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 14-Jul-2021 16:36:42 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/2_msa/O95202_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/2_msa/O95202_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 809 sites

WARNING: Sequences tr_B4QC06_B4QC06_DROSI_7240 and tr_B4IH25_B4IH25_DROSE_7238 are exactly identical!
WARNING: Sequences tr_J3K3R1_J3K3R1_COCIM_246410 and tr_A0A0J6YE89_A0A0J6YE89_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2WCT6_B2WCT6_PYRTR_426418 and tr_A0A2W1F4A2_A0A2W1F4A2_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_B8N047_B8N047_ASPFN_332952 and tr_Q2UPY9_Q2UPY9_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_F9G7N8_F9G7N8_FUSOF_660025 and tr_N4UDI5_N4UDI5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G7N8_F9G7N8_FUSOF_660025 and tr_A0A2H3TAT4_A0A2H3TAT4_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0E0G9P2_A0A0E0G9P2_ORYNI_4536 and tr_B8AF39_B8AF39_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0G9P2_A0A0E0G9P2_ORYNI_4536 and tr_A0A0E0NHL0_A0A0E0NHL0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0G9P2_A0A0E0G9P2_ORYNI_4536 and tr_Q6K1Y0_Q6K1Y0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0H2P0_A0A0E0H2P0_ORYNI_4536 and tr_A0A0E0PB10_A0A0E0PB10_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1P230_I1P230_ORYGL_4538 and tr_A0A0D3F7F6_A0A0D3F7F6_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PMN2_I1PMN2_ORYGL_4538 and tr_A0A0D3FXH1_A0A0D3FXH1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_B3S8Z2_B3S8Z2_TRIAD_10228 and tr_A0A369RPF2_A0A369RPF2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G3Y1V0_G3Y1V0_ASPNA_380704 and tr_A0A319ALF6_A0A319ALF6_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7PD74_G7PD74_MACFA_9541 and tr_A0A096NYL8_A0A096NYL8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PD74_G7PD74_MACFA_9541 and tr_A0A2K5YKE7_A0A2K5YKE7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_S0DQV7_S0DQV7_GIBF5_1279085 and tr_A0A365NE24_A0A365NE24_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_V2XKL8_V2XKL8_MONRO_1381753 and tr_A0A0W0FU81_A0A0W0FU81_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015JKC1_A0A015JKC1_9GLOM_1432141 and tr_A0A2I1GVI1_A0A2I1GVI1_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015JKC1_A0A015JKC1_9GLOM_1432141 and tr_U9UBL7_U9UBL7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_V4TMR6_V4TMR6_9ROSI_85681 and tr_A0A2H5P573_A0A2H5P573_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2QVJ6_A0A0D2QVJ6_GOSRA_29730 and tr_A0A1U8KSN9_A0A1U8KSN9_GOSHI_3635 are exactly identical!
WARNING: Duplicate sequences found: 22

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/O95202/3_mltree/O95202.raxml.reduced.phy

Alignment comprises 1 partitions and 809 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 809 / 809
Gaps: 29.81 %
Invariant sites: 0.62 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 203 / 16240
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1070063.556047] Initial branch length optimization
[00:00:07 -932026.439103] Model parameter optimization (eps = 10.000000)
[00:01:17 -929393.716383] AUTODETECT spr round 1 (radius: 5)
[00:04:31 -658024.253067] AUTODETECT spr round 2 (radius: 10)
[00:08:09 -478660.741228] AUTODETECT spr round 3 (radius: 15)
[00:11:59 -405731.232666] AUTODETECT spr round 4 (radius: 20)
[00:16:50 -391142.989118] AUTODETECT spr round 5 (radius: 25)
[00:21:44 -373852.844321] SPR radius for FAST iterations: 25 (autodetect)
[00:21:44 -373852.844321] Model parameter optimization (eps = 3.000000)
[00:22:21 -373323.971494] FAST spr round 1 (radius: 25)
[00:26:23 -320348.428008] FAST spr round 2 (radius: 25)
[00:29:22 -318374.713616] FAST spr round 3 (radius: 25)
[00:32:00 -318195.361057] FAST spr round 4 (radius: 25)
[00:34:24 -318167.807312] FAST spr round 5 (radius: 25)
[00:36:38 -318152.653886] FAST spr round 6 (radius: 25)
[00:38:47 -318149.689573] FAST spr round 7 (radius: 25)
[00:40:53 -318149.689348] Model parameter optimization (eps = 1.000000)
[00:41:15 -318115.809035] SLOW spr round 1 (radius: 5)
[00:44:38 -318046.330962] SLOW spr round 2 (radius: 5)
[00:47:46 -318040.508358] SLOW spr round 3 (radius: 5)
[00:50:42 -318036.471174] SLOW spr round 4 (radius: 5)
[00:53:36 -318035.491618] SLOW spr round 5 (radius: 5)
[00:56:27 -318035.491600] SLOW spr round 6 (radius: 10)
[00:59:32 -318030.386152] SLOW spr round 7 (radius: 5)
[01:03:22 -318030.386112] SLOW spr round 8 (radius: 10)
[01:06:51 -318030.386111] SLOW spr round 9 (radius: 15)
[01:10:30] [worker #1] ML tree search #2, logLikelihood: -318040.741104
[01:12:05 -318030.386110] SLOW spr round 10 (radius: 20)
[01:20:15 -318030.386109] SLOW spr round 11 (radius: 25)
[01:30:30 -318030.386109] Model parameter optimization (eps = 0.100000)

