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 25-Jun-2021 07:35:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/2_msa/O00429_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/3_mltree/O00429.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624595759 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_040621/phylogeny-snakemake/results/O00429/2_msa/O00429_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 736 sites WARNING: Sequences tr_M3XMB9_M3XMB9_MUSPF_9669 and tr_A0A2Y9LGA7_A0A2Y9LGA7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_J3K853_J3K853_COCIM_246410 and tr_E9CSR4_E9CSR4_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K853_J3K853_COCIM_246410 and tr_A0A0J6Y9W7_A0A0J6Y9W7_COCIT_404692 are exactly identical! WARNING: Sequences tr_J3KL22_J3KL22_COCIM_246410 and tr_E9CU59_E9CU59_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KL22_J3KL22_COCIM_246410 and tr_A0A0J7BHQ3_A0A0J7BHQ3_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QMJ5_B6QMJ5_TALMQ_441960 and tr_A0A093UYG3_A0A093UYG3_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A2I3RYD0_A0A2I3RYD0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and sp_O00429_DNM1L_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_F7GI64_F7GI64_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A096NYR0_A0A096NYR0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A0D9R4X2_A0A0D9R4X2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A2K5KVQ8_A0A2K5KVQ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A2K6CW91_A0A2K6CW91_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2ZBB8_A0A2I2ZBB8_GORGO_9595 and tr_A0A2R9C0P6_A0A2R9C0P6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0A0HWS3_A0A0A0HWS3_PARBD_502780 and tr_C1H945_C1H945_PARBA_502779 are exactly identical! WARNING: Sequences tr_Q7SDJ3_Q7SDJ3_NEUCR_367110 and tr_G4U8X4_G4U8X4_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8NQ64_B8NQ64_ASPFN_332952 and tr_A0A1S9DS32_A0A1S9DS32_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UDD9_A0A179UDD9_BLAGS_559298 and tr_C5GIJ7_C5GIJ7_AJEDR_559297 are exactly identical! WARNING: Sequences tr_C6HAX1_C6HAX1_AJECH_544712 and tr_F0UD31_F0UD31_AJEC8_544711 are exactly identical! WARNING: Sequences tr_C6HFE6_C6HFE6_AJECH_544712 and tr_F0UP46_F0UP46_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4UJE8_J4UJE8_BEAB2_655819 and tr_A0A2N6NGU0_A0A2N6NGU0_BEABA_176275 are exactly identical! WARNING: Sequences tr_Q2TVY0_Q2TVY0_ASPOR_510516 and tr_A0A1S9DFU0_A0A1S9DFU0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A2QHI2_A2QHI2_ASPNC_425011 and tr_G3Y7Y3_G3Y7Y3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QHI2_A2QHI2_ASPNC_425011 and tr_A0A318ZVQ4_A0A318ZVQ4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XV65_G7XV65_ASPKW_1033177 and tr_A0A146FYX7_A0A146FYX7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XV65_G7XV65_ASPKW_1033177 and tr_A0A317V7Y1_A0A317V7Y1_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F9X1G0_F9X1G0_ZYMTI_336722 and tr_A0A1X7RI49_A0A1X7RI49_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F9XI80_F9XI80_ZYMTI_336722 and tr_A0A1X7S199_A0A1X7S199_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YDP7_G2YDP7_BOTF4_999810 and tr_M7USS1_M7USS1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SYU2_F2SYU2_TRIRC_559305 and tr_A0A178F5P8_A0A178F5P8_TRIRU_5551 are exactly identical! WARNING: Sequences tr_D4ARQ2_D4ARQ2_ARTBC_663331 and tr_F2PRV3_F2PRV3_TRIEC_559882 are exactly identical! WARNING: Sequences tr_D4ARQ2_D4ARQ2_ARTBC_663331 and tr_A0A059JHJ6_A0A059JHJ6_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2PGK6_F2PGK6_TRIEC_559882 and tr_A0A059J694_A0A059J694_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0PF72_L0PF72_PNEJ8_1209962 and tr_A0A0W4ZVI0_A0A0W4ZVI0_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L2G810_L2G810_COLFN_1213859 and tr_T0L2Q9_T0L2Q9_COLGC_1237896 are exactly identical! WARNING: Sequences tr_L2GF04_L2GF04_COLFN_1213859 and tr_T0KJB2_T0KJB2_COLGC_1237896 are exactly identical! WARNING: Sequences tr_A0A337SJJ1_A0A337SJJ1_FELCA_9685 and tr_A0A2U3WFZ0_A0A2U3WFZ0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M2UF26_M2UF26_COCH5_701091 and tr_W6XQ57_W6XQ57_COCCA_930089 are exactly identical! WARNING: Sequences tr_U5H5W1_U5H5W1_USTV1_683840 and tr_A0A2X0MRI4_A0A2X0MRI4_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2WXT5_V2WXT5_MONRO_1381753 and tr_A0A0W0G2V7_A0A0W0G2V7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PU56_W2PU56_PHYPN_761204 and tr_A0A0W8DGL2_A0A0W8DGL2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PU56_W2PU56_PHYPN_761204 and tr_W2KMW5_W2KMW5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015KE57_A0A015KE57_9GLOM_1432141 and tr_A0A2H5S4J4_A0A2H5S4J4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044T7Y0_A0A044T7Y0_ONCVO_6282 and tr_A0A182DZF9_A0A182DZF9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A094E610_A0A094E610_9PEZI_1420912 and tr_A0A1B8GJ74_A0A1B8GJ74_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094E6M2_A0A094E6M2_9PEZI_1420912 and tr_A0A1B8G8K7_A0A1B8G8K7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8U2H5_A0A0F8U2H5_9EURO_308745 and tr_A0A2T5LXY8_A0A2T5LXY8_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0F8UTH1_A0A0F8UTH1_9EURO_308745 and tr_A0A2T5M5D8_A0A2T5M5D8_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A100I935_A0A100I935_ASPNG_5061 and tr_A0A1L9N8A9_A0A1L9N8A9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A166QHZ8_A0A166QHZ8_9PEZI_708197 and tr_A0A167C3F4_A0A167C3F4_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A2S7Q8C4_A0A2S7Q8C4_9HELO_2070414 and tr_A0A2S7R4X7_A0A2S7R4X7_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2U4BCK8_A0A2U4BCK8_TURTR_9739 and tr_A0A2Y9F8U9_A0A2Y9F8U9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A319CBK1_A0A319CBK1_9EURO_1448315 and tr_A0A2V5H4A5_A0A2V5H4A5_9EURO_1450538 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_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.raxml.reduced.phy Alignment comprises 1 partitions and 736 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 736 Gaps: 10.05 % Invariant sites: 2.99 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.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_040621/phylogeny-snakemake/results/O00429/3_mltree/O00429.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 184 / 14720 [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: -201725.966749 [00:00:00 -201725.966749] Initial branch length optimization [00:00:01 -201298.692555] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -200432.505210 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.298859,0.207369) (0.260649,0.299180) (0.238750,1.047706) (0.201743,3.023186) 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_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O00429/4_raxmlng_ancestral/O00429.raxml.log Analysis started: 25-Jun-2021 07:35:59 / finished: 25-Jun-2021 07:36:47 Elapsed time: 48.120 seconds