SAM Tools version 0.1.18 loaded. OpenMPI libraries (GNU) version 1.6.3 loaded. GMP arithmetic library version 5.1.1 loaded. MPFR version 3.1.1 loaded. Mpc version 1.0.1 loaded. gcc version 4.9.2 loaded. R version 3.1.1 loaded Boost version 1.52.0 loaded. Sun/Oracle Java SE Development Kit version 1.7.0_51 loaded. RAxML version 8.0.26 loaded. RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file IMPORTANT WARNING: Sequences Paramecium-caudatum-PCAUDG02994 and Paramecium-caudatum-PCAUDG10616 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189424234 and Karenia-brevis-SP3-CAMPEP_0189258408 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189424234 and Karenia-brevis-CCMP2229-CAMPEP_0188909504 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189424234 and Karenia-brevis-SP1-CAMPEP_0189087650 are exactly identical IMPORTANT WARNING: Sequences Perkinsus_marinus-EER04402.1 and Perkinsus_marinus-EEQ99722.1 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP3-CAMPEP_0189192184 and Karenia-brevis-CCMP2229-CAMPEP_0188903032 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP3-CAMPEP_0189192184 and Karenia-brevis-SP1-CAMPEP_0189015932 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-SP1-CAMPEP_0189058320 and Karenia-brevis-CCMP2229-CAMPEP_0188887872 are exactly identical IMPORTANT WARNING Found 8 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. Just in case you might need it, an alignment file with sequence duplicates removed is printed to file /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/H2A-variants/H2A-with-other-lineages-more-H2A.Z.muscle.minCov50.fa.reduced This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 This is RAxML Worker Pthread Number: 2 This is RAxML Worker Pthread Number: 3 This is RAxML Worker Pthread Number: 4 This is RAxML Worker Pthread Number: 5 This is RAxML Worker Pthread Number: 6 This is RAxML Worker Pthread Number: 7 This is RAxML Worker Pthread Number: 8 This is RAxML Worker Pthread Number: 10 This is RAxML Worker Pthread Number: 9 This is RAxML Worker Pthread Number: 11 This is RAxML Worker Pthread Number: 12 This is RAxML Worker Pthread Number: 13 This is RAxML Worker Pthread Number: 14 This is RAxML Worker Pthread Number: 15 This is RAxML version 8.1.3 released by Alexandros Stamatakis on August 13 2014. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 142 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 6.79% RAxML rapid bootstrapping and subsequent ML search Using 1 distinct models/data partitions with joint branch length optimization Executing 100 rapid bootstrap inferences and thereafter a thorough ML search All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 142 Name: No Name Provided DataType: AA Substitution Matrix: LG Using fixed base frequencies RAxML was called as follows: raxml -f a -s /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/H2A-variants/H2A-with-other-lineages-more-H2A.Z.muscle.minCov50.fa -n RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 -m PROTGAMMALG -T 16 -p 12345 -N 100 -x 12345 Time for BS model parameter optimization 0.464334 Bootstrap[0]: Time 8.726030 seconds, bootstrap likelihood -12445.932046, best rearrangement setting 13 Bootstrap[1]: Time 7.119650 seconds, bootstrap likelihood -12425.473069, best rearrangement setting 13 Bootstrap[2]: Time 7.744009 seconds, bootstrap likelihood -13055.929371, best