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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM

RAxML-NG was called at 26-Jul-2021 05:25:32 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/2_msa/A6NHP3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/2_msa/A6NHP3_trimmed_msa.fasta
[00:00:00] Loaded alignment with 310 taxa and 130 sites

WARNING: Sequences sp_Q5IBH7_SPDYA_MOUSE_10090 and tr_A0A3Q0CW52_A0A3Q0CW52_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2I2Z3X8_A0A2I2Z3X8_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2I3RDX2_A0A2I3RDX2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and sp_Q5MJ68_SPDYC_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_F7GKM1_F7GKM1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_G7PPI9_G7PPI9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A096NWU0_A0A096NWU0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2K5P120_A0A2K5P120_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2K6C373_A0A2K6C373_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2K5ZM41_A0A2K5ZM41_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1R0G6_G1R0G6_NOMLE_61853 and tr_A0A2R9C0H7_A0A2R9C0H7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_A0A2J8VNB9_A0A2J8VNB9_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and sp_Q5MJ70_SPDYA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_F6Y2M5_F6Y2M5_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_G7PLY1_G7PLY1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_A0A096P0B0_A0A096P0B0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_A0A2K5KPJ9_A0A2K5KPJ9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_A0A2K5Y683_A0A2K5Y683_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RZF2_G1RZF2_NOMLE_61853 and tr_A0A2R9BDL4_A0A2R9BDL4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_J9P8P8_J9P8P8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_I3N4M5_I3N4M5_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_G3TLJ3_G3TLJ3_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_G1LEU3_G1LEU3_AILME_9646 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_L5KRL7_L5KRL7_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_M3X1C4_M3X1C4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_A0A1S3EYP5_A0A1S3EYP5_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_A0A2U3ZAG1_A0A2U3ZAG1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_A0A2U3YDC4_A0A2U3YDC4_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_A0A2Y9IEY1_A0A2Y9IEY1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1PZP9_G1PZP9_MYOLU_59463 and tr_A0A384CVH3_A0A384CVH3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G3S4R9_G3S4R9_GORGO_9595 and sp_A6NLX3_SPDE4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2RGM4_H2RGM4_PANTR_9598 and tr_H2RHU9_H2RHU9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_W5PY69_W5PY69_SHEEP_9940 and tr_G1MD09_G1MD09_AILME_9646 are exactly identical!
WARNING: Sequences tr_W5PY69_W5PY69_SHEEP_9940 and tr_A0A2U3Y0Y5_A0A2U3Y0Y5_LEPWE_9713 are exactly identical!
WARNING: Sequences sp_A6NHP3_SPE2B_HUMAN_9606 and sp_P0CI01_SPDE6_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_A6NHP3_SPE2B_HUMAN_9606 and sp_Q495Y8_SPDE2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6UB06_F6UB06_MACMU_9544 and tr_G7PTL7_G7PTL7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6UB06_F6UB06_MACMU_9544 and tr_A0A0D9RDE1_A0A0D9RDE1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6UB06_F6UB06_MACMU_9544 and tr_A0A2K6CY21_A0A2K6CY21_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G5C2Y3_G5C2Y3_HETGA_10181 and tr_A0A091CX93_A0A091CX93_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_G1MH23_G1MH23_AILME_9646 and tr_A0A384DJL9_A0A384DJL9_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A096P2V8_A0A096P2V8_PAPAN_9555 and tr_A0A2K5LTJ6_A0A2K5LTJ6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P2V8_A0A096P2V8_PAPAN_9555 and tr_A0A2K5YNK1_A0A2K5YNK1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096P4V9_A0A096P4V9_PAPAN_9555 and tr_A0A2K5ME39_A0A2K5ME39_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P4V9_A0A096P4V9_PAPAN_9555 and tr_A0A2K6D0S9_A0A2K6D0S9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A151MTP1_A0A151MTP1_ALLMI_8496 and tr_A0A1U8DL77_A0A1U8DL77_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2D0RLV5_A0A2D0RLV5_ICTPU_7998 and tr_A0A2D0RMW2_A0A2D0RMW2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4BZM8_A0A2U4BZM8_TURTR_9739 and tr_A0A2Y9N589_A0A2Y9N589_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4BZM8_A0A2U4BZM8_TURTR_9739 and tr_A0A2Y9EH13_A0A2Y9EH13_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 49