[01:30:39] [worker #0] ML tree search #1, logLikelihood: -318030.204869

[01:30:40 -1072142.333043] Initial branch length optimization
[01:30:47 -931416.722385] Model parameter optimization (eps = 10.000000)
[01:31:53 -928643.016359] AUTODETECT spr round 1 (radius: 5)
[01:35:09 -650427.513937] AUTODETECT spr round 2 (radius: 10)
[01:38:44 -470538.781899] AUTODETECT spr round 3 (radius: 15)
[01:42:23 -412491.400382] AUTODETECT spr round 4 (radius: 20)
[01:47:02 -368680.480635] AUTODETECT spr round 5 (radius: 25)
[01:52:58 -366835.242822] SPR radius for FAST iterations: 25 (autodetect)
[01:52:58 -366835.242822] Model parameter optimization (eps = 3.000000)
[01:53:28 -366326.937171] FAST spr round 1 (radius: 25)
[01:57:32 -320194.687811] FAST spr round 2 (radius: 25)
[02:00:38 -318257.995304] FAST spr round 3 (radius: 25)
[02:03:22 -318162.015735] FAST spr round 4 (radius: 25)
[02:05:44 -318146.732524] FAST spr round 5 (radius: 25)
[02:07:54 -318146.732331] Model parameter optimization (eps = 1.000000)
[02:08:30 -318133.604920] SLOW spr round 1 (radius: 5)
[02:11:54 -318043.300512] SLOW spr round 2 (radius: 5)
[02:15:09 -318031.660828] SLOW spr round 3 (radius: 5)
[02:18:07 -318029.530659] SLOW spr round 4 (radius: 5)
[02:21:02 -318029.530644] SLOW spr round 5 (radius: 10)
[02:24:06 -318024.749075] SLOW spr round 6 (radius: 5)
[02:26:25] [worker #1] ML tree search #4, logLikelihood: -318027.505877
[02:27:59 -318024.749043] SLOW spr round 7 (radius: 10)
[02:31:31 -318024.749042] SLOW spr round 8 (radius: 15)
[02:36:48 -318024.749042] SLOW spr round 9 (radius: 20)
[02:44:39 -318024.749042] SLOW spr round 10 (radius: 25)
[02:57:35 -318024.749042] Model parameter optimization (eps = 0.100000)