rearrangement setting 12 Bootstrap[3]: Time 6.986891 seconds, bootstrap likelihood -13186.999036, best rearrangement setting 15 Bootstrap[4]: Time 7.144647 seconds, bootstrap likelihood -13353.725907, best rearrangement setting 10 Bootstrap[5]: Time 6.369263 seconds, bootstrap likelihood -12211.371144, best rearrangement setting 10 Bootstrap[6]: Time 6.795640 seconds, bootstrap likelihood -12342.986093, best rearrangement setting 6 Bootstrap[7]: Time 7.046084 seconds, bootstrap likelihood -11847.259654, best rearrangement setting 14 Bootstrap[8]: Time 6.195026 seconds, bootstrap likelihood -13012.999077, best rearrangement setting 5 Bootstrap[9]: Time 6.824075 seconds, bootstrap likelihood -11707.704130, best rearrangement setting 7 Bootstrap[10]: Time 7.347328 seconds, bootstrap likelihood -12483.183610, best rearrangement setting 7 Bootstrap[11]: Time 7.210260 seconds, bootstrap likelihood -13217.369570, best rearrangement setting 5 Bootstrap[12]: Time 6.506945 seconds, bootstrap likelihood -13389.766161, best rearrangement setting 8 Bootstrap[13]: Time 7.094918 seconds, bootstrap likelihood -12580.272813, best rearrangement setting 7 Bootstrap[14]: Time 8.144058 seconds, bootstrap likelihood -12348.635063, best rearrangement setting 12 Bootstrap[15]: Time 6.616189 seconds, bootstrap likelihood -12656.862738, best rearrangement setting 15 Bootstrap[16]: Time 8.290334 seconds, bootstrap likelihood -12915.043677, best rearrangement setting 12 Bootstrap[17]: Time 8.229069 seconds, bootstrap likelihood -13510.068113, best rearrangement setting 12 Bootstrap[18]: Time 6.813873 seconds, bootstrap likelihood -13333.035877, best rearrangement setting 5 Bootstrap[19]: Time 6.318439 seconds, bootstrap likelihood -12039.559870, best rearrangement setting 8 Bootstrap[20]: Time 7.153566 seconds, bootstrap likelihood -13781.217597, best rearrangement setting 10 Bootstrap[21]: Time 6.715516 seconds, bootstrap likelihood -13562.450928, best rearrangement setting 6 Bootstrap[22]: Time 6.365209 seconds, bootstrap likelihood -12359.007796, best rearrangement setting 5 Bootstrap[23]: Time 6.684045 seconds, bootstrap likelihood -14162.182700, best rearrangement setting 7 Bootstrap[24]: Time 8.105688 seconds, bootstrap likelihood -13086.301530, best rearrangement setting 8 Bootstrap[25]: Time 6.364471 seconds, bootstrap likelihood -13825.585302, best rearrangement setting 6 Bootstrap[26]: Time 6.975499 seconds, bootstrap likelihood -12442.746497, best rearrangement setting 12 Bootstrap[27]: Time 6.812971 seconds, bootstrap likelihood -12957.133693, best rearrangement setting 10 Bootstrap[28]: Time 8.042479 seconds, bootstrap likelihood -12570.437435, best rearrangement setting 11 Bootstrap[29]: Time 6.681834 seconds, bootstrap likelihood -12249.534831, best rearrangement setting 12 Bootstrap[30]: Time 6.668223 seconds, bootstrap likelihood -13479.010311, best rearrangement setting 15 Bootstrap[31]: Time 7.107742 seconds, bootstrap likelihood -13484.038155, best rearrangement setting 15 Bootstrap[32]: Time 6.599003 seconds, bootstrap likelihood -13719.727524, best rearrangement setting 6 Bootstrap[33]: Time 6.887436 seconds, bootstrap likelihood -13706.256991, best rearrangement setting 15 Bootstrap[34]: Time 7.210825 seconds, bootstrap likelihood -12941.944299, best rearrangement setting 11 Bootstrap[35]: Time 6.691243 seconds, bootstrap