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 18-Jun-2021 17:07:02 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/2_msa/Q05086_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/2_msa/Q05086_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 573 sites

WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_G1NPJ3_G1NPJ3_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_H0ZJ61_H0ZJ61_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_U3JN35_U3JN35_FICAL_59894 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_U3J4R2_U3J4R2_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A0Q3U4V9_A0A0Q3U4V9_AMAAE_12930 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A091EWQ8_A0A091EWQ8_CORBR_85066 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A093QGF8_A0A093QGF8_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A091VQX0_A0A091VQX0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A087QJ00_A0A087QJ00_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A093HCA2_A0A093HCA2_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A091VDL4_A0A091VDL4_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A099Z8T9_A0A099Z8T9_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A0A0ACC0_A0A0A0ACC0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A093GK00_A0A093GK00_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A091I9Y4_A0A091I9Y4_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A1V4JB33_A0A1V4JB33_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A218V507_A0A218V507_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A226MQF8_A0A226MQF8_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1D5PTI9_A0A1D5PTI9_CHICK_9031 and tr_A0A226P5L4_A0A226P5L4_COLVI_9014 are exactly identical!
WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_G1N136_G1N136_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3XTJ3_M3XTJ3_MUSPF_9669 and tr_F1PBV3_F1PBV3_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XTJ3_M3XTJ3_MUSPF_9669 and tr_A0A2U3ZVJ1_A0A2U3ZVJ1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3XTJ3_M3XTJ3_MUSPF_9669 and tr_A0A2U3XDU8_A0A2U3XDU8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3XTJ3_M3XTJ3_MUSPF_9669 and tr_A0A2Y9L642_A0A2Y9L642_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YKL4_M3YKL4_MUSPF_9669 and tr_A0A2U3VG86_A0A2U3VG86_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YKL4_M3YKL4_MUSPF_9669 and tr_A0A2Y9J1T5_A0A2Y9J1T5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0D8JUQ9_A0A0D8JUQ9_COCIM_246410 and tr_A0A0J6YDW7_A0A0J6YDW7_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QKL2_B6QKL2_TALMQ_441960 and tr_A0A093UTG2_A0A093UTG2_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_A0A2I2YX52_A0A2I2YX52_GORGO_9595 and tr_A0A2I3SJZ1_A0A2I3SJZ1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YX52_A0A2I2YX52_GORGO_9595 and sp_Q05086_UBE3A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YX52_A0A2I2YX52_GORGO_9595 and tr_F7H5M4_F7H5M4_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3R445_G3R445_GORGO_9595 and tr_A0A2I3RAM0_A0A2I3RAM0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R445_G3R445_GORGO_9595 and sp_Q5U5R9_HECD2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NAR8_H2NAR8_PONAB_9601 and tr_G1U7C7_G1U7C7_RABIT_9986 are exactly identical!
WARNING: Sequences tr_H2NAR8_H2NAR8_PONAB_9601 and tr_K7B173_K7B173_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NAR8_H2NAR8_PONAB_9601 and tr_A0A2R9BDZ0_A0A2R9BDZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A179URI7_A0A179URI7_BLAGS_559298 and tr_C5GDD8_C5GDD8_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_W5P440_W5P440_SHEEP_9940 and tr_E1BAV2_E1BAV2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A4IFN7_A4IFN7_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A0A2U3V2G7_A0A2U3V2G7_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A0A2Y9QGX9_A0A2Y9QGX9_DELLE_9749 are exactly identical!
WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A0A2Y9F4C9_A0A2Y9F4C9_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A0A383ZW85_A0A383ZW85_BALAS_310752 are exactly identical!
WARNING: Sequences tr_C6HAR4_C6HAR4_AJECH_544712 and tr_F0UI26_F0UI26_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0K0JUU3_A0A0K0JUU3_BRUMA_6279 and tr_A0A0N4TLT6_A0A0N4TLT6_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A1D5R2K6_A0A1D5R2K6_MACMU_9544 and tr_G7PDJ5_G7PDJ5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R2K6_A0A1D5R2K6_MACMU_9544 and tr_A0A2I3MGE3_A0A2I3MGE3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R2K6_A0A1D5R2K6_MACMU_9544 and tr_A0A2K6DXW4_A0A2K6DXW4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6RKN5_F6RKN5_MACMU_9544 and tr_A0A0D9R273_A0A0D9R273_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6RKN5_F6RKN5_MACMU_9544 and tr_A0A2K5MR62_A0A2K5MR62_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6RKN5_F6RKN5_MACMU_9544 and tr_A0A2K6BA20_A0A2K6BA20_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6RKN5_F6RKN5_MACMU_9544 and tr_A0A2K6A2Y9_A0A2K6A2Y9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_G7PDD3_G7PDD3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G2YCG1_G2YCG1_BOTF4_999810 and tr_M7TH54_M7TH54_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2STK2_F2STK2_TRIRC_559305 and tr_A0A178EV54_A0A178EV54_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G1LKJ5_G1LKJ5_AILME_9646 and tr_A0A384DBX2_A0A384DBX2_URSMA_29073 are exactly identical!
WARNING: Sequences tr_S0DXK5_S0DXK5_GIBF5_1279085 and tr_A0A365N362_A0A365N362_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_W2PRJ4_W2PRJ4_PHYPN_761204 and tr_W2KHV7_W2KHV7_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A0D9R593_A0A0D9R593_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K5MP27_A0A2K5MP27_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K6C0X7_A0A2K6C0X7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K5YV13_A0A2K5YV13_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A094EDZ8_A0A094EDZ8_9PEZI_1420912 and tr_A0A1B8GGE8_A0A1B8GGE8_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_X0D2Y0_X0D2Y0_FUSOX_1089458 and tr_A0A2H3HFM4_A0A2H3HFM4_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A151NXE7_A0A151NXE7_ALLMI_8496 and tr_A0A1U7RMT8_A0A1U7RMT8_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151P0V4_A0A151P0V4_ALLMI_8496 and tr_A0A1U8D3T6_A0A1U8D3T6_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A1S3MYE0_A0A1S3MYE0_SALSA_8030 and tr_A0A1S3QGR7_A0A1S3QGR7_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A2U4BEW1_A0A2U4BEW1_TURTR_9739 and tr_A0A2Y9PTV6_A0A2Y9PTV6_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4BEW1_A0A2U4BEW1_TURTR_9739 and tr_A0A2Y9FEP9_A0A2Y9FEP9_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 69

