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 Perkinsus_marinus-EER04402.1 and Perkinsus_marinus-EER15538.1 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189324718 and Karenia-brevis-SP3-CAMPEP_0189192184 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189324718 and Karenia-brevis-CCMP2229-CAMPEP_0188903032 are exactly identical IMPORTANT WARNING: Sequences Karenia-brevis-Wilson-CAMPEP_0189324718 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 10 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. An alignment file with sequence duplicates removed has already been 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: 11 This is RAxML Worker Pthread Number: 9 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 143 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 7.07% 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: 143 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 0.765197 Bootstrap[0]: Time 14.229301 seconds, bootstrap likelihood -12532.187645, best rearrangement setting 13 Bootstrap[1]: Time 11.498453 seconds, bootstrap likelihood -13340.509954, best rearrangement setting 13 Bootstrap[2]: Time 10.460018 seconds, bootstrap likelihood -12601.903989, best rearrangement setting 12 Bootstrap[3]: Time 12.493127 seconds, bootstrap likelihood -11948.732633, best rearrangement setting 15 Bootstrap[4]: Time 10.235546 seconds, bootstrap likelihood -13507.650097, best rearrangement setting 10 Bootstrap[5]: Time 8.866686 seconds, bootstrap likelihood -11799.468534, best rearrangement setting 10 Bootstrap[6]: Time 10.428007 seconds, bootstrap likelihood -12804.136137, best rearrangement setting 6 Bootstrap[7]: Time 11.248527 seconds, bootstrap likelihood -12099.006275, best rearrangement setting 14 Bootstrap[8]: Time 10.089855 seconds, bootstrap likelihood -13504.621723, best rearrangement setting 5 Bootstrap[9]: Time 9.134323 seconds, bootstrap likelihood -13134.092343, best rearrangement setting 7 Bootstrap[10]: Time 9.936902 seconds, bootstrap likelihood -13498.854877, best rearrangement setting 7 Bootstrap[11]: Time 11.309365 seconds, bootstrap likelihood -12646.037519, best rearrangement setting 5 Bootstrap[12]: Time 10.685649 seconds, bootstrap likelihood -13265.008389, best rearrangement setting 8 Bootstrap[13]: Time 11.078216 seconds, bootstrap likelihood -13089.241908, best rearrangement setting 7 Bootstrap[14]: Time 10.977220 seconds, bootstrap likelihood -12754.827628, best rearrangement setting 12 Bootstrap[15]: Time 13.038036 seconds, bootstrap likelihood -12849.727725, best rearrangement setting 15 Bootstrap[16]: Time 11.473882 seconds, bootstrap likelihood -13767.127826, best rearrangement setting 12 Bootstrap[17]: Time 11.070267 seconds, bootstrap likelihood -13230.806301, best rearrangement setting 12 Bootstrap[18]: Time 10.864108 seconds, bootstrap likelihood -12330.248029, best rearrangement setting 5 Bootstrap[19]: Time 7.990705 seconds, bootstrap likelihood -11938.532550, best rearrangement setting 8 Bootstrap[20]: Time 11.904142 seconds, bootstrap likelihood -14165.186318, best rearrangement setting 10 Bootstrap[21]: Time 8.482678 seconds, bootstrap likelihood -13003.449357, best rearrangement setting 6 Bootstrap[22]: Time 9.358851 seconds, bootstrap likelihood -12763.397309, best rearrangement setting 5 Bootstrap[23]: Time 10.170359 seconds, bootstrap likelihood -14062.763667, best rearrangement setting 7 Bootstrap[24]: Time 12.584639 seconds, bootstrap likelihood -13737.661673, best rearrangement setting 8 Bootstrap[25]: Time 11.289247 seconds, bootstrap likelihood -13869.429852, best rearrangement setting 6 Bootstrap[26]: Time 12.037621 seconds, bootstrap likelihood -12521.466195, best rearrangement setting 12 Bootstrap[27]: Time 10.755134 seconds, bootstrap likelihood -13558.439282, best rearrangement setting 10 Bootstrap[28]: Time 10.409365 seconds, bootstrap likelihood -11975.438632, best rearrangement setting 11 Bootstrap[29]: Time 11.633831 seconds, bootstrap likelihood -12718.153452, best rearrangement setting 12 Bootstrap[30]: Time 11.923059 seconds, bootstrap likelihood -13243.987111, best rearrangement setting 15 Bootstrap[31]: Time 12.413109 seconds, bootstrap likelihood -14575.295288, best rearrangement setting 15 Bootstrap[32]: Time 10.769152 seconds, bootstrap likelihood -14554.228180, best rearrangement setting 6 Bootstrap[33]: Time 10.742770 seconds, bootstrap likelihood -13179.961212, best rearrangement setting 15 Bootstrap[34]: Time 11.796033 seconds, bootstrap likelihood -12992.171224, best rearrangement setting 11 Bootstrap[35]: Time 10.867741 seconds, bootstrap likelihood -12990.921458, best rearrangement setting 8 Bootstrap[36]: Time 11.892807 seconds, bootstrap likelihood -12352.237215, best rearrangement setting 9 Bootstrap[37]: Time 9.958855 seconds, bootstrap likelihood -12396.745618, best rearrangement setting 11 Bootstrap[38]: Time 10.595716 seconds, bootstrap likelihood -13213.052799, best rearrangement setting 8 Bootstrap[39]: Time 12.666339 seconds, bootstrap likelihood -14018.135198, best rearrangement setting 13 Bootstrap[40]: Time 10.982997 seconds, bootstrap likelihood -14457.569168, best rearrangement setting 13 Bootstrap[41]: Time 13.643245 seconds, bootstrap likelihood -14334.031408, best rearrangement setting 10 Bootstrap[42]: Time 10.548180 seconds, bootstrap likelihood -12481.397261, best rearrangement setting 5 Bootstrap[43]: Time 11.345048 seconds, bootstrap likelihood -12435.071615, best rearrangement setting 14 Bootstrap[44]: Time 9.629760 seconds, bootstrap likelihood -13856.456161, best rearrangement setting 10 Bootstrap[45]: Time 9.996907 seconds, bootstrap likelihood -13498.572291, best rearrangement setting 15 Bootstrap[46]: Time 10.303639 seconds, bootstrap likelihood -13365.749944, best rearrangement setting 14 Bootstrap[47]: Time 10.767368 seconds, bootstrap likelihood -13728.419781, best rearrangement setting 8 Bootstrap[48]: Time 10.230951 seconds, bootstrap likelihood -13834.224913, best rearrangement setting 6 Bootstrap[49]: Time 10.754005 seconds, bootstrap likelihood -12966.151593, best rearrangement setting 7 Bootstrap[50]: Time 10.293005 seconds, bootstrap likelihood -13488.982445, best rearrangement setting 7 Bootstrap[51]: Time 9.763340 seconds, bootstrap likelihood -12683.712940, best rearrangement setting 11 Bootstrap[52]: Time 12.010263 seconds, bootstrap likelihood -13217.311311, best rearrangement setting 12 Bootstrap[53]: Time 11.186285 seconds, bootstrap likelihood -12446.908891, best rearrangement setting 8 Bootstrap[54]: Time 10.748796 seconds, bootstrap likelihood -14590.458021, best rearrangement setting 9 Bootstrap[55]: Time 11.892818 seconds, bootstrap likelihood -13792.166544, best rearrangement setting 11 Bootstrap[56]: Time 10.257570 seconds, bootstrap likelihood -13458.609566, best rearrangement setting 5 Bootstrap[57]: Time 11.443282 seconds, bootstrap likelihood -12008.410224, best rearrangement setting 7 Bootstrap[58]: Time 10.845851 seconds, bootstrap likelihood -13318.695475, best rearrangement setting 10 Bootstrap[59]: Time 11.781741 seconds, bootstrap likelihood -13933.104459, best rearrangement setting 9 Bootstrap[60]: Time 10.126093 seconds, bootstrap likelihood -13296.355759, best rearrangement setting 7 Bootstrap[61]: Time 9.501086 seconds, bootstrap likelihood -12434.906369, best rearrangement setting 5 Bootstrap[62]: Time 12.880767 seconds, bootstrap likelihood -13329.017463, best rearrangement setting 11 Bootstrap[63]: Time 13.598003 seconds, bootstrap likelihood -12889.102397, best rearrangement setting 12 Bootstrap[64]: Time 8.685532 seconds, bootstrap likelihood -12956.980521, best rearrangement setting 7 Bootstrap[65]: Time 10.041766 seconds, bootstrap likelihood -12963.393841, best rearrangement setting 5 Bootstrap[66]: Time 9.953382 seconds, bootstrap likelihood -13016.552369, best rearrangement setting 5 Bootstrap[67]: Time 10.971177 seconds, bootstrap likelihood -12967.432712, best rearrangement setting 15 Bootstrap[68]: Time 10.010136 seconds, bootstrap likelihood -13181.014837, best rearrangement setting 11 Bootstrap[69]: Time 9.431216 seconds, bootstrap likelihood -14007.672174, best rearrangement setting 5 Bootstrap[70]: Time 11.477321 seconds, bootstrap likelihood -12698.665702, best rearrangement setting 8 Bootstrap[71]: Time 