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 01-Jul-2021 12:27:46 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/2_msa/Q9Y2I8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/2_msa/Q9Y2I8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 446 taxa and 328 sites

WARNING: Sequences tr_B4QUE5_B4QUE5_DROSI_7240 and tr_Q9VE73_Q9VE73_DROME_7227 are exactly identical!
WARNING: Sequences tr_E1C008_E1C008_CHICK_9031 and tr_G3UTJ8_G3UTJ8_MELGA_9103 are exactly identical!
WARNING: Sequences tr_B4JP78_B4JP78_DROGR_7222 and tr_B4K1U9_B4K1U9_DROGR_7222 are exactly identical!
WARNING: Sequences tr_A0A2I3GEP3_A0A2I3GEP3_NOMLE_61853 and tr_G3S190_G3S190_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GEP3_A0A2I3GEP3_NOMLE_61853 and sp_Q5R650_WDR37_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3GEP3_A0A2I3GEP3_NOMLE_61853 and tr_K7BL02_K7BL02_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GEP3_A0A2I3GEP3_NOMLE_61853 and tr_A0A2R8ZMD1_A0A2R8ZMD1_PANPA_9597 are exactly identical!
WARNING: Sequences sp_Q5REE6_WDR12_PONAB_9601 and sp_Q9GZL7_WDR12_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q299M0_Q299M0_DROPS_46245 and tr_B4G5D9_B4G5D9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_G7N1H3_G7N1H3_MACMU_9544 and tr_G7PE37_G7PE37_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7N1H3_G7N1H3_MACMU_9544 and tr_A0A096P375_A0A096P375_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7N1H3_G7N1H3_MACMU_9544 and tr_A0A0D9RNL0_A0A0D9RNL0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7N1H3_G7N1H3_MACMU_9544 and tr_A0A1U7TV65_A0A1U7TV65_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G7N1H3_G7N1H3_MACMU_9544 and tr_A0A2K6CIS1_A0A2K6CIS1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0YRF5_H0YRF5_TAEGU_59729 and tr_A0A218UR72_A0A218UR72_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A8X840_A8X840_CAEBR_6238 and tr_A0A2G5URY7_A0A2G5URY7_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_G1L578_G1L578_AILME_9646 and tr_A0A2U3ZVV6_A0A2U3ZVV6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1L578_G1L578_AILME_9646 and tr_A0A2U3XIJ8_A0A2U3XIJ8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G1L578_G1L578_AILME_9646 and tr_A0A384D225_A0A384D225_URSMA_29073 are exactly identical!
WARNING: Sequences tr_U5H0S6_U5H0S6_USTV1_683840 and tr_A0A238FJ81_A0A238FJ81_9BASI_269621 are exactly identical!
WARNING: Sequences tr_U5H0S6_U5H0S6_USTV1_683840 and tr_A0A2X0P054_A0A2X0P054_9BASI_796604 are exactly identical!
WARNING: Sequences tr_A0A091K2S6_A0A091K2S6_EGRGA_188379 and tr_A0A091UQH9_A0A091UQH9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091K2S6_A0A091K2S6_EGRGA_188379 and tr_A0A091VL54_A0A091VL54_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A2I0MQ95_A0A2I0MQ95_COLLI_8932 and tr_A0A1V4KLR2_A0A1V4KLR2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CZI5_A0A0V1CZI5_TRIBR_45882 and tr_A0A0V0ZJL5_A0A0V0ZJL5_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0UZS1_A0A0V0UZS1_9BILA_181606 and tr_A0A0V1KVZ5_A0A0V1KVZ5_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0UZS1_A0A0V0UZS1_9BILA_181606 and tr_A0A0V1NJJ4_A0A0V1NJJ4_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0XRP0_A0A0V0XRP0_TRIPS_6337 and tr_A0A0V1MFB0_A0A0V1MFB0_9BILA_268474 are exactly identical!
WARNING: Sequences tr_A0A1S3IJ74_A0A1S3IJ74_LINUN_7574 and tr_A0A1S3K066_A0A1S3K066_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3LVJ5_A0A1S3LVJ5_SALSA_8030 and tr_A0A060W6A1_A0A060W6A1_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3RU93_A0A1S3RU93_SALSA_8030 and tr_A0A060Y0R3_A0A060Y0R3_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2D0STL6_A0A2D0STL6_ICTPU_7998 and tr_A0A2D0STL9_A0A2D0STL9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0STL6_A0A2D0STL6_ICTPU_7998 and tr_A0A2D0SU44_A0A2D0SU44_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0STL6_A0A2D0STL6_ICTPU_7998 and tr_A0A2D0SUP5_A0A2D0SUP5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4C7A0_A0A2U4C7A0_TURTR_9739 and tr_A0A2Y9LN86_A0A2Y9LN86_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4C7A0_A0A2U4C7A0_TURTR_9739 and tr_A0A2Y9T4T9_A0A2Y9T4T9_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4C7A0_A0A2U4C7A0_TURTR_9739 and tr_A0A383YXY3_A0A383YXY3_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 37

