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 04-Jun-2021 14:16:44 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/2_msa/Q9H2U2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/3_mltree/Q9H2U2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805404 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_020621/phylogeny-snakemake/results/Q9H2U2/2_msa/Q9H2U2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 334 sites WARNING: Sequences tr_B4QC15_B4QC15_DROSI_7240 and tr_B4IH35_B4IH35_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3RLE5_G3RLE5_GORGO_9595 and tr_H2Q212_H2Q212_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RLE5_G3RLE5_GORGO_9595 and tr_A0A2R9AJJ7_A0A2R9AJJ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8PF53_B8PF53_POSPM_561896 and tr_A0A1X6NE72_A0A1X6NE72_9APHY_670580 are exactly identical! WARNING: Sequences tr_A0A179UCU0_A0A179UCU0_BLAGS_559298 and tr_C5GHC7_C5GHC7_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3RXN7_A0A2I3RXN7_PANTR_9598 and tr_A0A2R9CH95_A0A2R9CH95_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QPZ6_H2QPZ6_PANTR_9598 and sp_Q9H2U2_IPYR2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QPZ6_H2QPZ6_PANTR_9598 and tr_A0A2R9CNU0_A0A2R9CNU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_E9EW13_E9EW13_METRA_655844 and tr_A0A0B4IAJ2_A0A0B4IAJ2_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EW13_E9EW13_METRA_655844 and tr_A0A0D9P2M4_A0A0D9P2M4_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4UFJ6_J4UFJ6_BEAB2_655819 and tr_A0A0A2WF44_A0A0A2WF44_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A2QER8_A2QER8_ASPNC_425011 and tr_G3Y1W7_G3Y1W7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QER8_A2QER8_ASPNC_425011 and tr_A0A319AZU5_A0A319AZU5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7GWS5_F7GWS5_MACMU_9544 and tr_A0A096P4X1_A0A096P4X1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GWS5_F7GWS5_MACMU_9544 and tr_A0A2K5L3N8_A0A2K5L3N8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GWS5_F7GWS5_MACMU_9544 and tr_A0A2K6AAV8_A0A2K6AAV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7XC47_G7XC47_ASPKW_1033177 and tr_A0A146FDD9_A0A146FDD9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XC47_G7XC47_ASPKW_1033177 and tr_A0A317V2H5_A0A317V2H5_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F4P1P1_F4P1P1_BATDJ_684364 and tr_A0A177WNI8_A0A177WNI8_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9XC11_F9XC11_ZYMTI_336722 and tr_A0A1X7RTU3_A0A1X7RTU3_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2T0R6_F2T0R6_TRIRC_559305 and tr_A0A178EWA6_A0A178EWA6_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G0R715_G0R715_HYPJQ_431241 and tr_A0A2T4CD97_A0A2T4CD97_TRILO_983965 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_A0A0D2X9J5_A0A0D2X9J5_FUSO4_426428 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_N4TTW5_N4TTW5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_X0C1T0_X0C1T0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_A0A2H3SWH5_A0A2H3SWH5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_A0A2H3I7L3_A0A2H3I7L3_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W7LPB0_W7LPB0_GIBM7_334819 and tr_A0A2K0W510_A0A2K0W510_GIBNY_42673 are exactly identical! WARNING: Sequences tr_L2FTT5_L2FTT5_COLFN_1213859 and tr_T0LE87_T0LE87_COLGC_1237896 are exactly identical! WARNING: Sequences tr_U5H4G5_U5H4G5_USTV1_683840 and tr_A0A2X0MYP8_A0A2X0MYP8_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A015JTX0_A0A015JTX0_9GLOM_1432141 and tr_A0A2I1G1G8_A0A2I1G1G8_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A094CZS8_A0A094CZS8_9PEZI_1420910 and tr_A0A1B8DNL2_A0A1B8DNL2_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A0F8WG89_A0A0F8WG89_9EURO_308745 and tr_A0A2T5LMP1_A0A2T5LMP1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0N1J319_A0A0N1J319_FUSLA_179993 and tr_A0A1B8B1F8_A0A1B8B1F8_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0A1MKK1_A0A0A1MKK1_9FUNG_58291 and tr_A0A367JC01_A0A367JC01_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1CKD8_A0A0V1CKD8_TRIBR_45882 and tr_A0A0V0WIS8_A0A0V0WIS8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CKD8_A0A0V1CKD8_TRIBR_45882 and tr_A0A0V0UBI5_A0A0V0UBI5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100IU80_A0A100IU80_ASPNG_5061 and tr_A0A1L9N988_A0A1L9N988_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1C3YI53_A0A1C3YI53_GIBZE_229533 and tr_A0A2T4H8K6_A0A2T4H8K6_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A2S7Q307_A0A2S7Q307_9HELO_2070414 and tr_A0A2S7QKY8_A0A2S7QKY8_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A319DJV8_A0A319DJV8_9EURO_1448315 and tr_A0A2V5IAL6_A0A2V5IAL6_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319DJV8_A0A319DJV8_9EURO_1448315 and tr_A0A2V5GR75_A0A2V5GR75_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.raxml.reduced.phy Alignment comprises 1 partitions and 334 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 334 Gaps: 17.81 % Invariant sites: 0.60 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.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_020621/phylogeny-snakemake/results/Q9H2U2/3_mltree/Q9H2U2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 84 / 6720 [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: -130536.982264 [00:00:00 -130536.982264] Initial branch length optimization [00:00:01 -121553.347691] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -121233.488213 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.180861,0.319199) (0.235474,0.405357) (0.266354,0.760220) (0.317310,2.030601) 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_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9H2U2/4_raxmlng_ancestral/Q9H2U2.raxml.log Analysis started: 04-Jun-2021 14:16:44 / finished: 04-Jun-2021 14:17:12 Elapsed time: 27.371 seconds