[02:57:57] [worker #0] ML tree search #3, logLikelihood: -318024.261814

[02:57:57 -1070687.819209] Initial branch length optimization
[02:58:08 -933817.682919] Model parameter optimization (eps = 10.000000)
[02:59:16 -931022.908380] AUTODETECT spr round 1 (radius: 5)
[03:04:39 -645416.288717] AUTODETECT spr round 2 (radius: 10)
[03:11:26 -474278.701418] AUTODETECT spr round 3 (radius: 15)
[03:18:15 -409342.092443] AUTODETECT spr round 4 (radius: 20)
[03:25:46 -372658.709659] AUTODETECT spr round 5 (radius: 25)
[03:34:01 -367738.613644] SPR radius for FAST iterations: 25 (autodetect)
[03:34:01 -367738.613644] Model parameter optimization (eps = 3.000000)
[03:34:41 -367303.564635] FAST spr round 1 (radius: 25)
[03:41:05 -320013.523519] FAST spr round 2 (radius: 25)
[03:45:45 -318387.572339] FAST spr round 3 (radius: 25)
[03:48:48 -318241.867813] FAST spr round 4 (radius: 25)
[03:51:32 -318206.519553] FAST spr round 5 (radius: 25)
[03:52:36] [worker #1] ML tree search #6, logLikelihood: -318040.565494
[03:54:32 -318199.538107] FAST spr round 6 (radius: 25)
[03:56:50 -318199.538082] Model parameter optimization (eps = 1.000000)
[03:57:14 -318170.267761] SLOW spr round 1 (radius: 5)
[04:00:50 -318089.945104] SLOW spr round 2 (radius: 5)
[04:04:05 -318088.012027] SLOW spr round 3 (radius: 5)
[04:07:14 -318088.009780] SLOW spr round 4 (radius: 10)
[04:14:57 -318063.161440] SLOW spr round 5 (radius: 5)
[04:25:03 -318035.532250] SLOW spr round 6 (radius: 5)
[04:32:15 -318027.232873] SLOW spr round 7 (radius: 5)
[04:37:52 -318024.553462] SLOW spr round 8 (radius: 5)
[04:43:08 -318024.553461] SLOW spr round 9 (radius: 10)
[04:49:56 -318023.835325] SLOW spr round 10 (radius: 5)
[04:57:07 -318021.152189] SLOW spr round 11 (radius: 5)
[05:04:17 -318021.152103] SLOW spr round 12 (radius: 10)
[05:09:58 -318021.152103] SLOW spr round 13 (radius: 15)
[05:19:39 -318021.152103] SLOW spr round 14 (radius: 20)
[05:29:12 -318021.152103] SLOW spr round 15 (radius: 25)
[05:41:12 -318021.152103] Model parameter optimization (eps = 0.100000)

[05:41:30] [worker #0] ML tree search #5, logLikelihood: -318020.865394

[05:41:30 -1066931.008183] Initial branch length optimization
[05:41:37 -929904.601520] Model parameter optimization (eps = 10.000000)
[05:42:42 -927262.690657] AUTODETECT spr round 1 (radius: 5)
[05:47:48 -642866.781743] AUTODETECT spr round 2 (radius: 10)
[05:53:16 -485194.499893] AUTODETECT spr round 3 (radius: 15)
[05:59:21 -410850.688713] AUTODETECT spr round 4 (radius: 20)
[06:05:58 -377500.314732] AUTODETECT spr round 5 (radius: 25)
[06:13:37 -368988.959341] SPR radius for FAST iterations: 25 (autodetect)
[06:13:37 -368988.959341] Model parameter optimization (eps = 3.000000)
[06:14:18 -368550.217600] FAST spr round 1 (radius: 25)
[06:20:09 -321287.749467] FAST spr round 2 (radius: 25)
[06:24:44 -318304.040377] FAST spr round 3 (radius: 25)
[06:28:22 -318161.809824] FAST spr round 4 (radius: 25)
[06:33:27 -318131.238138] FAST spr round 5 (radius: 25)
[06:36:29 -318126.423375] FAST spr round 6 (radius: 25)
[06:37:18] [worker #1] ML tree search #8, logLikelihood: -318021.761595
[06:39:40 -318126.423337] Model parameter optimization (eps = 1.000000)
[06:40:08 -318111.450804] SLOW spr round 1 (radius: 5)
[06:54:24 -318038.753362] SLOW spr round 2 (radius: 5)
[07:03:54 -318032.364678] SLOW spr round 3 (radius: 5)
[07:21:50 -318032.364572] SLOW spr round 4 (radius: 10)
[07:44:59 -318032.364569] SLOW spr round 5 (radius: 15)
[07:50:40 -318032.364569] SLOW spr round 6 (radius: 20)
[08:36:04] [worker #1] ML tree search #10, logLikelihood: -318037.212569
[09:01:10 -318032.364569] SLOW spr round 7 (radius: 25)
[10:14:42 -318032.364569] Model parameter optimization (eps = 0.100000)