likelihood -12822.646019, best rearrangement setting 8 Bootstrap[36]: Time 6.259815 seconds, bootstrap likelihood -12675.162932, best rearrangement setting 9 Bootstrap[37]: Time 7.659564 seconds, bootstrap likelihood -13021.396443, best rearrangement setting 11 Bootstrap[38]: Time 6.829021 seconds, bootstrap likelihood -12986.487756, best rearrangement setting 8 Bootstrap[39]: Time 7.520005 seconds, bootstrap likelihood -12892.063692, best rearrangement setting 13 Bootstrap[40]: Time 6.732603 seconds, bootstrap likelihood -14044.273877, best rearrangement setting 13 Bootstrap[41]: Time 6.701839 seconds, bootstrap likelihood -13766.466698, best rearrangement setting 10 Bootstrap[42]: Time 5.900327 seconds, bootstrap likelihood -12388.444556, best rearrangement setting 5 Bootstrap[43]: Time 6.732621 seconds, bootstrap likelihood -12466.851336, best rearrangement setting 14 Bootstrap[44]: Time 6.294365 seconds, bootstrap likelihood -12793.600341, best rearrangement setting 10 Bootstrap[45]: Time 7.700835 seconds, bootstrap likelihood -13672.635682, best rearrangement setting 15 Bootstrap[46]: Time 6.312336 seconds, bootstrap likelihood -13371.591106, best rearrangement setting 14 Bootstrap[47]: Time 6.885830 seconds, bootstrap likelihood -11946.798971, best rearrangement setting 8 Bootstrap[48]: Time 6.318883 seconds, bootstrap likelihood -13957.156429, best rearrangement setting 6 Bootstrap[49]: Time 6.572200 seconds, bootstrap likelihood -12857.968141, best rearrangement setting 7 Bootstrap[50]: Time 7.915722 seconds, bootstrap likelihood -12298.489705, best rearrangement setting 7 Bootstrap[51]: Time 6.749798 seconds, bootstrap likelihood -13308.542864, best rearrangement setting 11 Bootstrap[52]: Time 6.890758 seconds, bootstrap likelihood -13021.797497, best rearrangement setting 12 Bootstrap[53]: Time 6.313173 seconds, bootstrap likelihood -12679.957424, best rearrangement setting 8 Bootstrap[54]: Time 6.670292 seconds, bootstrap likelihood -13801.463588, best rearrangement setting 9 Bootstrap[55]: Time 6.486655 seconds, bootstrap likelihood -14755.287999, best rearrangement setting 11 Bootstrap[56]: Time 6.810691 seconds, bootstrap likelihood -12266.978174, best rearrangement setting 5 Bootstrap[57]: Time 6.508273 seconds, bootstrap likelihood -13242.751965, best rearrangement setting 7 Bootstrap[58]: Time 7.383074 seconds, bootstrap likelihood -12256.626305, best rearrangement setting 10 Bootstrap[59]: Time 6.382528 seconds, bootstrap likelihood -13184.484463, best rearrangement setting 9 Bootstrap[60]: Time 6.691589 seconds, bootstrap likelihood -12820.305948, best rearrangement setting 7 Bootstrap[61]: Time 6.353867 seconds, bootstrap likelihood -13156.757164, best rearrangement setting 5 Bootstrap[62]: Time 5.683540 seconds, bootstrap likelihood -12745.093408, best rearrangement setting 11 Bootstrap[63]: Time 6.919436 seconds, bootstrap likelihood -12650.408031, best rearrangement setting 12 Bootstrap[64]: Time 6.115498 seconds, bootstrap likelihood -13034.018929, best rearrangement setting 7 Bootstrap[65]: Time 5.708456 seconds, bootstrap likelihood -12587.774254, best rearrangement setting 5 Bootstrap[66]: Time 6.126223 seconds, bootstrap likelihood -13575.271166, best rearrangement setting 5 Bootstrap[67]: Time 7.345049 seconds, bootstrap likelihood -13516.917695, best rearrangement setting 15 Bootstrap[68]: Time 