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.reduced.phy

Alignment comprises 1 partitions and 328 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 328 / 328
Gaps: 13.11 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.rba

Parallelization scheme autoconfig: 5 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 446 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 328 / 26240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -239116.456437] Initial branch length optimization
[00:00:03 -180738.550487] Model parameter optimization (eps = 10.000000)
[00:00:43 -179879.583558] AUTODETECT spr round 1 (radius: 5)
[00:01:50 -147311.720310] AUTODETECT spr round 2 (radius: 10)
[00:03:11 -120415.239648] AUTODETECT spr round 3 (radius: 15)
[00:04:39 -107952.592883] AUTODETECT spr round 4 (radius: 20)
[00:06:31 -95951.472594] AUTODETECT spr round 5 (radius: 25)
[00:09:12 -93952.938942] SPR radius for FAST iterations: 25 (autodetect)
[00:09:12 -93952.938942] Model parameter optimization (eps = 3.000000)
[00:09:44 -93747.325342] FAST spr round 1 (radius: 25)
[00:11:34 -86424.519018] FAST spr round 2 (radius: 25)
[00:12:58 -85944.719470] FAST spr round 3 (radius: 25)
[00:14:07 -85905.831805] FAST spr round 4 (radius: 25)
[00:15:05 -85892.303011] FAST spr round 5 (radius: 25)
[00:15:57 -85873.086094] FAST spr round 6 (radius: 25)
[00:16:44 -85873.075301] Model parameter optimization (eps = 1.000000)
[00:16:57 -85867.928305] SLOW spr round 1 (radius: 5)
[00:18:32 -85848.989524] SLOW spr round 2 (radius: 5)
[00:19:58 -85848.222521] SLOW spr round 3 (radius: 5)
[00:21:22 -85847.210406] SLOW spr round 4 (radius: 5)
[00:22:42 -85847.045067] SLOW spr round 5 (radius: 5)
[00:24:02 -85847.044681] SLOW spr round 6 (radius: 10)
[00:25:26 -85846.626426] SLOW spr round 7 (radius: 5)
[00:27:13 -85846.626120] SLOW spr round 8 (radius: 10)
[00:28:55 -85846.471191] SLOW spr round 9 (radius: 5)
[00:30:40 -85846.470936] SLOW spr round 10 (radius: 10)
[00:32:17 -85846.470935] SLOW spr round 11 (radius: 15)
[00:32:52] [worker #3] ML tree search #4, logLikelihood: -85841.281865
[00:34:38 -85846.470934] SLOW spr round 12 (radius: 20)
[00:37:44 -85846.470934] SLOW spr round 13 (radius: 25)
[00:40:53 -85846.470934] Model parameter optimization (eps = 0.100000)

