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 03-Jun-2021 02:37:47 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/2_msa/P50897_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/3_mltree/P50897.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/4_raxmlng_ancestral/P50897 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1622677067
  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/P50897/2_msa/P50897_nogap_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 306 sites

WARNING: Sequences tr_B6Q4J9_B6Q4J9_TALMQ_441960 and tr_A0A093VK79_A0A093VK79_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2W3M7_B2W3M7_PYRTR_426418 and tr_A0A2W1DQY8_A0A2W1DQY8_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_D8QMJ1_D8QMJ1_SELML_88036 and tr_D8R7P1_D8R7P1_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A2I2YE01_A0A2I2YE01_GORGO_9595 and tr_A0A2I3TV74_A0A2I3TV74_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YE01_A0A2I2YE01_GORGO_9595 and tr_A0A2R9C0Y5_A0A2R9C0Y5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29M27_Q29M27_DROPS_46245 and tr_B4G6M7_B4G6M7_DROPE_7234 are exactly identical!
WARNING: Sequences tr_F9F6Q8_F9F6Q8_FUSOF_660025 and tr_X0CMN4_X0CMN4_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_Q2UC65_Q2UC65_ASPOR_510516 and tr_A0A1S9DQU4_A0A1S9DQU4_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0IWJ7_A0A0E0IWJ7_ORYNI_4536 and tr_B8BI74_B8BI74_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0IWJ7_A0A0E0IWJ7_ORYNI_4536 and tr_A0A0E0R2J2_A0A0E0R2J2_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0IWJ7_A0A0E0IWJ7_ORYNI_4536 and tr_Q336S3_Q336S3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0K0J1N7_A0A0K0J1N7_BRUMA_6279 and tr_A0A0R3QVW2_A0A0R3QVW2_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A2QU69_A2QU69_ASPNC_425011 and tr_G3XMX7_G3XMX7_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QU69_A2QU69_ASPNC_425011 and tr_A0A319BW79_A0A319BW79_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5QL55_A0A1D5QL55_MACMU_9544 and tr_A0A0D9S7N4_A0A0D9S7N4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QL55_A0A1D5QL55_MACMU_9544 and tr_A0A2K6CP84_A0A2K6CP84_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QL55_A0A1D5QL55_MACMU_9544 and tr_A0A2K6AHB7_A0A2K6AHB7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XMQ6_G7XMQ6_ASPKW_1033177 and tr_A0A146FRU8_A0A146FRU8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_B8AL03_B8AL03_ORYSI_39946 and tr_Q10T53_Q10T53_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4NYV0_F4NYV0_BATDJ_684364 and tr_A0A177WJH7_A0A177WJH7_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1QVZ8_I1QVZ8_ORYGL_4538 and tr_A0A0D3HGN2_A0A0D3HGN2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_G2Y373_G2Y373_BOTF4_999810 and tr_M7U606_M7U606_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A080WDW6_A0A080WDW6_TRIRC_559305 and tr_A0A178EU90_A0A178EU90_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_N4UNW2_N4UNW2_FUSC1_1229664 and tr_A0A2H3TH56_A0A2H3TH56_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_V2X0U9_V2X0U9_MONRO_1381753 and tr_A0A0W0FE05_A0A0W0FE05_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2PPS2_W2PPS2_PHYPN_761204 and tr_W2G2N6_W2G2N6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015KRI0_A0A015KRI0_9GLOM_1432141 and tr_A0A2H5UI28_A0A2H5UI28_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A078GL44_A0A078GL44_BRANA_3708 and tr_A0A0D3E779_A0A0D3E779_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0V0W4I5_A0A0V0W4I5_9BILA_92179 and tr_A0A0V1KV16_A0A0V1KV16_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A2D0PV41_A0A2D0PV41_ICTPU_7998 and tr_W5UCH3_W5UCH3_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 30

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/P50897/4_raxmlng_ancestral/P50897.raxml.reduced.phy

Alignment comprises 1 partitions and 306 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 306
Gaps: 12.93 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/4_raxmlng_ancestral/P50897.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/P50897/3_mltree/P50897.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 77 / 6160
[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: -188592.334241

[00:00:00 -188592.334241] Initial branch length optimization
[00:00:00 -188132.471176] Model parameter optimization (eps = 0.100000)

[00:00:27] Tree #1, final logLikelihood: -187482.176120


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.167219,0.351374) (0.251068,0.395108) (0.302614,0.925937) (0.279099,2.013059) 
   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/P50897/4_raxmlng_ancestral/P50897.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/4_raxmlng_ancestral/P50897.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/4_raxmlng_ancestral/P50897.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P50897/4_raxmlng_ancestral/P50897.raxml.log

Analysis started: 03-Jun-2021 02:37:47 / finished: 03-Jun-2021 02:38:18

Elapsed time: 30.649 seconds

Consumed energy: 2.122 Wh