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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:24:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/2_msa/Q07912_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/3_mltree/Q07912.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647473 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/020621_run/phylogeny-snakemake/results/Q07912/2_msa/Q07912_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1038 sites WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_R0LH93_R0LH93_ANAPL_8839 are exactly identical! WARNING: Sequences sp_P08630_BTKL_DROME_7227 and tr_B4HYH7_B4HYH7_DROSE_7238 are exactly identical! WARNING: Sequences sp_P08630_BTKL_DROME_7227 and tr_B3MPH0_B3MPH0_DROAN_7217 are exactly identical! WARNING: Sequences sp_P08630_BTKL_DROME_7227 and tr_A0A1W4V8B2_A0A1W4V8B2_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2I3RYF9_A0A2I3RYF9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and sp_P00533_EGFR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2R9CTL6_A0A2R9CTL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_F7G3H1_F7G3H1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_G7PLC3_G7PLC3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K5NV86_A0A2K5NV86_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K6DNJ0_A0A2K6DNJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Z667_A0A2I2Z667_GORGO_9595 and sp_Q15303_ERBB4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R9U2_G3R9U2_GORGO_9595 and tr_H2R453_H2R453_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9U2_G3R9U2_GORGO_9595 and sp_P07948_LYN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RF60_A0A2I3RF60_PANTR_9598 and tr_A0A2R9C6L4_A0A2R9C6L4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8PYX8_A0A2J8PYX8_PANTR_9598 and sp_P08631_HCK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8PYX8_A0A2J8PYX8_PANTR_9598 and tr_A0A2R9BT02_A0A2R9BT02_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and sp_P42685_FRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and tr_A0A2R9BRU0_A0A2R9BRU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RE09_A0A1D5RE09_MACMU_9544 and sp_P55245_EGFR_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A1D5RE09_A0A1D5RE09_MACMU_9544 and tr_G7P1R4_G7P1R4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RE09_A0A1D5RE09_MACMU_9544 and tr_A0A0D9RU37_A0A0D9RU37_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5RE09_A0A1D5RE09_MACMU_9544 and tr_A0A2K6B1P2_A0A2K6B1P2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_G7PBV3_G7PBV3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A096MX07_A0A096MX07_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A0D9RQ35_A0A0D9RQ35_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BV42_F7BV42_MACMU_9544 and tr_A0A2K6DNJ8_A0A2K6DNJ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H8A7_F7H8A7_MACMU_9544 and tr_G7PGN2_G7PGN2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H8A7_F7H8A7_MACMU_9544 and tr_A0A2K6DQ69_A0A2K6DQ69_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZLG0_H0ZLG0_TAEGU_59729 and tr_A0A218VBI1_A0A218VBI1_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4W469_F4W469_ACREC_103372 and tr_A0A151X1X9_A0A151X1X9_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4W469_F4W469_ACREC_103372 and tr_A0A195E5N9_A0A195E5N9_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A096MT35_A0A096MT35_PAPAN_9555 and tr_A0A2K5XRB5_A0A2K5XRB5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MVJ9_A0A096MVJ9_PAPAN_9555 and tr_A0A2K5N7J8_A0A2K5N7J8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MVJ9_A0A096MVJ9_PAPAN_9555 and tr_A0A2K5Z8B7_A0A2K5Z8B7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NUZ0_A0A096NUZ0_PAPAN_9555 and tr_A0A2K5M7C8_A0A2K5M7C8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091VSQ5_A0A091VSQ5_NIPNI_128390 and tr_A0A091FK40_A0A091FK40_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091GP40_A0A091GP40_9AVES_55661 and tr_A0A0A0APC0_A0A0A0APC0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091GP40_A0A091GP40_9AVES_55661 and tr_A0A2I0MIN8_A0A2I0MIN8_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091GP40_A0A091GP40_9AVES_55661 and tr_A0A1V4K778_A0A1V4K778_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A195DQM7_A0A195DQM7_9HYME_471704 and tr_A0A151I5L4_A0A151I5L4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A195DQM7_A0A195DQM7_9HYME_471704 and tr_A0A195CJM0_A0A195CJM0_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A195ET97_A0A195ET97_9HYME_34720 and tr_A0A195CLJ5_A0A195CLJ5_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A226NGR7_A0A226NGR7_CALSU_9009 and tr_A0A226NY66_A0A226NY66_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PSY2_A0A2D0PSY2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PW58_A0A2D0PW58_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PX14_A0A2D0PX14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3A6_A0A2D0R3A6_ICTPU_7998 and tr_A0A2D0R5J2_A0A2D0R5J2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SJ06_A0A2D0SJ06_ICTPU_7998 and tr_W5U9K8_W5U9K8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T7X8_A0A2D0T7X8_ICTPU_7998 and tr_A0A2D0T7Y0_A0A2D0T7Y0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T7X8_A0A2D0T7X8_ICTPU_7998 and tr_A0A2D0T8L0_A0A2D0T8L0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AJ04_A0A2U4AJ04_TURTR_9739 and tr_A0A2Y9LZZ2_A0A2Y9LZZ2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BML0_A0A2U4BML0_TURTR_9739 and tr_A0A2Y9MQV3_A0A2Y9MQV3_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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.raxml.reduced.phy Alignment comprises 1 partitions and 1038 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1038 Gaps: 50.92 % Invariant sites: 0.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.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/020621_run/phylogeny-snakemake/results/Q07912/3_mltree/Q07912.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 260 / 20800 [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: -295761.375688 [00:00:00 -295761.375688] Initial branch length optimization [00:00:02 -275327.672226] Model parameter optimization (eps = 0.100000) [00:01:20] Tree #1, final logLikelihood: -274719.342198 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.083251,0.183370) (0.097451,0.254673) (0.303197,0.669023) (0.516102,1.466902) 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/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q07912/4_raxmlng_ancestral/Q07912.raxml.log Analysis started: 02-Jun-2021 18:24:33 / finished: 02-Jun-2021 18:26:04 Elapsed time: 90.782 seconds Consumed energy: 4.786 Wh