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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 17:33:49 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/2_msa/O43374_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/3_mltree/O43374.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100429 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/2_msa/O43374_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 803 sites WARNING: Sequences sp_P63318_KPCG_MOUSE_10090 and sp_P63319_KPCG_RAT_10116 are exactly identical! WARNING: Sequences sp_P68404_KPCB_MOUSE_10090 and sp_P05772_KPCB_RABIT_9986 are exactly identical! WARNING: Sequences sp_P68404_KPCB_MOUSE_10090 and sp_P68403_KPCB_RAT_10116 are exactly identical! WARNING: Sequences sp_P68404_KPCB_MOUSE_10090 and tr_A0A3Q0CN94_A0A3Q0CN94_MESAU_10036 are exactly identical! WARNING: Sequences sp_P05130_KPC1_DROME_7227 and tr_B4HTB4_B4HTB4_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2I3NI95_A0A2I3NI95_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2K5YD37_A0A2K5YD37_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_G3R5W0_G3R5W0_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_H2NQF5_H2NQF5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_H2QAS6_H2QAS6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_F7I4K8_F7I4K8_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_A0A2I3N8C1_A0A2I3N8C1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_A0A2K5L6M3_A0A2K5L6M3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HJQ3_A0A2I3HJQ3_NOMLE_61853 and tr_A0A2K6B2U4_A0A2K6B2U4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QHE4_G1QHE4_NOMLE_61853 and tr_G7PV75_G7PV75_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2YKG4_A0A2I2YKG4_GORGO_9595 and tr_H2QH30_H2QH30_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YKG4_A0A2I2YKG4_GORGO_9595 and sp_P05129_KPCG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YRH5_A0A2I2YRH5_GORGO_9595 and sp_Q9BQG1_SYT3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QNK0_G3QNK0_GORGO_9595 and sp_Q9Y6V0_PCLO_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RIN3_G3RIN3_GORGO_9595 and tr_A0A096NTX9_A0A096NTX9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RIN3_G3RIN3_GORGO_9595 and tr_A0A2K5LMT6_A0A2K5LMT6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RIN3_G3RIN3_GORGO_9595 and tr_A0A2K6CYI9_A0A2K6CYI9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8U8Z9_A0A2J8U8Z9_PONAB_9601 and tr_A0A0D9S4W8_A0A0D9S4W8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_E2R521_E2R521_CANLF_9615 and tr_G1M2R5_G1M2R5_AILME_9646 are exactly identical! WARNING: Sequences tr_E2R521_E2R521_CANLF_9615 and tr_A0A2U3WLZ8_A0A2U3WLZ8_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2R521_E2R521_CANLF_9615 and tr_A0A2Y9L0S9_A0A2Y9L0S9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F6R0R1_F6R0R1_HORSE_9796 and tr_I3MXX7_I3MXX7_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P05696_KPCA_RAT_10116 and tr_A0A1U7QLD2_A0A1U7QLD2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A158P293_A0A158P293_ATTCE_12957 and tr_A0A151I099_A0A151I099_9HYME_520822 are exactly identical! WARNING: Sequences sp_P05771_KPCB_HUMAN_9606 and tr_F7BYI4_F7BYI4_MACMU_9544 are exactly identical! WARNING: Sequences sp_P05771_KPCB_HUMAN_9606 and tr_A0A0D9R2T7_A0A0D9R2T7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0H5SPI7_A0A0H5SPI7_BRUMA_6279 and tr_A0A0R3R0T2_A0A0R3R0T2_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A1D5R7T9_A0A1D5R7T9_MACMU_9544 and tr_A0A2I3LWE8_A0A2I3LWE8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R7T9_A0A1D5R7T9_MACMU_9544 and tr_A0A2K5NCN7_A0A2K5NCN7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R7T9_A0A1D5R7T9_MACMU_9544 and tr_A0A2K6CE51_A0A2K6CE51_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SWS4_F6SWS4_MACMU_9544 and tr_A0A2K6DMP2_A0A2K6DMP2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H3B3_F7H3B3_MACMU_9544 and tr_F6W4P5_F6W4P5_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7H3B3_F7H3B3_MACMU_9544 and tr_A0A0D9S5H3_A0A0D9S5H3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7H3B3_F7H3B3_MACMU_9544 and tr_A0A2K5M7E0_A0A2K5M7E0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H3B3_F7H3B3_MACMU_9544 and tr_A0A2K6CYX1_A0A2K6CYX1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1RH13_F1RH13_PIG_9823 and tr_E1BJ13_E1BJ13_BOVIN_9913 are exactly identical! WARNING: Sequences tr_D2HYP8_D2HYP8_AILME_9646 and tr_M3VWV6_M3VWV6_FELCA_9685 are exactly identical! WARNING: Sequences tr_D2HYP8_D2HYP8_AILME_9646 and tr_A0A2U3WL05_A0A2U3WL05_ODORO_9708 are exactly identical! WARNING: Sequences tr_D2HYP8_D2HYP8_AILME_9646 and tr_A0A2Y9IG42_A0A2Y9IG42_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G7Q0R2_G7Q0R2_MACFA_9541 and tr_A0A2R9B4X0_A0A2R9B4X0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0A0MVP0_A0A0A0MVP0_PAPAN_9555 and tr_A0A2K5LZ34_A0A2K5LZ34_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A094EEW7_A0A094EEW7_9PEZI_1420912 and tr_A0A1B8G9B8_A0A1B8G9B8_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A091J9P6_A0A091J9P6_EGRGA_188379 and tr_A0A0A0ANL6_A0A0A0ANL6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0N0PDY1_A0A0N0PDY1_PAPMA_76193 and tr_A0A194PUL4_A0A194PUL4_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A1S3N085_A0A1S3N085_SALSA_8030 and tr_A0A1S3SH72_A0A1S3SH72_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2I4ASP5_A0A2I4ASP5_9TELE_52670 and tr_A0A2I4D2Y4_A0A2I4D2Y4_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A226N661_A0A226N661_CALSU_9009 and tr_A0A226PAY6_A0A226PAY6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4A1B7_A0A2U4A1B7_TURTR_9739 and tr_A0A2Y9SAH2_A0A2Y9SAH2_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 53 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.raxml.reduced.phy Alignment comprises 1 partitions and 803 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 803 Gaps: 41.38 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/3_mltree/O43374.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080 [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: -219081.426061 [00:00:00 -219081.426061] Initial branch length optimization [00:00:02 -217709.837050] Model parameter optimization (eps = 0.100000) [00:01:04] Tree #1, final logLikelihood: -216603.548210 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.130929,0.813091) (0.075713,0.631193) (0.422100,0.716560) (0.371259,1.463383) 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43374/4_raxmlng_ancestral/O43374.raxml.log Analysis started: 12-Jul-2021 17:33:49 / finished: 12-Jul-2021 17:35:02 Elapsed time: 72.689 seconds Consumed energy: 6.327 Wh