~/Programs/tassel4/run_pipeline.pl -fork1 -DiscoverySNPCallerPlugin -i ~/Projects/4Acer/mergedTBT/myMastertag.tbt.byte -y -m ~/Projects/4Acer/topm/myMasterTags.topm -mUpd ~/Projects/4Acer/topm/myMasterTagsWithVariants.topm -o ~/Projects/4Acer/hapmap/raw/myGBSGenos_chr+.hmp.txt -mnMAF 0.01 -mnMAC 100000 -ref ~/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa -sC 1 -eC 4765 -endPlugin -runfork1 ---- last lins Exception in thread "Thread-0" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getMaxScore(FractionalIdentityScorer.java:92) at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:40) at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:35) at org.biojava3.alignment.GuideTree.(GuideTree.java:80) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176) at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514) at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) _____ Memory Settings: -Xms12G -Xmx14G Tassel Pipeline Arguments: -fork1 -DiscoverySNPCallerPlugin -i /Users/admin/Projects/4Acer/mergedTBT/myMastertag.tbt.byte -y -m /Users/admin/Projects/4Acer/topm/myMasterTags.topm -mUpd /Users/admin/Projects/4Acer/topm/myMasterTagsWithVariants.topm -o /Users/admin/Projects/4Acer/hapmap/raw/myGBSGenos_chr+.hmp.txt -mnMAF 0.01 -mnMAC 100000 -ref /Users/admin/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa -sC 1 -eC 4765 -endPlugin -runfork1 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 4.3.7 Date: April 17, 2014 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 12743 MB nBytes to end of taxa names: 3090 Read tag0 Read tag1000000 Number of Taxa in file:80 Number of Haplotypes in file:1685220 File = /Users/admin/Projects/4Acer/topm/myMasterTags.topm TagMapFile Row Read:0 TagMapFile Row Read:1000000 Count of Tags=1685220 initPhysicalSort Position index sort begin. Position index sort end. [main] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - minTaxaWithLocus:8 MinF:-2.00000 MinMAF:0.0100000 MinMAC:100000 [main] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - includeRare:false includeGaps:false net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Finding SNPs in /Users/admin/Projects/4Acer/mergedTBT/myMastertag.tbt.byte. [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - StartChr:1 EndChr:4765 Starting Read Table Sort ...Done in 316ms initPhysicalSort Position index sort begin. Position index sort end. [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - As a check, here are the first 5 tags in the TOPM (sorted by position): CTGCGAAAATTATAAGAAGTAAAAAAATATAAAAATACTTTCGCACGAATGGAGTCTGATTGCA 64 1 1 1 3608 3671 2 * * * * * * * CAGCCATCTTGTGAAGGTCGAAATATCGCAGAACAATGGGAGAAATGACGAAACCAACTTGTTC 64 1 1 -1 8583 8520 1 * * * * * * * CAGCCACAACTAAGCATTTTGTCAGTATCAAACGTCCTATCGATTTTACCTAAGGAAACTAGTC 64 1 1 1 8802 8865 2 * * * * * * * CAGCGAGTTCACTCCGGTTCCCTCTTGTGTCTCTGAATTCGTTAACATGATAACACCAGAAAGT 64 1 1 -1 10220 10157 0 * * * * * * * CAGCCAATAATTTCTATTGACAAAGACAGTAACAACCCTATTTTTATTGAAACTTTATTTTCCA 64 1 1 1 11308 11371 0 * * * * * * * [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Processing chromosome 1... [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Creating Mutable Alignment to hold genotypes for chr1 (maximum number of sites = 200000) [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Determining the length (in bases) of target chromosome 1 in the reference genome fasta file: /Users/admin/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Currently reading chromosome 1 (target chromosome = 1) [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - The target chromosome 1 is 1590019 bases long [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Reading in the target chromosome 1 from the reference genome fasta file: /Users/admin/Projects/4Acer/Acropora_genome/adi_v1.0.scaffold_2.fa [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Currently reading chromosome 1 (target chromosome = 1) [Thread-0] INFO net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin - Finished reading target chromosome 1 into a total of 49689 32bp chunks Initializing the cutoffs for quantitative SNP calling likelihood ratio (pHet/pErr) >1 totalReadsForSNPInIndiv minLessTaggedAlleleCountForHet 2 1 3 1 4 1 5 1 6 1 7 2 8 2 9 2 10 2 11 2 12 2 13 2 14 3 15 3 16 3 17 3 18 3 19 3 20 3 21 4 22 4 23 4 24 4 25 4 26 4 27 4 28 5 29 5 30 5 31 5 32 5 33 5 34 6 35 6 36 6 37 6 38 6 39 6 40 6 41 7 42 7 43 7 44 7 45 7 46 7 47 7 48 8 49 8 50 8 51 8 52 8 53 8 54 8 55 9 56 9 57 9 58 9 59 9 60 9 61 10 62 10 63 10 64 10 65 10 66 10 67 10 68 11 69 11 70 11 71 11 72 11 73 11 74 11 75 12 76 12 77 12 78 12 79 12 80 12 81 13 82 13 83 13 84 13 85 13 86 13 87 13 88 14 89 14 90 14 91 14 92 14 93 14 94 14 95 15 96 15 97 15 98 15 99 15 100 15 101 15 102 16 103 16 104 16 105 16 106 16 107 16 108 17 109 17 110 17 111 17 112 17 113 17 114 17 115 18 116 18 117 18 118 18 119 18 120 18 121 18 122 19 123 19 124 19 125 19 126 19 127 19 128 19 129 20 130 20 131 20 132 21 133 21 134 21 135 21 136 22 137 22 138 22 139 23 140 23 141 23 142 24 143 24 144 24 145 25 146 25 147 25 148 26 149 26 150 26 151 27 152 27 153 27 154 28 155 28 156 28 157 29 158 29 159 29 160 30 161 30 162 30 163 30 164 31 165 31 166 31 167 32 168 32 169 32 170 33 171 33 172 33 173 34 174 34 175 35 176 35 177 35 178 36 179 36 180 36 181 37 182 