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.reduced.phy

Alignment comprises 1 partitions and 130 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 130 / 130
Gaps: 5.44 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.rba

Parallelization scheme autoconfig: 3 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 310 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 130 / 10400
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -60155.162344] Initial branch length optimization
[00:00:01 -47937.017817] Model parameter optimization (eps = 10.000000)
[00:00:17 -47773.055664] AUTODETECT spr round 1 (radius: 5)
[00:00:42 -29489.125634] AUTODETECT spr round 2 (radius: 10)
[00:01:14 -22436.891732] AUTODETECT spr round 3 (radius: 15)
[00:01:53 -20375.071835] AUTODETECT spr round 4 (radius: 20)
[00:02:40 -19083.219074] AUTODETECT spr round 5 (radius: 25)
[00:03:24 -18730.886150] SPR radius for FAST iterations: 25 (autodetect)
[00:03:24 -18730.886150] Model parameter optimization (eps = 3.000000)
[00:03:38 -18684.198995] FAST spr round 1 (radius: 25)
[00:04:13 -17108.973326] FAST spr round 2 (radius: 25)
[00:04:42 -17071.018753] FAST spr round 3 (radius: 25)
[00:05:04 -17070.388970] FAST spr round 4 (radius: 25)
[00:05:25 -17070.374065] Model parameter optimization (eps = 1.000000)
[00:05:32 -17069.267208] SLOW spr round 1 (radius: 5)
[00:06:08 -17068.591799] SLOW spr round 2 (radius: 5)
[00:06:40 -17068.591773] SLOW spr round 3 (radius: 10)
[00:07:14 -17065.007892] SLOW spr round 4 (radius: 5)
[00:08:04 -17061.481588] SLOW spr round 5 (radius: 5)
[00:08:45 -17061.481371] SLOW spr round 6 (radius: 10)
[00:09:20 -17061.481340] SLOW spr round 7 (radius: 15)
[00:10:14 -17060.043644] SLOW spr round 8 (radius: 5)
[00:11:08 -17058.186086] SLOW spr round 9 (radius: 5)
[00:11:50 -17058.184204] SLOW spr round 10 (radius: 10)
[00:12:25 -17058.184194] SLOW spr round 11 (radius: 15)
[00:13:20 -17057.983104] SLOW spr round 12 (radius: 5)
[00:14:12 -17057.983005] SLOW spr round 13 (radius: 10)
[00:14:38] [worker #2] ML tree search #3, logLikelihood: -16925.033254
[00:14:52 -17057.982980] SLOW spr round 14 (radius: 15)
[00:15:45 -17057.982980] SLOW spr round 15 (radius: 20)
[00:16:50 -17057.982980] SLOW spr round 16 (radius: 25)
[00:18:01 -17013.946441] SLOW spr round 17 (radius: 5)
[00:18:19] [worker #1] ML tree search #2, logLikelihood: -16928.278216
[00:18:59 -16932.519460] SLOW spr round 18 (radius: 5)
[00:19:43 -16932.518830] SLOW spr round 19 (radius: 10)
[00:20:20 -16924.456776] SLOW spr round 20 (radius: 5)
[00:21:08 -16924.455860] SLOW spr round 21 (radius: 10)
[00:21:46 -16924.455812] SLOW spr round 22 (radius: 15)
[00:22:45 -16924.455809] SLOW spr round 23 (radius: 20)
[00:23:58 -16924.455809] SLOW spr round 24 (radius: 25)
[00:25:14 -16924.455809] Model parameter optimization (eps = 0.100000)

