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 31-Jul-2021 02:44:47 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/2_msa/Q13332_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/2_msa/Q13332_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1059 sites

WARNING: Sequences tr_B4QA19_B4QA19_DROSI_7240 and sp_P16621_LAR_DROME_7227 are exactly identical!
WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_H2NVW2_H2NVW2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and sp_P28827_PTPRM_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YYP7_A0A2I2YYP7_GORGO_9595 and tr_A0A2R9BYW7_A0A2R9BYW7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SQY6_A0A2I3SQY6_PANTR_9598 and tr_F6V5S0_F6V5S0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3SQY6_A0A2I3SQY6_PANTR_9598 and tr_A0A2I3LW03_A0A2I3LW03_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3SQY6_A0A2I3SQY6_PANTR_9598 and tr_A0A2K5ZG26_A0A2K5ZG26_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3SQY6_A0A2I3SQY6_PANTR_9598 and tr_A0A2R8ZP60_A0A2R8ZP60_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QE85_H2QE85_PANTR_9598 and tr_A0A2R8ZLI9_A0A2R8ZLI9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R1K1_H2R1K1_PANTR_9598 and tr_A0A2K5YH94_A0A2K5YH94_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2R1K1_H2R1K1_PANTR_9598 and tr_A0A2R9B7Y1_A0A2R9B7Y1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R3E7_H2R3E7_PANTR_9598 and tr_A0A2R8ZB11_A0A2R8ZB11_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5PVQ2_W5PVQ2_SHEEP_9940 and tr_F1MME1_F1MME1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5PWC2_W5PWC2_SHEEP_9940 and tr_F1MJR2_F1MJR2_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_O14522_PTPRT_HUMAN_9606 and tr_F6PVC0_F6PVC0_MACMU_9544 are exactly identical!
WARNING: Sequences sp_P18433_PTPRA_HUMAN_9606 and tr_A0A2R8ZSE8_A0A2R8ZSE8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_G7PWE3_G7PWE3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_A0A096N2E3_A0A096N2E3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_A0A0D9RYA9_A0A0D9RYA9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_A0A2K5LED7_A0A2K5LED7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_A0A2K6C632_A0A2K6C632_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6TLA3_F6TLA3_MACMU_9544 and tr_A0A2I3NAL0_A0A2I3NAL0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DWH2_F7DWH2_MACMU_9544 and tr_G7PSD1_G7PSD1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HG97_F7HG97_MACMU_9544 and tr_A0A2I3LET0_A0A2I3LET0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HG97_F7HG97_MACMU_9544 and tr_A0A0D9RC69_A0A0D9RC69_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1LLN7_G1LLN7_AILME_9646 and tr_A0A384C7G9_A0A384C7G9_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G7P370_G7P370_MACFA_9541 and tr_A0A0D9RV87_A0A0D9RV87_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PEC8_G7PEC8_MACFA_9541 and tr_A0A2K6BYF7_A0A2K6BYF7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096N7E0_A0A096N7E0_PAPAN_9555 and tr_A0A2K5Y7Q0_A0A2K5Y7Q0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A0D9R9K5_A0A0D9R9K5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A2K5KQ07_A0A2K5KQ07_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A2K6A4P9_A0A2K6A4P9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9QWP4_A0A0D9QWP4_CHLSB_60711 and tr_A0A2K5LWU5_A0A2K5LWU5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RLM0_A0A0D9RLM0_CHLSB_60711 and tr_A0A2K5KVH8_A0A2K5KVH8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A087RBA8_A0A087RBA8_APTFO_9233 and tr_A0A093GT42_A0A093GT42_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091VX05_A0A091VX05_OPIHO_30419 and tr_A0A091G8Y5_A0A091G8Y5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A2I0LQJ0_A0A2I0LQJ0_COLLI_8932 and tr_A0A1V4KWQ8_A0A1V4KWQ8_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A195BU66_A0A195BU66_9HYME_520822 and tr_A0A195F635_A0A195F635_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A1S3HQ57_A0A1S3HQ57_LINUN_7574 and tr_A0A1S3HRJ8_A0A1S3HRJ8_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A226MUA2_A0A226MUA2_CALSU_9009 and tr_A0A226P042_A0A226P042_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PV98_A0A2D0PV98_ICTPU_7998 and tr_A0A2D0PYE1_A0A2D0PYE1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PV98_A0A2D0PV98_ICTPU_7998 and tr_A0A2D0PZB7_A0A2D0PZB7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PVC0_A0A2D0PVC0_ICTPU_7998 and tr_A0A2D0PYG0_A0A2D0PYG0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFL7_A0A2D0QFL7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFM4_A0A2D0QFM4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QH24_A0A2D0QH24_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RWZ5_A0A2D0RWZ5_ICTPU_7998 and tr_A0A2D0RXW6_A0A2D0RXW6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T9D0_A0A2D0T9D0_ICTPU_7998 and tr_A0A2D0T9D3_A0A2D0T9D3_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 48

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/Q13332/3_mltree/Q13332.raxml.reduced.phy

