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 12-Jul-2021 15:45:12 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/2_msa/P0CG30_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/2_msa/P0CG30_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 92 sites

WARNING: Sequences tr_B4QHB9_B4QHB9_DROSI_7240 and tr_B4HT23_B4HT23_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QSW6_B4QSW6_DROSI_7240 and tr_B7Z0S9_B7Z0S9_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QSW6_B4QSW6_DROSI_7240 and tr_B4HGZ7_B4HGZ7_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4R2Y9_B4R2Y9_DROSI_7240 and tr_E1JJS1_E1JJS1_DROME_7227 are exactly identical!
WARNING: Sequences tr_G3UYJ7_G3UYJ7_MOUSE_10090 and sp_Q99L20_GSTT3_MOUSE_10090 are exactly identical!
WARNING: Sequences tr_M3XV21_M3XV21_MUSPF_9669 and tr_A0A2Y9IVH2_A0A2Y9IVH2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_B4JRE8_B4JRE8_DROGR_7222 and tr_B4JU18_B4JU18_DROGR_7222 are exactly identical!
WARNING: Sequences tr_B4IH77_B4IH77_DROSE_7238 and tr_A0A1W4UMC1_A0A1W4UMC1_DROFC_30025 are exactly identical!
WARNING: Sequences tr_D8QNB8_D8QNB8_SELML_88036 and tr_D8R6V3_D8R6V3_SELML_88036 are exactly identical!
WARNING: Sequences tr_D8QND3_D8QND3_SELML_88036 and tr_D8R6U7_D8R6U7_SELML_88036 are exactly identical!
WARNING: Sequences tr_A0A2I2Z3W6_A0A2I2Z3W6_GORGO_9595 and tr_A0A2I3NA75_A0A2I3NA75_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2Z3W6_A0A2I2Z3W6_GORGO_9595 and tr_A0A2K6CDE6_A0A2K6CDE6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Z3W6_A0A2I2Z3W6_GORGO_9595 and tr_A0A2K5Y7V2_A0A2K5Y7V2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Z8A9_A0A2I2Z8A9_GORGO_9595 and tr_A0A2R8ZPY7_A0A2R8ZPY7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R4P4_G3R4P4_GORGO_9595 and tr_H2QLD4_H2QLD4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R4P4_G3R4P4_GORGO_9595 and sp_P30711_GSTT1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R4P4_G3R4P4_GORGO_9595 and tr_A0A2R8ZLH9_A0A2R8ZLH9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2P4Y9_H2P4Y9_PONAB_9601 and tr_A0A2R9B3V8_A0A2R9B3V8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q28Y07_Q28Y07_DROPS_46245 and tr_B4GGE4_B4GGE4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q28YS8_Q28YS8_DROPS_46245 and tr_B4GIX5_B4GIX5_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q28YS9_Q28YS9_DROPS_46245 and tr_B4GIX4_B4GIX4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29B39_Q29B39_DROPS_46245 and tr_B4GZ48_B4GZ48_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29B41_Q29B41_DROPS_46245 and tr_B4GZ46_B4GZ46_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A158NGR5_A0A158NGR5_ATTCE_12957 and tr_A0A195B7Q3_A0A195B7Q3_9HYME_520822 are exactly identical!
WARNING: Sequences tr_H3H341_H3H341_PHYRM_164328 and tr_H3HEB8_H3HEB8_PHYRM_164328 are exactly identical!
WARNING: Sequences sp_A0A1W2PR19_GSTT4_HUMAN_9606 and tr_A0A1W2PRG0_A0A1W2PRG0_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P0CG29_GST2_HUMAN_9606 and sp_P0CG30_GSTT2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A0E0J3P4_A0A0E0J3P4_ORYNI_4536 and tr_A2ZG26_A2ZG26_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0J3P4_A0A0E0J3P4_ORYNI_4536 and tr_A0A0E0RAA8_A0A0E0RAA8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0J3P4_A0A0E0J3P4_ORYNI_4536 and tr_Q945X2_Q945X2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F7A219_F7A219_MACMU_9544 and tr_G8F5L3_G8F5L3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7A219_F7A219_MACMU_9544 and tr_A0A2I3MAK1_A0A2I3MAK1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7A219_F7A219_MACMU_9544 and tr_A0A0D9REZ6_A0A0D9REZ6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7A219_F7A219_MACMU_9544 and tr_A0A2K6B7V5_A0A2K6B7V5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7A219_F7A219_MACMU_9544 and tr_A0A2K5Z8K4_A0A2K5Z8K4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H9H5L3_H9H5L3_MACMU_9544 and tr_A0A096P6A9_A0A096P6A9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H9H5L3_H9H5L3_MACMU_9544 and tr_A0A2K5KNU7_A0A2K5KNU7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H9H5L3_H9H5L3_MACMU_9544 and tr_A0A2K5YK90_A0A2K5YK90_MANLE_9568 are exactly identical!
WARNING: Sequences tr_I1R199_I1R199_ORYGL_4538 and tr_A0A0D3HNI2_A0A0D3HNI2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_H0ZIZ2_H0ZIZ2_TAEGU_59729 and tr_A0A218V3C1_A0A218V3C1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G1M5C5_G1M5C5_AILME_9646 and tr_A0A384CLP3_A0A384CLP3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_B3RZD9_B3RZD9_TRIAD_10228 and tr_A0A369S6F1_A0A369S6F1_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3S2J1_B3S2J1_TRIAD_10228 and tr_A0A369SNC8_A0A369SNC8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3S535_B3S535_TRIAD_10228 and tr_A0A369SJ71_A0A369SJ71_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3S555_B3S555_TRIAD_10228 and tr_A0A369SJ60_A0A369SJ60_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3S556_B3S556_TRIAD_10228 and tr_A0A369SKJ8_A0A369SKJ8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3S557_B3S557_TRIAD_10228 and tr_A0A369SJ68_A0A369SJ68_9METZ_287889 are exactly identical!
WARNING: Sequences tr_M7YEA9_M7YEA9_TRIUA_4572 and tr_A0A3B6N4H3_A0A3B6N4H3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M7YEA9_M7YEA9_TRIUA_4572 and tr_A0A3B6SB90_A0A3B6SB90_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B1IWT1_A0A3B1IWT1_ASTMX_7994 and tr_A0A3B1K046_A0A3B1K046_ASTMX_7994 are exactly identical!
WARNING: Sequences tr_W2PF29_W2PF29_PHYPN_761204 and tr_W2JYJ6_W2JYJ6_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PLH3_W2PLH3_PHYPN_761204 and tr_A0A0W8D6I5_A0A0W8D6I5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PLH3_W2PLH3_PHYPN_761204 and tr_W2KB01_W2KB01_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PLZ0_W2PLZ0_PHYPN_761204 and tr_W2MJ30_W2MJ30_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2PMM8_W2PMM8_PHYPN_761204 and tr_A0A0W8BYG3_A0A0W8BYG3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PMM8_W2PMM8_PHYPN_761204 and tr_A0A0W8DIX1_A0A0W8DIX1_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PMM8_W2PMM8_PHYPN_761204 and tr_W2KD23_W2KD23_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2QK87_W2QK87_PHYPN_761204 and tr_A0A0W8DDR3_A0A0W8DDR3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QK87_W2QK87_PHYPN_761204 and tr_W2LTI5_W2LTI5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_K3W5M1_K3W5M1_PYTUL_431595 and tr_K3W5M2_K3W5M2_PYTUL_431595 are exactly identical!
WARNING: Sequences tr_K3W5M1_K3W5M1_PYTUL_431595 and tr_K3W5M3_K3W5M3_PYTUL_431595 are exactly identical!
WARNING: Sequences tr_A0A078HPG9_A0A078HPG9_BRANA_3708 and tr_A0A078I948_A0A078I948_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A078HPG9_A0A078HPG9_BRANA_3708 and tr_A0A0D3C0E7_A0A0D3C0E7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078K289_A0A078K289_BRANA_3708 and tr_A0A0D3CT81_A0A0D3CT81_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_V4SY43_V4SY43_9ROSI_85681 and tr_A0A2H5NFX4_A0A2H5NFX4_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4THI9_V4THI9_9ROSI_85681 and tr_A0A2H5NHF3_A0A2H5NHF3_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A151N469_A0A151N469_ALLMI_8496 and tr_A0A1U7RVV5_A0A1U7RVV5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0L9VQD0_A0A0L9VQD0_PHAAN_3914 and tr_A0A1S3ULU9_A0A1S3ULU9_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3XDD6_A0A1S3XDD6_TOBAC_4097 and tr_A0A1S3Z880_A0A1S3Z880_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3XDD6_A0A1S3XDD6_TOBAC_4097 and tr_A0A1U7WB56_A0A1U7WB56_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4AC68_A0A1S4AC68_TOBAC_4097 and tr_A0A1U7YBI6_A0A1U7YBI6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_B5X6K0_B5X6K0_SALSA_8030 and tr_A0A060WR63_A0A060WR63_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A251SP47_A0A251SP47_HELAN_4232 and tr_A0A251UAV5_A0A251UAV5_HELAN_4232 are exactly identical!
WARNING: Sequences tr_A0A1U8GDH9_A0A1U8GDH9_CAPAN_4072 and tr_A0A2G3DB71_A0A2G3DB71_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2G3AE24_A0A2G3AE24_CAPAN_4072 and tr_A0A2G3DB52_A0A2G3DB52_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2P5EGE4_A0A2P5EGE4_TREOI_63057 and tr_A0A2P5CP76_A0A2P5CP76_PARAD_3476 are exactly identical!
WARNING: Sequences tr_A0A2U3VYC6_A0A2U3VYC6_ODORO_9708 and tr_A0A2U3YRS6_A0A2U3YRS6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9LEG9_A0A2Y9LEG9_DELLE_9749 and tr_A0A2Y9FQM6_A0A2Y9FQM6_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9LEG9_A0A2Y9LEG9_DELLE_9749 and tr_A0A384BA29_A0A384BA29_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 79