6.644158 seconds, bootstrap likelihood -12176.446383, best rearrangement setting 11 Bootstrap[69]: Time 6.566476 seconds, bootstrap likelihood -13337.956434, best rearrangement setting 5 Bootstrap[70]: Time 7.169015 seconds, bootstrap likelihood -13787.042638, best rearrangement setting 8 Bootstrap[71]: Time 8.154208 seconds, bootstrap likelihood -12108.909756, best rearrangement setting 10 Bootstrap[72]: Time 8.531742 seconds, bootstrap likelihood -14532.352350, best rearrangement setting 11 Bootstrap[73]: Time 6.845257 seconds, bootstrap likelihood -12726.801838, best rearrangement setting 9 Bootstrap[74]: Time 6.853767 seconds, bootstrap likelihood -12593.251259, best rearrangement setting 5 Bootstrap[75]: Time 7.132922 seconds, bootstrap likelihood -13565.964195, best rearrangement setting 8 Bootstrap[76]: Time 7.057743 seconds, bootstrap likelihood -12555.653758, best rearrangement setting 9 Bootstrap[77]: Time 7.635481 seconds, bootstrap likelihood -13113.637882, best rearrangement setting 11 Bootstrap[78]: Time 8.173248 seconds, bootstrap likelihood -13609.159339, best rearrangement setting 15 Bootstrap[79]: Time 7.456919 seconds, bootstrap likelihood -13674.406553, best rearrangement setting 9 Bootstrap[80]: Time 8.036333 seconds, bootstrap likelihood -12843.050674, best rearrangement setting 15 Bootstrap[81]: Time 5.932656 seconds, bootstrap likelihood -11695.220265, best rearrangement setting 7 Bootstrap[82]: Time 6.239449 seconds, bootstrap likelihood -14059.280394, best rearrangement setting 6 Bootstrap[83]: Time 6.614569 seconds, bootstrap likelihood -13478.858725, best rearrangement setting 10 Bootstrap[84]: Time 6.948863 seconds, bootstrap likelihood -14066.886646, best rearrangement setting 11 Bootstrap[85]: Time 7.010471 seconds, bootstrap likelihood -12074.021375, best rearrangement setting 8 Bootstrap[86]: Time 6.648626 seconds, bootstrap likelihood -14143.796635, best rearrangement setting 7 Bootstrap[87]: Time 7.107776 seconds, bootstrap likelihood -12721.424138, best rearrangement setting 7 Bootstrap[88]: Time 7.275106 seconds, bootstrap likelihood -12611.612671, best rearrangement setting 12 Bootstrap[89]: Time 7.521396 seconds, bootstrap likelihood -13777.043458, best rearrangement setting 10 Bootstrap[90]: Time 7.428554 seconds, bootstrap likelihood -12788.057478, best rearrangement setting 8 Bootstrap[91]: Time 6.636480 seconds, bootstrap likelihood -13164.379953, best rearrangement setting 12 Bootstrap[92]: Time 6.716960 seconds, bootstrap likelihood -13188.103400, best rearrangement setting 13 Bootstrap[93]: Time 7.974836 seconds, bootstrap likelihood -13294.028377, best rearrangement setting 15 Bootstrap[94]: Time 6.355555 seconds, bootstrap likelihood -12588.007049, best rearrangement setting 5 Bootstrap[95]: Time 6.762352 seconds, bootstrap likelihood -12510.013009, best rearrangement setting 5 Bootstrap[96]: Time 6.357933 seconds, bootstrap likelihood -12538.390608, best rearrangement setting 13 Bootstrap[97]: Time 7.659857 seconds, bootstrap likelihood -13871.749573, best rearrangement setting 11 Bootstrap[98]: Time 7.281123 seconds, bootstrap likelihood -11518.618156, best rearrangement setting 6 Bootstrap[99]: Time 6.978723 seconds, bootstrap likelihood -13352.812062, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 695.912472 seconds Average Time per Rapid Bootstrap 6.959125 