Alignment comprises 1 partitions and 1059 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1059 / 1059
Gaps: 16.46 %
Invariant sites: 0.09 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 9 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 / 118 / 9440
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1446887.736155] Initial branch length optimization
[00:00:06 -1163225.332391] Model parameter optimization (eps = 10.000000)
[00:00:40 -1162496.433307] AUTODETECT spr round 1 (radius: 5)
[00:02:52 -631823.500037] AUTODETECT spr round 2 (radius: 10)
[00:05:13 -390774.097155] AUTODETECT spr round 3 (radius: 15)
[00:07:40 -315287.693205] AUTODETECT spr round 4 (radius: 20)
[00:10:29 -285539.092107] AUTODETECT spr round 5 (radius: 25)
[00:13:30 -264869.605490] SPR radius for FAST iterations: 25 (autodetect)
[00:13:30 -264869.605490] Model parameter optimization (eps = 3.000000)
[00:13:54 -264457.895038] FAST spr round 1 (radius: 25)
[00:16:23 -220880.125447] FAST spr round 2 (radius: 25)
[00:18:27 -216301.289409] FAST spr round 3 (radius: 25)
[00:20:19 -216047.960754] FAST spr round 4 (radius: 25)
[00:22:05 -215903.415405] FAST spr round 5 (radius: 25)
[00:23:40 -215899.959446] FAST spr round 6 (radius: 25)
[00:25:15 -215895.340668] FAST spr round 7 (radius: 25)
[00:26:46 -215895.339965] Model parameter optimization (eps = 1.000000)
[00:27:05 -215869.944908] SLOW spr round 1 (radius: 5)
[00:29:07 -215832.752414] SLOW spr round 2 (radius: 5)
[00:31:09 -215825.603219] SLOW spr round 3 (radius: 5)
[00:33:07 -215825.527032] SLOW spr round 4 (radius: 10)
[00:35:10 -215819.174625] SLOW spr round 5 (radius: 5)
[00:37:38 -215810.063883] SLOW spr round 6 (radius: 5)
[00:39:48 -215810.061011] SLOW spr round 7 (radius: 10)
[00:41:54 -215810.059424] SLOW spr round 8 (radius: 15)
[00:44:50 -215810.058395] SLOW spr round 9 (radius: 20)
[00:49:18 -215810.057706] SLOW spr round 10 (radius: 25)
[00:54:53 -215810.057228] Model parameter optimization (eps = 0.100000)

[00:54:58] ML tree search #1, logLikelihood: -215809.989806

[00:54:59 -1447844.039647] Initial branch length optimization
[00:55:04 -1152733.629049] Model parameter optimization (eps = 10.000000)
[00:55:32 -1151894.485840] AUTODETECT spr round 1 (radius: 5)
[00:57:48 -641034.901626] AUTODETECT spr round 2 (radius: 10)
[01:00:16 -420510.443759] AUTODETECT spr round 3 (radius: 15)
[01:02:39 -336617.877130] AUTODETECT spr round 4 (radius: 20)
[01:05:31 -287495.246514] AUTODETECT spr round 5 (radius: 25)
[01:08:36 -264749.610552] SPR radius for FAST iterations: 25 (autodetect)
[01:08:36 -264749.610552] Model parameter optimization (eps = 3.000000)
[01:08:59 -264268.090381] FAST spr round 1 (radius: 25)
[01:11:30 -220744.133139] FAST spr round 2 (radius: 25)
[01:13:32 -216130.559632] FAST spr round 3 (radius: 25)
[01:15:19 -215896.383447] FAST spr round 4 (radius: 25)
[01:16:57 -215892.232138] FAST spr round 5 (radius: 25)
[01:18:31 -215890.930849] FAST spr round 6 (radius: 25)
[01:20:03 -215890.930359] Model parameter optimization (eps = 1.000000)
[01:20:17 -215885.277125] SLOW spr round 1 (radius: 5)
[01:22:18 -215837.466998] SLOW spr round 2 (radius: 5)
[01:24:20 -215827.950421] SLOW spr round 3 (radius: 5)
[01:26:21 -215821.403907] SLOW spr round 4 (radius: 5)
[01:28:21 -215813.519829] SLOW spr round 5 (radius: 5)
[01:30:19 -215813.519459] SLOW spr round 6 (radius: 10)
[01:32:19 -215813.519184] SLOW spr round 7 (radius: 15)
[01:35:17 -215813.517827] SLOW spr round 8 (radius: 20)
[01:39:43 -215813.517651] SLOW spr round 9 (radius: 25)
[01:45:14 -215813.517491] Model parameter optimization (eps = 0.100000)

[01:45:23] ML tree search #2, logLikelihood: -215813.313850

[01:45:23 -1443608.407116] Initial branch length optimization
[01:45:28 -1155900.774869] Model parameter optimization (eps = 10.000000)
[01:45:59 -1155026.144841] AUTODETECT spr round 1 (radius: 5)
[01:48:13 -640794.681921] AUTODETECT spr round 2 (radius: 10)
[01:50:42 -406191.812745] AUTODETECT spr round 3 (radius: 15)
[01:53:10 -306568.680255] AUTODETECT spr round 4 (radius: 20)
[01:56:10 -260976.795343] AUTODETECT spr round 5 (radius: 25)
[01:59:27 -245751.108759] SPR radius for FAST iterations: 25 (autodetect)
[01:59:27 -245751.108759] Model parameter optimization (eps = 3.000000)
[01:59:55 -245268.503264] FAST spr round 1 (radius: 25)
[02:02:12 -217744.647552] FAST spr round 2 (radius: 25)
[02:04:07 -215969.872477] FAST spr round 3 (radius: 25)
[02:05:53 -215882.004447] FAST spr round 4 (radius: 25)
[02:07:32 -215874.102321] FAST spr round 5 (radius: 25)
[02:09:06 -215874.102083] Model parameter optimization (eps = 1.000000)
[02:09:19 -215872.149627] SLOW spr round 1 (radius: 5)
[02:11:23 -215814.995663] SLOW spr round 2 (radius: 5)
[02:13:26 -215813.682950] SLOW spr round 3 (radius: 5)
[02:15:26 -215813.682592] SLOW spr round 4 (radius: 10)
[02:17:29 -215811.285342] SLOW spr round 5 (radius: 5)
[02:19:54 -215810.441632] SLOW spr round 6 (radius: 5)
[02:22:05 -215810.441124] SLOW spr round 7 (radius: 10)
[02:24:13 -215810.440812] SLOW spr round 8 (radius: 15)
[02:27:08 -215810.440563] SLOW spr round 9 (radius: 20)
[02:31:34 -215810.440353] SLOW spr round 10 (radius: 25)
[02:36:55 -215810.440169] Model parameter optimization (eps = 0.100000)