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.reduced.phy

Alignment comprises 1 partitions and 573 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 573 / 573
Gaps: 5.25 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 7 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 / 82 / 6560
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1032442.135347] Initial branch length optimization
[00:00:05 -866885.946102] Model parameter optimization (eps = 10.000000)
[00:00:30 -865127.478193] AUTODETECT spr round 1 (radius: 5)
[00:02:24 -560893.512886] AUTODETECT spr round 2 (radius: 10)
[00:04:32 -432256.094001] AUTODETECT spr round 3 (radius: 15)
[00:06:45 -357519.845003] AUTODETECT spr round 4 (radius: 20)
[00:09:13 -330910.043553] AUTODETECT spr round 5 (radius: 25)
[00:12:16 -322930.420776] SPR radius for FAST iterations: 25 (autodetect)
[00:12:16 -322930.420776] Model parameter optimization (eps = 3.000000)
[00:12:32 -322714.409652] FAST spr round 1 (radius: 25)
[00:15:07 -272185.371479] FAST spr round 2 (radius: 25)
[00:17:08 -268083.298699] FAST spr round 3 (radius: 25)
[00:18:59 -267646.317652] FAST spr round 4 (radius: 25)
[00:20:37 -267581.752593] FAST spr round 5 (radius: 25)
[00:22:08 -267571.122484] FAST spr round 6 (radius: 25)
[00:23:37 -267571.121612] Model parameter optimization (eps = 1.000000)
[00:23:49 -267567.605471] SLOW spr round 1 (radius: 5)
[00:25:47 -267524.713064] SLOW spr round 2 (radius: 5)
[00:27:39 -267518.784639] SLOW spr round 3 (radius: 5)
[00:29:27 -267518.784412] SLOW spr round 4 (radius: 10)
[00:31:23 -267516.920885] SLOW spr round 5 (radius: 5)
[00:33:37 -267512.141885] SLOW spr round 6 (radius: 5)
[00:35:36 -267512.141652] SLOW spr round 7 (radius: 10)
[00:37:33 -267512.141647] SLOW spr round 8 (radius: 15)
[00:40:20 -267512.141645] SLOW spr round 9 (radius: 20)
[00:44:21 -267512.141643] SLOW spr round 10 (radius: 25)
[00:49:22 -267512.141641] Model parameter optimization (eps = 0.100000)

[00:49:30] ML tree search #1, logLikelihood: -267511.985960

[00:49:30 -1034114.028239] Initial branch length optimization
[00:49:33 -872962.825034] Model parameter optimization (eps = 10.000000)
[00:49:57 -871279.600099] AUTODETECT spr round 1 (radius: 5)
[00:51:56 -583482.373107] AUTODETECT spr round 2 (radius: 10)
[00:54:12 -420665.985041] AUTODETECT spr round 3 (radius: 15)
[00:56:26 -350931.051358] AUTODETECT spr round 4 (radius: 20)
[00:58:53 -318028.745156] AUTODETECT spr round 5 (radius: 25)
[01:01:46 -312028.868133] SPR radius for FAST iterations: 25 (autodetect)
[01:01:46 -312028.868133] Model parameter optimization (eps = 3.000000)
[01:02:07 -311774.195392] FAST spr round 1 (radius: 25)
[01:04:39 -269210.389548] FAST spr round 2 (radius: 25)
[01:06:39 -267692.748618] FAST spr round 3 (radius: 25)
[01:08:20 -267597.238250] FAST spr round 4 (radius: 25)
[01:09:55 -267580.642892] FAST spr round 5 (radius: 25)
[01:11:26 -267580.639511] Model parameter optimization (eps = 1.000000)
[01:11:38 -267578.788343] SLOW spr round 1 (radius: 5)
[01:13:35 -267533.710734] SLOW spr round 2 (radius: 5)
[01:15:30 -267521.256629] SLOW spr round 3 (radius: 5)
[01:17:22 -267519.366778] SLOW spr round 4 (radius: 5)
[01:19:14 -267518.326974] SLOW spr round 5 (radius: 5)
[01:21:04 -267518.326961] SLOW spr round 6 (radius: 10)
[01:23:01 -267516.318966] SLOW spr round 7 (radius: 5)
[01:25:16 -267516.318599] SLOW spr round 8 (radius: 10)
[01:27:23 -267516.318590] SLOW spr round 9 (radius: 15)
[01:30:14 -267516.318586] SLOW spr round 10 (radius: 20)
[01:34:29 -267516.318583] SLOW spr round 11 (radius: 25)
[01:39:48 -267516.318582] Model parameter optimization (eps = 0.100000)

[01:39:56] ML tree search #2, logLikelihood: -267516.050576

[01:39:57 -1037366.260215] Initial branch length optimization
[01:40:00 -870146.417913] Model parameter optimization (eps = 10.000000)
[01:40:29 -868309.343605] AUTODETECT spr round 1 (radius: 5)
[01:42:28 -559358.365539] AUTODETECT spr round 2 (radius: 10)
[01:44:43 -420786.324963] AUTODETECT spr round 3 (radius: 15)
[01:46:57 -355243.067031] AUTODETECT spr round 4 (radius: 20)
[01:49:26 -315996.961161] AUTODETECT spr round 5 (radius: 25)
[01:52:04 -311916.981023] SPR radius for FAST iterations: 25 (autodetect)
[01:52:04 -311916.981023] Model parameter optimization (eps = 3.000000)
[01:52:21 -311811.310800] FAST spr round 1 (radius: 25)
[01:54:46 -269462.414065] FAST spr round 2 (radius: 25)
[01:56:41 -267708.358282] FAST spr round 3 (radius: 25)
[01:58:24 -267617.644772] FAST spr round 4 (radius: 25)
[02:00:00 -267609.161619] FAST spr round 5 (radius: 25)
[02:01:31 -267602.912063] FAST spr round 6 (radius: 25)
[02:03:01 -267602.910509] Model parameter optimization (eps = 1.000000)
[02:03:18 -267591.918999] SLOW spr round 1 (radius: 5)
[02:05:17 -267533.299858] SLOW spr round 2 (radius: 5)
[02:07:11 -267531.265222] SLOW spr round 3 (radius: 5)
[02:09:03 -267531.265050] SLOW spr round 4 (radius: 10)
[02:10:58 -267531.265033] SLOW spr round 5 (radius: 15)
[02:13:51 -267531.265025] SLOW spr round 6 (radius: 20)
[02:17:56 -267531.265020] SLOW spr round 7 (radius: 25)
[02:22:58 -267531.265016] Model parameter optimization (eps = 0.100000)