10.855769 seconds, bootstrap likelihood -13354.720863, best rearrangement setting 10 Bootstrap[72]: Time 11.666204 seconds, bootstrap likelihood -13745.041383, best rearrangement setting 11 Bootstrap[73]: Time 10.321480 seconds, bootstrap likelihood -13478.470852, best rearrangement setting 9 Bootstrap[74]: Time 9.929996 seconds, bootstrap likelihood -14035.591400, best rearrangement setting 5 Bootstrap[75]: Time 11.320437 seconds, bootstrap likelihood -13465.371959, best rearrangement setting 8 Bootstrap[76]: Time 9.902882 seconds, bootstrap likelihood -12436.247520, best rearrangement setting 9 Bootstrap[77]: Time 10.969085 seconds, bootstrap likelihood -14343.377642, best rearrangement setting 11 Bootstrap[78]: Time 12.782433 seconds, bootstrap likelihood -13865.701925, best rearrangement setting 15 Bootstrap[79]: Time 9.938920 seconds, bootstrap likelihood -14411.353017, best rearrangement setting 9 Bootstrap[80]: Time 11.744869 seconds, bootstrap likelihood -11999.300148, best rearrangement setting 15 Bootstrap[81]: Time 11.088605 seconds, bootstrap likelihood -13094.230516, best rearrangement setting 7 Bootstrap[82]: Time 10.396730 seconds, bootstrap likelihood -13122.911669, best rearrangement setting 6 Bootstrap[83]: Time 13.388723 seconds, bootstrap likelihood -13541.435412, best rearrangement setting 10 Bootstrap[84]: Time 11.851476 seconds, bootstrap likelihood -13548.933068, best rearrangement setting 11 Bootstrap[85]: Time 11.095287 seconds, bootstrap likelihood -13349.601092, best rearrangement setting 8 Bootstrap[86]: Time 9.456831 seconds, bootstrap likelihood -13085.517761, best rearrangement setting 7 Bootstrap[87]: Time 10.173071 seconds, bootstrap likelihood -12587.984895, best rearrangement setting 7 Bootstrap[88]: Time 12.674585 seconds, bootstrap likelihood -13333.808274, best rearrangement setting 12 Bootstrap[89]: Time 10.756555 seconds, bootstrap likelihood -14400.849523, best rearrangement setting 10 Bootstrap[90]: Time 10.361482 seconds, bootstrap likelihood -11910.057490, best rearrangement setting 8 Bootstrap[91]: Time 12.152152 seconds, bootstrap likelihood -13141.174063, best rearrangement setting 12 Bootstrap[92]: Time 11.518466 seconds, bootstrap likelihood -12399.338921, best rearrangement setting 13 Bootstrap[93]: Time 11.905331 seconds, bootstrap likelihood -13531.068465, best rearrangement setting 15 Bootstrap[94]: Time 10.314858 seconds, bootstrap likelihood -12234.844822, best rearrangement setting 5 Bootstrap[95]: Time 9.937077 seconds, bootstrap likelihood -14012.847990, best rearrangement setting 5 Bootstrap[96]: Time 10.709337 seconds, bootstrap likelihood -13447.177927, best rearrangement setting 13 Bootstrap[97]: Time 11.864870 seconds, bootstrap likelihood -12752.320446, best rearrangement setting 11 Bootstrap[98]: Time 10.300744 seconds, bootstrap likelihood -12214.122472, best rearrangement setting 6 Bootstrap[99]: Time 10.311029 seconds, bootstrap likelihood -14828.381187, best rearrangement setting 14 Overall Time for 100 Rapid Bootstraps 1094.241233 seconds Average Time per Rapid Bootstrap 10.942412 seconds Starting ML Search ... Fast ML optimization finished Fast ML search Time: 1374.221011 seconds Slow ML Search 0 Likelihood: -13345.676709 Slow ML Search 1 Likelihood: -13344.965626 Slow ML Search 2 Likelihood: -13347.908341 Slow ML Search 3 Likelihood: -13348.114769 Slow ML Search 4 Likelihood: -13345.254394 Slow ML Search 5 Likelihood: -13350.811379 Slow ML Search 6 Likelihood: -13352.189899 Slow ML Search 7 Likelihood: -13352.251242 Slow ML Search 8 Likelihood: -13347.898240 Slow ML Search 9 Likelihood: -13353.194490 Slow ML optimization finished Slow ML search Time: 635.932279 seconds Thorough ML search Time: 40.536850 seconds Final ML Optimization Likelihood: -13344.873419 Model Information: Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA alpha: 0.786493 Tree-Length: 71.274809 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 2050.789366 secs or 0.569664 hours Combined Bootstrap and ML search took 3145.031507 secs or 0.873620 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: 3145.083497 secs or 0.873634 hours or 0.036401 days