[02:37:00] ML tree search #3, logLikelihood: -215810.399123

[02:37:00 -1440253.389871] Initial branch length optimization
[02:37:06 -1156415.489997] Model parameter optimization (eps = 10.000000)
[02:37:36 -1155653.991578] AUTODETECT spr round 1 (radius: 5)
[02:39:50 -649085.803643] AUTODETECT spr round 2 (radius: 10)
[02:42:18 -426356.806860] AUTODETECT spr round 3 (radius: 15)
[02:44:42 -301694.375506] AUTODETECT spr round 4 (radius: 20)
[02:47:18 -270654.655274] AUTODETECT spr round 5 (radius: 25)
[02:50:25 -250957.220181] SPR radius for FAST iterations: 25 (autodetect)
[02:50:25 -250957.220181] Model parameter optimization (eps = 3.000000)
[02:50:59 -250548.757245] FAST spr round 1 (radius: 25)
[02:53:19 -216987.074477] FAST spr round 2 (radius: 25)
[02:55:13 -215999.557871] FAST spr round 3 (radius: 25)
[02:56:57 -215891.669502] FAST spr round 4 (radius: 25)
[02:58:37 -215882.061044] FAST spr round 5 (radius: 25)
[03:00:11 -215882.060713] Model parameter optimization (eps = 1.000000)
[03:00:24 -215879.773546] SLOW spr round 1 (radius: 5)
[03:02:27 -215816.045695] SLOW spr round 2 (radius: 5)
[03:04:30 -215815.536941] SLOW spr round 3 (radius: 5)
[03:06:31 -215815.536292] SLOW spr round 4 (radius: 10)
[03:08:33 -215812.200158] SLOW spr round 5 (radius: 5)
[03:11:00 -215812.183931] SLOW spr round 6 (radius: 10)
[03:13:16 -215812.183450] SLOW spr round 7 (radius: 15)
[03:16:07 -215810.810367] SLOW spr round 8 (radius: 5)
[03:18:41 -215810.810111] SLOW spr round 9 (radius: 10)
[03:21:06 -215810.809965] SLOW spr round 10 (radius: 15)
[03:23:54 -215810.809821] SLOW spr round 11 (radius: 20)
[03:28:37 -215810.809679] SLOW spr round 12 (radius: 25)
[03:34:07 -215810.809538] Model parameter optimization (eps = 0.100000)

[03:34:16] ML tree search #4, logLikelihood: -215810.681686

[03:34:16 -1439931.254592] Initial branch length optimization
[03:34:21 -1152796.948552] Model parameter optimization (eps = 10.000000)
[03:34:51 -1151987.816120] AUTODETECT spr round 1 (radius: 5)
[03:37:06 -638446.138932] AUTODETECT spr round 2 (radius: 10)
[03:39:30 -402884.851975] AUTODETECT spr round 3 (radius: 15)
[03:41:56 -306614.515949] AUTODETECT spr round 4 (radius: 20)
[03:44:39 -261709.046068] AUTODETECT spr round 5 (radius: 25)
[03:47:51 -253342.289297] SPR radius for FAST iterations: 25 (autodetect)
[03:47:51 -253342.289297] Model parameter optimization (eps = 3.000000)
[03:48:19 -252863.879788] FAST spr round 1 (radius: 25)
[03:50:48 -217373.440790] FAST spr round 2 (radius: 25)
[03:52:47 -215989.454280] FAST spr round 3 (radius: 25)
[03:54:38 -215894.136306] FAST spr round 4 (radius: 25)
[03:56:14 -215892.156404] FAST spr round 5 (radius: 25)
[03:57:47 -215892.154850] Model parameter optimization (eps = 1.000000)
[03:58:02 -215888.402798] SLOW spr round 1 (radius: 5)
[04:00:09 -215829.904325] SLOW spr round 2 (radius: 5)
[04:02:11 -215826.247497] SLOW spr round 3 (radius: 5)
[04:04:10 -215826.245932] SLOW spr round 4 (radius: 10)
[04:06:11 -215826.244974] SLOW spr round 5 (radius: 15)
[04:09:14 -215826.244771] SLOW spr round 6 (radius: 20)
[04:13:51 -215826.244659] SLOW spr round 7 (radius: 25)
[04:19:41 -215826.244585] Model parameter optimization (eps = 0.100000)

[04:19:46] ML tree search #5, logLikelihood: -215826.204940

[04:19:46 -1434238.227716] Initial branch length optimization
[04:19:51 -1146375.240964] Model parameter optimization (eps = 10.000000)
[04:20:25 -1145475.100663] AUTODETECT spr round 1 (radius: 5)
[04:22:38 -621881.056975] AUTODETECT spr round 2 (radius: 10)
[04:24:59 -410573.624353] AUTODETECT spr round 3 (radius: 15)
[04:27:29 -296764.916058] AUTODETECT spr round 4 (radius: 20)
[04:30:17 -258639.261210] AUTODETECT spr round 5 (radius: 25)
[04:33:37 -249522.858020] SPR radius for FAST iterations: 25 (autodetect)
[04:33:37 -249522.858020] Model parameter optimization (eps = 3.000000)
[04:34:00 -249094.347835] FAST spr round 1 (radius: 25)
[04:36:28 -217774.740750] FAST spr round 2 (radius: 25)
[04:38:35 -216030.681236] FAST spr round 3 (radius: 25)
[04:40:27 -215894.186150] FAST spr round 4 (radius: 25)
[04:42:05 -215893.008324] FAST spr round 5 (radius: 25)
[04:43:39 -215893.007754] Model parameter optimization (eps = 1.000000)
[04:43:56 -215879.578033] SLOW spr round 1 (radius: 5)
[04:46:06 -215827.555379] SLOW spr round 2 (radius: 5)
[04:48:09 -215814.239252] SLOW spr round 3 (radius: 5)
[04:50:07 -215814.204224] SLOW spr round 4 (radius: 10)
[04:52:09 -215813.861152] SLOW spr round 5 (radius: 5)
[04:54:33 -215813.860489] SLOW spr round 6 (radius: 10)
[04:56:48 -215813.860261] SLOW spr round 7 (radius: 15)
[04:59:41 -215813.860114] SLOW spr round 8 (radius: 20)
[05:04:19 -215813.860014] SLOW spr round 9 (radius: 25)
[05:09:56 -215813.859942] Model parameter optimization (eps = 0.100000)