[02:23:09] ML tree search #3, logLikelihood: -267530.685993

[02:23:09 -1035982.400957] Initial branch length optimization
[02:23:15 -875053.573273] Model parameter optimization (eps = 10.000000)
[02:23:41 -873196.803584] AUTODETECT spr round 1 (radius: 5)
[02:25:38 -569680.604777] AUTODETECT spr round 2 (radius: 10)
[02:27:47 -429960.216370] AUTODETECT spr round 3 (radius: 15)
[02:30:03 -366574.653563] AUTODETECT spr round 4 (radius: 20)
[02:32:29 -329839.149718] AUTODETECT spr round 5 (radius: 25)
[02:35:02 -316594.648227] SPR radius for FAST iterations: 25 (autodetect)
[02:35:02 -316594.648227] Model parameter optimization (eps = 3.000000)
[02:35:21 -316412.328114] FAST spr round 1 (radius: 25)
[02:37:57 -269527.358628] FAST spr round 2 (radius: 25)
[02:39:47 -267731.367276] FAST spr round 3 (radius: 25)
[02:41:29 -267629.660867] FAST spr round 4 (radius: 25)
[02:43:05 -267622.380784] FAST spr round 5 (radius: 25)
[02:44:37 -267622.379607] Model parameter optimization (eps = 1.000000)
[02:44:51 -267619.620011] SLOW spr round 1 (radius: 5)
[02:46:51 -267526.883679] SLOW spr round 2 (radius: 5)
[02:48:46 -267514.986490] SLOW spr round 3 (radius: 5)
[02:50:39 -267512.096353] SLOW spr round 4 (radius: 5)
[02:52:29 -267512.095870] SLOW spr round 5 (radius: 10)
[02:54:25 -267512.095861] SLOW spr round 6 (radius: 15)
[02:57:20 -267512.095858] SLOW spr round 7 (radius: 20)
[03:01:27 -267512.095855] SLOW spr round 8 (radius: 25)
[03:06:40 -267512.095852] Model parameter optimization (eps = 0.100000)

[03:06:46] ML tree search #4, logLikelihood: -267511.894737

[03:06:46 -1034460.911146] Initial branch length optimization
[03:06:51 -868480.335815] Model parameter optimization (eps = 10.000000)
[03:07:22 -866767.102967] AUTODETECT spr round 1 (radius: 5)
[03:09:20 -569674.170683] AUTODETECT spr round 2 (radius: 10)
[03:11:30 -416854.222960] AUTODETECT spr round 3 (radius: 15)
[03:13:41 -359313.134879] AUTODETECT spr round 4 (radius: 20)
[03:16:08 -324589.288200] AUTODETECT spr round 5 (radius: 25)
[03:19:01 -311600.183812] SPR radius for FAST iterations: 25 (autodetect)
[03:19:01 -311600.183812] Model parameter optimization (eps = 3.000000)
[03:19:17 -311349.822852] FAST spr round 1 (radius: 25)
[03:21:46 -269050.213113] FAST spr round 2 (radius: 25)
[03:23:46 -267708.375627] FAST spr round 3 (radius: 25)
[03:25:38 -267623.448538] FAST spr round 4 (radius: 25)
[03:27:16 -267604.488470] FAST spr round 5 (radius: 25)
[03:28:50 -267595.532119] FAST spr round 6 (radius: 25)
[03:30:21 -267595.531168] Model parameter optimization (eps = 1.000000)
[03:30:35 -267584.721321] SLOW spr round 1 (radius: 5)
[03:32:34 -267526.490628] SLOW spr round 2 (radius: 5)
[03:34:28 -267521.851259] SLOW spr round 3 (radius: 5)
[03:36:18 -267521.850929] SLOW spr round 4 (radius: 10)
[03:38:16 -267521.850899] SLOW spr round 5 (radius: 15)
[03:41:13 -267521.850891] SLOW spr round 6 (radius: 20)
[03:45:26 -267521.850887] SLOW spr round 7 (radius: 25)
[03:50:41 -267521.850884] Model parameter optimization (eps = 0.100000)

[03:50:47] ML tree search #5, logLikelihood: -267521.757623

[03:50:47 -1034275.477053] Initial branch length optimization
[03:50:50 -870410.107471] Model parameter optimization (eps = 10.000000)
[03:51:21 -868520.981711] AUTODETECT spr round 1 (radius: 5)
[03:53:19 -571388.593645] AUTODETECT spr round 2 (radius: 10)
[03:55:31 -427238.752006] AUTODETECT spr round 3 (radius: 15)
[03:57:47 -350352.951834] AUTODETECT spr round 4 (radius: 20)
[04:00:15 -323002.875643] AUTODETECT spr round 5 (radius: 25)
[04:03:05 -315526.345657] SPR radius for FAST iterations: 25 (autodetect)
[04:03:05 -315526.345657] Model parameter optimization (eps = 3.000000)
[04:03:24 -315357.249719] FAST spr round 1 (radius: 25)
[04:05:54 -269016.842669] FAST spr round 2 (radius: 25)
[04:07:52 -267686.932308] FAST spr round 3 (radius: 25)
[04:09:39 -267633.386808] FAST spr round 4 (radius: 25)
[04:11:14 -267614.833987] FAST spr round 5 (radius: 25)
[04:12:45 -267614.242579] FAST spr round 6 (radius: 25)
[04:14:15 -267614.241870] Model parameter optimization (eps = 1.000000)
[04:14:22 -267612.906050] SLOW spr round 1 (radius: 5)
[04:16:19 -267536.240821] SLOW spr round 2 (radius: 5)
[04:18:14 -267532.756733] SLOW spr round 3 (radius: 5)
[04:20:05 -267532.756644] SLOW spr round 4 (radius: 10)
[04:22:03 -267527.963092] SLOW spr round 5 (radius: 5)
[04:24:19 -267527.962864] SLOW spr round 6 (radius: 10)
[04:26:25 -267527.962843] SLOW spr round 7 (radius: 15)
[04:29:13 -267527.962832] SLOW spr round 8 (radius: 20)
[04:33:17 -267527.962826] SLOW spr round 9 (radius: 25)
[04:38:07 -267527.962823] Model parameter optimization (eps = 0.100000)

