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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 05-Jul-2021 22:46:45 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/2_msa/Q5SQ80_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80 --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/Q5SQ80/2_msa/Q5SQ80_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 262 sites

WARNING: Sequences tr_A0A0J9YUH2_A0A0J9YUH2_MOUSE_10090 and tr_A0A0J9YUZ3_A0A0J9YUZ3_MOUSE_10090 are exactly identical!
WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_E9Q637_E9Q637_MOUSE_10090 are exactly identical!
WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_Q8C646_Q8C646_MOUSE_10090 are exactly identical!
WARNING: Sequences tr_H2NA10_H2NA10_PONAB_9601 and sp_Q9UPS8_ANR26_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and sp_Q92527_ANKR7_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and tr_A0A2R8ZJB4_A0A2R8ZJB4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TX65_A0A2I3TX65_PANTR_9598 and tr_A0A2R9B0Y1_A0A2R9B0Y1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q1R5_H2Q1R5_PANTR_9598 and tr_A0A2R9CCJ6_A0A2R9CCJ6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QB11_H2QB11_PANTR_9598 and tr_A0A2R8ZAT3_A0A2R8ZAT3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7CR95_F7CR95_MONDO_13616 and tr_G3VYV3_G3VYV3_SARHA_9305 are exactly identical!
WARNING: Sequences sp_A0A0A6YYL3_POTEB_HUMAN_9606 and sp_H3BUK9_POTB2_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q5SQ80_A20A2_HUMAN_9606 and sp_Q5VUR7_A20A3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q2U9G2_Q2U9G2_ASPOR_510516 and tr_A0A1S9D9N6_A0A1S9D9N6_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_Q2UGY0_Q2UGY0_ASPOR_510516 and tr_A0A1S9DZ77_A0A1S9DZ77_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0GU17_A0A0E0GU17_ORYNI_4536 and tr_I1PFP1_I1PFP1_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GU17_A0A0E0GU17_ORYNI_4536 and tr_A0A0E0P1K0_A0A0E0P1K0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_F6W8P2_F6W8P2_MACMU_9544 and tr_G7Q115_G7Q115_MACFA_9541 are exactly identical!
WARNING: Sequences tr_B8AK75_B8AK75_ORYSI_39946 and tr_Q9AUW0_Q9AUW0_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A091EUN4_A0A091EUN4_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A093QHA6_A0A093QHA6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H0YUX9_H0YUX9_TAEGU_59729 and tr_A0A218UXQ1_A0A218UXQ1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G7NX83_G7NX83_MACFA_9541 and tr_A0A0D9S5X0_A0A0D9S5X0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096MVX0_A0A096MVX0_PAPAN_9555 and tr_A0A2K5KKK9_A0A2K5KKK9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A078I827_A0A078I827_BRANA_3708 and tr_A0A0D3E7P7_A0A0D3E7P7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0B4GGJ3_A0A0B4GGJ3_METMF_1276143 and tr_A0A0B4IJM0_A0A0B4IJM0_METMF_1276143 are exactly identical!
WARNING: Sequences tr_A0A0F0IF66_A0A0F0IF66_ASPPU_1403190 and tr_A0A2G7FX58_A0A2G7FX58_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A091ILE9_A0A091ILE9_EGRGA_188379 and tr_A0A091V6X4_A0A091V6X4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091ILE9_A0A091ILE9_EGRGA_188379 and tr_A0A087RGP9_A0A087RGP9_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091ILE9_A0A091ILE9_EGRGA_188379 and tr_A0A0A0AE38_A0A0A0AE38_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087QKS1_A0A087QKS1_APTFO_9233 and tr_A0A091GFV8_A0A091GFV8_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A087QKS1_A0A087QKS1_APTFO_9233 and tr_A0A099ZVA7_A0A099ZVA7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087QKS1_A0A087QKS1_APTFO_9233 and tr_A0A2I0MGU1_A0A2I0MGU1_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A1S4APP5_A0A1S4APP5_TOBAC_4097 and tr_A0A1U7VUI0_A0A1U7VUI0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K5LZW8_A0A2K5LZW8_CERAT_9531 and tr_A0A2K5ZEI9_A0A2K5ZEI9_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 34