[05:10:06] ML tree search #6, logLikelihood: -215813.748169

[05:10:06 -1431695.067083] Initial branch length optimization
[05:10:11 -1146781.944469] Model parameter optimization (eps = 10.000000)
[05:10:49 -1145928.896085] AUTODETECT spr round 1 (radius: 5)
[05:13:01 -668093.931472] AUTODETECT spr round 2 (radius: 10)
[05:15:32 -420562.973802] AUTODETECT spr round 3 (radius: 15)
[05:17:58 -321236.457833] AUTODETECT spr round 4 (radius: 20)
[05:20:31 -265113.731393] AUTODETECT spr round 5 (radius: 25)
[05:23:20 -249675.331067] SPR radius for FAST iterations: 25 (autodetect)
[05:23:20 -249675.331067] Model parameter optimization (eps = 3.000000)
[05:23:43 -249222.157252] FAST spr round 1 (radius: 25)
[05:26:10 -217860.729052] FAST spr round 2 (radius: 25)
[05:28:12 -216030.837768] FAST spr round 3 (radius: 25)
[05:30:02 -215912.542186] FAST spr round 4 (radius: 25)
[05:31:41 -215893.807589] FAST spr round 5 (radius: 25)
[05:33:16 -215893.242813] FAST spr round 6 (radius: 25)
[05:34:49 -215893.242335] Model parameter optimization (eps = 1.000000)
[05:35:08 -215876.565335] SLOW spr round 1 (radius: 5)
[05:37:11 -215812.034176] SLOW spr round 2 (radius: 5)
[05:39:12 -215811.552423] SLOW spr round 3 (radius: 5)
[05:41:11 -215811.551867] SLOW spr round 4 (radius: 10)
[05:43:13 -215811.448612] SLOW spr round 5 (radius: 5)
[05:45:38 -215811.447922] SLOW spr round 6 (radius: 10)
[05:47:55 -215811.447801] SLOW spr round 7 (radius: 15)
[05:50:48 -215811.385166] SLOW spr round 8 (radius: 20)
[05:55:35 -215811.371942] SLOW spr round 9 (radius: 25)
[06:01:25 -215811.370155] Model parameter optimization (eps = 0.100000)

[06:01:30] ML tree search #7, logLikelihood: -215811.345022

[06:01:30 -1412766.074629] Initial branch length optimization
[06:01:35 -1133765.645156] Model parameter optimization (eps = 10.000000)
[06:02:04 -1132936.672665] AUTODETECT spr round 1 (radius: 5)
[06:04:18 -617525.272562] AUTODETECT spr round 2 (radius: 10)
[06:06:36 -424559.532138] AUTODETECT spr round 3 (radius: 15)
[06:09:00 -314085.754385] AUTODETECT spr round 4 (radius: 20)
[06:11:56 -260436.556363] AUTODETECT spr round 5 (radius: 25)
[06:15:06 -249096.457645] SPR radius for FAST iterations: 25 (autodetect)
[06:15:06 -249096.457645] Model parameter optimization (eps = 3.000000)
[06:15:33 -248668.988627] FAST spr round 1 (radius: 25)
[06:17:57 -217585.872640] FAST spr round 2 (radius: 25)
[06:19:48 -216058.688344] FAST spr round 3 (radius: 25)
[06:21:32 -215922.904343] FAST spr round 4 (radius: 25)
[06:23:13 -215920.734746] FAST spr round 5 (radius: 25)
[06:24:48 -215920.733597] Model parameter optimization (eps = 1.000000)
[06:25:05 -215903.033830] SLOW spr round 1 (radius: 5)
[06:27:14 -215853.553354] SLOW spr round 2 (radius: 5)
[06:29:16 -215852.666055] SLOW spr round 3 (radius: 5)
[06:31:18 -215849.956832] SLOW spr round 4 (radius: 5)
[06:33:15 -215849.956587] SLOW spr round 5 (radius: 10)
[06:35:17 -215844.105308] SLOW spr round 6 (radius: 5)
[06:37:43 -215842.893934] SLOW spr round 7 (radius: 5)
[06:39:54 -215842.893693] SLOW spr round 8 (radius: 10)
[06:41:59 -215842.893538] SLOW spr round 9 (radius: 15)
[06:44:56 -215835.496599] SLOW spr round 10 (radius: 5)
[06:47:33 -215818.887516] SLOW spr round 11 (radius: 5)
[06:49:50 -215808.473531] SLOW spr round 12 (radius: 5)
[06:51:55 -215808.473352] SLOW spr round 13 (radius: 10)
[06:53:59 -215808.473218] SLOW spr round 14 (radius: 15)
[06:56:58 -215808.473085] SLOW spr round 15 (radius: 20)
[07:01:37 -215808.472953] SLOW spr round 16 (radius: 25)
[07:07:13 -215808.472821] Model parameter optimization (eps = 0.100000)

[07:07:18] ML tree search #8, logLikelihood: -215808.442193

[07:07:18 -1436006.395661] Initial branch length optimization
[07:07:23 -1152804.118414] Model parameter optimization (eps = 10.000000)
[07:07:56 -1151983.283792] AUTODETECT spr round 1 (radius: 5)
[07:10:09 -635262.894647] AUTODETECT spr round 2 (radius: 10)
[07:12:29 -416718.196914] AUTODETECT spr round 3 (radius: 15)
[07:14:52 -293544.855470] AUTODETECT spr round 4 (radius: 20)
[07:17:35 -255906.900328] AUTODETECT spr round 5 (radius: 25)
[07:20:28 -246408.550778] SPR radius for FAST iterations: 25 (autodetect)
[07:20:28 -246408.550778] Model parameter optimization (eps = 3.000000)
[07:20:50 -245846.296603] FAST spr round 1 (radius: 25)
[07:23:21 -217612.547161] FAST spr round 2 (radius: 25)
[07:25:22 -215959.398144] FAST spr round 3 (radius: 25)
[07:27:09 -215850.151970] FAST spr round 4 (radius: 25)
[07:28:47 -215848.601877] FAST spr round 5 (radius: 25)
[07:30:21 -215848.599645] Model parameter optimization (eps = 1.000000)
[07:30:35 -215844.568112] SLOW spr round 1 (radius: 5)
[07:32:42 -215815.912044] SLOW spr round 2 (radius: 5)
[07:34:44 -215815.862313] SLOW spr round 3 (radius: 10)
[07:36:46 -215812.730713] SLOW spr round 4 (radius: 5)
[07:39:12 -215812.714474] SLOW spr round 5 (radius: 10)
[07:41:28 -215812.714126] SLOW spr round 6 (radius: 15)
[07:44:19 -215812.713897] SLOW spr round 7 (radius: 20)
[07:49:00 -215812.713743] SLOW spr round 8 (radius: 25)
[07:54:44 -215812.713637] Model parameter optimization (eps = 0.100000)

