MrBayes Stepping-stone analysis error: DEBUG ERROR: Log likelihood nan after move 'Slider(Ratemultiplier{all})'
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Entering edit mode
12 weeks ago
klo • 0

I am trying to run a stepping-stone analysis in MrBayes to get accurate marginal likelihood estimates for two different constrained trees. I am using the following MrBayes command block in my nexus file:

begin mrbayes;
[Define pairs for the doublet model]
pairs 77:90, 76:96, 75:97, 74:98, 73:99, 72:100, 71:101, 61:102, 60:103, 
     57:111, 56:112, 55:113, 53:115, 52:116, 51:117, 50:118, 49:122, 48:123, 47:124, 
     46:125, 133:137, 132:138, 129:143, 128:144, 127:145, 126:146, 163:170, 162:171, 
     161:172, 160:173, 159:174, 158:175, 157:176, 154:177, 153:178, 152:179, 151:180, 
     150:181, 242:246, 241:247, 240:248, 239:249, 238:250, 237:251, 236:252, 276:283, 
     275:284, 274:285, 273:286, 272:287, 271:288, 269:290, 268:292, 267:293, 266:294, 
     265:295, 309:317, 308:318, 307:319, 306:320, 305:321, 304:322, 263:323, 262:324, 
     261:325, 260:326, 259:327, 257:328, 256:329, 255:330, 254:331, 206:332, 205:333, 
     204:334, 203:335, 202:336, 201:337, 200:338, 199:339, 198:340, 197:341, 191:342, 
     190:343, 189:344, 188:345, 187:346, 186:347, 185:350, 184:351, 183:352, 182:353, 
     413:419, 412:420, 411:421, 408:424, 407:425, 406:426, 405:427, 404:428, 403:429, 
     402:430, 399:435, 398:436, 397:437, 396:438, 395:439, 394:440, 391:443, 390:444, 
     389:454, 388:455, 387:456, 386:457, 385:459, 384:460, 383:461, 382:462, 371:467, 
     370:468, 369:469, 368:470, 367:471, 366:472, 365:473;


    charset  12s-stems = 46 47 48 49 50 51 52 53 55 56 57 60 61 71 72 73 74 
       75 76 77 90 96 97 98 99 100 101 102 103 111 112 113 115 116 117 118 122 123 
       124 125 126 127 128 129 132 133 137 138 143 144 145 146 150 151 152 153 154 
       157 158 159 160 161 162 163 170 171 172 173 174 175 176 177 178 179 180 181 
       182 183 184 185 186 187 188 189 190 191 197 198 199 200 201 202 203 204 205 
       206 236 237 238 239 240 241 242 246 247 248 249 250 251 252 254 255 256 257 
       259 260 261 262 263 265 266 267 268 269 271 272 273 274 275 276 283 284 285 
       286 287 288 290 292 293 294 295 304 305 306 307 308 309 317 318 319 320 321 
       322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 
       341 342 343 344 345 346 347 350 351 352 353 365 366 367 368 369 370 371 382 
       383 384 385 386 387 388 389 390 391 394 395 396 397 398 399 402 403 404 405 
       406 407 408 411 412 413 419 420 421 424 425 426 427 428 429 430 435 436 437 
       438 439 440 443 444 454 455 456 457 459 460 461 462 467 468 469 470 471 472 
       473;


    charset  12s-loops = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
       21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 
       54 58 59 62 63 64 65 66 67 68 69 70 78 79 80 81 82 83 84 85 86 87 88 89 91 
       92 93 94 95 104 105 106 107 108 109 110 114 119 120 121 130 131 134 135 136 
       139 140 141 142 147 148 149 155 156 164 165 166 167 168 169 192 193 194 195 
       196 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 
       225 226 227 228 229 230 231 232 233 234 235 243 244 245 253 258 264 270 277 
       278 279 280 281 282 289 291 296 297 298 299 300 301 302 303 310 311 312 313 
       314 315 316 348 349 354 355 356 357 358 359 360 361 362 363 364 372 373 374 
       375 376 377 378 379 380 381 392 393 400 401 409 410 414 415 416 417 418 422 
       423 431 432 433 434 441 442 445 446 447 448 449 450 451 452 453 458 463 464 
       465 466 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 
       491 492 493 494 495 496;

  charset coiii_pos1 =  497 - 1160\3;
  charset coiii_pos2 =  498 - 1160\3;
  charset coiii_pos3 =  499 - 1160\3;
  charset cytb_pos1 =  1161 - 1926\3;
  charset cytb_pos2 =  1162 - 1926\3;
  charset cytb_pos3 =  1163 - 1926\3;