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.reduced.phy

Alignment comprises 1 partitions and 92 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 92 / 92
Gaps: 2.37 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.rba

Parallelization scheme autoconfig: 2 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 / 92 / 7360
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -171279.508780] Initial branch length optimization
[00:00:02 -145412.151696] Model parameter optimization (eps = 10.000000)
[00:00:31 -144968.083382] AUTODETECT spr round 1 (radius: 5)
[00:02:28 -112198.153614] AUTODETECT spr round 2 (radius: 10)
[00:04:38 -88133.579768] AUTODETECT spr round 3 (radius: 15)
[00:06:53 -77846.810897] AUTODETECT spr round 4 (radius: 20)
[00:09:37 -70196.222062] AUTODETECT spr round 5 (radius: 25)
[00:12:36 -68309.305868] SPR radius for FAST iterations: 25 (autodetect)
[00:12:36 -68309.305868] Model parameter optimization (eps = 3.000000)
[00:12:55 -68270.564658] FAST spr round 1 (radius: 25)
[00:15:33 -58217.049813] FAST spr round 2 (radius: 25)
[00:17:33 -57672.035128] FAST spr round 3 (radius: 25)
[00:19:23 -57609.907503] FAST spr round 4 (radius: 25)
[00:21:03 -57605.631853] FAST spr round 5 (radius: 25)
[00:22:40 -57596.779847] FAST spr round 6 (radius: 25)
[00:24:15 -57594.263804] FAST spr round 7 (radius: 25)
[00:25:46 -57594.263658] Model parameter optimization (eps = 1.000000)
[00:25:55 -57592.609625] SLOW spr round 1 (radius: 5)
[00:27:55 -57573.841678] SLOW spr round 2 (radius: 5)
[00:29:53 -57571.055979] SLOW spr round 3 (radius: 5)
[00:31:47 -57568.732134] SLOW spr round 4 (radius: 5)
[00:33:37 -57568.732037] SLOW spr round 5 (radius: 10)
[00:35:29 -57567.542192] SLOW spr round 6 (radius: 5)
[00:37:41 -57567.542191] SLOW spr round 7 (radius: 10)
[00:39:44 -57567.077111] SLOW spr round 8 (radius: 5)
[00:41:56 -57565.934856] SLOW spr round 9 (radius: 5)
[00:43:58 -57564.470637] SLOW spr round 10 (radius: 5)
[00:45:53 -57564.373794] SLOW spr round 11 (radius: 10)
[00:47:47 -57562.961053] SLOW spr round 12 (radius: 5)
[00:49:59 -57562.960959] SLOW spr round 13 (radius: 10)
[00:52:02 -57562.960957] SLOW spr round 14 (radius: 15)
[00:54:44 -57561.605486] SLOW spr round 15 (radius: 5)
[00:57:02 -57560.992519] SLOW spr round 16 (radius: 5)
[00:59:05 -57560.992307] SLOW spr round 17 (radius: 10)
[01:01:02 -57560.992289] SLOW spr round 18 (radius: 15)
[01:03:47 -57560.691304] SLOW spr round 19 (radius: 5)
[01:06:05 -57560.400516] SLOW spr round 20 (radius: 5)
[01:08:08 -57559.911132] SLOW spr round 21 (radius: 5)
[01:10:05 -57559.341401] SLOW spr round 22 (radius: 5)
[01:11:57 -57559.341333] SLOW spr round 23 (radius: 10)
[01:13:50 -57559.341330] SLOW spr round 24 (radius: 15)
[01:16:41 -57559.341329] SLOW spr round 25 (radius: 20)
[01:18:31] [worker #1] ML tree search #2, logLikelihood: -57554.615454
[01:20:22 -57555.664710] SLOW spr round 26 (radius: 5)
[01:22:42 -57555.163956] SLOW spr round 27 (radius: 5)
[01:24:46 -57555.163928] SLOW spr round 28 (radius: 10)
[01:26:42 -57555.163927] SLOW spr round 29 (radius: 15)
[01:29:28 -57555.163926] SLOW spr round 30 (radius: 20)
[01:33:13 -57555.163925] SLOW spr round 31 (radius: 25)
[01:37:32 -57555.163924] Model parameter optimization (eps = 0.100000)