[07:54:52] ML tree search #9, logLikelihood: -215812.644101

[07:54:52 -1442450.853388] Initial branch length optimization
[07:54:56 -1150322.957835] Model parameter optimization (eps = 10.000000)
[07:55:30 -1149438.080876] AUTODETECT spr round 1 (radius: 5)
[07:57:43 -663206.536225] AUTODETECT spr round 2 (radius: 10)
[08:00:10 -392908.022754] AUTODETECT spr round 3 (radius: 15)
[08:02:33 -306540.820843] AUTODETECT spr round 4 (radius: 20)
[08:05:06 -276870.664385] AUTODETECT spr round 5 (radius: 25)
[08:08:01 -262260.112014] SPR radius for FAST iterations: 25 (autodetect)
[08:08:01 -262260.112014] Model parameter optimization (eps = 3.000000)
[08:08:32 -261839.321522] FAST spr round 1 (radius: 25)
[08:11:07 -218882.401267] FAST spr round 2 (radius: 25)
[08:13:10 -216142.170047] FAST spr round 3 (radius: 25)
[08:14:55 -215955.328187] FAST spr round 4 (radius: 25)
[08:16:35 -215908.196854] FAST spr round 5 (radius: 25)
[08:18:13 -215899.245645] FAST spr round 6 (radius: 25)
[08:19:47 -215899.243966] Model parameter optimization (eps = 1.000000)
[08:20:07 -215868.212774] SLOW spr round 1 (radius: 5)
[08:22:09 -215826.699024] SLOW spr round 2 (radius: 5)
[08:24:11 -215820.485949] SLOW spr round 3 (radius: 5)
[08:26:09 -215820.485434] SLOW spr round 4 (radius: 10)
[08:28:11 -215816.922100] SLOW spr round 5 (radius: 5)
[08:30:36 -215816.906351] SLOW spr round 6 (radius: 10)
[08:32:52 -215816.905857] SLOW spr round 7 (radius: 15)
[08:35:45 -215816.905485] SLOW spr round 8 (radius: 20)
[08:40:24 -215816.905193] SLOW spr round 9 (radius: 25)
[08:46:01 -215816.904955] Model parameter optimization (eps = 0.100000)

[08:46:09] ML tree search #10, logLikelihood: -215816.791564

[08:46:10 -1442329.915494] Initial branch length optimization
[08:46:14 -1151584.819710] Model parameter optimization (eps = 10.000000)
[08:46:51 -1150825.618062] AUTODETECT spr round 1 (radius: 5)
[08:49:06 -614600.412166] AUTODETECT spr round 2 (radius: 10)
[08:51:24 -397673.083217] AUTODETECT spr round 3 (radius: 15)
[08:53:47 -305418.464006] AUTODETECT spr round 4 (radius: 20)
[08:56:53 -259435.628978] AUTODETECT spr round 5 (radius: 25)
[08:59:52 -252920.445505] SPR radius for FAST iterations: 25 (autodetect)
[08:59:52 -252920.445505] Model parameter optimization (eps = 3.000000)
[09:00:28 -252397.244932] FAST spr round 1 (radius: 25)
[09:02:53 -217676.109594] FAST spr round 2 (radius: 25)
[09:04:48 -216011.663146] FAST spr round 3 (radius: 25)
[09:06:32 -215913.241289] FAST spr round 4 (radius: 25)
[09:08:09 -215912.645142] FAST spr round 5 (radius: 25)
[09:09:42 -215912.643987] Model parameter optimization (eps = 1.000000)
[09:10:02 -215900.235974] SLOW spr round 1 (radius: 5)
[09:12:06 -215843.678264] SLOW spr round 2 (radius: 5)
[09:14:08 -215841.938730] SLOW spr round 3 (radius: 5)
[09:16:06 -215841.938184] SLOW spr round 4 (radius: 10)
[09:18:10 -215836.776219] SLOW spr round 5 (radius: 5)
[09:20:34 -215835.928256] SLOW spr round 6 (radius: 5)
[09:22:46 -215835.927761] SLOW spr round 7 (radius: 10)
[09:24:53 -215824.153339] SLOW spr round 8 (radius: 5)
[09:27:17 -215819.380788] SLOW spr round 9 (radius: 5)
[09:29:27 -215819.380565] SLOW spr round 10 (radius: 10)
[09:31:34 -215819.380408] SLOW spr round 11 (radius: 15)
[09:34:32 -215818.012297] SLOW spr round 12 (radius: 5)
[09:37:04 -215818.012116] SLOW spr round 13 (radius: 10)
[09:39:30 -215818.011976] SLOW spr round 14 (radius: 15)
[09:42:20 -215818.011836] SLOW spr round 15 (radius: 20)
[09:47:07 -215818.011696] SLOW spr round 16 (radius: 25)
[09:52:42 -215818.011557] Model parameter optimization (eps = 0.100000)

[09:52:48] ML tree search #11, logLikelihood: -215817.962817

[09:52:48 -1443689.605630] Initial branch length optimization
[09:52:52 -1149548.252730] Model parameter optimization (eps = 10.000000)
[09:53:25 -1148781.061011] AUTODETECT spr round 1 (radius: 5)
[09:55:41 -665899.812113] AUTODETECT spr round 2 (radius: 10)
[09:58:09 -433139.814356] AUTODETECT spr round 3 (radius: 15)
[10:00:41 -358385.204424] AUTODETECT spr round 4 (radius: 20)
[10:03:48 -280985.191162] AUTODETECT spr round 5 (radius: 25)
[10:07:07 -262229.498128] SPR radius for FAST iterations: 25 (autodetect)
[10:07:07 -262229.498128] Model parameter optimization (eps = 3.000000)
[10:07:32 -261733.935699] FAST spr round 1 (radius: 25)
[10:10:04 -218217.723412] FAST spr round 2 (radius: 25)
[10:12:08 -216089.102417] FAST spr round 3 (radius: 25)
[10:13:57 -215964.518503] FAST spr round 4 (radius: 25)
[10:15:38 -215938.794126] FAST spr round 5 (radius: 25)
[10:17:13 -215936.090841] FAST spr round 6 (radius: 25)
[10:18:47 -215936.090745] Model parameter optimization (eps = 1.000000)
[10:19:08 -215900.452228] SLOW spr round 1 (radius: 5)
[10:21:14 -215834.590874] SLOW spr round 2 (radius: 5)
[10:23:20 -215825.988773] SLOW spr round 3 (radius: 5)
[10:25:19 -215825.987761] SLOW spr round 4 (radius: 10)
[10:27:23 -215822.156645] SLOW spr round 5 (radius: 5)
[10:29:49 -215822.109102] SLOW spr round 6 (radius: 10)
[10:32:07 -215822.108867] SLOW spr round 7 (radius: 15)
[10:35:00 -215822.108667] SLOW spr round 8 (radius: 20)
[10:39:42 -215822.108488] SLOW spr round 9 (radius: 25)
[10:45:25 -215822.108322] Model parameter optimization (eps = 0.100000)