[10:15:51] [worker #0] ML tree search #7, logLikelihood: -318032.209551

[10:15:51 -1068841.747391] Initial branch length optimization
[10:21:45 -932656.848777] Model parameter optimization (eps = 10.000000)
[10:24:47 -929863.725283] AUTODETECT spr round 1 (radius: 5)
[10:43:48 -645577.779689] AUTODETECT spr round 2 (radius: 10)
[10:59:30 -485487.931658] AUTODETECT spr round 3 (radius: 15)
[11:08:14 -426969.438081] AUTODETECT spr round 4 (radius: 20)
[11:17:02 -382649.807793] AUTODETECT spr round 5 (radius: 25)
[11:23:46 -375727.051296] SPR radius for FAST iterations: 25 (autodetect)
[11:23:46 -375727.051296] Model parameter optimization (eps = 3.000000)
[11:23:57 -375723.849173] FAST spr round 1 (radius: 25)
[11:29:43 -320900.147657] FAST spr round 2 (radius: 25)
[11:34:25 -318766.062503] FAST spr round 3 (radius: 25)
[11:38:11 -318643.367330] FAST spr round 4 (radius: 25)
[11:41:38 -318609.022303] FAST spr round 5 (radius: 25)
[11:44:53 -318603.807114] FAST spr round 6 (radius: 25)
[11:47:49 -318603.807088] Model parameter optimization (eps = 1.000000)
[11:48:25 -318116.062902] SLOW spr round 1 (radius: 5)
[11:54:13 -318024.891689] SLOW spr round 2 (radius: 5)
[11:59:23 -318019.032823] SLOW spr round 3 (radius: 5)
[12:04:23 -318019.032781] SLOW spr round 4 (radius: 10)
[12:11:14 -318019.032768] SLOW spr round 5 (radius: 15)
[12:22:04 -318019.032762] SLOW spr round 6 (radius: 20)
[12:32:53] [worker #1] ML tree search #12, logLikelihood: -318019.602331
[13:16:26 -318019.032759] SLOW spr round 7 (radius: 25)
[13:37:05 -318019.032757] Model parameter optimization (eps = 0.100000)

[13:37:15] [worker #0] ML tree search #9, logLikelihood: -318018.959814

[13:37:15 -1064431.655093] Initial branch length optimization
[13:37:27 -926626.852614] Model parameter optimization (eps = 10.000000)
[13:38:52 -924144.070177] AUTODETECT spr round 1 (radius: 5)
[13:43:45 -647682.582797] AUTODETECT spr round 2 (radius: 10)
[13:49:20 -482761.957151] AUTODETECT spr round 3 (radius: 15)
[13:54:06 -419608.456531] AUTODETECT spr round 4 (radius: 20)
[14:07:04 -381377.127567] AUTODETECT spr round 5 (radius: 25)
[14:14:21 -369088.484838] SPR radius for FAST iterations: 25 (autodetect)
[14:14:21 -369088.484838] Model parameter optimization (eps = 3.000000)
[14:14:56 -368657.028662] FAST spr round 1 (radius: 25)
[14:20:56 -320065.856620] FAST spr round 2 (radius: 25)
[14:26:40 -318298.906682] FAST spr round 3 (radius: 25)
[14:31:36 -318189.071949] FAST spr round 4 (radius: 25)
[14:35:58 -318170.170311] FAST spr round 5 (radius: 25)
[14:38:55 -318170.170046] Model parameter optimization (eps = 1.000000)
[14:39:18 -318141.606242] SLOW spr round 1 (radius: 5)
[14:44:43 -318053.276705] SLOW spr round 2 (radius: 5)
[14:48:54 -318029.095735] SLOW spr round 3 (radius: 5)
[14:52:46 -318024.647037] SLOW spr round 4 (radius: 5)
[14:57:28 -318024.646962] SLOW spr round 5 (radius: 10)
[15:01:06 -318024.646951] SLOW spr round 6 (radius: 15)
[15:10:51 -318024.646944] SLOW spr round 7 (radius: 20)
[15:23:00 -318024.646939] SLOW spr round 8 (radius: 25)
[15:36:56 -318024.646936] Model parameter optimization (eps = 0.100000)