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/Q5SQ80/3_mltree/Q5SQ80.raxml.reduced.phy

Alignment comprises 1 partitions and 262 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 262 / 262
Gaps: 20.99 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 262 / 20960
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -451935.302878] Initial branch length optimization
[00:00:10 -390161.073466] Model parameter optimization (eps = 10.000000)
[00:01:14 -388710.826153] AUTODETECT spr round 1 (radius: 5)
[00:04:59 -315988.261365] AUTODETECT spr round 2 (radius: 10)
[00:09:13 -251191.455930] AUTODETECT spr round 3 (radius: 15)
[00:13:51 -218458.975336] AUTODETECT spr round 4 (radius: 20)
[00:18:57 -211563.617218] AUTODETECT spr round 5 (radius: 25)
[00:24:42 -210050.720283] SPR radius for FAST iterations: 25 (autodetect)
[00:24:42 -210050.720283] Model parameter optimization (eps = 3.000000)
[00:24:51 -210049.942589] FAST spr round 1 (radius: 25)
[00:32:26 -195051.465389] FAST spr round 2 (radius: 25)
[00:38:05 -194348.638370] FAST spr round 3 (radius: 25)
[00:42:29 -194221.384942] FAST spr round 4 (radius: 25)
[00:46:16 -194214.958825] FAST spr round 5 (radius: 25)
[00:49:44 -194214.237983] FAST spr round 6 (radius: 25)
[00:53:07 -194214.237303] Model parameter optimization (eps = 1.000000)
[00:53:14 -194214.034558] SLOW spr round 1 (radius: 5)
[00:57:44 -194138.972240] SLOW spr round 2 (radius: 5)
[01:02:01 -194122.292041] SLOW spr round 3 (radius: 5)
[01:06:12 -194116.478721] SLOW spr round 4 (radius: 5)
[01:10:10 -194114.335363] SLOW spr round 5 (radius: 5)
[01:13:57 -194114.234806] SLOW spr round 6 (radius: 5)
[01:17:35 -194114.234785] SLOW spr round 7 (radius: 10)
[01:22:00 -194098.346449] SLOW spr round 8 (radius: 5)
[01:26:50 -194090.461141] SLOW spr round 9 (radius: 5)
[01:31:02 -194090.345097] SLOW spr round 10 (radius: 5)
[01:34:50 -194090.343947] SLOW spr round 11 (radius: 10)
[01:38:55 -194089.313935] SLOW spr round 12 (radius: 5)
[01:43:15 -194087.069489] SLOW spr round 13 (radius: 5)
[01:47:24 -194086.140683] SLOW spr round 14 (radius: 5)
[01:51:26 -194085.174266] SLOW spr round 15 (radius: 5)
[01:55:07 -194085.173965] SLOW spr round 16 (radius: 10)
[01:59:05 -194085.038108] SLOW spr round 17 (radius: 5)
[02:03:21 -194084.751841] SLOW spr round 18 (radius: 5)
[02:07:15 -194084.751619] SLOW spr round 19 (radius: 10)
[02:11:23 -194084.751608] SLOW spr round 20 (radius: 15)
[02:18:11 -194081.050725] SLOW spr round 21 (radius: 5)
[02:23:01 -194079.302306] SLOW spr round 22 (radius: 5)
[02:27:10 -194079.300388] SLOW spr round 23 (radius: 10)
[02:31:26 -194076.302916] SLOW spr round 24 (radius: 5)
[02:35:44 -194076.140466] SLOW spr round 25 (radius: 5)
[02:39:40 -194076.140102] SLOW spr round 26 (radius: 10)
[02:44:06 -194076.140085] SLOW spr round 27 (radius: 15)
[02:51:24 -194074.076694] SLOW spr round 28 (radius: 5)
[02:55:54 -194073.628351] SLOW spr round 29 (radius: 5)
[03:00:06 -194073.628184] SLOW spr round 30 (radius: 10)
[03:04:35 -194073.628174] SLOW spr round 31 (radius: 15)
[03:11:48 -194073.628171] SLOW spr round 32 (radius: 20)
[03:21:07 -194073.147933] SLOW spr round 33 (radius: 5)
[03:25:49 -194067.866198] SLOW spr round 34 (radius: 5)
[03:29:04] [worker #3] ML tree search #4, logLikelihood: -193814.876827
[03:30:08 -194065.803654] SLOW spr round 35 (radius: 5)
[03:34:16 -194063.211778] SLOW spr round 36 (radius: 5)
[03:38:14 -194063.211609] SLOW spr round 37 (radius: 10)
[03:42:24 -194063.211603] SLOW spr round 38 (radius: 15)
[03:49:13 -194063.211601] SLOW spr round 39 (radius: 20)
[03:57:43 -194063.211600] SLOW spr round 40 (radius: 25)
[04:08:07 -194063.211599] Model parameter optimization (eps = 0.100000)