[04:38:10] ML tree search #6, logLikelihood: -267527.961780

[04:38:10 -1039583.006796] Initial branch length optimization
[04:38:15 -877478.883665] Model parameter optimization (eps = 10.000000)
[04:38:40 -875586.342166] AUTODETECT spr round 1 (radius: 5)
[04:40:36 -560550.336963] AUTODETECT spr round 2 (radius: 10)
[04:42:51 -413083.630780] AUTODETECT spr round 3 (radius: 15)
[04:45:09 -341805.694107] AUTODETECT spr round 4 (radius: 20)
[04:47:25 -314267.671569] AUTODETECT spr round 5 (radius: 25)
[04:50:15 -307901.263829] SPR radius for FAST iterations: 25 (autodetect)
[04:50:15 -307901.263829] Model parameter optimization (eps = 3.000000)
[04:50:31 -307733.393745] FAST spr round 1 (radius: 25)
[04:52:57 -268786.485847] FAST spr round 2 (radius: 25)
[04:54:56 -267700.923406] FAST spr round 3 (radius: 25)
[04:56:43 -267623.771025] FAST spr round 4 (radius: 25)
[04:58:19 -267614.549979] FAST spr round 5 (radius: 25)
[04:59:50 -267614.549978] Model parameter optimization (eps = 1.000000)
[05:00:03 -267606.670362] SLOW spr round 1 (radius: 5)
[05:02:02 -267533.084942] SLOW spr round 2 (radius: 5)
[05:03:58 -267530.798798] SLOW spr round 3 (radius: 5)
[05:05:49 -267530.638542] SLOW spr round 4 (radius: 5)
[05:07:39 -267530.638526] SLOW spr round 5 (radius: 10)
[05:09:34 -267529.610379] SLOW spr round 6 (radius: 5)
[05:11:48 -267529.607869] SLOW spr round 7 (radius: 10)
[05:13:55 -267529.607001] SLOW spr round 8 (radius: 15)
[05:16:42 -267529.606704] SLOW spr round 9 (radius: 20)
[05:20:56 -267529.606603] SLOW spr round 10 (radius: 25)
[05:26:16 -267529.606568] Model parameter optimization (eps = 0.100000)

[05:26:24] ML tree search #7, logLikelihood: -267529.142607

[05:26:24 -1028599.711176] Initial branch length optimization
[05:26:28 -864499.798263] Model parameter optimization (eps = 10.000000)
[05:26:55 -862679.577865] AUTODETECT spr round 1 (radius: 5)
[05:28:54 -566599.895243] AUTODETECT spr round 2 (radius: 10)
[05:31:09 -422561.235007] AUTODETECT spr round 3 (radius: 15)
[05:33:27 -348566.986163] AUTODETECT spr round 4 (radius: 20)
[05:36:02 -312542.728200] AUTODETECT spr round 5 (radius: 25)
[05:38:51 -305842.146926] SPR radius for FAST iterations: 25 (autodetect)
[05:38:51 -305842.146926] Model parameter optimization (eps = 3.000000)
[05:39:08 -305653.597320] FAST spr round 1 (radius: 25)
[05:41:41 -268526.988158] FAST spr round 2 (radius: 25)
[05:43:40 -267712.117744] FAST spr round 3 (radius: 25)
[05:45:27 -267629.747714] FAST spr round 4 (radius: 25)
[05:47:01 -267626.234531] FAST spr round 5 (radius: 25)
[05:48:33 -267626.234186] Model parameter optimization (eps = 1.000000)
[05:48:49 -267619.028922] SLOW spr round 1 (radius: 5)
[05:50:52 -267545.370647] SLOW spr round 2 (radius: 5)
[05:52:47 -267537.568914] SLOW spr round 3 (radius: 5)
[05:54:41 -267535.839156] SLOW spr round 4 (radius: 5)
[05:56:32 -267535.839006] SLOW spr round 5 (radius: 10)
[05:58:27 -267533.818331] SLOW spr round 6 (radius: 5)
[06:00:41 -267533.818137] SLOW spr round 7 (radius: 10)
[06:02:46 -267533.818134] SLOW spr round 8 (radius: 15)
[06:05:35 -267533.818132] SLOW spr round 9 (radius: 20)
[06:09:47 -267533.818131] SLOW spr round 10 (radius: 25)
[06:14:58 -267533.818130] Model parameter optimization (eps = 0.100000)

[06:15:09] ML tree search #8, logLikelihood: -267533.340212

[06:15:09 -1030325.916585] Initial branch length optimization
[06:15:13 -861366.716249] Model parameter optimization (eps = 10.000000)
[06:15:38 -859744.626061] AUTODETECT spr round 1 (radius: 5)
[06:17:34 -569763.152283] AUTODETECT spr round 2 (radius: 10)
[06:19:46 -445915.247797] AUTODETECT spr round 3 (radius: 15)
[06:22:02 -371410.509049] AUTODETECT spr round 4 (radius: 20)
[06:24:27 -338106.128073] AUTODETECT spr round 5 (radius: 25)
[06:27:02 -321425.867664] SPR radius for FAST iterations: 25 (autodetect)
[06:27:02 -321425.867664] Model parameter optimization (eps = 3.000000)
[06:27:08 -321418.595660] FAST spr round 1 (radius: 25)
[06:29:32 -269819.569651] FAST spr round 2 (radius: 25)
[06:31:26 -267912.884031] FAST spr round 3 (radius: 25)
[06:33:06 -267833.302878] FAST spr round 4 (radius: 25)
[06:34:44 -267787.883155] FAST spr round 5 (radius: 25)
[06:36:15 -267781.382604] FAST spr round 6 (radius: 25)
[06:37:44 -267781.382577] Model parameter optimization (eps = 1.000000)
[06:38:03 -267643.995297] SLOW spr round 1 (radius: 5)
[06:40:00 -267564.717933] SLOW spr round 2 (radius: 5)
[06:41:55 -267555.549968] SLOW spr round 3 (radius: 5)
[06:43:45 -267555.549844] SLOW spr round 4 (radius: 10)
[06:45:42 -267553.762428] SLOW spr round 5 (radius: 5)
[06:47:55 -267553.762167] SLOW spr round 6 (radius: 10)
[06:49:59 -267553.762165] SLOW spr round 7 (radius: 15)
[06:52:44 -267553.762163] SLOW spr round 8 (radius: 20)
[06:56:52 -267553.762161] SLOW spr round 9 (radius: 25)
[07:01:48 -267553.762160] Model parameter optimization (eps = 0.100000)