[01:37:39] [worker #0] ML tree search #1, logLikelihood: -57554.812761

[01:37:39 -172060.085818] Initial branch length optimization
[01:37:44 -146152.742889] Model parameter optimization (eps = 10.000000)
[01:38:10 -145762.678951] AUTODETECT spr round 1 (radius: 5)

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-Jul-2021 08:02:36 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/2_msa/P0CG30_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 92 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 92 / 92
Gaps: 2.37 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 2 worker(s) x 1 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -145762.68, ML trees: 2, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 92 / 7360
[00:00:00] Data distribution: max. searches per worker: 9

Starting ML tree search with 20 distinct starting trees

[00:00:00 -145762.678951] AUTODETECT spr round 1 (radius: 5)
[00:01:57 -112782.535042] AUTODETECT spr round 2 (radius: 10)
[00:04:09 -87327.564835] AUTODETECT spr round 3 (radius: 15)
[00:06:29 -73874.684060] AUTODETECT spr round 4 (radius: 20)
[00:09:09 -70295.745433] AUTODETECT spr round 5 (radius: 25)
[00:12:29 -66989.973960] SPR radius for FAST iterations: 25 (autodetect)
[00:12:29 -66989.973960] Model parameter optimization (eps = 3.000000)
[00:12:49 -66935.849088] FAST spr round 1 (radius: 25)
[00:15:24 -58228.048444] FAST spr round 2 (radius: 25)
[00:17:23 -57751.989037] FAST spr round 3 (radius: 25)
[00:19:08 -57716.838151] FAST spr round 4 (radius: 25)
[00:20:46 -57709.563043] FAST spr round 5 (radius: 25)
[00:22:23 -57703.227675] FAST spr round 6 (radius: 25)
[00:23:57 -57701.762658] FAST spr round 7 (radius: 25)
[00:25:28 -57701.761499] Model parameter optimization (eps = 1.000000)
[00:25:38 -57698.688742] SLOW spr round 1 (radius: 5)
[00:27:41 -57680.287311] SLOW spr round 2 (radius: 5)
[00:29:37 -57678.605619] SLOW spr round 3 (radius: 5)
[00:31:29 -57678.605601] SLOW spr round 4 (radius: 10)
[00:33:25 -57674.404310] SLOW spr round 5 (radius: 5)
[00:35:41 -57671.198694] SLOW spr round 6 (radius: 5)
[00:37:43 -57671.198132] SLOW spr round 7 (radius: 10)
[00:39:40 -57669.286118] SLOW spr round 8 (radius: 5)
[00:41:53 -57669.286023] SLOW spr round 9 (radius: 10)
[00:43:56 -57668.768950] SLOW spr round 10 (radius: 5)
[00:46:11 -57664.107917] SLOW spr round 11 (radius: 5)
[00:48:12 -57664.097805] SLOW spr round 12 (radius: 10)
[00:50:08 -57663.880001] SLOW spr round 13 (radius: 5)
[00:52:22 -57663.730334] SLOW spr round 14 (radius: 5)
[00:54:23 -57663.730325] SLOW spr round 15 (radius: 10)
[00:56:20 -57663.730324] SLOW spr round 16 (radius: 15)
[00:59:04 -57661.494606] SLOW spr round 17 (radius: 5)
[01:01:24 -57655.650516] SLOW spr round 18 (radius: 5)
[01:03:28 -57655.649352] SLOW spr round 19 (radius: 10)
[01:05:25 -57655.649334] SLOW spr round 20 (radius: 15)
[01:08:06 -57655.649334] SLOW spr round 21 (radius: 20)
[01:11:42 -57655.649333] SLOW spr round 22 (radius: 25)
[01:15:57 -57654.190251] SLOW spr round 23 (radius: 5)
[01:18:19 -57643.998901] SLOW spr round 24 (radius: 5)
[01:20:25 -57643.998901] SLOW spr round 25 (radius: 10)
[01:22:22 -57643.998900] SLOW spr round 26 (radius: 15)
[01:25:05 -57643.998900] SLOW spr round 27 (radius: 20)
[01:28:44 -57643.998900] SLOW spr round 28 (radius: 25)
[01:32:58 -57643.998899] Model parameter optimization (eps = 0.100000)