[00:40:58] [worker #0] ML tree search #1, logLikelihood: -85846.444750

[00:40:58 -237221.942072] Initial branch length optimization
[00:41:00 -180954.547571] Model parameter optimization (eps = 10.000000)
[00:41:41 -180067.552015] AUTODETECT spr round 1 (radius: 5)
[00:42:47 -148268.796939] AUTODETECT spr round 2 (radius: 10)
[00:44:07 -119787.495067] AUTODETECT spr round 3 (radius: 15)
[00:45:05] [worker #4] ML tree search #5, logLikelihood: -85833.511700
[00:45:34 -107607.690694] AUTODETECT spr round 4 (radius: 20)
[00:47:13 -102796.414469] AUTODETECT spr round 5 (radius: 25)
[00:49:14 -96280.536872] SPR radius for FAST iterations: 25 (autodetect)
[00:49:14 -96280.536872] Model parameter optimization (eps = 3.000000)
[00:49:43 -95998.115657] FAST spr round 1 (radius: 25)
[00:51:26 -86461.310277] FAST spr round 2 (radius: 25)
[00:52:46 -85931.017511] FAST spr round 3 (radius: 25)
[00:53:07] [worker #1] ML tree search #2, logLikelihood: -85874.819288
[00:53:56 -85897.861682] FAST spr round 4 (radius: 25)
[00:54:50 -85885.522744] FAST spr round 5 (radius: 25)
[00:55:40 -85882.169197] FAST spr round 6 (radius: 25)
[00:56:27 -85882.168832] Model parameter optimization (eps = 1.000000)
[00:56:39 -85877.093826] SLOW spr round 1 (radius: 5)
[00:58:08 -85855.555466] SLOW spr round 2 (radius: 5)
[00:58:12] [worker #2] ML tree search #3, logLikelihood: -85834.020978
[00:59:33 -85848.143767] SLOW spr round 3 (radius: 5)
[01:00:53 -85848.031944] SLOW spr round 4 (radius: 5)
[01:02:12 -85848.031247] SLOW spr round 5 (radius: 10)
[01:03:32 -85847.836567] SLOW spr round 6 (radius: 5)
[01:05:19 -85846.842665] SLOW spr round 7 (radius: 5)
[01:06:51 -85846.841878] SLOW spr round 8 (radius: 10)
[01:08:20 -85846.841866] SLOW spr round 9 (radius: 15)
[01:11:05 -85846.023278] SLOW spr round 10 (radius: 5)
[01:12:56 -85845.128347] SLOW spr round 11 (radius: 5)
[01:14:29 -85845.128141] SLOW spr round 12 (radius: 10)
[01:15:59 -85845.128140] SLOW spr round 13 (radius: 15)
[01:17:43] [worker #3] ML tree search #9, logLikelihood: -85867.192052
[01:18:42 -85845.128140] SLOW spr round 14 (radius: 20)
[01:22:07 -85845.128140] SLOW spr round 15 (radius: 25)
[01:22:25] [worker #4] ML tree search #10, logLikelihood: -85849.169535
[01:25:25 -85845.128140] Model parameter optimization (eps = 0.100000)

[01:25:34] [worker #0] ML tree search #6, logLikelihood: -85845.015053

[01:25:34 -239207.527218] Initial branch length optimization
[01:25:37 -180529.262443] Model parameter optimization (eps = 10.000000)
[01:26:20 -179699.614560] AUTODETECT spr round 1 (radius: 5)
[01:27:05] [worker #1] ML tree search #7, logLikelihood: -85828.064329
[01:27:27 -146838.281391] AUTODETECT spr round 2 (radius: 10)
[01:28:44 -117190.264066] AUTODETECT spr round 3 (radius: 15)
[01:30:10] [worker #2] ML tree search #8, logLikelihood: -85842.630926
[01:30:16 -101337.647291] AUTODETECT spr round 4 (radius: 20)
[01:32:12 -94222.374516] AUTODETECT spr round 5 (radius: 25)
[01:34:26 -92361.519897] SPR radius for FAST iterations: 25 (autodetect)
[01:34:26 -92361.519897] Model parameter optimization (eps = 3.000000)
[01:34:52 -92137.611601] FAST spr round 1 (radius: 25)
[01:36:41 -86134.607177] FAST spr round 2 (radius: 25)
[01:38:04 -85912.199286] FAST spr round 3 (radius: 25)
[01:39:11 -85881.069015] FAST spr round 4 (radius: 25)
[01:40:07 -85867.279651] FAST spr round 5 (radius: 25)
[01:40:59 -85863.858332] FAST spr round 6 (radius: 25)
[01:41:47 -85862.999328] FAST spr round 7 (radius: 25)
[01:42:35 -85862.700165] FAST spr round 8 (radius: 25)
[01:43:21 -85862.700110] Model parameter optimization (eps = 1.000000)
[01:43:33 -85860.001677] SLOW spr round 1 (radius: 5)
[01:45:02 -85848.437416] SLOW spr round 2 (radius: 5)
[01:46:28 -85846.609263] SLOW spr round 3 (radius: 5)
[01:47:50 -85846.609185] SLOW spr round 4 (radius: 10)
[01:49:12 -85844.737959] SLOW spr round 5 (radius: 5)
[01:51:00 -85844.056707] SLOW spr round 6 (radius: 5)
[01:52:32 -85844.056513] SLOW spr round 7 (radius: 10)
[01:53:48] [worker #3] ML tree search #14, logLikelihood: -85855.180645
[01:54:00 -85843.901537] SLOW spr round 8 (radius: 5)
[01:55:50 -85842.013415] SLOW spr round 9 (radius: 5)
[01:57:22 -85842.013403] SLOW spr round 10 (radius: 10)
[01:58:49 -85842.013403] SLOW spr round 11 (radius: 15)
[01:59:18] [worker #4] ML tree search #15, logLikelihood: -85864.185787
[02:01:16 -85842.013403] SLOW spr round 12 (radius: 20)
[02:04:32 -85842.013403] SLOW spr round 13 (radius: 25)
[02:07:56 -85842.013403] Model parameter optimization (eps = 0.100000)