[00:25:23] [worker #0] ML tree search #1, logLikelihood: -16923.489138

[00:25:23 -61806.816652] Initial branch length optimization
[00:25:23 -49598.506598] Model parameter optimization (eps = 10.000000)
[00:25:40 -49392.083624] AUTODETECT spr round 1 (radius: 5)
[00:26:05 -30379.994025] AUTODETECT spr round 2 (radius: 10)
[00:26:37 -24078.126045] AUTODETECT spr round 3 (radius: 15)
[00:27:17 -19343.543838] AUTODETECT spr round 4 (radius: 20)
[00:28:01 -18808.384071] AUTODETECT spr round 5 (radius: 25)
[00:28:47 -18789.329475] SPR radius for FAST iterations: 25 (autodetect)
[00:28:47 -18789.329475] Model parameter optimization (eps = 3.000000)
[00:29:00 -18717.492202] FAST spr round 1 (radius: 25)
[00:29:34 -17066.734840] FAST spr round 2 (radius: 25)
[00:30:01] [worker #1] ML tree search #5, logLikelihood: -16928.912869
[00:30:02 -16943.901064] FAST spr round 3 (radius: 25)
[00:30:24 -16942.089960] FAST spr round 4 (radius: 25)
[00:30:45 -16941.563464] FAST spr round 5 (radius: 25)
[00:31:01] [worker #2] ML tree search #6, logLikelihood: -16930.383020
[00:31:06 -16941.563442] Model parameter optimization (eps = 1.000000)
[00:31:12 -16940.849158] SLOW spr round 1 (radius: 5)
[00:31:49 -16936.524663] SLOW spr round 2 (radius: 5)
[00:32:22 -16936.511035] SLOW spr round 3 (radius: 10)
[00:32:56 -16935.841797] SLOW spr round 4 (radius: 5)
[00:33:44 -16935.841709] SLOW spr round 5 (radius: 10)
[00:34:24 -16935.841709] SLOW spr round 6 (radius: 15)
[00:35:15 -16935.841709] SLOW spr round 7 (radius: 20)
[00:36:23 -16935.841709] SLOW spr round 8 (radius: 25)
[00:37:31 -16935.841709] Model parameter optimization (eps = 0.100000)

[00:37:35] [worker #0] ML tree search #4, logLikelihood: -16935.798919

[00:37:35 -61213.277724] Initial branch length optimization
[00:37:36 -49171.393899] Model parameter optimization (eps = 10.000000)
[00:37:51 -49017.126584] AUTODETECT spr round 1 (radius: 5)
[00:38:17 -31467.890629] AUTODETECT spr round 2 (radius: 10)
[00:38:49 -24270.657303] AUTODETECT spr round 3 (radius: 15)
[00:39:28 -20845.689294] AUTODETECT spr round 4 (radius: 20)
[00:40:15 -19232.066561] AUTODETECT spr round 5 (radius: 25)
[00:41:13 -19081.340954] SPR radius for FAST iterations: 25 (autodetect)
[00:41:13 -19081.340954] Model parameter optimization (eps = 3.000000)
[00:41:25 -19002.765217] FAST spr round 1 (radius: 25)
[00:42:00 -17105.051294] FAST spr round 2 (radius: 25)
[00:42:27 -16958.471649] FAST spr round 3 (radius: 25)
[00:42:35] [worker #1] ML tree search #8, logLikelihood: -16929.022294
[00:42:51 -16948.009818] FAST spr round 4 (radius: 25)
[00:43:14 -16942.940894] FAST spr round 5 (radius: 25)
[00:43:35 -16942.853786] Model parameter optimization (eps = 1.000000)
[00:43:41 -16941.655458] SLOW spr round 1 (radius: 5)
[00:44:17 -16935.862057] SLOW spr round 2 (radius: 5)
[00:44:52 -16933.163505] SLOW spr round 3 (radius: 5)
[00:45:25 -16933.161413] SLOW spr round 4 (radius: 10)
[00:46:00 -16926.965378] SLOW spr round 5 (radius: 5)
[00:46:51 -16925.674426] SLOW spr round 6 (radius: 5)
[00:47:16] [worker #2] ML tree search #9, logLikelihood: -16933.215266
[00:47:32 -16925.674186] SLOW spr round 7 (radius: 10)
[00:48:08 -16925.548463] SLOW spr round 8 (radius: 5)
[00:48:56 -16925.548449] SLOW spr round 9 (radius: 10)
[00:49:36 -16925.548449] SLOW spr round 10 (radius: 15)
[00:50:34 -16924.461930] SLOW spr round 11 (radius: 5)
[00:51:27 -16924.461839] SLOW spr round 12 (radius: 10)
[00:52:11 -16922.935462] SLOW spr round 13 (radius: 5)
[00:52:58 -16922.935426] SLOW spr round 14 (radius: 10)
[00:53:37 -16922.935425] SLOW spr round 15 (radius: 15)
[00:54:41 -16922.935425] SLOW spr round 16 (radius: 20)
[00:56:02 -16921.861715] SLOW spr round 17 (radius: 5)
[00:56:57 -16920.800831] SLOW spr round 18 (radius: 5)
[00:57:41 -16920.800691] SLOW spr round 19 (radius: 10)
[00:58:19 -16920.800689] SLOW spr round 20 (radius: 15)
[00:59:22 -16920.615740] SLOW spr round 21 (radius: 5)
[00:59:34] [worker #2] ML tree search #12, logLikelihood: -16928.021752
[01:00:15 -16919.185943] SLOW spr round 22 (radius: 5)
[01:00:57 -16919.184783] SLOW spr round 23 (radius: 10)
[01:01:35 -16919.184695] SLOW spr round 24 (radius: 15)
[01:02:38 -16919.184688] SLOW spr round 25 (radius: 20)
[01:03:59 -16919.184688] SLOW spr round 26 (radius: 25)
[01:05:14 -16919.184688] Model parameter optimization (eps = 0.100000)