[07:02:00] ML tree search #9, logLikelihood: -267553.249352

[07:02:00 -1036490.746900] Initial branch length optimization
[07:02:06 -874653.155278] Model parameter optimization (eps = 10.000000)
[07:02:42 -872662.953195] AUTODETECT spr round 1 (radius: 5)
[07:04:38 -571835.619677] AUTODETECT spr round 2 (radius: 10)
[07:06:52 -427754.313279] AUTODETECT spr round 3 (radius: 15)
[07:09:12 -337348.359477] AUTODETECT spr round 4 (radius: 20)
[07:11:50 -312955.018908] AUTODETECT spr round 5 (radius: 25)
[07:14:27 -303992.048942] SPR radius for FAST iterations: 25 (autodetect)
[07:14:27 -303992.048942] Model parameter optimization (eps = 3.000000)
[07:14:45 -303836.016062] FAST spr round 1 (radius: 25)
[07:17:10 -269131.981660] FAST spr round 2 (radius: 25)
[07:19:05 -267693.270120] FAST spr round 3 (radius: 25)
[07:20:49 -267593.741641] FAST spr round 4 (radius: 25)
[07:22:21 -267587.502200] FAST spr round 5 (radius: 25)
[07:23:50 -267587.502108] Model parameter optimization (eps = 1.000000)
[07:24:04 -267570.909468] SLOW spr round 1 (radius: 5)
[07:26:00 -267525.678126] SLOW spr round 2 (radius: 5)
[07:27:55 -267519.574082] SLOW spr round 3 (radius: 5)
[07:29:43 -267519.574041] SLOW spr round 4 (radius: 10)
[07:31:36 -267519.574040] SLOW spr round 5 (radius: 15)
[07:34:33 -267519.574038] SLOW spr round 6 (radius: 20)
[07:38:38 -267519.574036] SLOW spr round 7 (radius: 25)
[07:43:46 -267519.574035] Model parameter optimization (eps = 0.100000)

[07:43:50] ML tree search #10, logLikelihood: -267519.553371

[07:43:50 -1028636.484079] Initial branch length optimization
[07:43:55 -865316.110571] Model parameter optimization (eps = 10.000000)
[07:44:21 -863547.661167] AUTODETECT spr round 1 (radius: 5)
[07:46:17 -566567.562004] AUTODETECT spr round 2 (radius: 10)
[07:48:26 -433613.951184] AUTODETECT spr round 3 (radius: 15)
[07:50:40 -348794.815350] AUTODETECT spr round 4 (radius: 20)
[07:53:01 -322165.274886] AUTODETECT spr round 5 (radius: 25)
[07:56:10 -315152.956489] SPR radius for FAST iterations: 25 (autodetect)
[07:56:10 -315152.956489] Model parameter optimization (eps = 3.000000)
[07:56:27 -315021.775617] FAST spr round 1 (radius: 25)
[07:58:57 -269297.929026] FAST spr round 2 (radius: 25)
[08:00:56 -267819.154473] FAST spr round 3 (radius: 25)
[08:02:45 -267658.114952] FAST spr round 4 (radius: 25)
[08:04:22 -267627.722895] FAST spr round 5 (radius: 25)
[08:05:52 -267615.628666] FAST spr round 6 (radius: 25)
[08:07:22 -267612.470608] FAST spr round 7 (radius: 25)
[08:08:51 -267604.276291] FAST spr round 8 (radius: 25)
[08:10:19 -267604.276153] Model parameter optimization (eps = 1.000000)
[08:10:32 -267595.736831] SLOW spr round 1 (radius: 5)
[08:12:28 -267536.044776] SLOW spr round 2 (radius: 5)
[08:14:18 -267534.265985] SLOW spr round 3 (radius: 5)
[08:16:06 -267534.265981] SLOW spr round 4 (radius: 10)
[08:18:00 -267534.265980] SLOW spr round 5 (radius: 15)
[08:20:57 -267534.265980] SLOW spr round 6 (radius: 20)
[08:24:59 -267534.265980] SLOW spr round 7 (radius: 25)
[08:30:02 -267534.265980] Model parameter optimization (eps = 0.100000)

[08:30:12] ML tree search #11, logLikelihood: -267533.969342

[08:30:12 -1031331.859358] Initial branch length optimization
[08:30:16 -864475.092420] Model parameter optimization (eps = 10.000000)
[08:30:42 -862820.942363] AUTODETECT spr round 1 (radius: 5)
[08:32:38 -568750.267855] AUTODETECT spr round 2 (radius: 10)
[08:34:49 -431211.192181] AUTODETECT spr round 3 (radius: 15)
[08:36:58 -360231.675934] AUTODETECT spr round 4 (radius: 20)
[08:39:25 -313366.813331] AUTODETECT spr round 5 (radius: 25)
[08:42:15 -304565.268917] SPR radius for FAST iterations: 25 (autodetect)
[08:42:15 -304565.268917] Model parameter optimization (eps = 3.000000)
[08:42:37 -304393.700986] FAST spr round 1 (radius: 25)
[08:45:02 -269128.742077] FAST spr round 2 (radius: 25)
[08:46:56 -267760.293388] FAST spr round 3 (radius: 25)
[08:48:40 -267702.851575] FAST spr round 4 (radius: 25)
[08:50:18 -267622.288447] FAST spr round 5 (radius: 25)
[08:51:49 -267608.109915] FAST spr round 6 (radius: 25)
[08:53:17 -267608.109704] Model parameter optimization (eps = 1.000000)
[08:53:29 -267599.972601] SLOW spr round 1 (radius: 5)
[08:55:24 -267539.117247] SLOW spr round 2 (radius: 5)
[08:57:17 -267535.217961] SLOW spr round 3 (radius: 5)
[08:59:05 -267535.217749] SLOW spr round 4 (radius: 10)
[09:00:58 -267535.217728] SLOW spr round 5 (radius: 15)
[09:03:48 -267535.217714] SLOW spr round 6 (radius: 20)
[09:07:43 -267535.217701] SLOW spr round 7 (radius: 25)
[09:12:34 -267535.217689] Model parameter optimization (eps = 0.100000)

