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 10-Jul-2021 06:09:45 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/2_msa/A6NHQ4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/2_msa/A6NHQ4_trimmed_msa.fasta
[00:00:00] Loaded alignment with 116 taxa and 293 sites

WARNING: Sequences tr_H2N9X9_H2N9X9_PONAB_9601 and tr_F7H1M0_F7H1M0_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2QCS9_H2QCS9_PANTR_9598 and sp_A6NHQ4_EPOP_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F7ABR5_F7ABR5_MACMU_9544 and tr_A0A2K5L251_A0A2K5L251_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7ABR5_F7ABR5_MACMU_9544 and tr_A0A2K6B3L5_A0A2K6B3L5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2U3VEC2_A0A2U3VEC2_ODORO_9708 and tr_A0A2U3XEH4_A0A2U3XEH4_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 5

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.reduced.phy

Alignment comprises 1 partitions and 293 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 293 / 293
Gaps: 7.68 %
Invariant sites: 0.68 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.rba

Parallelization scheme autoconfig: 6 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 116 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 293 / 23440
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -53459.428177] Initial branch length optimization
[00:00:00 -39205.341888] Model parameter optimization (eps = 10.000000)
[00:00:08 -39086.288200] AUTODETECT spr round 1 (radius: 5)
[00:00:13 -25687.458586] AUTODETECT spr round 2 (radius: 10)
[00:00:21 -21972.880570] AUTODETECT spr round 3 (radius: 15)
[00:00:30 -19577.540441] AUTODETECT spr round 4 (radius: 20)
[00:00:38 -19527.277277] AUTODETECT spr round 5 (radius: 25)
[00:00:44 -19527.274042] SPR radius for FAST iterations: 20 (autodetect)
[00:00:44 -19527.274042] Model parameter optimization (eps = 3.000000)
[00:00:55 -19425.721896] FAST spr round 1 (radius: 20)
[00:01:03 -17920.036566] FAST spr round 2 (radius: 20)
[00:01:09 -17882.878997] FAST spr round 3 (radius: 20)
[00:01:14 -17881.437458] FAST spr round 4 (radius: 20)
[00:01:19 -17881.436383] Model parameter optimization (eps = 1.000000)
[00:01:24 -17875.604335] SLOW spr round 1 (radius: 5)
[00:01:35 -17871.914925] SLOW spr round 2 (radius: 5)
[00:01:47 -17868.294166] SLOW spr round 3 (radius: 5)
[00:01:58 -17868.293757] SLOW spr round 4 (radius: 10)
[00:02:08 -17868.293751] SLOW spr round 5 (radius: 15)
[00:02:22 -17868.293750] SLOW spr round 6 (radius: 20)
[00:02:32] [worker #1] ML tree search #2, logLikelihood: -17864.538518
[00:02:36 -17868.293750] SLOW spr round 7 (radius: 25)
[00:02:38] [worker #5] ML tree search #6, logLikelihood: -17864.433870
[00:02:40] [worker #3] ML tree search #4, logLikelihood: -17864.433747
[00:02:43] [worker #2] ML tree search #3, logLikelihood: -17864.538683
[00:02:46 -17868.293750] Model parameter optimization (eps = 0.100000)

[00:02:47] [worker #0] ML tree search #1, logLikelihood: -17868.235031

[00:02:47 -54150.567026] Initial branch length optimization
[00:02:48 -39764.834290] Model parameter optimization (eps = 10.000000)
[00:02:51] [worker #4] ML tree search #5, logLikelihood: -17864.434292
[00:02:55 -39629.319380] AUTODETECT spr round 1 (radius: 5)
[00:03:01 -24391.656061] AUTODETECT spr round 2 (radius: 10)
[00:03:10 -19747.086687] AUTODETECT spr round 3 (radius: 15)
[00:03:20 -19080.293313] AUTODETECT spr round 4 (radius: 20)
[00:03:30 -19079.658232] AUTODETECT spr round 5 (radius: 25)
[00:03:36 -19079.639677] SPR radius for FAST iterations: 20 (autodetect)
[00:03:36 -19079.639677] Model parameter optimization (eps = 3.000000)
[00:03:44 -18988.848941] FAST spr round 1 (radius: 20)
[00:03:54 -17921.801045] FAST spr round 2 (radius: 20)
[00:04:00 -17896.007399] FAST spr round 3 (radius: 20)
[00:04:05 -17896.005816] Model parameter optimization (eps = 1.000000)
[00:04:09 -17885.235540] SLOW spr round 1 (radius: 5)
[00:04:23 -17873.680202] SLOW spr round 2 (radius: 5)
[00:04:35 -17867.651375] SLOW spr round 3 (radius: 5)
[00:04:46 -17864.705487] SLOW spr round 4 (radius: 5)
[00:04:57 -17864.705306] SLOW spr round 5 (radius: 10)
[00:05:07 -17864.705197] SLOW spr round 6 (radius: 15)
[00:05:13] [worker #2] ML tree search #9, logLikelihood: -17868.235012
[00:05:21] [worker #5] ML tree search #12, logLikelihood: -17864.677623
[00:05:21 -17864.705124] SLOW spr round 7 (radius: 20)
[00:05:22] [worker #3] ML tree search #10, logLikelihood: -17864.538760
[00:05:35 -17864.705074] SLOW spr round 8 (radius: 25)
[00:05:38] [worker #4] ML tree search #11, logLikelihood: -17864.433574
[00:05:45 -17864.705033] Model parameter optimization (eps = 0.100000)