[01:05:17] [worker #0] ML tree search #7, logLikelihood: -16919.086059

[01:05:17 -61960.514141] Initial branch length optimization
[01:05:18 -49878.908115] Model parameter optimization (eps = 10.000000)
[01:05:37] [worker #1] ML tree search #11, logLikelihood: -16937.186095
[01:05:40 -49668.152195] AUTODETECT spr round 1 (radius: 5)
[01:06:05 -29198.453478] AUTODETECT spr round 2 (radius: 10)
[01:06:39 -22476.462217] AUTODETECT spr round 3 (radius: 15)
[01:07:19 -19672.110368] AUTODETECT spr round 4 (radius: 20)
[01:08:00 -19010.742852] AUTODETECT spr round 5 (radius: 25)
[01:08:43 -18864.123503] SPR radius for FAST iterations: 25 (autodetect)
[01:08:43 -18864.123503] Model parameter optimization (eps = 3.000000)
[01:08:57 -18781.342795] FAST spr round 1 (radius: 25)
[01:09:29 -16997.284390] FAST spr round 2 (radius: 25)
[01:09:56 -16941.848823] FAST spr round 3 (radius: 25)
[01:10:19 -16940.754636] FAST spr round 4 (radius: 25)
[01:10:40 -16940.753097] Model parameter optimization (eps = 1.000000)
[01:10:49 -16939.292952] SLOW spr round 1 (radius: 5)
[01:11:25 -16938.006502] SLOW spr round 2 (radius: 5)
[01:11:59 -16936.982637] SLOW spr round 3 (radius: 5)
[01:12:32 -16936.982628] SLOW spr round 4 (radius: 10)
[01:13:07 -16928.283550] SLOW spr round 5 (radius: 5)
[01:14:00 -16923.504607] SLOW spr round 6 (radius: 5)
[01:14:41 -16922.822719] SLOW spr round 7 (radius: 5)
[01:15:18 -16922.822715] SLOW spr round 8 (radius: 10)
[01:15:53 -16921.111300] SLOW spr round 9 (radius: 5)
[01:16:30] [worker #2] ML tree search #15, logLikelihood: -16934.274951
[01:16:41 -16921.111295] SLOW spr round 10 (radius: 10)
[01:17:22 -16921.111295] SLOW spr round 11 (radius: 15)
[01:18:24 -16921.111295] SLOW spr round 12 (radius: 20)
[01:19:44 -16921.111295] SLOW spr round 13 (radius: 25)
[01:20:06] [worker #1] ML tree search #14, logLikelihood: -16926.966712
[01:21:00 -16921.111295] Model parameter optimization (eps = 0.100000)