[15:37:06] [worker #0] ML tree search #11, logLikelihood: -318024.412650

[15:37:06 -1068550.789628] Initial branch length optimization
[15:37:24 -929662.543829] Model parameter optimization (eps = 10.000000)
[15:38:39 -927220.007731] AUTODETECT spr round 1 (radius: 5)
[15:47:36 -641326.059300] AUTODETECT spr round 2 (radius: 10)
[15:58:49 -464203.373833] AUTODETECT spr round 3 (radius: 15)
[16:13:57 -389613.223070] AUTODETECT spr round 4 (radius: 20)
[16:30:51 -368614.171116] AUTODETECT spr round 5 (radius: 25)
[16:50:17 -360972.278635] SPR radius for FAST iterations: 25 (autodetect)
[16:50:17 -360972.278635] Model parameter optimization (eps = 3.000000)
[16:50:51 -360611.918138] FAST spr round 1 (radius: 25)
[16:56:25 -319675.403068] FAST spr round 2 (radius: 25)
[17:00:32 -318293.397340] FAST spr round 3 (radius: 25)
[17:04:51 -318186.038218] FAST spr round 4 (radius: 25)
[17:07:34 -318172.107549] FAST spr round 5 (radius: 25)
[17:10:34 -318172.107449] Model parameter optimization (eps = 1.000000)
[17:10:57 -318147.846277] SLOW spr round 1 (radius: 5)
[17:17:52 -318038.567350] SLOW spr round 2 (radius: 5)
[17:22:43 -318031.214258] SLOW spr round 3 (radius: 5)
[17:27:38 -318031.213834] SLOW spr round 4 (radius: 10)
[17:31:52 -318031.213816] SLOW spr round 5 (radius: 15)
[17:40:21 -318031.213815] SLOW spr round 6 (radius: 20)
[17:52:39 -318031.213815] SLOW spr round 7 (radius: 25)
[18:06:27 -318031.213815] Model parameter optimization (eps = 0.100000)

[18:06:43] [worker #0] ML tree search #13, logLikelihood: -318031.016331

[18:06:44 -1067884.192784] Initial branch length optimization
[18:06:50 -930327.094916] Model parameter optimization (eps = 10.000000)
[18:08:00 -927618.630764] AUTODETECT spr round 1 (radius: 5)
[18:12:41 -656637.159592] AUTODETECT spr round 2 (radius: 10)
[18:19:38 -482514.139297] AUTODETECT spr round 3 (radius: 15)
[18:24:28 -423562.420435] AUTODETECT spr round 4 (radius: 20)
[18:37:57 -393126.418727] AUTODETECT spr round 5 (radius: 25)
[19:14:11 -376569.905126] SPR radius for FAST iterations: 25 (autodetect)
[19:14:12 -376569.905126] Model parameter optimization (eps = 3.000000)
[19:14:37 -376562.554123] FAST spr round 1 (radius: 25)
[19:29:16 -321416.246741] FAST spr round 2 (radius: 25)
[19:57:09] [worker #1] ML tree search #14, logLikelihood: -318053.600862
[20:06:51 -318830.653199] FAST spr round 3 (radius: 25)
[20:21:48 -318689.729063] FAST spr round 4 (radius: 25)
[21:43:20 -318685.041006] FAST spr round 5 (radius: 25)
[23:57:36 -318683.868756] FAST spr round 6 (radius: 25)
[26:01:24 -318683.756474] FAST spr round 7 (radius: 25)
[27:53:41 -318683.756472] Model parameter optimization (eps = 1.000000)
[28:15:25 -318154.571620] SLOW spr round 1 (radius: 5)
[30:13:23 -318047.532475] SLOW spr round 2 (radius: 5)
[30:22:08 -318029.730198] SLOW spr round 3 (radius: 5)
[30:29:30 -318027.468813] SLOW spr round 4 (radius: 5)
[30:35:15 -318027.468767] SLOW spr round 5 (radius: 10)
[30:40:38 -318027.468741] SLOW spr round 6 (radius: 15)
[30:55:06 -318027.468724] SLOW spr round 7 (radius: 20)
[31:28:30 -318027.468712] SLOW spr round 8 (radius: 25)
[31:59:32 -318027.468704] Model parameter optimization (eps = 0.100000)