[04:08:14] [worker #0] ML tree search #1, logLikelihood: -194063.188237

[04:08:14 -452417.173143] Initial branch length optimization
[04:08:19 -389629.573543] Model parameter optimization (eps = 10.000000)
[04:09:20 -388252.644478] AUTODETECT spr round 1 (radius: 5)
[04:13:01 -316192.563033] AUTODETECT spr round 2 (radius: 10)
[04:17:18 -252523.717236] AUTODETECT spr round 3 (radius: 15)
[04:22:01 -231194.576749] AUTODETECT spr round 4 (radius: 20)
[04:27:40 -215887.031087] AUTODETECT spr round 5 (radius: 25)
[04:29:53] [worker #2] ML tree search #3, logLikelihood: -193658.092156
[04:33:38] [worker #4] ML tree search #5, logLikelihood: -193596.418082
[04:34:06 -209613.758061] SPR radius for FAST iterations: 25 (autodetect)
[04:34:06 -209613.758061] Model parameter optimization (eps = 3.000000)
[04:34:15 -209613.282617] FAST spr round 1 (radius: 25)
[04:36:34] [worker #1] ML tree search #2, logLikelihood: -194043.049570
[04:41:48 -195026.298013] FAST spr round 2 (radius: 25)
[04:47:22 -194176.364486] FAST spr round 3 (radius: 25)
[04:52:36 -194087.609525] FAST spr round 4 (radius: 25)
[04:56:56 -194050.879573] FAST spr round 5 (radius: 25)
[05:00:52 -194029.003723] FAST spr round 6 (radius: 25)
[05:04:30 -194016.941059] FAST spr round 7 (radius: 25)
[05:07:57 -194012.109964] FAST spr round 8 (radius: 25)
[05:11:13 -194010.843530] FAST spr round 9 (radius: 25)
[05:14:26 -194010.842282] Model parameter optimization (eps = 1.000000)
[05:14:35 -194010.394654] SLOW spr round 1 (radius: 5)
[05:19:01 -193949.695124] SLOW spr round 2 (radius: 5)
[05:23:11 -193939.518243] SLOW spr round 3 (radius: 5)
[05:27:27 -193936.844981] SLOW spr round 4 (radius: 5)
[05:31:24 -193936.027646] SLOW spr round 5 (radius: 5)
[05:35:15 -193936.027393] SLOW spr round 6 (radius: 10)
[05:39:32 -193923.838572] SLOW spr round 7 (radius: 5)
[05:44:04 -193913.961356] SLOW spr round 8 (radius: 5)
[05:48:04 -193912.875327] SLOW spr round 9 (radius: 5)
[05:50:11] [worker #3] ML tree search #9, logLikelihood: -193847.754738
[05:51:52 -193911.720981] SLOW spr round 10 (radius: 5)