[01:21:03] [worker #0] ML tree search #10, logLikelihood: -16921.056582

[01:21:04 -61898.406035] Initial branch length optimization
[01:21:05 -50328.682128] Model parameter optimization (eps = 10.000000)
[01:21:24 -50109.415987] AUTODETECT spr round 1 (radius: 5)
[01:21:50 -29150.984786] AUTODETECT spr round 2 (radius: 10)
[01:22:22 -23136.233264] AUTODETECT spr round 3 (radius: 15)
[01:23:03 -19614.422158] AUTODETECT spr round 4 (radius: 20)
[01:23:46 -18966.665032] AUTODETECT spr round 5 (radius: 25)
[01:24:27 -18898.735251] SPR radius for FAST iterations: 25 (autodetect)
[01:24:27 -18898.735251] Model parameter optimization (eps = 3.000000)
[01:24:40 -18820.796999] FAST spr round 1 (radius: 25)
[01:25:12 -16988.325722] FAST spr round 2 (radius: 25)
[01:25:39 -16939.851540] FAST spr round 3 (radius: 25)
[01:26:03 -16934.053546] FAST spr round 4 (radius: 25)
[01:26:25 -16933.539885] FAST spr round 5 (radius: 25)
[01:26:46 -16933.539874] Model parameter optimization (eps = 1.000000)
[01:26:51 -16932.905496] SLOW spr round 1 (radius: 5)
[01:27:27 -16931.602533] SLOW spr round 2 (radius: 5)
[01:28:02 -16931.602396] SLOW spr round 3 (radius: 10)
[01:28:37 -16929.776735] SLOW spr round 4 (radius: 5)
[01:29:28 -16923.432161] SLOW spr round 5 (radius: 5)
[01:30:11 -16923.431009] SLOW spr round 6 (radius: 10)
[01:30:48 -16922.345968] SLOW spr round 7 (radius: 5)
[01:31:37 -16922.191481] SLOW spr round 8 (radius: 5)
[01:32:16 -16922.191339] SLOW spr round 9 (radius: 10)
[01:32:52 -16922.191308] SLOW spr round 10 (radius: 15)
[01:33:50 -16922.090431] SLOW spr round 11 (radius: 5)
[01:34:28] [worker #2] ML tree search #18, logLikelihood: -16922.368645
[01:34:42 -16922.090350] SLOW spr round 12 (radius: 10)
[01:35:24 -16922.090344] SLOW spr round 13 (radius: 15)
[01:36:20 -16922.090339] SLOW spr round 14 (radius: 20)
[01:37:35 -16922.090333] SLOW spr round 15 (radius: 25)
[01:38:01] [worker #1] ML tree search #17, logLikelihood: -16925.257571
[01:38:45 -16922.090326] Model parameter optimization (eps = 0.100000)