[01:33:03] [worker #0] ML tree search #3, logLikelihood: -57643.975390

[01:33:03 -171800.010916] Initial branch length optimization
[01:33:06 -146033.681121] Model parameter optimization (eps = 10.000000)
[01:33:36 -145606.388576] AUTODETECT spr round 1 (radius: 5)
[01:35:33 -112842.880384] AUTODETECT spr round 2 (radius: 10)
[01:37:46 -90678.516806] AUTODETECT spr round 3 (radius: 15)
[01:40:26 -73844.572222] AUTODETECT spr round 4 (radius: 20)
[01:43:25 -69336.372468] AUTODETECT spr round 5 (radius: 25)
[01:46:20 -66495.553218] SPR radius for FAST iterations: 25 (autodetect)
[01:46:20 -66495.553218] Model parameter optimization (eps = 3.000000)
[01:46:26 -66493.282577] FAST spr round 1 (radius: 25)
[01:48:56 -58252.655164] FAST spr round 2 (radius: 25)
[01:50:56 -57698.312800] FAST spr round 3 (radius: 25)
[01:52:47 -57626.367944] FAST spr round 4 (radius: 25)
[01:54:27 -57611.686271] FAST spr round 5 (radius: 25)
[01:56:01 -57610.082316] FAST spr round 6 (radius: 25)
[01:57:33 -57610.081782] Model parameter optimization (eps = 1.000000)
[01:57:48 -57582.148126] SLOW spr round 1 (radius: 5)
[01:59:50 -57560.665902] SLOW spr round 2 (radius: 5)
[02:01:46 -57559.192783] SLOW spr round 3 (radius: 5)
[02:03:37 -57559.191268] SLOW spr round 4 (radius: 10)
[02:05:31 -57556.253053] SLOW spr round 5 (radius: 5)
[02:07:46 -57556.252376] SLOW spr round 6 (radius: 10)
[02:09:50 -57553.848482] SLOW spr round 7 (radius: 5)
[02:11:16] [worker #1] ML tree search #4, logLikelihood: -59172.493482
[02:12:03 -57552.612654] SLOW spr round 8 (radius: 5)
[02:14:05 -57551.227883] SLOW spr round 9 (radius: 5)
[02:16:00 -57550.932901] SLOW spr round 10 (radius: 5)
[02:17:52 -57550.805984] SLOW spr round 11 (radius: 5)
[02:19:43 -57550.805980] SLOW spr round 12 (radius: 10)
[02:21:36 -57546.195398] SLOW spr round 13 (radius: 5)
[02:23:50 -57546.054393] SLOW spr round 14 (radius: 5)
[02:25:51 -57546.053834] SLOW spr round 15 (radius: 10)
[02:27:48 -57544.009068] SLOW spr round 16 (radius: 5)
[02:30:01 -57540.641985] SLOW spr round 17 (radius: 5)
[02:32:02 -57540.641982] SLOW spr round 18 (radius: 10)
[02:33:58 -57540.439574] SLOW spr round 19 (radius: 5)
[02:36:11 -57540.439570] SLOW spr round 20 (radius: 10)
[02:38:13 -57540.259817] SLOW spr round 21 (radius: 5)
[02:40:24 -57540.259791] SLOW spr round 22 (radius: 10)
[02:42:25 -57540.259790] SLOW spr round 23 (radius: 15)
[02:45:09 -57540.131164] SLOW spr round 24 (radius: 5)
[02:47:27 -57540.129556] SLOW spr round 25 (radius: 10)
[02:49:34 -57540.129458] SLOW spr round 26 (radius: 15)
[02:52:16 -57540.129452] SLOW spr round 27 (radius: 20)
[02:55:56 -57540.129451] SLOW spr round 28 (radius: 25)
[03:00:24 -57538.670347] SLOW spr round 29 (radius: 5)
[03:02:44 -57538.670347] SLOW spr round 30 (radius: 10)
[03:04:55 -57538.670346] SLOW spr round 31 (radius: 15)
[03:07:37 -57538.670346] SLOW spr round 32 (radius: 20)
[03:11:18 -57538.670345] SLOW spr round 33 (radius: 25)
[03:15:45 -57538.670345] Model parameter optimization (eps = 0.100000)

[03:15:50] [worker #0] ML tree search #5, logLikelihood: -57538.601707

[03:15:51 -171480.593837] Initial branch length optimization
[03:15:53 -145936.310900] Model parameter optimization (eps = 10.000000)
[03:16:21 -145396.527657] AUTODETECT spr round 1 (radius: 5)
[03:18:17 -110619.375499] AUTODETECT spr round 2 (radius: 10)
[03:20:28 -88481.057540] AUTODETECT spr round 3 (radius: 15)
[03:22:47 -78600.735962] AUTODETECT spr round 4 (radius: 20)
[03:25:30 -68896.237108] AUTODETECT spr round 5 (radius: 25)
[03:29:04 -66901.057704] SPR radius for FAST iterations: 25 (autodetect)
[03:29:04 -66901.057704] Model parameter optimization (eps = 3.000000)
[03:29:17 -66878.959485] FAST spr round 1 (radius: 25)
[03:31:57 -58110.097369] FAST spr round 2 (radius: 25)
[03:33:59 -57633.015274] FAST spr round 3 (radius: 25)
[03:35:49 -57581.395438] FAST spr round 4 (radius: 25)
[03:37:26 -57578.381295] FAST spr round 5 (radius: 25)
[03:39:00 -57578.380948] Model parameter optimization (eps = 1.000000)
[03:39:13 -57570.799595] SLOW spr round 1 (radius: 5)
[03:41:18 -57556.381502] SLOW spr round 2 (radius: 5)
[03:43:18 -57549.341020] SLOW spr round 3 (radius: 5)
[03:45:13 -57549.340513] SLOW spr round 4 (radius: 10)
[03:47:07 -57547.938815] SLOW spr round 5 (radius: 5)
[03:49:23 -57546.635483] SLOW spr round 6 (radius: 5)
[03:51:26 -57546.634611] SLOW spr round 7 (radius: 10)
[03:53:22 -57546.454547] SLOW spr round 8 (radius: 5)
[03:55:37 -57545.258490] SLOW spr round 9 (radius: 5)
[03:57:39 -57545.258458] SLOW spr round 10 (radius: 10)
[03:59:35 -57544.871301] SLOW spr round 11 (radius: 5)
[04:01:49 -57544.867540] SLOW spr round 12 (radius: 10)
[04:03:50 -57544.867540] SLOW spr round 13 (radius: 15)
[04:06:31 -57532.344751] SLOW spr round 14 (radius: 5)
[04:08:50 -57532.070231] SLOW spr round 15 (radius: 5)
[04:10:55 -57532.068280] SLOW spr round 16 (radius: 10)
[04:12:51 -57531.715149] SLOW spr round 17 (radius: 5)
[04:15:07 -57531.083428] SLOW spr round 18 (radius: 5)
[04:17:09 -57531.082731] SLOW spr round 19 (radius: 10)
[04:19:04 -57531.082711] SLOW spr round 20 (radius: 15)
[04:21:50 -57527.338812] SLOW spr round 21 (radius: 5)
[04:24:11 -57523.887839] SLOW spr round 22 (radius: 5)
[04:26:16 -57523.611501] SLOW spr round 23 (radius: 5)
[04:28:15 -57523.611338] SLOW spr round 24 (radius: 10)
[04:30:11 -57523.611337] SLOW spr round 25 (radius: 15)
[04:30:27] [worker #1] ML tree search #6, logLikelihood: -57529.938279
[04:33:05 -57523.611337] SLOW spr round 26 (radius: 20)
[04:36:36 -57523.611337] SLOW spr round 27 (radius: 25)
[04:40:57 -57522.152329] SLOW spr round 28 (radius: 5)
[04:43:19 -57522.152329] SLOW spr round 29 (radius: 10)
[04:45:29 -57522.152329] SLOW spr round 30 (radius: 15)
[04:48:06 -57522.152329] SLOW spr round 31 (radius: 20)
[04:51:44 -57522.152329] SLOW spr round 32 (radius: 25)
[04:56:01 -57522.152329] Model parameter optimization (eps = 0.100000)

