RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 14-Jul-2021 17:49:20 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/2_msa/A6NDS4_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/3_mltree/A6NDS4.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626274160 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/2_msa/A6NDS4_nogap_msa.fasta [00:00:00] Loaded alignment with 960 taxa and 549 sites WARNING: Sequences tr_M3YRR1_M3YRR1_MUSPF_9669 and tr_W5PWX7_W5PWX7_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q9VGL8_TBWKD_DROME_7227 and tr_B4HI08_B4HI08_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1S5X3_G1S5X3_NOMLE_61853 and tr_G3QMT1_G3QMT1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S5X3_G1S5X3_NOMLE_61853 and sp_Q5RAN1_RBGP1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S5X3_G1S5X3_NOMLE_61853 and sp_Q9Y3P9_RBGP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A0E1RY19_A0A0E1RY19_COCIM_246410 and tr_E9D5V0_E9D5V0_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1RY19_A0A0E1RY19_COCIM_246410 and tr_A0A0J6XXF6_A0A0J6XXF6_COCIT_404692 are exactly identical! WARNING: Sequences tr_D8QWZ0_D8QWZ0_SELML_88036 and tr_D8RL25_D8RL25_SELML_88036 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_H0Z9C8_H0Z9C8_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_R0KWV7_R0KWV7_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A0Q3X3R1_A0A0Q3X3R1_AMAAE_12930 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A091FW49_A0A091FW49_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A093SY20_A0A093SY20_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A091VTQ3_A0A091VTQ3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A087R4L4_A0A087R4L4_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A091V3D3_A0A091V3D3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1N7Q7_G1N7Q7_MELGA_9103 and tr_A0A0A0AX42_A0A0A0AX42_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1PC09_F1PC09_CANLF_9615 and tr_A0A2Y9J631_A0A2Y9J631_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3S7C2_A0A2I3S7C2_PANTR_9598 and tr_A0A2R8Z943_A0A2R8Z943_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SEY8_A0A2I3SEY8_PANTR_9598 and tr_A0A2R9BFS6_A0A2R9BFS6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2REZ6_H2REZ6_PANTR_9598 and tr_A0A2R9BBZ3_A0A2R9BBZ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7A3S3_K7A3S3_PANTR_9598 and sp_Q9BXI6_TB10A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7A3S3_K7A3S3_PANTR_9598 and tr_A0A2R9BKM8_A0A2R9BKM8_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and sp_Q6ZT07_TBCD9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and tr_G7P6B8_G7P6B8_MACFA_9541 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and tr_A0A096N0N7_A0A096N0N7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and tr_A0A0D9S105_A0A0D9S105_CHLSB_60711 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and tr_A0A2K6DL73_A0A2K6DL73_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7BPQ8_K7BPQ8_PANTR_9598 and tr_A0A2K5XEW7_A0A2K5XEW7_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q6IPX1_TBC3C_HUMAN_9606 and sp_Q8IZP1_TBC3A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5R538_A0A1D5R538_MACMU_9544 and tr_G7PE75_G7PE75_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R8F2_A0A1D5R8F2_MACMU_9544 and tr_G7PTV9_G7PTV9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NFU3_G7NFU3_MACMU_9544 and tr_A0A096P0M8_A0A096P0M8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NFU3_G7NFU3_MACMU_9544 and tr_A0A0D9RLV2_A0A0D9RLV2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NFU3_G7NFU3_MACMU_9544 and tr_A0A2K5KR41_A0A2K5KR41_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NFU3_G7NFU3_MACMU_9544 and tr_A0A2K6D7A3_A0A2K6D7A3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NFU3_G7NFU3_MACMU_9544 and tr_A0A2K5XTY1_A0A2K5XTY1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7X709_G7X709_ASPKW_1033177 and tr_A0A146FTH3_A0A146FTH3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X709_G7X709_ASPKW_1033177 and tr_A0A317WAF8_A0A317WAF8_9EURO_1448314 are exactly identical! WARNING: Sequences tr_I3LCN0_I3LCN0_PIG_9823 and tr_D2HDF8_D2HDF8_AILME_9646 are exactly identical! WARNING: Sequences tr_W2RHV4_W2RHV4_PHYPN_761204 and tr_A0A0W8B4B7_A0A0W8B4B7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RHV4_W2RHV4_PHYPN_761204 and tr_W2HLB5_W2HLB5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2I0M418_A0A2I0M418_COLLI_8932 and tr_A0A1V4J744_A0A1V4J744_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0S6W6_A0A0V0S6W6_9BILA_6336 and tr_A0A0V0VSS0_A0A0V0VSS0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WRD2_A0A0V0WRD2_9BILA_92179 and tr_A0A0V1KQ11_A0A0V1KQ11_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2D0RFJ2_A0A2D0RFJ2_ICTPU_7998 and tr_A0A2D0RGQ3_A0A2D0RGQ3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RFJ2_A0A2D0RFJ2_ICTPU_7998 and tr_A0A2D0RHD5_A0A2D0RHD5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3R2_A0A2D0T3R2_ICTPU_7998 and tr_A0A2D0T3S1_A0A2D0T3S1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3R2_A0A2D0T3R2_ICTPU_7998 and tr_A0A2D0T4M0_A0A2D0T4M0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NJ23_A0A2K5NJ23_CERAT_9531 and tr_A0A2K6BYJ1_A0A2K6BYJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K6DBW7_A0A2K6DBW7_MACNE_9545 and tr_A0A2K5YT21_A0A2K5YT21_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4B6G9_A0A2U4B6G9_TURTR_9739 and tr_A0A2Y9NLK8_A0A2Y9NLK8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CH17_A0A2U4CH17_TURTR_9739 and tr_A0A2Y9NNP2_A0A2Y9NNP2_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 53 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.reduced.phy Alignment comprises 1 partitions and 549 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 549 Gaps: 32.88 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/3_mltree/A6NDS4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -193992.551533 [00:00:00 -193992.551533] Initial branch length optimization [00:00:01 -192432.943954] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -191915.224667 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.110662,0.453069) (0.091542,0.442384) (0.309893,0.621097) (0.487902,1.469335) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NDS4/4_raxmlng_ancestral/A6NDS4.raxml.log Analysis started: 14-Jul-2021 17:49:20 / finished: 14-Jul-2021 17:50:02 Elapsed time: 41.822 seconds