[10:45:37] ML tree search #12, logLikelihood: -215821.731449

[10:45:37 -1445178.773796] Initial branch length optimization
[10:45:42 -1154525.557072] Model parameter optimization (eps = 10.000000)
[10:46:13 -1153739.175692] AUTODETECT spr round 1 (radius: 5)
[10:48:30 -651944.363128] AUTODETECT spr round 2 (radius: 10)
[10:50:54 -434676.214138] AUTODETECT spr round 3 (radius: 15)
[10:53:20 -301806.316063] AUTODETECT spr round 4 (radius: 20)
[10:56:01 -269232.952826] AUTODETECT spr round 5 (radius: 25)
[10:58:53 -255674.473366] SPR radius for FAST iterations: 25 (autodetect)
[10:58:53 -255674.473366] Model parameter optimization (eps = 3.000000)
[10:59:16 -255122.444230] FAST spr round 1 (radius: 25)
[11:01:49 -219638.234503] FAST spr round 2 (radius: 25)
[11:03:52 -216178.502544] FAST spr round 3 (radius: 25)
[11:05:37 -215930.757016] FAST spr round 4 (radius: 25)
[11:07:17 -215927.683114] FAST spr round 5 (radius: 25)
[11:08:51 -215927.682391] Model parameter optimization (eps = 1.000000)
[11:09:10 -215907.350070] SLOW spr round 1 (radius: 5)
[11:11:15 -215818.865056] SLOW spr round 2 (radius: 5)
[11:13:18 -215818.862861] SLOW spr round 3 (radius: 10)
[11:15:20 -215818.861645] SLOW spr round 4 (radius: 15)
[11:18:21 -215818.860668] SLOW spr round 5 (radius: 20)
[11:22:55 -215818.860046] SLOW spr round 6 (radius: 25)
[11:28:36 -215818.859877] Model parameter optimization (eps = 0.100000)

[11:28:43] ML tree search #13, logLikelihood: -215818.838901

[11:28:43 -1441316.226625] Initial branch length optimization
[11:28:47 -1159333.347118] Model parameter optimization (eps = 10.000000)
[11:29:18 -1158557.448553] AUTODETECT spr round 1 (radius: 5)
[11:31:33 -627366.192238] AUTODETECT spr round 2 (radius: 10)
[11:33:53 -414107.579414] AUTODETECT spr round 3 (radius: 15)
[11:36:13 -291534.485373] AUTODETECT spr round 4 (radius: 20)
[11:39:02 -253790.056292] AUTODETECT spr round 5 (radius: 25)
[11:42:22 -247895.379674] SPR radius for FAST iterations: 25 (autodetect)
[11:42:22 -247895.379674] Model parameter optimization (eps = 3.000000)
[11:42:45 -247427.520748] FAST spr round 1 (radius: 25)
[11:45:05 -217374.432240] FAST spr round 2 (radius: 25)
[11:46:59 -215967.931422] FAST spr round 3 (radius: 25)
[11:48:44 -215888.091858] FAST spr round 4 (radius: 25)
[11:50:24 -215886.152920] FAST spr round 5 (radius: 25)
[11:52:00 -215886.152765] Model parameter optimization (eps = 1.000000)
[11:52:13 -215884.308097] SLOW spr round 1 (radius: 5)
[11:54:17 -215827.542657] SLOW spr round 2 (radius: 5)
[11:56:20 -215822.684307] SLOW spr round 3 (radius: 5)
[11:58:22 -215817.970018] SLOW spr round 4 (radius: 5)
[12:00:21 -215817.969550] SLOW spr round 5 (radius: 10)
[12:02:23 -215817.943936] SLOW spr round 6 (radius: 15)
[12:05:25 -215817.942945] SLOW spr round 7 (radius: 20)
[12:09:57 -215817.942719] SLOW spr round 8 (radius: 25)
[12:15:32 -215817.942541] Model parameter optimization (eps = 0.100000)

[12:15:36] ML tree search #14, logLikelihood: -215817.933314

[12:15:37 -1448973.684328] Initial branch length optimization
[12:15:41 -1158125.696570] Model parameter optimization (eps = 10.000000)
[12:16:12 -1157237.476992] AUTODETECT spr round 1 (radius: 5)
[12:18:27 -638951.325083] AUTODETECT spr round 2 (radius: 10)
[12:20:54 -400259.435423] AUTODETECT spr round 3 (radius: 15)
[12:23:25 -291298.281918] AUTODETECT spr round 4 (radius: 20)
[12:26:15 -258585.227298] AUTODETECT spr round 5 (radius: 25)
[12:29:35 -245059.710314] SPR radius for FAST iterations: 25 (autodetect)
[12:29:35 -245059.710314] Model parameter optimization (eps = 3.000000)
[12:29:57 -244682.676314] FAST spr round 1 (radius: 25)
[12:32:22 -217536.055789] FAST spr round 2 (radius: 25)
[12:34:20 -216087.804479] FAST spr round 3 (radius: 25)
[12:36:09 -215923.406832] FAST spr round 4 (radius: 25)
[12:37:49 -215922.918987] FAST spr round 5 (radius: 25)
[12:39:26 -215922.917884] Model parameter optimization (eps = 1.000000)
[12:39:47 -215889.029418] SLOW spr round 1 (radius: 5)
[12:41:54 -215823.212705] SLOW spr round 2 (radius: 5)
[12:43:57 -215822.006245] SLOW spr round 3 (radius: 5)
[12:45:58 -215822.005661] SLOW spr round 4 (radius: 10)
[12:48:00 -215821.905353] SLOW spr round 5 (radius: 5)
[12:50:26 -215821.904866] SLOW spr round 6 (radius: 10)
[12:52:43 -215821.904645] SLOW spr round 7 (radius: 15)
[12:55:35 -215821.904456] SLOW spr round 8 (radius: 20)
[13:00:18 -215821.904287] SLOW spr round 9 (radius: 25)
[13:05:54 -215821.904131] Model parameter optimization (eps = 0.100000)