[04:56:09] [worker #0] ML tree search #7, logLikelihood: -57521.994519

[04:56:10 -170115.875343] Initial branch length optimization
[04:56:12 -144513.966368] Model parameter optimization (eps = 10.000000)
[04:56:46 -144121.195160] AUTODETECT spr round 1 (radius: 5)
[04:58:44 -112808.034500] AUTODETECT spr round 2 (radius: 10)
[05:00:56 -90898.063317] AUTODETECT spr round 3 (radius: 15)
[05:03:23 -80002.398316] AUTODETECT spr round 4 (radius: 20)
[05:06:21 -70400.543273] AUTODETECT spr round 5 (radius: 25)
[05:09:44 -68021.875899] SPR radius for FAST iterations: 25 (autodetect)
[05:09:44 -68021.875899] Model parameter optimization (eps = 3.000000)
[05:10:01 -67972.151443] FAST spr round 1 (radius: 25)
[05:12:39 -58338.432102] FAST spr round 2 (radius: 25)
[05:14:43 -57663.381980] FAST spr round 3 (radius: 25)
[05:16:32 -57608.097161] FAST spr round 4 (radius: 25)
[05:18:13 -57601.095483] FAST spr round 5 (radius: 25)
[05:19:49 -57599.755082] FAST spr round 6 (radius: 25)
[05:21:24 -57599.755045] Model parameter optimization (eps = 1.000000)
[05:21:33 -57598.907267] SLOW spr round 1 (radius: 5)
[05:23:38 -57582.738843] SLOW spr round 2 (radius: 5)
[05:25:36 -57582.578111] SLOW spr round 3 (radius: 5)
[05:27:29 -57582.577684] SLOW spr round 4 (radius: 10)
[05:29:23 -57581.508993] SLOW spr round 5 (radius: 5)
[05:31:42 -57580.283367] SLOW spr round 6 (radius: 5)
[05:33:45 -57580.283267] SLOW spr round 7 (radius: 10)
[05:34:45] [worker #1] ML tree search #8, logLikelihood: -57595.826783
[05:35:41 -57579.948940] SLOW spr round 8 (radius: 5)
[05:37:57 -57578.132961] SLOW spr round 9 (radius: 5)
[05:40:00 -57578.132957] SLOW spr round 10 (radius: 10)
[05:41:56 -57578.132954] SLOW spr round 11 (radius: 15)
[05:44:41 -57574.543098] SLOW spr round 12 (radius: 5)
[05:47:00 -57573.870741] SLOW spr round 13 (radius: 5)
[05:49:05 -57573.870707] SLOW spr round 14 (radius: 10)
[05:51:01 -57573.870705] SLOW spr round 15 (radius: 15)
[05:53:46 -57570.914638] SLOW spr round 16 (radius: 5)
[05:56:09 -57567.634619] SLOW spr round 17 (radius: 5)
[05:58:17 -57565.922159] SLOW spr round 18 (radius: 5)
[06:00:16 -57565.922055] SLOW spr round 19 (radius: 10)
[06:02:11 -57563.406158] SLOW spr round 20 (radius: 5)
[06:04:32 -57561.212660] SLOW spr round 21 (radius: 5)
[06:06:37 -57561.211969] SLOW spr round 22 (radius: 10)
[06:08:33 -57561.211954] SLOW spr round 23 (radius: 15)
[06:11:19 -57561.211953] SLOW spr round 24 (radius: 20)
[06:14:59 -57561.211951] SLOW spr round 25 (radius: 25)
[06:19:27 -57561.211950] Model parameter optimization (eps = 0.100000)