[05:55:34 -193911.360737] SLOW spr round 11 (radius: 5)
[05:59:13 -193911.360593] SLOW spr round 12 (radius: 10)
[06:03:05 -193911.360501] SLOW spr round 13 (radius: 15)
[06:10:08 -193910.149488] SLOW spr round 14 (radius: 5)
[06:14:54 -193910.149347] SLOW spr round 15 (radius: 10)
[06:19:57 -193910.149254] SLOW spr round 16 (radius: 15)
[06:26:50 -193909.959876] SLOW spr round 17 (radius: 5)
[06:31:40 -193909.928176] SLOW spr round 18 (radius: 10)
[06:36:41 -193909.927230] SLOW spr round 19 (radius: 15)
[06:43:06 -193909.927165] SLOW spr round 20 (radius: 20)
[06:52:24 -193906.655926] SLOW spr round 21 (radius: 5)
[06:57:17 -193905.316345] SLOW spr round 22 (radius: 5)
[07:01:42 -193905.088594] SLOW spr round 23 (radius: 5)
[07:05:57 -193903.321596] SLOW spr round 24 (radius: 5)
[07:10:02 -193900.326111] SLOW spr round 25 (radius: 5)
[07:14:09 -193895.456526] SLOW spr round 26 (radius: 5)
[07:18:04 -193895.456401] SLOW spr round 27 (radius: 10)
[07:22:13 -193895.456399] SLOW spr round 28 (radius: 15)
[07:29:11 -193895.456398] SLOW spr round 29 (radius: 20)
[07:38:11 -193894.559030] SLOW spr round 30 (radius: 5)
[07:39:43] [worker #2] ML tree search #8, logLikelihood: -193610.111205
[07:42:52 -193887.446497] SLOW spr round 31 (radius: 5)
[07:47:08 -193886.167281] SLOW spr round 32 (radius: 5)
[07:51:14 -193886.167254] SLOW spr round 33 (radius: 10)
[07:55:33 -193886.167253] SLOW spr round 34 (radius: 15)
[08:02:41 -193886.167253] SLOW spr round 35 (radius: 20)
[08:11:51 -193886.167252] SLOW spr round 36 (radius: 25)
[08:22:54 -193885.042033] SLOW spr round 37 (radius: 5)
[08:27:54 -193883.513430] SLOW spr round 38 (radius: 5)
[08:32:05 -193883.513206] SLOW spr round 39 (radius: 10)
[08:36:17] [worker #3] ML tree search #14, logLikelihood: -193851.070336
[08:36:23 -193883.513204] SLOW spr round 40 (radius: 15)
[08:43:04 -193883.513204] SLOW spr round 41 (radius: 20)
[08:51:58 -193883.513204] SLOW spr round 42 (radius: 25)
[08:57:26] [worker #4] ML tree search #10, logLikelihood: -194065.049996
[09:03:04 -193883.513204] Model parameter optimization (eps = 0.100000)