[09:12:42] ML tree search #12, logLikelihood: -267535.082101

[09:12:42 -1037109.181594] Initial branch length optimization
[09:12:46 -871493.495839] Model parameter optimization (eps = 10.000000)
[09:13:13 -869718.877585] AUTODETECT spr round 1 (radius: 5)
[09:15:10 -560924.809809] AUTODETECT spr round 2 (radius: 10)
[09:17:20 -409060.153020] AUTODETECT spr round 3 (radius: 15)
[09:19:34 -330324.588861] AUTODETECT spr round 4 (radius: 20)
[09:22:00 -310324.896174] AUTODETECT spr round 5 (radius: 25)
[09:24:46 -304551.112027] SPR radius for FAST iterations: 25 (autodetect)
[09:24:46 -304551.112027] Model parameter optimization (eps = 3.000000)
[09:25:00 -304406.320654] FAST spr round 1 (radius: 25)
[09:27:24 -268930.764961] FAST spr round 2 (radius: 25)
[09:29:21 -267709.290920] FAST spr round 3 (radius: 25)
[09:31:01 -267598.655397] FAST spr round 4 (radius: 25)
[09:32:35 -267586.422548] FAST spr round 5 (radius: 25)
[09:34:03 -267586.418587] Model parameter optimization (eps = 1.000000)
[09:34:18 -267579.616228] SLOW spr round 1 (radius: 5)
[09:36:15 -267525.548335] SLOW spr round 2 (radius: 5)
[09:38:05 -267524.796120] SLOW spr round 3 (radius: 5)
[09:39:54 -267524.796090] SLOW spr round 4 (radius: 10)
[09:41:48 -267524.795693] SLOW spr round 5 (radius: 15)
[09:44:40 -267524.795691] SLOW spr round 6 (radius: 20)
[09:48:36 -267524.795690] SLOW spr round 7 (radius: 25)
[09:53:22 -267524.795688] Model parameter optimization (eps = 0.100000)

[09:53:26] ML tree search #13, logLikelihood: -267524.752542

[09:53:27 -1036716.830157] Initial branch length optimization
[09:53:31 -873163.175526] Model parameter optimization (eps = 10.000000)
[09:53:56 -871280.788791] AUTODETECT spr round 1 (radius: 5)
[09:55:54 -580537.275603] AUTODETECT spr round 2 (radius: 10)
[09:58:03 -421696.842706] AUTODETECT spr round 3 (radius: 15)
[10:00:14 -351979.492230] AUTODETECT spr round 4 (radius: 20)
[10:02:38 -314004.798995] AUTODETECT spr round 5 (radius: 25)
[10:05:25 -308205.021074] SPR radius for FAST iterations: 25 (autodetect)
[10:05:25 -308205.021074] Model parameter optimization (eps = 3.000000)
[10:05:46 -308019.852654] FAST spr round 1 (radius: 25)
[10:08:12 -268862.501637] FAST spr round 2 (radius: 25)
[10:10:07 -267680.997889] FAST spr round 3 (radius: 25)
[10:11:49 -267616.016212] FAST spr round 4 (radius: 25)
[10:13:21 -267607.461180] FAST spr round 5 (radius: 25)
[10:14:50 -267607.461136] Model parameter optimization (eps = 1.000000)
[10:15:02 -267604.445508] SLOW spr round 1 (radius: 5)
[10:17:02 -267560.075185] SLOW spr round 2 (radius: 5)
[10:18:55 -267552.628413] SLOW spr round 3 (radius: 5)
[10:20:45 -267552.627804] SLOW spr round 4 (radius: 10)
[10:22:38 -267552.627762] SLOW spr round 5 (radius: 15)
[10:25:30 -267552.627751] SLOW spr round 6 (radius: 20)
[10:29:27 -267552.627746] SLOW spr round 7 (radius: 25)
[10:34:23 -267552.627743] Model parameter optimization (eps = 0.100000)

[10:34:27] ML tree search #14, logLikelihood: -267552.594450

[10:34:27 -1038078.477299] Initial branch length optimization
[10:34:31 -874124.365997] Model parameter optimization (eps = 10.000000)
[10:35:01 -872265.995008] AUTODETECT spr round 1 (radius: 5)
[10:36:56 -571542.379534] AUTODETECT spr round 2 (radius: 10)
[10:39:03 -425929.086749] AUTODETECT spr round 3 (radius: 15)
[10:41:10 -367895.014704] AUTODETECT spr round 4 (radius: 20)
[10:43:39 -332903.926083] AUTODETECT spr round 5 (radius: 25)
[10:46:24 -320793.240579] SPR radius for FAST iterations: 25 (autodetect)
[10:46:24 -320793.240579] Model parameter optimization (eps = 3.000000)
[10:46:32 -320788.139903] FAST spr round 1 (radius: 25)
[10:48:58 -270187.356780] FAST spr round 2 (radius: 25)
[10:50:53 -267903.988172] FAST spr round 3 (radius: 25)
[10:52:36 -267759.991453] FAST spr round 4 (radius: 25)
[10:54:09 -267732.810225] FAST spr round 5 (radius: 25)
[10:55:37 -267732.809658] Model parameter optimization (eps = 1.000000)
[10:55:52 -267615.700446] SLOW spr round 1 (radius: 5)
[10:57:50 -267531.991422] SLOW spr round 2 (radius: 5)
[10:59:45 -267517.737719] SLOW spr round 3 (radius: 5)
[11:01:34 -267517.737691] SLOW spr round 4 (radius: 10)
[11:03:28 -267513.858470] SLOW spr round 5 (radius: 5)
[11:05:42 -267511.765244] SLOW spr round 6 (radius: 5)
[11:07:42 -267511.765191] SLOW spr round 7 (radius: 10)
[11:09:38 -267511.765180] SLOW spr round 8 (radius: 15)
[11:12:26 -267511.765178] SLOW spr round 9 (radius: 20)
[11:16:29 -267511.765177] SLOW spr round 10 (radius: 25)
[11:21:33 -267511.765176] Model parameter optimization (eps = 0.100000)