[06:19:32] [worker #0] ML tree search #9, logLikelihood: -57561.196797

[06:19:32 -171329.255812] Initial branch length optimization
[06:19:35 -145496.619662] Model parameter optimization (eps = 10.000000)
[06:20:02 -145047.090111] AUTODETECT spr round 1 (radius: 5)
[06:22:02 -112244.141191] AUTODETECT spr round 2 (radius: 10)
[06:24:15 -89148.384720] AUTODETECT spr round 3 (radius: 15)
[06:26:42 -78502.198873] AUTODETECT spr round 4 (radius: 20)
[06:29:37 -71381.246600] AUTODETECT spr round 5 (radius: 25)
[06:32:39 -67417.281496] SPR radius for FAST iterations: 25 (autodetect)
[06:32:39 -67417.281496] Model parameter optimization (eps = 3.000000)
[06:32:57 -67385.125886] FAST spr round 1 (radius: 25)
[06:35:34 -58130.152603] FAST spr round 2 (radius: 25)
[06:37:31 -57643.773850] FAST spr round 3 (radius: 25)
[06:39:19 -57608.338771] FAST spr round 4 (radius: 25)
[06:40:58 -57604.945754] FAST spr round 5 (radius: 25)
[06:42:33 -57604.750356] FAST spr round 6 (radius: 25)
[06:44:07 -57604.749830] Model parameter optimization (eps = 1.000000)
[06:44:21 -57602.624391] SLOW spr round 1 (radius: 5)
[06:46:23 -57580.836379] SLOW spr round 2 (radius: 5)
[06:48:22 -57568.325637] SLOW spr round 3 (radius: 5)
[06:50:20 -57563.342543] SLOW spr round 4 (radius: 5)
[06:52:15 -57562.347706] SLOW spr round 5 (radius: 5)
[06:54:08 -57562.347309] SLOW spr round 6 (radius: 10)
[06:56:05 -57556.501255] SLOW spr round 7 (radius: 5)
[06:58:24 -57555.914703] SLOW spr round 8 (radius: 5)
[07:00:30 -57554.665844] SLOW spr round 9 (radius: 5)
[07:02:28 -57554.665809] SLOW spr round 10 (radius: 10)
[07:04:26 -57552.342212] SLOW spr round 11 (radius: 5)
[07:06:48 -57546.616548] SLOW spr round 12 (radius: 5)
[07:08:56 -57546.364345] SLOW spr round 13 (radius: 5)
[07:10:56 -57546.073937] SLOW spr round 14 (radius: 5)
[07:12:51 -57546.073933] SLOW spr round 15 (radius: 10)
[07:14:46 -57545.563194] SLOW spr round 16 (radius: 5)
[07:17:02 -57545.563110] SLOW spr round 17 (radius: 10)
[07:19:06 -57545.251623] SLOW spr round 18 (radius: 5)
[07:21:20 -57545.121561] SLOW spr round 19 (radius: 5)
[07:22:23] [worker #1] ML tree search #10, logLikelihood: -57534.138408
[07:23:23 -57545.121551] SLOW spr round 20 (radius: 10)
[07:25:20 -57544.997510] SLOW spr round 21 (radius: 5)
[07:27:36 -57544.997426] SLOW spr round 22 (radius: 10)
[07:29:40 -57544.526397] SLOW spr round 23 (radius: 5)
[07:31:54 -57544.526106] SLOW spr round 24 (radius: 10)
[07:33:56 -57544.526076] SLOW spr round 25 (radius: 15)
[07:36:35 -57544.526071] SLOW spr round 26 (radius: 20)
[07:40:08 -57544.526069] SLOW spr round 27 (radius: 25)
[07:44:13 -57543.066999] SLOW spr round 28 (radius: 5)
[07:46:36 -57543.066998] SLOW spr round 29 (radius: 10)
[07:48:47 -57543.066996] SLOW spr round 30 (radius: 15)
[07:51:23 -57543.066995] SLOW spr round 31 (radius: 20)
[07:54:57 -57543.066993] SLOW spr round 32 (radius: 25)
[07:58:59 -57543.066991] Model parameter optimization (eps = 0.100000)

[07:59:06] [worker #0] ML tree search #11, logLikelihood: -57542.839915

[07:59:06 -171423.344642] Initial branch length optimization
[07:59:09 -145599.212467] Model parameter optimization (eps = 10.000000)
[07:59:34 -145210.581095] AUTODETECT spr round 1 (radius: 5)
[08:01:33 -113788.057195] AUTODETECT spr round 2 (radius: 10)
[08:03:52 -87179.392185] AUTODETECT spr round 3 (radius: 15)
[08:06:14 -76145.087256] AUTODETECT spr round 4 (radius: 20)
[08:08:51 -67841.116827] AUTODETECT spr round 5 (radius: 25)
[08:11:46 -67230.772866] SPR radius for FAST iterations: 25 (autodetect)
[08:11:46 -67230.772866] Model parameter optimization (eps = 3.000000)
[08:11:53 -67228.277365] FAST spr round 1 (radius: 25)
[08:14:35 -58268.450205] FAST spr round 2 (radius: 25)
[08:16:45 -57768.738524] FAST spr round 3 (radius: 25)
[08:18:41 -57733.059483] FAST spr round 4 (radius: 25)
[08:20:29 -57725.871825] FAST spr round 5 (radius: 25)
[08:22:09 -57723.921673] FAST spr round 6 (radius: 25)
[08:23:46 -57723.921524] Model parameter optimization (eps = 1.000000)
[08:24:02 -57689.950308] SLOW spr round 1 (radius: 5)
[08:26:10 -57671.140193] SLOW spr round 2 (radius: 5)
[08:28:09 -57670.937986] SLOW spr round 3 (radius: 5)
[08:30:07 -57668.049691] SLOW spr round 4 (radius: 5)
[08:32:02 -57667.903667] SLOW spr round 5 (radius: 5)
[08:33:56 -57667.903630] SLOW spr round 6 (radius: 10)
[08:35:52 -57663.596996] SLOW spr round 7 (radius: 5)
[08:38:09 -57657.956228] SLOW spr round 8 (radius: 5)
[08:40:12 -57657.956151] SLOW spr round 9 (radius: 10)
[08:42:09 -57657.087439] SLOW spr round 10 (radius: 5)
[08:44:25 -57657.087335] SLOW spr round 11 (radius: 10)
[08:46:30 -57652.344444] SLOW spr round 12 (radius: 5)
[08:48:45 -57649.333873] SLOW spr round 13 (radius: 5)
[08:50:49 -57649.333753] SLOW spr round 14 (radius: 10)
[08:52:47 -57649.333745] SLOW spr round 15 (radius: 15)
[08:55:36 -57649.333743] SLOW spr round 16 (radius: 20)
[08:59:17 -57649.333743] SLOW spr round 17 (radius: 25)
[09:02:43] [worker #1] ML tree search #12, logLikelihood: -57521.397838
[09:03:39 -57649.333743] Model parameter optimization (eps = 0.100000)