[02:08:02] [worker #0] ML tree search #11, logLikelihood: -85841.952035

[02:08:02 -239262.610801] Initial branch length optimization
[02:08:04 -180487.754968] Model parameter optimization (eps = 10.000000)
[02:08:21] [worker #2] ML tree search #13, logLikelihood: -85864.476666
[02:08:52 -179585.545000] AUTODETECT spr round 1 (radius: 5)
[02:09:57 -145861.751684] AUTODETECT spr round 2 (radius: 10)
[02:11:19 -120896.437540] AUTODETECT spr round 3 (radius: 15)
[02:12:53 -106270.509857] AUTODETECT spr round 4 (radius: 20)
[02:14:37 -95868.862221] AUTODETECT spr round 5 (radius: 25)
[02:16:35 -93607.870672] SPR radius for FAST iterations: 25 (autodetect)
[02:16:35 -93607.870672] Model parameter optimization (eps = 3.000000)
[02:17:01 -93385.906616] FAST spr round 1 (radius: 25)
[02:18:39 -86301.290723] FAST spr round 2 (radius: 25)
[02:19:48] [worker #1] ML tree search #12, logLikelihood: -85867.525923
[02:19:53 -85962.421428] FAST spr round 3 (radius: 25)
[02:20:58 -85918.110309] FAST spr round 4 (radius: 25)
[02:21:55 -85902.842926] FAST spr round 5 (radius: 25)
[02:22:44 -85902.050109] FAST spr round 6 (radius: 25)
[02:23:33 -85901.374323] FAST spr round 7 (radius: 25)
[02:24:21 -85901.373700] Model parameter optimization (eps = 1.000000)
[02:24:35 -85896.864603] SLOW spr round 1 (radius: 5)
[02:26:04 -85871.083878] SLOW spr round 2 (radius: 5)
[02:27:29 -85870.530897] SLOW spr round 3 (radius: 5)
[02:28:51 -85870.524746] SLOW spr round 4 (radius: 10)
[02:29:58] [worker #3] ML tree search #19, logLikelihood: -85851.972110
[02:30:16 -85865.794409] SLOW spr round 5 (radius: 5)
[02:32:03 -85864.944740] SLOW spr round 6 (radius: 5)
[02:33:36 -85864.944691] SLOW spr round 7 (radius: 10)
[02:35:04 -85864.944690] SLOW spr round 8 (radius: 15)
[02:37:36 -85864.944690] SLOW spr round 9 (radius: 20)
[02:40:47 -85864.944690] SLOW spr round 10 (radius: 25)
[02:44:02 -85864.944690] Model parameter optimization (eps = 0.100000)

[02:44:15] [worker #0] ML tree search #16, logLikelihood: -85864.394855

[02:49:39] [worker #4] ML tree search #20, logLikelihood: -85843.829513
[02:59:24] [worker #2] ML tree search #18, logLikelihood: -85868.226943
[03:13:51] [worker #1] ML tree search #17, logLikelihood: -85837.309371

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.185367,0.471852) (0.276894,0.646527) (0.396874,1.119366) (0.140865,2.053508) 
   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: -85828.064329

AIC score: 173446.128658 / AICc score: 1777286.128658 / BIC score: 176840.875837
Free parameters (model + branch lengths): 895

WARNING: Number of free parameters (K=895) is larger than alignment size (n=328).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 67 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y2I8/3_mltree/Q9Y2I8.raxml.log

Analysis started: 01-Jul-2021 12:27:46 / finished: 01-Jul-2021 15:41:38

Elapsed time: 11631.107 seconds

Consumed energy: 831.419 Wh (= 4 km in an electric car, or 21 km with an e-scooter!)