[09:03:12] [worker #0] ML tree search #6, logLikelihood: -193883.454905

[09:03:12 -453627.424527] Initial branch length optimization
[09:03:18 -390758.992506] Model parameter optimization (eps = 10.000000)
[09:04:26 -389424.616288] AUTODETECT spr round 1 (radius: 5)
[09:08:24 -313087.233876] AUTODETECT spr round 2 (radius: 10)
[09:12:48 -248333.661232] AUTODETECT spr round 3 (radius: 15)
[09:17:28 -221064.922693] AUTODETECT spr round 4 (radius: 20)
[09:22:50 -212624.065419] AUTODETECT spr round 5 (radius: 25)
[09:29:07 -210858.615517] SPR radius for FAST iterations: 25 (autodetect)
[09:29:07 -210858.615517] Model parameter optimization (eps = 3.000000)
[09:29:17 -210856.652353] FAST spr round 1 (radius: 25)
[09:36:29 -195740.642974] FAST spr round 2 (radius: 25)
[09:41:39 -194462.618282] FAST spr round 3 (radius: 25)
[09:43:28] [worker #1] ML tree search #7, logLikelihood: -193822.713414
[09:46:04 -194228.469199] FAST spr round 4 (radius: 25)
[09:50:21 -194097.060850] FAST spr round 5 (radius: 25)
[09:53:57 -194074.633046] FAST spr round 6 (radius: 25)
[09:57:17 -194074.632263] Model parameter optimization (eps = 1.000000)
[09:57:24 -194074.304553] SLOW spr round 1 (radius: 5)
[10:01:46 -194038.111556] SLOW spr round 2 (radius: 5)
[10:05:57 -194029.653852] SLOW spr round 3 (radius: 5)
[10:10:03 -194028.330393] SLOW spr round 4 (radius: 5)
[10:14:08 -194024.867058] SLOW spr round 5 (radius: 5)
[10:17:58 -194024.494484] SLOW spr round 6 (radius: 5)
[10:21:38 -194023.796481] SLOW spr round 7 (radius: 5)
[10:25:21 -194023.795918] SLOW spr round 8 (radius: 10)
[10:29:42 -194015.188448] SLOW spr round 9 (radius: 5)
[10:34:26 -194013.873096] SLOW spr round 10 (radius: 5)
[10:38:32 -194013.872933] SLOW spr round 11 (radius: 10)
[10:42:46 -194013.317079] SLOW spr round 12 (radius: 5)
[10:47:03 -194013.317016] SLOW spr round 13 (radius: 10)
[10:51:45 -194012.914181] SLOW spr round 14 (radius: 5)
[10:56:20 -194012.015530] SLOW spr round 15 (radius: 5)
[11:00:30 -194012.015326] SLOW spr round 16 (radius: 10)
[11:04:58 -194012.015315] SLOW spr round 17 (radius: 15)
[11:12:32 -194005.295253] SLOW spr round 18 (radius: 5)
[11:17:09 -194004.552029] SLOW spr round 19 (radius: 5)
[11:21:27 -194000.730525] SLOW spr round 20 (radius: 5)
[11:25:33 -193999.955897] SLOW spr round 21 (radius: 5)
[11:29:30 -193999.955698] SLOW spr round 22 (radius: 10)
[11:33:48 -193999.955694] SLOW spr round 23 (radius: 15)
[11:41:43 -193995.495823] SLOW spr round 24 (radius: 5)
[11:46:36 -193991.198497] SLOW spr round 25 (radius: 5)
[11:50:55 -193991.195960] SLOW spr round 26 (radius: 10)
[11:55:27 -193991.195531] SLOW spr round 27 (radius: 15)
[12:02:32 -193991.195454] SLOW spr round 28 (radius: 20)
[12:12:10 -193991.195441] SLOW spr round 29 (radius: 25)
[12:19:57] [worker #2] ML tree search #13, logLikelihood: -193847.265314
[12:23:24 -193991.195438] Model parameter optimization (eps = 0.100000)