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 790.740336 seconds Slow ML Search 0 Likelihood: -13167.952897 Slow ML Search 1 Likelihood: -13168.166198 Slow ML Search 2 Likelihood: -13175.840215 Slow ML Search 3 Likelihood: -13170.866245 Slow ML Search 4 Likelihood: -13175.208122 Slow ML Search 5 Likelihood: -13176.258840 Slow ML Search 6 Likelihood: -13173.695851 Slow ML Search 7 Likelihood: -13178.294298 Slow ML Search 8 Likelihood: -13177.692213 Slow ML Search 9 Likelihood: -13176.980419 Slow ML optimization finished Slow ML search Time: 514.814164 seconds Thorough ML search Time: 29.691212 seconds Final ML Optimization Likelihood: -13167.945856 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.715602 Tree-Length: 71.782491 rate A <-> R: 0.399182 rate A <-> N: 0.259945 rate A <-> D: 0.371058 rate A <-> C: 2.337364 rate A <-> Q: 0.910775 rate A <-> E: 0.975241 rate A <-> G: 1.940106 rate A <-> H: 0.336984 rate A <-> I: 0.140697 rate A <-> L: 0.371240 rate A <-> K: 0.503815 rate A <-> M: 1.055520 rate A <-> F: 0.238237 rate A <-> P: 1.105868 rate A <-> S: 4.439041 rate A <-> T: 2.009090 rate A <-> W: 0.169702 rate A <-> Y: 0.205613 rate A <-> V: 2.392567 rate R <-> N: 0.706048 rate R <-> D: 0.116398 rate R <-> C: 0.501968 rate R <-> Q: 2.636754 rate R <-> E: 0.341785 rate R <-> G: 0.366408 rate R <-> H: 2.278690 rate R <-> I: 0.119250 rate R <-> L: 0.283449 rate R <-> K: 5.940467 rate R <-> M: 0.454623 rate R <-> F: 0.049508 rate R <-> P: 0.312264 rate R <-> S: 0.805843 rate R <-> T: 0.543695 rate R <-> W: 0.557424 rate R <-> Y: 0.295274 rate R <-> V: 0.160471 rate N <-> D: 4.766737 rate N <-> C: 0.496537 rate N <-> Q: 1.592389 rate N <-> E: 0.508692 rate N <-> G: 1.350015 rate N <-> H: 4.234381 rate N <-> I: 0.179830 rate N <-> L: 0.064256 rate N <-> K: 2.014327 rate N <-> M: 0.348390 rate N <-> F: 0.084068 rate N <-> P: 0.151925 rate N <-> S: 3.764032 rate N <-> T: 1.878729 rate N <-> W: 0.042610 rate N <-> Y: 0.574720 rate N <-> V: 0.078587 rate D <-> C: 0.058743 rate D <-> Q: 0.491483 rate D <-> E: 4.924234 rate D <-> G: 0.793424 rate D <-> H: 0.870603 rate D <-> I: 0.010038 rate D <-> L: 0.014157 rate D <-> K: 0.265711 rate D <-> M: 0.023991 rate D <-> F: 0.016354 rate D <-> P: 0.370412 rate D <-> S: 1.164675 rate D <-> T: 0.399902 rate D <-> W: 0.028068 rate D <-> Y: 0.126872 rate D <-> V: 0.035653 rate C <-> Q: 0.079639 rate C <-> E: 0.003286 rate C <-> G: 0.534566 rate C <-> H: 0.601499 rate C <-> I: 0.301083 rate C <-> L: 0.557800 rate C <-> K: 0.012457 rate C <-> M: 0.839207 rate C <-> F: 1.037881 rate C <-> P: 0.070787 rate C <-> S: 2.614753 rate C <-> T: 1.073780 rate C <-> W: 0.629281 rate C <-> Y: 1.094488 rate C <-> V: 1.839864 rate Q <-> E: 3.876936 rate Q <-> G: 0.251626 rate Q <-> H: 4.520102 rate Q <-> I: 0.068413 rate Q <-> L: 0.546954 rate Q <-> K: 3.037150 rate Q <-> M: 1.570619 rate Q <-> F: 0.033669 rate Q <-> P: 0.586241 rate Q <-> S: 1.149231 rate Q <-> T: 1.014297 rate Q <-> W: 0.221802 rate Q <-> Y: 0.241650 rate Q <-> V: 0.197511 rate E <-> G: 0.327583 rate E <-> H: 0.398044 rate E <-> I: 0.041567 rate E <-> L: 0.065426 rate E <-> K: 1.697022 rate E <-> M: 0.163145 rate E <-> F: 0.017664 rate E <-> P: 0.393844 rate E <-> S: 0.574671 rate E <-> T: 0.567695 rate E <-> W: 0.073107 rate E <-> Y: 0.112720 rate E <-> V: 0.230098 rate G <-> H: 0.292498 rate G <-> I: 0.008174 rate G <-> L: 0.041563 rate G <-> K: 0.278555 rate G <-> M: 0.131033 rate G <-> F: 0.084125 rate G <-> P: 0.184955 rate G <-> S: 1.633930 rate G <-> T: 0.121922 rate G <-> W: 0.252125 rate G <-> Y: 0.051346 rate G <-> V: 0.072026 rate H <-> I: 0.102245 rate H <-> L: 0.343988 rate H <-> K: 0.654763 rate H <-> M: 0.415502 rate H <-> F: 0.640560 rate H <-> P: 0.477834 rate H <-> S: 0.929667 rate H <-> T: 0.548649 rate H <-> W: 0.560661 rate H <-> Y: 4.983361 rate H <-> V: 0.111759 rate I <-> L: 3.892408 rate I <-> K: 0.149373 rate I <-> M: 4.013113 rate I <-> F: 1.044902 rate I <-> P: 0.073509 rate I <-> S: 0.060198 rate I <-> T: 0.970728 rate I <-> W: 0.104854 rate I <-> Y: 0.218350 rate I <-> V: 10.000000 rate L <-> K: 0.129119 rate L <-> M: 5.927594 rate L <-> F: 2.434657 rate L <-> P: 0.233879 rate L <-> S: 0.171176 rate L <-> T: 0.284471 rate L <-> W: 0.581863 rate L <-> Y: 0.281383 rate L <-> V: 1.598956 rate K <-> M: 0.616581 rate K <-> F: 0.022460 rate K <-> P: 0.366530 rate K <-> S: 0.703048 rate K <-> T: 1.067567 rate K <-> W: 0.046864 rate K <-> Y: 0.123890 rate K <-> V: 0.173913 rate M <-> F: 1.689205 rate M <-> P: 0.093763 rate M <-> S: 0.325811 rate M <-> T: 1.897216 rate M <-> W: 0.653740 rate M <-> Y: 0.451968 rate M <-> V: 1.782983 rate F <-> P: 0.088706 rate F <-> S: 0.339765 rate F <-> T: 0.154944 rate F <-> W: 2.307349 rate F <-> Y: 7.328222 rate F <-> V: 0.614777 rate P <-> S: 1.256567 rate P <-> T: 0.536635 rate P <-> W: 0.089332 rate P <-> Y: 0.084151 rate P <-> V: 0.278428 rate S <-> T: 6.077767 rate S <-> W: 0.233693 rate S <-> Y: 0.376132 rate S <-> V: 0.092373 rate T <-> W: 0.132241 rate T <-> Y: 0.230856 rate T <-> V: 2.054781 rate W <-> Y: 2.959699 rate W <-> V: 0.177959 rate Y <-> V: 0.234116 freq pi(A): 0.079060 freq pi(R): 0.055940 freq pi(N): 0.041980 freq pi(D): 0.053050 freq pi(C): 0.012940 freq pi(Q): 0.040770 freq pi(E): 0.071580 freq pi(G): 0.057340 freq pi(H): 0.022350 freq pi(I): 0.062160 freq pi(L): 0.099080 freq pi(K): 0.064600 freq pi(M): 0.022950 freq pi(F): 0.042300 freq pi(P): 0.044040 freq pi(S): 0.061200 freq pi(T): 0.053290 freq pi(W): 0.012070 freq pi(Y): 0.034150 freq pi(V): 0.069150 ML search took 1335.356486 secs or 0.370932 hours Combined Bootstrap and ML search took 2031.269933 secs or 0.564242 hours Drawing Bootstrap Support Values on best-scoring ML tree ... Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Found 1 tree in File /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Program execution info written to /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_info.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 All 100 bootstrapped trees written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bootstrap.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Best-scoring ML tree written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bestTree.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Best-scoring ML tree with support values written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bipartitions.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Best-scoring ML tree with support values as branch labels written to: /N/dc2/projects/marinovg/2014-06-19-MMETSP/2015-07-10-final-analysis/RAxML/RAxML_bipartitionsBranchLabels.RAxML-H2A-with-other-lineages-more-H2A.Z.muscle.minCov50 Overall execution time for full ML analysis: 2031.316389 secs or 0.564255 hours or 0.023511 days