[11:21:45] ML tree search #15, logLikelihood: -267511.137870

[11:21:45 -1036233.999442] Initial branch length optimization
[11:21:49 -870156.188202] Model parameter optimization (eps = 10.000000)
[11:22:14 -868351.652153] AUTODETECT spr round 1 (radius: 5)
[11:24:10 -578472.075405] AUTODETECT spr round 2 (radius: 10)
[11:26:17 -449005.228503] AUTODETECT spr round 3 (radius: 15)
[11:28:34 -376330.301915] AUTODETECT spr round 4 (radius: 20)
[11:30:56 -330329.028547] AUTODETECT spr round 5 (radius: 25)
[11:33:57 -319294.124436] SPR radius for FAST iterations: 25 (autodetect)
[11:33:57 -319294.124436] Model parameter optimization (eps = 3.000000)
[11:34:04 -319287.035731] FAST spr round 1 (radius: 25)
[11:36:34 -269550.767132] FAST spr round 2 (radius: 25)
[11:38:31 -267880.327245] FAST spr round 3 (radius: 25)
[11:40:16 -267761.425845] FAST spr round 4 (radius: 25)
[11:41:50 -267748.862769] FAST spr round 5 (radius: 25)
[11:43:20 -267745.264824] FAST spr round 6 (radius: 25)
[11:44:49 -267745.264666] Model parameter optimization (eps = 1.000000)
[11:45:07 -267608.301234] SLOW spr round 1 (radius: 5)
[11:47:02 -267538.576178] SLOW spr round 2 (radius: 5)
[11:48:55 -267529.898020] SLOW spr round 3 (radius: 5)
[11:50:45 -267525.756405] SLOW spr round 4 (radius: 5)
[11:52:33 -267525.756242] SLOW spr round 5 (radius: 10)
[11:54:29 -267523.810511] SLOW spr round 6 (radius: 5)
[11:56:42 -267523.810198] SLOW spr round 7 (radius: 10)
[11:58:47 -267523.810184] SLOW spr round 8 (radius: 15)
[12:01:34 -267523.810177] SLOW spr round 9 (radius: 20)
[12:05:44 -267523.810173] SLOW spr round 10 (radius: 25)
[12:10:51 -267523.810169] Model parameter optimization (eps = 0.100000)

[12:10:57] ML tree search #16, logLikelihood: -267523.720592

[12:10:57 -1035324.241450] Initial branch length optimization
[12:11:00 -868899.595979] Model parameter optimization (eps = 10.000000)
[12:11:30 -867166.738255] AUTODETECT spr round 1 (radius: 5)
[12:13:25 -565262.945024] AUTODETECT spr round 2 (radius: 10)
[12:15:32 -419095.958977] AUTODETECT spr round 3 (radius: 15)
[12:17:44 -356722.044502] AUTODETECT spr round 4 (radius: 20)
[12:20:05 -331753.312422] AUTODETECT spr round 5 (radius: 25)
[12:23:05 -318476.966811] SPR radius for FAST iterations: 25 (autodetect)
[12:23:05 -318476.966811] Model parameter optimization (eps = 3.000000)
[12:23:29 -318265.746504] FAST spr round 1 (radius: 25)
[12:25:57 -269620.041097] FAST spr round 2 (radius: 25)
[12:27:54 -267757.069423] FAST spr round 3 (radius: 25)
[12:29:41 -267620.143878] FAST spr round 4 (radius: 25)
[12:31:14 -267594.446733] FAST spr round 5 (radius: 25)
[12:32:43 -267594.446444] Model parameter optimization (eps = 1.000000)
[12:32:56 -267590.573768] SLOW spr round 1 (radius: 5)
[12:34:55 -267532.042783] SLOW spr round 2 (radius: 5)
[12:36:47 -267525.575269] SLOW spr round 3 (radius: 5)
[12:38:35 -267525.575254] SLOW spr round 4 (radius: 10)
[12:40:31 -267519.858168] SLOW spr round 5 (radius: 5)
[12:42:44 -267517.862618] SLOW spr round 6 (radius: 5)
[12:44:45 -267517.862565] SLOW spr round 7 (radius: 10)
[12:46:42 -267517.862563] SLOW spr round 8 (radius: 15)
[12:49:35 -267517.862561] SLOW spr round 9 (radius: 20)
[12:53:35 -267517.862559] SLOW spr round 10 (radius: 25)
[12:58:21 -267517.862557] Model parameter optimization (eps = 0.100000)

[12:58:28] ML tree search #17, logLikelihood: -267517.757862

[12:58:29 -1027297.308762] Initial branch length optimization
[12:58:33 -868558.300949] Model parameter optimization (eps = 10.000000)
[12:59:05 -866679.284982] AUTODETECT spr round 1 (radius: 5)
[13:01:00 -570249.964889] AUTODETECT spr round 2 (radius: 10)
[13:03:09 -417805.667878] AUTODETECT spr round 3 (radius: 15)
[13:05:20 -355002.081212] AUTODETECT spr round 4 (radius: 20)
[13:07:40 -339812.088259] AUTODETECT spr round 5 (radius: 25)
[13:10:23 -321901.911803] SPR radius for FAST iterations: 25 (autodetect)
[13:10:23 -321901.911803] Model parameter optimization (eps = 3.000000)
[13:10:50 -321682.936893] FAST spr round 1 (radius: 25)
[13:13:17 -270251.844730] FAST spr round 2 (radius: 25)
[13:15:13 -267715.786605] FAST spr round 3 (radius: 25)
[13:16:59 -267591.059417] FAST spr round 4 (radius: 25)
[13:18:31 -267576.582954] FAST spr round 5 (radius: 25)
[13:19:59 -267576.582648] Model parameter optimization (eps = 1.000000)
[13:20:11 -267573.200282] SLOW spr round 1 (radius: 5)
[13:22:07 -267521.936020] SLOW spr round 2 (radius: 5)
[13:23:58 -267516.488719] SLOW spr round 3 (radius: 5)
[13:25:47 -267515.915578] SLOW spr round 4 (radius: 5)
[13:27:35 -267515.915532] SLOW spr round 5 (radius: 10)
[13:29:29 -267515.915087] SLOW spr round 6 (radius: 15)
[13:32:24 -267515.915085] SLOW spr round 7 (radius: 20)
[13:36:19 -267515.915084] SLOW spr round 8 (radius: 25)
[13:41:06 -267515.915082] Model parameter optimization (eps = 0.100000)