[09:03:44] [worker #0] ML tree search #13, logLikelihood: -57649.262386

[09:03:44 -171826.517292] Initial branch length optimization
[09:03:46 -145757.623586] Model parameter optimization (eps = 10.000000)
[09:04:19 -145246.772340] AUTODETECT spr round 1 (radius: 5)
[09:06:18 -111539.310568] AUTODETECT spr round 2 (radius: 10)
[09:08:30 -87673.110759] AUTODETECT spr round 3 (radius: 15)
[09:10:51 -77860.381499] AUTODETECT spr round 4 (radius: 20)
[09:13:31 -70990.855664] AUTODETECT spr round 5 (radius: 25)
[09:16:31 -67259.217658] SPR radius for FAST iterations: 25 (autodetect)
[09:16:31 -67259.217658] Model parameter optimization (eps = 3.000000)
[09:16:36 -67257.542651] FAST spr round 1 (radius: 25)
[09:19:15 -58352.595894] FAST spr round 2 (radius: 25)
[09:21:14 -57713.729472] FAST spr round 3 (radius: 25)
[09:23:04 -57626.872729] FAST spr round 4 (radius: 25)
[09:24:48 -57606.331563] FAST spr round 5 (radius: 25)
[09:26:24 -57603.916459] FAST spr round 6 (radius: 25)
[09:27:57 -57603.916438] Model parameter optimization (eps = 1.000000)
[09:28:17 -57578.884049] SLOW spr round 1 (radius: 5)
[09:30:22 -57557.452188] SLOW spr round 2 (radius: 5)
[09:32:23 -57551.694470] SLOW spr round 3 (radius: 5)
[09:34:17 -57551.571467] SLOW spr round 4 (radius: 5)
[09:36:09 -57551.570360] SLOW spr round 5 (radius: 10)
[09:38:06 -57548.148233] SLOW spr round 6 (radius: 5)
[09:40:27 -57547.836854] SLOW spr round 7 (radius: 5)
[09:42:33 -57546.112167] SLOW spr round 8 (radius: 5)
[09:44:33 -57546.111793] SLOW spr round 9 (radius: 10)
[09:46:29 -57546.111734] SLOW spr round 10 (radius: 15)
[09:49:20 -57545.609716] SLOW spr round 11 (radius: 5)
[09:51:42 -57545.609488] SLOW spr round 12 (radius: 10)
[09:53:50 -57545.609471] SLOW spr round 13 (radius: 15)
[09:56:31 -57545.609469] SLOW spr round 14 (radius: 20)
[10:00:20 -57545.609469] SLOW spr round 15 (radius: 25)
[10:04:51 -57545.609469] Model parameter optimization (eps = 0.100000)

[10:04:57] [worker #0] ML tree search #15, logLikelihood: -57545.555664

[10:04:57 -172271.256345] Initial branch length optimization
[10:05:00 -146137.696170] Model parameter optimization (eps = 10.000000)
[10:05:26 -145712.293994] AUTODETECT spr round 1 (radius: 5)
[10:07:26 -112988.765535] AUTODETECT spr round 2 (radius: 10)
[10:09:42 -90439.705568] AUTODETECT spr round 3 (radius: 15)
[10:12:04 -77863.954991] AUTODETECT spr round 4 (radius: 20)
[10:15:06 -71914.468892] AUTODETECT spr round 5 (radius: 25)
[10:18:20 -68280.558136] SPR radius for FAST iterations: 25 (autodetect)
[10:18:20 -68280.558136] Model parameter optimization (eps = 3.000000)
[10:18:26 -68278.976837] FAST spr round 1 (radius: 25)
[10:21:06 -58343.937335] FAST spr round 2 (radius: 25)
[10:23:08 -57735.411917] FAST spr round 3 (radius: 25)
[10:24:58 -57679.122921] FAST spr round 4 (radius: 25)
[10:26:37 -57671.998695] FAST spr round 5 (radius: 25)
[10:28:14 -57670.414234] FAST spr round 6 (radius: 25)
[10:29:49 -57670.414190] Model parameter optimization (eps = 1.000000)
[10:30:02 -57652.067619] SLOW spr round 1 (radius: 5)
[10:32:07 -57635.062106] SLOW spr round 2 (radius: 5)
[10:34:04] [worker #1] ML tree search #14, logLikelihood: -57530.360514
[10:34:08 -57622.886689] SLOW spr round 3 (radius: 5)
[10:36:07 -57620.929681] SLOW spr round 4 (radius: 5)
[10:38:01 -57620.929147] SLOW spr round 5 (radius: 10)
[10:39:56 -57618.818678] SLOW spr round 6 (radius: 5)
[10:42:18 -57615.619302] SLOW spr round 7 (radius: 5)
[10:44:24 -57612.399530] SLOW spr round 8 (radius: 5)
[10:46:25 -57611.323524] SLOW spr round 9 (radius: 5)
[10:48:20 -57611.322186] SLOW spr round 10 (radius: 10)
[10:50:14 -57610.148986] SLOW spr round 11 (radius: 5)
[10:52:29 -57610.148984] SLOW spr round 12 (radius: 10)
[10:54:31 -57608.987610] SLOW spr round 13 (radius: 5)
[10:56:48 -57608.169317] SLOW spr round 14 (radius: 5)
[10:58:52 -57606.813448] SLOW spr round 15 (radius: 5)
[11:00:51 -57606.096623] SLOW spr round 16 (radius: 5)
[11:02:45 -57606.096532] SLOW spr round 17 (radius: 10)
[11:04:39 -57605.624550] SLOW spr round 18 (radius: 5)
[11:06:56 -57605.538960] SLOW spr round 19 (radius: 10)
[11:08:59 -57604.590869] SLOW spr round 20 (radius: 5)
[11:11:14 -57604.122740] SLOW spr round 21 (radius: 5)
[11:13:17 -57604.122475] SLOW spr round 22 (radius: 10)
[11:15:13 -57602.788691] SLOW spr round 23 (radius: 5)
[11:17:28 -57602.741783] SLOW spr round 24 (radius: 10)
[11:19:31 -57602.516337] SLOW spr round 25 (radius: 5)
[11:21:45 -57602.516274] SLOW spr round 26 (radius: 10)
[11:23:47 -57602.483838] SLOW spr round 27 (radius: 15)
[11:26:25 -57601.529625] SLOW spr round 28 (radius: 5)
[11:28:48 -57595.585571] SLOW spr round 29 (radius: 5)
[11:30:55 -57593.969741] SLOW spr round 30 (radius: 5)
[11:32:56 -57593.969568] SLOW spr round 31 (radius: 10)
[11:35:03 -57593.969565] SLOW spr round 32 (radius: 15)
[11:37:51 -57593.969564] SLOW spr round 33 (radius: 20)
[11:41:17 -57589.076396] SLOW spr round 34 (radius: 5)
[11:41:59] [worker #1] ML tree search #16, logLikelihood: -57541.999251
[11:43:40 -57577.306471] SLOW spr round 35 (radius: 5)
[11:45:49 -57575.135195] SLOW spr round 36 (radius: 5)
[11:47:48 -57575.134839] SLOW spr round 37 (radius: 10)
[11:49:44 -57573.830433] SLOW spr round 38 (radius: 5)
[11:52:02 -57569.836638] SLOW spr round 39 (radius: 5)
[11:54:06 -57569.835952] SLOW spr round 40 (radius: 10)
[11:56:04 -57566.381367] SLOW spr round 41 (radius: 5)
[11:58:20 -57546.784499] SLOW spr round 42 (radius: 5)
[12:00:26 -57543.935125] SLOW spr round 43 (radius: 5)
[12:02:23 -57543.931538] SLOW spr round 44 (radius: 10)
[12:04:18 -57542.644401] SLOW spr round 45 (radius: 5)
[12:06:35 -57542.430710] SLOW spr round 46 (radius: 5)
[12:08:39 -57542.430379] SLOW spr round 47 (radius: 10)
[12:10:36 -57542.430360] SLOW spr round 48 (radius: 15)
[12:13:20 -57542.430358] SLOW spr round 49 (radius: 20)
[12:16:47 -57542.430357] SLOW spr round 50 (radius: 25)
[12:20:51 -57540.971276] SLOW spr round 51 (radius: 5)
[12:23:13 -57540.971276] SLOW spr round 52 (radius: 10)
[12:25:23 -57540.971275] SLOW spr round 53 (radius: 15)
[12:27:58 -57540.971274] SLOW spr round 54 (radius: 20)
[12:31:30 -57540.971273] SLOW spr round 55 (radius: 25)
[12:35:31 -57540.971273] Model parameter optimization (eps = 0.100000)