[31:59:40] [worker #0] ML tree search #15, logLikelihood: -318027.417391

[31:59:41 -1066064.277399] Initial branch length optimization
[32:01:16 -928707.935505] Model parameter optimization (eps = 10.000000)
[32:02:36 -925735.293946] AUTODETECT spr round 1 (radius: 5)
[32:07:59 -645164.037913] AUTODETECT spr round 2 (radius: 10)
[32:12:12 -473247.455153] AUTODETECT spr round 3 (radius: 15)
[32:18:06 -392804.590338] AUTODETECT spr round 4 (radius: 20)
[32:23:32] [worker #1] ML tree search #16, logLikelihood: -318031.158393
[32:24:50 -373470.356684] AUTODETECT spr round 5 (radius: 25)
[32:35:03 -368851.023562] SPR radius for FAST iterations: 25 (autodetect)
[32:35:03 -368851.023562] Model parameter optimization (eps = 3.000000)
[32:35:46 -368222.542461] FAST spr round 1 (radius: 25)
[32:50:26 -319849.619529] FAST spr round 2 (radius: 25)
[32:55:02 -318198.339158] FAST spr round 3 (radius: 25)
[33:02:50 -318109.594544] FAST spr round 4 (radius: 25)
[33:08:14 -318105.801224] FAST spr round 5 (radius: 25)
[33:12:40 -318105.801193] Model parameter optimization (eps = 1.000000)
[33:13:22 -318090.528363] SLOW spr round 1 (radius: 5)
[33:20:27 -318037.861593] SLOW spr round 2 (radius: 5)
[33:26:34 -318031.565440] SLOW spr round 3 (radius: 5)
[33:32:24 -318029.314245] SLOW spr round 4 (radius: 5)
[33:38:05 -318029.314225] SLOW spr round 5 (radius: 10)
[33:45:08 -318029.314225] SLOW spr round 6 (radius: 15)
[33:51:28 -318029.314225] SLOW spr round 7 (radius: 20)
[33:59:09 -318029.314225] SLOW spr round 8 (radius: 25)
[34:08:56 -318029.314225] Model parameter optimization (eps = 0.100000)

[34:09:04] [worker #0] ML tree search #17, logLikelihood: -318029.302354

[34:09:04 -1074017.502450] Initial branch length optimization
[34:09:10 -937503.726605] Model parameter optimization (eps = 10.000000)
[34:10:02 -934625.657010] AUTODETECT spr round 1 (radius: 5)
[34:13:16 -640568.360419] AUTODETECT spr round 2 (radius: 10)
[34:16:44 -460303.582557] AUTODETECT spr round 3 (radius: 15)
[34:20:13 -398715.006901] AUTODETECT spr round 4 (radius: 20)
[34:24:38 -373913.127486] AUTODETECT spr round 5 (radius: 25)
[34:29:42 -364022.819848] SPR radius for FAST iterations: 25 (autodetect)
[34:29:42 -364022.819848] Model parameter optimization (eps = 3.000000)
[34:30:05 -363698.432234] FAST spr round 1 (radius: 25)
[34:30:23] [worker #1] ML tree search #18, logLikelihood: -318044.581092
[34:34:00 -319330.962995] FAST spr round 2 (radius: 25)
[34:37:01 -318305.310920] FAST spr round 3 (radius: 25)
[34:39:35 -318230.432321] FAST spr round 4 (radius: 25)
[34:41:51 -318209.178362] FAST spr round 5 (radius: 25)
[34:44:02 -318192.164222] FAST spr round 6 (radius: 25)
[34:46:06 -318192.164218] Model parameter optimization (eps = 1.000000)
[34:46:29 -318162.366298] SLOW spr round 1 (radius: 5)
[34:49:50 -318074.352480] SLOW spr round 2 (radius: 5)
[34:52:59 -318055.386963] SLOW spr round 3 (radius: 5)
[34:55:57 -318054.558711] SLOW spr round 4 (radius: 5)
[34:58:55 -318054.558451] SLOW spr round 5 (radius: 10)
[35:02:04 -318050.515727] SLOW spr round 6 (radius: 5)
[35:05:57 -318050.515684] SLOW spr round 7 (radius: 10)
[35:09:30 -318050.515683] SLOW spr round 8 (radius: 15)
[35:14:45 -318050.515683] SLOW spr round 9 (radius: 20)
[35:22:41 -318050.515682] SLOW spr round 10 (radius: 25)
[35:32:24 -318050.515682] Model parameter optimization (eps = 0.100000)

[35:32:47] [worker #0] ML tree search #19, logLikelihood: -318049.949908

[35:41:37] [worker #1] ML tree search #20, logLikelihood: -318034.968725

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.128649,0.253094) (0.131272,0.262050) (0.315378,0.653131) (0.424701,1.711926) 
   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: -318018.959814

AIC score: 640047.919628 / AICc score: 8684107.919628 / BIC score: 649462.996457
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=809).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 26 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O95202/3_mltree/O95202.raxml.log

Analysis started: 14-Jul-2021 16:36:42 / finished: 16-Jul-2021 04:18:20

Elapsed time: 128497.693 seconds