[13:41:20] ML tree search #18, logLikelihood: -267515.064606

[13:41:20 -1033336.983743] Initial branch length optimization
[13:41:24 -872957.136568] Model parameter optimization (eps = 10.000000)
[13:41:50 -871263.317277] AUTODETECT spr round 1 (radius: 5)
[13:43:46 -579820.272735] AUTODETECT spr round 2 (radius: 10)
[13:45:58 -431140.315968] AUTODETECT spr round 3 (radius: 15)
[13:48:10 -349603.638095] AUTODETECT spr round 4 (radius: 20)
[13:50:35 -326879.787006] AUTODETECT spr round 5 (radius: 25)
[13:53:29 -320690.491266] SPR radius for FAST iterations: 25 (autodetect)
[13:53:29 -320690.491266] Model parameter optimization (eps = 3.000000)
[13:53:47 -320470.694273] FAST spr round 1 (radius: 25)
[13:56:13 -269793.076446] FAST spr round 2 (radius: 25)
[13:58:08 -267767.104064] FAST spr round 3 (radius: 25)
[13:59:50 -267630.378928] FAST spr round 4 (radius: 25)
[14:01:23 -267628.435996] FAST spr round 5 (radius: 25)
[14:02:53 -267628.435648] Model parameter optimization (eps = 1.000000)
[14:03:05 -267624.762742] SLOW spr round 1 (radius: 5)
[14:05:02 -267556.244361] SLOW spr round 2 (radius: 5)
[14:06:56 -267546.514878] SLOW spr round 3 (radius: 5)
[14:08:48 -267535.327606] SLOW spr round 4 (radius: 5)
[14:10:36 -267534.889224] SLOW spr round 5 (radius: 5)
[14:12:25 -267534.888871] SLOW spr round 6 (radius: 10)
[14:14:20 -267525.798084] SLOW spr round 7 (radius: 5)
[14:16:34 -267523.198545] SLOW spr round 8 (radius: 5)
[14:18:33 -267523.198479] SLOW spr round 9 (radius: 10)
[14:20:31 -267523.198477] SLOW spr round 10 (radius: 15)
[14:23:22 -267522.811985] SLOW spr round 11 (radius: 5)
[14:25:42 -267522.809759] SLOW spr round 12 (radius: 10)
[14:27:52 -267522.809052] SLOW spr round 13 (radius: 15)
[14:30:38 -267522.808830] SLOW spr round 14 (radius: 20)
[14:34:49 -267522.808760] SLOW spr round 15 (radius: 25)
[14:39:49 -267522.808738] Model parameter optimization (eps = 0.100000)

[14:39:58] ML tree search #19, logLikelihood: -267522.242248

[14:39:58 -1036052.321687] Initial branch length optimization
[14:40:03 -871940.792825] Model parameter optimization (eps = 10.000000)
[14:40:26 -869984.999360] AUTODETECT spr round 1 (radius: 5)
[14:42:20 -570651.652377] AUTODETECT spr round 2 (radius: 10)
[14:44:33 -419451.491237] AUTODETECT spr round 3 (radius: 15)
[14:46:45 -344107.271137] AUTODETECT spr round 4 (radius: 20)
[14:49:13 -328540.643730] AUTODETECT spr round 5 (radius: 25)
[14:52:04 -308981.965752] SPR radius for FAST iterations: 25 (autodetect)
[14:52:04 -308981.965752] Model parameter optimization (eps = 3.000000)
[14:52:22 -308841.366462] FAST spr round 1 (radius: 25)
[14:54:46 -269856.509290] FAST spr round 2 (radius: 25)
[14:56:46 -267752.986356] FAST spr round 3 (radius: 25)
[14:58:28 -267599.981672] FAST spr round 4 (radius: 25)
[15:00:02 -267588.741241] FAST spr round 5 (radius: 25)
[15:01:32 -267586.024032] FAST spr round 6 (radius: 25)
[15:03:01 -267586.023792] Model parameter optimization (eps = 1.000000)
[15:03:11 -267583.423338] SLOW spr round 1 (radius: 5)
[15:05:05 -267537.799097] SLOW spr round 2 (radius: 5)
[15:06:59 -267529.841232] SLOW spr round 3 (radius: 5)
[15:08:48 -267529.109305] SLOW spr round 4 (radius: 5)
[15:10:36 -267529.109229] SLOW spr round 5 (radius: 10)
[15:12:31 -267526.298246] SLOW spr round 6 (radius: 5)
[15:14:45 -267526.297966] SLOW spr round 7 (radius: 10)
[15:16:50 -267526.297957] SLOW spr round 8 (radius: 15)
[15:19:42 -267525.518024] SLOW spr round 9 (radius: 5)
[15:22:03 -267525.517971] SLOW spr round 10 (radius: 10)
[15:24:15 -267525.517967] SLOW spr round 11 (radius: 15)
[15:27:03 -267525.517964] SLOW spr round 12 (radius: 20)
[15:31:15 -267525.517961] SLOW spr round 13 (radius: 25)
[15:36:26 -267525.517959] Model parameter optimization (eps = 0.100000)

[15:36:39] ML tree search #20, logLikelihood: -267524.474663


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.183907,0.405883) (0.232959,0.481112) (0.371857,0.999322) (0.211277,2.090487) 
   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: -267511.137870

AIC score: 539032.275740 / AICc score: 8583092.275740 / BIC score: 547755.801602
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=573).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.log

Analysis started: 18-Jun-2021 17:07:02 / finished: 19-Jun-2021 08:43:42

Elapsed time: 56199.954 seconds