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 14:02:40 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/2_msa/Q59H18_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/3_mltree/Q59H18.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/4_raxmlng_ancestral/Q59H18 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804560 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/Q59H18/2_msa/Q59H18_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 835 sites WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_A2XXC2_A2XXC2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_I1PPK1_I1PPK1_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H5R9_A0A0E0H5R9_ORYNI_4536 and tr_Q8GV29_Q8GV29_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H803_A0A0E0H803_ORYNI_4536 and tr_A0A0D9ZSQ5_A0A0D9ZSQ5_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HN24_A0A0E0HN24_ORYNI_4536 and tr_A0A0D3GEJ8_A0A0D3GEJ8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_Q6DTV6_Q6DTV6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_I1QGL4_I1QGL4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_A0A0E0QFT0_A0A0E0QFT0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_A0A0D3GXK0_A0A0D3GXK0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0I705_A0A0E0I705_ORYNI_4536 and tr_Q8GV30_Q8GV30_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2WJR5_A2WJR5_ORYSI_39946 and tr_I1NJK5_I1NJK5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2WJR5_A2WJR5_ORYSI_39946 and tr_A0A0E0MQD6_A0A0E0MQD6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2WJR5_A2WJR5_ORYSI_39946 and tr_A0A0D3EIQ3_A0A0D3EIQ3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2Z3N4_A2Z3N4_ORYSI_39946 and tr_A0A0E0B5Z4_A0A0E0B5Z4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2Z3N4_A2Z3N4_ORYSI_39946 and tr_Q7XXN2_Q7XXN2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8B4X3_B8B4X3_ORYSI_39946 and tr_I1QCI4_I1QCI4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_I1QQW9_I1QQW9_ORYGL_4538 and tr_A0A0D3H9K3_A0A0D3H9K3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1R4C3_I1R4C3_ORYGL_4538 and tr_A0A0E0RE68_A0A0E0RE68_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1R4C3_I1R4C3_ORYGL_4538 and tr_Q2QXA8_Q2QXA8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0DZH4_A0A0E0DZH4_9ORYZ_40149 and tr_A0A0E0A762_A0A0E0A762_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_M4D446_M4D446_BRARP_51351 and tr_A0A078GSW5_A0A078GSW5_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2PYG7_W2PYG7_PHYPN_761204 and tr_A0A0W8C9C0_A0A0W8C9C0_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PYG7_W2PYG7_PHYPN_761204 and tr_W2IMN9_W2IMN9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2Q694_W2Q694_PHYPN_761204 and tr_A0A0W8CIY8_A0A0W8CIY8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A3B6LRR0_A0A3B6LRR0_WHEAT_4565 and tr_A0A3B6MVS1_A0A3B6MVS1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067FLE1_A0A067FLE1_CITSI_2711 and tr_V4U926_V4U926_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FVA6_A0A067FVA6_CITSI_2711 and tr_V4UBC1_V4UBC1_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078G3J2_A0A078G3J2_BRANA_3708 and tr_A0A0D3E4U5_A0A0D3E4U5_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078HI36_A0A078HI36_BRANA_3708 and tr_A0A0D3BM14_A0A0D3BM14_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JCE5_A0A078JCE5_BRANA_3708 and tr_A0A0D3BVQ9_A0A0D3BVQ9_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0LML1_A0A0A0LML1_CUCSA_3659 and tr_A0A1S3BQ63_A0A1S3BQ63_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4W9U6_V4W9U6_9ROSI_85681 and tr_A0A2H5N6A2_A0A2H5N6A2_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2M4W2_A0A0D2M4W2_GOSRA_29730 and tr_A0A1U8LM17_A0A1U8LM17_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2NCP6_A0A0D2NCP6_GOSRA_29730 and tr_A0A1U8JX70_A0A1U8JX70_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RH99_A0A0D2RH99_GOSRA_29730 and tr_A0A1U8NB07_A0A1U8NB07_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0L9THB5_A0A0L9THB5_PHAAN_3914 and tr_A0A1S3USP9_A0A1S3USP9_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0V0X475_A0A0V0X475_9BILA_92179 and tr_A0A0V1LTX1_A0A0V1LTX1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X475_A0A0V0X475_9BILA_92179 and tr_A0A0V1PLG4_A0A0V1PLG4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3XTN8_A0A1S3XTN8_TOBAC_4097 and tr_A0A1U7YJI0_A0A1U7YJI0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZCD7_A0A1S3ZCD7_TOBAC_4097 and tr_A0A1U7W0L8_A0A1U7W0L8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AA74_A0A1S4AA74_TOBAC_4097 and tr_A0A1U7YTV3_A0A1U7YTV3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AL66_A0A1S4AL66_TOBAC_4097 and tr_A0A1U7Y7C5_A0A1U7Y7C5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BE03_A0A1S4BE03_TOBAC_4097 and tr_A0A1U7WCE7_A0A1U7WCE7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CIV7_A0A1S4CIV7_TOBAC_4097 and tr_A0A1U7X550_A0A1U7X550_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8L8S5_A0A1U8L8S5_GOSHI_3635 and tr_A0A1U8LS64_A0A1U8LS64_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A2G2Z197_A0A2G2Z197_CAPAN_4072 and tr_A0A2G3D1K9_A0A2G3D1K9_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G2Z1K5_A0A2G2Z1K5_CAPAN_4072 and tr_A0A2G3BZP5_A0A2G3BZP5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4A3F5_A0A2U4A3F5_TURTR_9739 and tr_A0A384A6M3_A0A384A6M3_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 48 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/Q59H18/4_raxmlng_ancestral/Q59H18.raxml.reduced.phy Alignment comprises 1 partitions and 835 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 835 Gaps: 45.59 % Invariant sites: 0.48 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/4_raxmlng_ancestral/Q59H18.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/Q59H18/3_mltree/Q59H18.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 209 / 16720 [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: -209363.852380 [00:00:00 -209363.852380] Initial branch length optimization [00:00:01 -207109.264058] Model parameter optimization (eps = 0.100000) [00:01:05] Tree #1, final logLikelihood: -206455.863723 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.116552,0.297135) (0.111211,0.289704) (0.433348,0.832614) (0.338889,1.688866) 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/Q59H18/4_raxmlng_ancestral/Q59H18.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/4_raxmlng_ancestral/Q59H18.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/4_raxmlng_ancestral/Q59H18.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q59H18/4_raxmlng_ancestral/Q59H18.raxml.log Analysis started: 04-Jun-2021 14:02:40 / finished: 04-Jun-2021 14:03:53 Elapsed time: 73.264 seconds