[01:38:51] [worker #0] ML tree search #13, logLikelihood: -16921.687993

[01:38:51 -61533.562923] Initial branch length optimization
[01:38:52 -49555.026579] Model parameter optimization (eps = 10.000000)
[01:39:06 -49379.597033] AUTODETECT spr round 1 (radius: 5)
[01:39:33 -30292.436066] AUTODETECT spr round 2 (radius: 10)
[01:40:06 -23997.729692] AUTODETECT spr round 3 (radius: 15)
[01:40:49 -19581.077267] AUTODETECT spr round 4 (radius: 20)
[01:41:32 -18854.715514] AUTODETECT spr round 5 (radius: 25)
[01:42:17 -18665.873575] SPR radius for FAST iterations: 25 (autodetect)
[01:42:17 -18665.873575] Model parameter optimization (eps = 3.000000)
[01:42:31 -18604.890869] FAST spr round 1 (radius: 25)
[01:43:03 -17026.888359] FAST spr round 2 (radius: 25)
[01:43:30 -16943.377432] FAST spr round 3 (radius: 25)
[01:43:53 -16934.909390] FAST spr round 4 (radius: 25)
[01:44:15 -16932.095646] FAST spr round 5 (radius: 25)
[01:44:36 -16932.095254] Model parameter optimization (eps = 1.000000)
[01:44:43 -16931.006666] SLOW spr round 1 (radius: 5)
[01:45:19 -16929.710702] SLOW spr round 2 (radius: 5)
[01:45:53 -16929.709157] SLOW spr round 3 (radius: 10)
[01:46:26 -16929.709151] SLOW spr round 4 (radius: 15)
[01:47:26 -16929.709151] SLOW spr round 5 (radius: 20)
[01:48:34 -16929.709151] SLOW spr round 6 (radius: 25)
[01:48:34] [worker #1] ML tree search #20, logLikelihood: -16924.529414
[01:49:43 -16929.709151] Model parameter optimization (eps = 0.100000)

[01:49:47] [worker #0] ML tree search #16, logLikelihood: -16929.706100

[01:49:47 -61122.176618] Initial branch length optimization
[01:49:47 -49182.914675] Model parameter optimization (eps = 10.000000)
[01:50:07 -48991.404524] AUTODETECT spr round 1 (radius: 5)
[01:50:33 -30288.781261] AUTODETECT spr round 2 (radius: 10)
[01:51:04 -23296.890196] AUTODETECT spr round 3 (radius: 15)
[01:51:45 -19398.677463] AUTODETECT spr round 4 (radius: 20)
[01:52:31 -18869.472519] AUTODETECT spr round 5 (radius: 25)
[01:53:23 -18861.961340] SPR radius for FAST iterations: 25 (autodetect)
[01:53:23 -18861.961340] Model parameter optimization (eps = 3.000000)
[01:53:35 -18795.589964] FAST spr round 1 (radius: 25)
[01:54:06 -16969.228533] FAST spr round 2 (radius: 25)
[01:54:33 -16939.531055] FAST spr round 3 (radius: 25)
[01:54:57 -16931.767146] FAST spr round 4 (radius: 25)
[01:55:18 -16931.008220] FAST spr round 5 (radius: 25)
[01:55:39 -16930.919629] Model parameter optimization (eps = 1.000000)
[01:55:47 -16929.109643] SLOW spr round 1 (radius: 5)
[01:56:23 -16926.857031] SLOW spr round 2 (radius: 5)
[01:56:57 -16926.841259] SLOW spr round 3 (radius: 10)
[01:57:31 -16926.841039] SLOW spr round 4 (radius: 15)
[01:58:34 -16924.684155] SLOW spr round 5 (radius: 5)
[01:59:29 -16924.269510] SLOW spr round 6 (radius: 5)
[02:00:13 -16924.268766] SLOW spr round 7 (radius: 10)
[02:00:49 -16924.268727] SLOW spr round 8 (radius: 15)
[02:01:45 -16924.268721] SLOW spr round 9 (radius: 20)
[02:02:53 -16924.268720] SLOW spr round 10 (radius: 25)
[02:04:05 -16924.268720] Model parameter optimization (eps = 0.100000)

[02:04:09] [worker #0] ML tree search #19, logLikelihood: -16924.251527


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.156384,0.444457) (0.175658,0.782519) (0.394567,0.709868) (0.273391,1.876244) 
   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: -16919.086059

AIC score: 35084.172117 / AICc score: 812588.172117 / BIC score: 36870.646080
Free parameters (model + branch lengths): 623

WARNING: Number of free parameters (K=623) is larger than alignment size (n=130).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 97 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NHP3/3_mltree/A6NHP3.raxml.log

Analysis started: 26-Jul-2021 05:25:32 / finished: 26-Jul-2021 07:29:41

Elapsed time: 7449.368 seconds

Consumed energy: 312.847 Wh (= 2 km in an electric car, or 8 km with an e-scooter!)