[12:35:39] [worker #0] ML tree search #17, logLikelihood: -57540.842159

[12:35:39 -172343.597195] Initial branch length optimization
[12:35:42 -146189.299326] Model parameter optimization (eps = 10.000000)
[12:36:09 -145769.773982] AUTODETECT spr round 1 (radius: 5)
[12:38:09 -113658.378808] AUTODETECT spr round 2 (radius: 10)
[12:40:23 -90534.702143] AUTODETECT spr round 3 (radius: 15)
[12:42:56 -76477.940505] AUTODETECT spr round 4 (radius: 20)
[12:45:36 -70015.170939] AUTODETECT spr round 5 (radius: 25)
[12:48:29 -67804.973458] SPR radius for FAST iterations: 25 (autodetect)
[12:48:29 -67804.973458] Model parameter optimization (eps = 3.000000)
[12:48:49 -67755.246721] FAST spr round 1 (radius: 25)
[12:51:29 -58180.160987] FAST spr round 2 (radius: 25)
[12:53:33 -57690.971739] FAST spr round 3 (radius: 25)
[12:55:24 -57611.351701] FAST spr round 4 (radius: 25)
[12:57:07 -57596.740870] FAST spr round 5 (radius: 25)
[12:58:42 -57596.739918] Model parameter optimization (eps = 1.000000)
[12:58:53 -57593.930355] SLOW spr round 1 (radius: 5)
[13:00:59 -57571.480359] SLOW spr round 2 (radius: 5)
[13:02:57 -57566.342080] SLOW spr round 3 (radius: 5)
[13:04:52 -57565.424729] SLOW spr round 4 (radius: 5)
[13:06:08] [worker #1] ML tree search #18, logLikelihood: -57580.206403
[13:06:45 -57565.424171] SLOW spr round 5 (radius: 10)
[13:08:40 -57564.477513] SLOW spr round 6 (radius: 5)
[13:10:56 -57562.505780] SLOW spr round 7 (radius: 5)
[13:13:02 -57560.440027] SLOW spr round 8 (radius: 5)
[13:14:59 -57560.439964] SLOW spr round 9 (radius: 10)
[13:16:54 -57560.439964] SLOW spr round 10 (radius: 15)
[13:19:49 -57560.439963] SLOW spr round 11 (radius: 20)
[13:23:47 -57560.439962] SLOW spr round 12 (radius: 25)
[13:28:42 -57558.980800] SLOW spr round 13 (radius: 5)
[13:31:06 -57558.980799] SLOW spr round 14 (radius: 10)
[13:33:20 -57558.980799] SLOW spr round 15 (radius: 15)
[13:36:06 -57558.980798] SLOW spr round 16 (radius: 20)
[13:40:13 -57558.980797] SLOW spr round 17 (radius: 25)
[13:45:07 -57558.980797] Model parameter optimization (eps = 0.100000)

[13:45:11] [worker #0] ML tree search #19, logLikelihood: -57558.959050

[14:31:58] [worker #1] ML tree search #20, logLikelihood: -57566.611796

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.163069,0.330066) (0.271754,0.629225) (0.391254,1.028339) (0.173923,2.143707) 
   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: -57521.397838

AIC score: 119052.795677 / AICc score: 8163112.795677 / BIC score: 124108.981774
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=92).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 135 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P0CG30/3_mltree/P0CG30.raxml.log

Analysis started: 18-Jul-2021 08:02:36 / finished: 18-Jul-2021 22:34:34

Elapsed time: 52318.500 seconds (this run) / 58209.148 seconds (total with restarts)