[12:23:31] [worker #0] ML tree search #11, logLikelihood: -193991.183281

[12:23:31 -453164.147686] Initial branch length optimization
[12:23:36 -390726.837830] Model parameter optimization (eps = 10.000000)
[12:24:35 -389408.869771] AUTODETECT spr round 1 (radius: 5)
[12:28:25 -315302.193313] AUTODETECT spr round 2 (radius: 10)
[12:32:40 -249627.562597] AUTODETECT spr round 3 (radius: 15)
[12:37:09 -222038.798599] AUTODETECT spr round 4 (radius: 20)
[12:42:32 -213435.951240] AUTODETECT spr round 5 (radius: 25)
[12:49:46 -211185.803847] SPR radius for FAST iterations: 25 (autodetect)
[12:49:46 -211185.803847] Model parameter optimization (eps = 3.000000)
[12:49:59 -211168.029151] FAST spr round 1 (radius: 25)
[12:56:56 -195369.417358] FAST spr round 2 (radius: 25)
[13:01:09] [worker #3] ML tree search #19, logLikelihood: -194003.060852
[13:02:08 -194016.983211] FAST spr round 3 (radius: 25)
[13:06:35 -193940.968237] FAST spr round 4 (radius: 25)
[13:10:25 -193931.512518] FAST spr round 5 (radius: 25)
[13:13:58 -193929.166525] FAST spr round 6 (radius: 25)
[13:17:20 -193929.163717] Model parameter optimization (eps = 1.000000)
[13:17:28 -193929.055233] SLOW spr round 1 (radius: 5)
[13:21:49 -193872.388181] SLOW spr round 2 (radius: 5)
[13:26:01 -193866.676858] SLOW spr round 3 (radius: 5)
[13:30:07 -193863.628370] SLOW spr round 4 (radius: 5)
[13:33:55 -193863.628016] SLOW spr round 5 (radius: 10)
[13:38:01 -193855.444781] SLOW spr round 6 (radius: 5)
[13:42:22 -193855.405957] SLOW spr round 7 (radius: 10)
[13:46:56 -193855.158595] SLOW spr round 8 (radius: 5)
[13:51:15 -193855.155019] SLOW spr round 9 (radius: 10)
[13:55:45 -193855.154985] SLOW spr round 10 (radius: 15)
[14:02:36 -193852.260075] SLOW spr round 11 (radius: 5)
[14:07:18 -193845.839395] SLOW spr round 12 (radius: 5)
[14:11:24 -193845.209571] SLOW spr round 13 (radius: 5)
[14:15:29 -193844.432155] SLOW spr round 14 (radius: 5)
[14:19:40 -193844.431912] SLOW spr round 15 (radius: 10)
[14:24:04 -193844.431900] SLOW spr round 16 (radius: 15)
[14:27:37] [worker #1] ML tree search #12, logLikelihood: -193645.860700
[14:32:03 -193841.823374] SLOW spr round 17 (radius: 5)
[14:36:55 -193841.558745] SLOW spr round 18 (radius: 5)
[14:41:25 -193841.557965] SLOW spr round 19 (radius: 10)
[14:46:10 -193839.263481] SLOW spr round 20 (radius: 5)
[14:50:57 -193836.551720] SLOW spr round 21 (radius: 5)
[14:55:21 -193836.203945] SLOW spr round 22 (radius: 5)
[14:59:51 -193836.203394] SLOW spr round 23 (radius: 10)
[15:01:22] [worker #4] ML tree search #15, logLikelihood: -193676.433186
[15:04:31 -193833.882687] SLOW spr round 24 (radius: 5)
[15:09:13 -193828.964481] SLOW spr round 25 (radius: 5)
[15:13:32 -193828.964418] SLOW spr round 26 (radius: 10)
[15:18:07 -193828.964415] SLOW spr round 27 (radius: 15)
[15:25:31 -193828.964414] SLOW spr round 28 (radius: 20)
[15:36:14 -193828.964413] SLOW spr round 29 (radius: 25)
[15:48:36 -193827.744303] SLOW spr round 30 (radius: 5)
[15:53:52 -193826.884197] SLOW spr round 31 (radius: 5)
[15:58:32 -193826.392113] SLOW spr round 32 (radius: 5)
[16:02:49 -193826.392098] SLOW spr round 33 (radius: 10)
[16:07:52 -193826.392097] SLOW spr round 34 (radius: 15)
[16:15:11 -193826.392096] SLOW spr round 35 (radius: 20)
[16:25:26 -193826.392096] SLOW spr round 36 (radius: 25)
[16:38:06 -193826.392095] Model parameter optimization (eps = 0.100000)

[16:38:14] [worker #0] ML tree search #16, logLikelihood: -193826.371772

[18:35:24] [worker #2] ML tree search #18, logLikelihood: -193589.310901
[19:49:11] [worker #4] ML tree search #20, logLikelihood: -193627.509917
[21:38:12] [worker #1] ML tree search #17, logLikelihood: -193645.719051

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.164598,0.451300) (0.144941,0.499767) (0.432996,0.999567) (0.257465,1.633124) 
   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: -193589.310901

AIC score: 391188.621802 / AICc score: 8435248.621802 / BIC score: 398343.152532
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=262).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 51 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5SQ80/3_mltree/Q5SQ80.raxml.log

Analysis started: 05-Jul-2021 22:46:45 / finished: 06-Jul-2021 20:24:57

Elapsed time: 77892.436 seconds

Consumed energy: 5631.495 Wh (= 28 km in an electric car, or 141 km with an e-scooter!)