  partition by_gene = 8:12s-stems,12s-loops,coiii_pos1,coiii_pos2,coiii_pos3,cytb_pos1,cytb_pos2,cytb_pos3;
    set partition = by_gene;

    constraint muusoctopus partial = Muusoctopus_eureka Muusoctopus_eureka_2 Muusoctopus_eureka_3 Muusoctopus_eureka_4 Muusoctopus_levis Muusoctopus_levis_2 Muusoctopus_oregonensis Muusoctopus_thielei Muusoctopus_yaquinae Muusoctopus_hydrothermalis Muusoctopus_hydrothermalis_2 Muusoctopus_longibranchus Muusoctopus_rigbyae Muusoctopus_rigbyae_2 Muusoctopus_tangaroa Muusoctopus_tangaroa_2 Muusoctopus_tangaroa_3 Muusoctopus_tangaroa_4 Muusoctopus_tangaroa_5 Muusoctopus_normani Muusoctopus_normani_2 Muusoctopus_normani_3 Muusoctopus_normani_4 Muusoctopus_longibrachus_akambei Muusoctopus_longibrachus_akambei_2 Muusoctopus_longibrachus_akambei_3 Muusoctopus_johnsonianus Muusoctopus_johnsonianus_2 Muusoctopus_sp._A Muusoctopus_sp._A_2 Muusoctopus_sp._A_3 Muusoctopus_cf._profundorum Muusoctopus_cf._profundorum_2 Muusoctopus_sp._B Muusoctopus_sp._B_2 Muusoctopus_sp._E Muusoctopus_cf._levis Muusoctopus_cf._rigbyae_AL Muusoctopus_cf._rigbyae_AS Muusoctopus_sp. Muusoctopus_sp._MV Muusoctopus_longibrachus_longibrachus Muusoctopus_longibrachus_longibrachus_2 Muusoctopus_longibrachus_longibrachus_3 Muusoctopus_longibrachus_longibrachus_4 Muusoctopus_longibrachus_longibrachus_5 Muusoctopus_longibrachus_longibrachus_6 Muusoctopus_longibrachus_longibrachus_7 Muusoctopus_longibrachus_longibrachus_8 Muusoctopus_longibrachus : Muusoctopus_leioderma_casiz31213 Muusoctopus_leioderma_burrows Muusoctopus_leioderma_neotype Muusoctopus_leioderma_rosario;
    constraint outg = Octopus_vulgaris Octopus_rubescens Octopus_bimaculoides Octopus_cyanea Amphioctopus_aegina Hapalochlaena_maculosa Abdopus_aculeatus Octopus_tetricus Octopus_berrima Macroctopus_maorum;
    prset topologypr = constraints (muusoctopus,outg);
    outgroup Octopus_vulgaris;

    lset applyto=(1)   nucmodel=doublet;
    lset applyto=(2,3,4,6,7,8)   nucmodel=4by4;
    prset ratepr=variable;
    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);
  lset applyto=(1) nst=6 rates=invgamma;
  lset applyto=(2) nst=2 rates=gamma;
  lset applyto=(3) nst=2 rates=gamma;
  lset applyto=(4) nst=2 rates=propinv;
  lset applyto=(5) nst=2 rates=gamma;
  lset applyto=(6) nst=2 rates=invgamma;
  lset applyto=(7) nst=2 rates=invgamma;
  lset applyto=(8) nst=2 rates=invgamma;
  prset applyto=(4) statefreqpr=fixed(equal);

  mcmcp ngen=20000000 printfreq=1000 samplefreq=1000 nruns=5 nchains=2;
  ss; 
end;

This analysis starts off fine and runs for about 9M generations of the 20M I have it set to run for, and I get the following error:

DEBUG ERROR: Log likelihood nan after move 'Slider(Ratemultiplier{all})'

After that all of the output from MrBayes stops, but the processors continue to run at 100% as if the analysis is still running. From what I can gather my Ratemultiplier has become so small that it can't be expressed with computer precision anymore, but I am completely at a loss for how to fix this. I ran this analysis and its pair (the only difference is in the 'muusoctopus' constraint) simultaneously using the MPI version of MrBayes, with each analysis spread across 10 processors. Both analyses get the same error somewhere between 9M and 10M generations.
Any ideas how to fix this problem? Thanks in advance!

stepping-stone mrbayes • 234 views
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Entering edit mode
11 weeks ago
klo • 0

I should add that I am using MPI version of MrBayes 3.2.6 on Ubuntu

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