37 183 37 184 38 185 38 186 38 187 39 188 39 189 39 190 40 191 40 192 40 193 41 194 41 195 41 196 42 197 42 198 42 199 43 200 43 201 43 202 44 203 44 204 44 205 45 206 45 207 46 208 46 209 46 210 47 211 47 212 47 213 48 214 48 215 48 216 49 217 49 218 49 219 50 220 50 221 50 222 51 223 51 224 52 225 52 226 52 227 53 228 53 229 53 230 54 231 54 232 54 233 55 234 55 235 56 236 56 237 56 238 57 239 57 240 57 241 58 242 58 243 58 244 59 245 59 246 60 247 60 248 60 249 61 250 61 251 61 252 62 253 62 254 62 255 63 256 63 257 64 258 64 259 64 260 65 261 65 262 65 263 66 264 66 265 66 266 67 267 67 268 68 269 68 270 68 271 69 272 69 273 69 274 70 275 70 276 71 277 71 278 71 279 72 280 72 281 72 282 73 283 73 284 74 285 74 286 74 287 75 288 75 289 75 290 76 291 76 292 77 293 77 294 77 295 78 296 78 297 78 298 79 299 79 300 80 301 80 302 80 303 81 304 81 305 81 306 82 307 82 308 83 309 83 310 83 311 84 312 84 313 85 314 85 315 85 316 86 317 86 318 86 319 87 320 87 321 88 322 88 323 88 324 89 325 89 326 89 327 90 328 90 329 91 330 91 331 91 332 92 333 92 334 93 335 93 336 93 337 94 338 94 339 94 340 95 341 95 342 96 343 96 344 96 345 97 346 97 347 98 348 98 349 98 350 99 351 99 352 99 353 100 354 100 355 101 356 101 357 101 358 102 359 102 360 103 361 103 362 103 363 104 364 104 365 105 366 105 367 105 368 106 369 106 370 106 371 107 372 107 373 108 374 108 375 108 376 109 377 109 378 110 379 110 380 110 381 111 382 111 383 112 384 112 385 112 386 113 387 113 388 114 389 114 390 114 391 115 392 115 393 116 394 116 395 116 396 117 397 117 398 117 399 118 400 118 401 119 402 119 403 119 404 120 405 120 406 121 407 121 408 121 409 122 410 122 411 123 412 123 413 123 414 124 415 124 416 125 417 125 418 125 419 126 420 126 421 127 422 127 423 127 424 128 425 128 426 129 427 129 428 129 429 130 430 130 431 131 432 131 433 131 434 132 435 132 436 133 437 133 438 133 439 134 440 134 441 135 442 135 443 135 444 136 445 136 446 137 447 137 448 137 449 138 450 138 451 139 452 139 453 139 454 140 455 140 456 141 457 141 458 141 459 142 460 142 461 143 462 143 463 143 464 144 465 144 466 145 467 145 468 145 469 146 470 146 471 147 472 147 473 147 474 148 475 148 476 149 477 149 478 149 479 150 480 150 481 151 482 151 483 151 484 152 485 152 486 153 487 153 488 153 489 154 490 154 491 155 492 155 493 156 494 156 495 156 496 157 497 157 498 158 499 158 java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173) at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514) at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:744) java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173) at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514) at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) Caused by: java.lang.ExceptionInInitializerError at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:744) Caused by: java.lang.NullPointerException at java.util.Collections$UnmodifiableCollection.(Collections.java:1086) at java.util.Collections$UnmodifiableList.(Collections.java:1362) at java.util.Collections.unmodifiableList(Collections.java:1347) at org.biojava3.core.sequence.location.template.AbstractLocation.(AbstractLocation.java:111) at org.biojava3.core.sequence.location.template.AbstractLocation.(AbstractLocation.java:85) at org.biojava3.core.sequence.location.SimpleLocation.(SimpleLocation.java:57) at org.biojava3.core.sequence.location.SimpleLocation.(SimpleLocation.java:53) at org.biojava3.core.sequence.location.template.Location.(Location.java:48) ... 16 more java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282) at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173) at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514) at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29) Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:744) Exception in thread "Thread-0" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358) at org.biojava3.alignment.SimpleAlignedSequence.(SimpleAlignedSequence.java:88) at org.biojava3.alignment.SimpleProfile.(SimpleProfile.java:118) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:86) at org.biojava3.alignment.SimpleSequencePair.(SimpleSequencePair.java:69) at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71) at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342) at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112) at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getMaxScore(FractionalIdentityScorer.java:92) at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:40) at org.biojava3.alignment.template.AbstractScorer.getDistance(AbstractScorer.java:35) at org.biojava3.alignment.GuideTree.(GuideTree.java:80) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176) at net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java:514) at net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java:309) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.addSitesToMutableAlignment(DiscoverySNPCallerPlugin.java:519) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.runTagsToSNPByAlignment(DiscoverySNPCallerPlugin.java:401) at net.maizegenetics.gbs.pipeline.DiscoverySNPCallerPlugin.performFunction(DiscoverySNPCallerPlugin.java:121) at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201) at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)