[13:06:01] ML tree search #15, logLikelihood: -215821.824799

[13:06:01 -1430596.019120] Initial branch length optimization
[13:06:06 -1149292.219245] Model parameter optimization (eps = 10.000000)
[13:06:39 -1148473.135253] AUTODETECT spr round 1 (radius: 5)
[13:08:54 -614370.111119] AUTODETECT spr round 2 (radius: 10)
[13:11:14 -388329.470647] AUTODETECT spr round 3 (radius: 15)
[13:13:40 -307020.345385] AUTODETECT spr round 4 (radius: 20)
[13:16:36 -264823.713572] AUTODETECT spr round 5 (radius: 25)
[13:20:09 -253292.109469] SPR radius for FAST iterations: 25 (autodetect)
[13:20:09 -253292.109469] Model parameter optimization (eps = 3.000000)
[13:20:31 -252849.714651] FAST spr round 1 (radius: 25)
[13:22:59 -218186.737458] FAST spr round 2 (radius: 25)
[13:25:02 -216030.364393] FAST spr round 3 (radius: 25)
[13:26:53 -215938.060932] FAST spr round 4 (radius: 25)
[13:28:33 -215928.246880] FAST spr round 5 (radius: 25)
[13:30:08 -215928.246337] Model parameter optimization (eps = 1.000000)
[13:30:32 -215891.597287] SLOW spr round 1 (radius: 5)
[13:32:41 -215826.000963] SLOW spr round 2 (radius: 5)
[13:34:45 -215822.098789] SLOW spr round 3 (radius: 5)
[13:36:46 -215822.097209] SLOW spr round 4 (radius: 10)
[13:38:48 -215822.040151] SLOW spr round 5 (radius: 15)
[13:41:46 -215820.706031] SLOW spr round 6 (radius: 5)
[13:44:20 -215820.705582] SLOW spr round 7 (radius: 10)
[13:46:46 -215820.704712] SLOW spr round 8 (radius: 15)
[13:49:31 -215820.704563] SLOW spr round 9 (radius: 20)
[13:54:14 -215820.704414] SLOW spr round 10 (radius: 25)
[13:59:41 -215820.704266] Model parameter optimization (eps = 0.100000)

[13:59:52] ML tree search #16, logLikelihood: -215820.517094

[13:59:52 -1436413.224892] Initial branch length optimization
[13:59:56 -1157266.545039] Model parameter optimization (eps = 10.000000)
[14:00:29 -1156482.117675] AUTODETECT spr round 1 (radius: 5)
[14:02:45 -616242.224912] AUTODETECT spr round 2 (radius: 10)
[14:05:06 -410532.157197] AUTODETECT spr round 3 (radius: 15)
[14:07:34 -307038.993919] AUTODETECT spr round 4 (radius: 20)
[14:10:19 -261691.171266] AUTODETECT spr round 5 (radius: 25)
[14:13:25 -251362.857557] SPR radius for FAST iterations: 25 (autodetect)
[14:13:25 -251362.857557] Model parameter optimization (eps = 3.000000)
[14:13:49 -250895.160188] FAST spr round 1 (radius: 25)
[14:16:15 -218344.364623] FAST spr round 2 (radius: 25)
[14:18:09 -216150.301861] FAST spr round 3 (radius: 25)
[14:19:57 -215916.881212] FAST spr round 4 (radius: 25)
[14:21:37 -215911.472972] FAST spr round 5 (radius: 25)
[14:23:14 -215910.921127] FAST spr round 6 (radius: 25)
[14:24:49 -215910.920993] Model parameter optimization (eps = 1.000000)
[14:25:03 -215906.283556] SLOW spr round 1 (radius: 5)
[14:27:06 -215838.878792] SLOW spr round 2 (radius: 5)
[14:29:10 -215822.661787] SLOW spr round 3 (radius: 5)
[14:31:12 -215822.659831] SLOW spr round 4 (radius: 10)
[14:33:16 -215822.659370] SLOW spr round 5 (radius: 15)
[14:36:16 -215822.659194] SLOW spr round 6 (radius: 20)
[14:40:44 -215822.659096] SLOW spr round 7 (radius: 25)
[14:46:23 -215822.659030] Model parameter optimization (eps = 0.100000)

