number of iterations: 396
1016 CPU time used for tree search: 114.612 sec (0h:1m:54s)
1017 Wall-clock time used for tree search: 119.058 sec (0h:1m:59s)
1018 Total CPU time used: 115.545 sec (0h:1m:55s)
1019 Total wall-clock time used: 120.013 sec (0h:2m:0s)
1020
1021 Analysis results written to:
1022 IQ-TREE report: clsReps.aln.iqtree
1023 Maximum-likelihood tree: clsReps.aln.treefile
1024 Likelihood distances: clsReps.aln.mldist
1025 Screen log file: clsReps.aln.log
1026
1027 Date and Time: Tue May 28 13:11:57 2019
1028 Working... done.
1029 Pressed and indexed 84 HMMs (84 names).
1030 Models pressed into binary file: pipelign.hmm.h3m
1031 SSI index for binary model file: pipelign.hmm.h3i
1032 Profiles (MSV part) pressed into: pipelign.hmm.h3f
1033 Profiles (remainder) pressed into: pipelign.hmm.h3p
1034
1035 Alignment files and HMMs can be found in <files>
1036 Long sequence alignments have names <long.xx.aln>
1037 HMM file written in <long.xx.hmm>
1038 HMM database written in <pipelign.hmm>
1039
1040 [28 May 13:12:16] Alignment with long sequences and fragments written in <final.noOrphans.aln>
1041
1042 [28 May 13:12:16] <final.noBadSeq.aln> file created