[00:05:47] [worker #0] ML tree search #7, logLikelihood: -17864.528121

[00:05:47 -51281.364482] Initial branch length optimization
[00:05:48 -37937.861957] Model parameter optimization (eps = 10.000000)
[00:05:55 -37809.875783] AUTODETECT spr round 1 (radius: 5)
[00:06:00] [worker #1] ML tree search #8, logLikelihood: -17868.306611
[00:06:01 -27274.226588] AUTODETECT spr round 2 (radius: 10)
[00:06:09 -21144.032933] AUTODETECT spr round 3 (radius: 15)
[00:06:19 -19779.844817] AUTODETECT spr round 4 (radius: 20)
[00:06:28 -19752.175512] AUTODETECT spr round 5 (radius: 25)
[00:06:35 -19752.123947] SPR radius for FAST iterations: 20 (autodetect)
[00:06:35 -19752.123947] Model parameter optimization (eps = 3.000000)
[00:06:43 -19629.307344] FAST spr round 1 (radius: 20)
[00:06:49 -18091.195773] FAST spr round 2 (radius: 20)
[00:06:56 -17881.096254] FAST spr round 3 (radius: 20)
[00:07:01 -17874.983647] FAST spr round 4 (radius: 20)
[00:07:06 -17872.522897] FAST spr round 5 (radius: 20)
[00:07:10 -17872.522616] Model parameter optimization (eps = 1.000000)
[00:07:15 -17866.592500] SLOW spr round 1 (radius: 5)
[00:07:27 -17864.457286] SLOW spr round 2 (radius: 5)
[00:07:38 -17864.456684] SLOW spr round 3 (radius: 10)
[00:07:49 -17864.456420] SLOW spr round 4 (radius: 15)
[00:07:57] [worker #2] ML tree search #15, logLikelihood: -17864.538625
[00:07:59] [worker #5] ML tree search #18, logLikelihood: -17868.234464
[00:08:02 -17864.456242] SLOW spr round 5 (radius: 20)
[00:08:16] [worker #3] ML tree search #16, logLikelihood: -17864.538576
[00:08:17 -17864.456121] SLOW spr round 6 (radius: 25)
[00:08:22] [worker #4] ML tree search #17, logLikelihood: -17864.433822
[00:08:27 -17864.456037] Model parameter optimization (eps = 0.100000)

[00:08:29] [worker #0] ML tree search #13, logLikelihood: -17864.433734

[00:08:29 -51540.973254] Initial branch length optimization
[00:08:29 -38988.290466] Model parameter optimization (eps = 10.000000)
[00:08:36 -38801.312731] AUTODETECT spr round 1 (radius: 5)
[00:08:42 -27859.876400] AUTODETECT spr round 2 (radius: 10)
[00:08:50 -20100.243615] AUTODETECT spr round 3 (radius: 15)
[00:09:00 -19683.809050] AUTODETECT spr round 4 (radius: 20)
[00:09:09 -19683.797034] SPR radius for FAST iterations: 15 (autodetect)
[00:09:09 -19683.797034] Model parameter optimization (eps = 3.000000)
[00:09:19 -19602.002012] FAST spr round 1 (radius: 15)
[00:09:26] [worker #1] ML tree search #14, logLikelihood: -17868.234750
[00:09:28 -18048.546821] FAST spr round 2 (radius: 15)
[00:09:35 -17887.839599] FAST spr round 3 (radius: 15)
[00:09:41 -17874.109000] FAST spr round 4 (radius: 15)
[00:09:45 -17874.108429] Model parameter optimization (eps = 1.000000)
[00:09:49 -17868.633589] SLOW spr round 1 (radius: 5)
[00:10:01 -17864.610886] SLOW spr round 2 (radius: 5)
[00:10:12 -17864.610122] SLOW spr round 3 (radius: 10)
[00:10:23 -17864.610077] SLOW spr round 4 (radius: 15)
[00:10:36 -17864.610067] SLOW spr round 5 (radius: 20)
[00:10:51 -17864.610066] SLOW spr round 6 (radius: 25)
[00:11:01 -17864.610066] Model parameter optimization (eps = 0.100000)

[00:11:02] [worker #0] ML tree search #19, logLikelihood: -17864.539061

[00:11:55] [worker #1] ML tree search #20, logLikelihood: -17864.677481

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.191557,0.595149) (0.109915,1.332416) (0.292222,0.583993) (0.406306,1.400144) 
   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 


Final LogLikelihood: -17864.433574

AIC score: 36198.867149 / AICc score: 38144.832061 / BIC score: 37063.707712
Free parameters (model + branch lengths): 235

WARNING: Best ML tree contains 21 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/A6NHQ4/3_mltree/A6NHQ4.raxml.log

Analysis started: 10-Jul-2021 06:09:45 / finished: 10-Jul-2021 06:21:41

Elapsed time: 715.967 seconds