[14:46:36] ML tree search #17, logLikelihood: -215821.721861

[14:46:36 -1442169.160785] Initial branch length optimization
[14:46:41 -1165203.619729] Model parameter optimization (eps = 10.000000)
[14:47:09 -1164427.235715] AUTODETECT spr round 1 (radius: 5)
[14:49:24 -628057.832227] AUTODETECT spr round 2 (radius: 10)
[14:51:49 -419544.032852] AUTODETECT spr round 3 (radius: 15)
[14:54:13 -316054.881647] AUTODETECT spr round 4 (radius: 20)
[14:57:05 -263826.521803] AUTODETECT spr round 5 (radius: 25)
[15:00:04 -247741.300898] SPR radius for FAST iterations: 25 (autodetect)
[15:00:04 -247741.300898] Model parameter optimization (eps = 3.000000)
[15:00:34 -247302.549234] FAST spr round 1 (radius: 25)
[15:03:10 -217594.716571] FAST spr round 2 (radius: 25)
[15:05:06 -216079.143752] FAST spr round 3 (radius: 25)
[15:06:53 -215961.888831] FAST spr round 4 (radius: 25)
[15:08:34 -215950.988087] FAST spr round 5 (radius: 25)
[15:10:10 -215948.296116] FAST spr round 6 (radius: 25)
[15:11:44 -215948.295916] Model parameter optimization (eps = 1.000000)
[15:12:01 -215939.182210] SLOW spr round 1 (radius: 5)
[15:14:12 -215846.787665] SLOW spr round 2 (radius: 5)
[15:16:16 -215826.136285] SLOW spr round 3 (radius: 5)
[15:18:17 -215824.042046] SLOW spr round 4 (radius: 5)
[15:20:15 -215824.041818] SLOW spr round 5 (radius: 10)
[15:22:20 -215818.755873] SLOW spr round 6 (radius: 5)
[15:24:47 -215816.226441] SLOW spr round 7 (radius: 5)
[15:26:59 -215816.224041] SLOW spr round 8 (radius: 10)
[15:29:06 -215816.222596] SLOW spr round 9 (radius: 15)
[15:32:06 -215814.813394] SLOW spr round 10 (radius: 5)
[15:34:39 -215814.813324] SLOW spr round 11 (radius: 10)
[15:37:04 -215814.813296] SLOW spr round 12 (radius: 15)
[15:39:55 -215814.813270] SLOW spr round 13 (radius: 20)
[15:44:45 -215814.813246] SLOW spr round 14 (radius: 25)
[15:50:25 -215814.813223] Model parameter optimization (eps = 0.100000)

[15:50:34] ML tree search #18, logLikelihood: -215814.584024

[15:50:34 -1447107.844994] Initial branch length optimization
[15:50:39 -1156632.577614] Model parameter optimization (eps = 10.000000)
[15:51:18 -1155769.904346] AUTODETECT spr round 1 (radius: 5)
[15:53:34 -640773.543922] AUTODETECT spr round 2 (radius: 10)
[15:56:05 -414180.004443] AUTODETECT spr round 3 (radius: 15)
[15:58:33 -321376.374920] AUTODETECT spr round 4 (radius: 20)
[16:01:18 -265573.642186] AUTODETECT spr round 5 (radius: 25)
[16:04:24 -252047.932392] SPR radius for FAST iterations: 25 (autodetect)
[16:04:24 -252047.932392] Model parameter optimization (eps = 3.000000)
[16:04:54 -251545.632998] FAST spr round 1 (radius: 25)
[16:07:27 -218034.736137] FAST spr round 2 (radius: 25)
[16:09:24 -216031.214142] FAST spr round 3 (radius: 25)
[16:11:15 -215890.279424] FAST spr round 4 (radius: 25)
[16:12:53 -215887.758825] FAST spr round 5 (radius: 25)
[16:14:29 -215887.758337] Model parameter optimization (eps = 1.000000)
[16:14:46 -215881.901147] SLOW spr round 1 (radius: 5)
[16:16:55 -215817.984207] SLOW spr round 2 (radius: 5)
[16:18:58 -215814.911913] SLOW spr round 3 (radius: 5)
[16:20:59 -215811.878055] SLOW spr round 4 (radius: 5)
[16:22:56 -215811.877704] SLOW spr round 5 (radius: 10)
[16:24:58 -215809.545105] SLOW spr round 6 (radius: 5)
[16:27:23 -215808.704612] SLOW spr round 7 (radius: 5)
[16:29:34 -215808.704192] SLOW spr round 8 (radius: 10)
[16:31:41 -215808.703885] SLOW spr round 9 (radius: 15)
[16:34:39 -215808.703642] SLOW spr round 10 (radius: 20)
[16:39:16 -215808.703440] SLOW spr round 11 (radius: 25)
[16:44:55 -215808.703264] Model parameter optimization (eps = 0.100000)

[16:45:05] ML tree search #19, logLikelihood: -215808.522678

[16:45:05 -1443868.715275] Initial branch length optimization
[16:45:10 -1155740.953648] Model parameter optimization (eps = 10.000000)
[16:45:39 -1154967.979860] AUTODETECT spr round 1 (radius: 5)
[16:47:54 -628771.409102] AUTODETECT spr round 2 (radius: 10)
[16:50:11 -413330.493341] AUTODETECT spr round 3 (radius: 15)
[16:52:37 -333545.211648] AUTODETECT spr round 4 (radius: 20)
[16:55:38 -280570.882293] AUTODETECT spr round 5 (radius: 25)
[16:59:23 -256523.670064] SPR radius for FAST iterations: 25 (autodetect)
[16:59:23 -256523.670064] Model parameter optimization (eps = 3.000000)
[16:59:49 -256050.978612] FAST spr round 1 (radius: 25)
[17:02:16 -219918.442070] FAST spr round 2 (radius: 25)
[17:04:21 -216156.208535] FAST spr round 3 (radius: 25)
[17:06:11 -215904.400123] FAST spr round 4 (radius: 25)
[17:07:53 -215889.215374] FAST spr round 5 (radius: 25)
[17:09:29 -215889.215015] Model parameter optimization (eps = 1.000000)
[17:09:44 -215886.719879] SLOW spr round 1 (radius: 5)
[17:11:49 -215844.437510] SLOW spr round 2 (radius: 5)
[17:13:54 -215840.484215] SLOW spr round 3 (radius: 5)
[17:15:57 -215835.392332] SLOW spr round 4 (radius: 5)
[17:17:57 -215835.391810] SLOW spr round 5 (radius: 10)
[17:19:58 -215835.391548] SLOW spr round 6 (radius: 15)
[17:22:58 -215835.391328] SLOW spr round 7 (radius: 20)
[17:27:20 -215835.391134] SLOW spr round 8 (radius: 25)
[17:32:43 -215835.390957] Model parameter optimization (eps = 0.100000)

[17:32:48] ML tree search #20, logLikelihood: -215835.352147


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.183416,0.383793) (0.169524,0.629829) (0.407252,0.784361) (0.239809,2.099183) 
   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: -215808.442193

AIC score: 435626.884386 / AICc score: 8479686.884386 / BIC score: 445581.870479
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1059).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 179 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q13332/3_mltree/Q13332.raxml.log

Analysis started: 31-Jul-2021 02:44:47 / finished: 31-Jul-2021 20:17:36

Elapsed time: 63168.709 seconds