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 17-Jun-2021 23:45:27 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/2_msa/Q5D862_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862 --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_040621/phylogeny-snakemake/results/Q5D862/2_msa/Q5D862_trimmed_msa.fasta
[00:00:00] Loaded alignment with 640 taxa and 90 sites

WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091ILC5_A0A091ILC5_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091VLU4_A0A091VLU4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A087QP91_A0A087QP91_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A2I0LLS9_A0A2I0LLS9_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A1V4JZG4_A0A1V4JZG4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226MEW3_A0A226MEW3_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226NI21_A0A226NI21_COLVI_9014 are exactly identical!
WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_G1MRY2_G1MRY2_MELGA_9103 are exactly identical!
WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226N1K0_A0A226N1K0_CALSU_9009 are exactly identical!
WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226P850_A0A226P850_COLVI_9014 are exactly identical!
WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_G3H328_G3H328_CRIGR_10029 are exactly identical!
WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_A0A1U7Q6F1_A0A1U7Q6F1_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3XUC8_M3XUC8_MUSPF_9669 and tr_A0A2Y9LDZ9_A0A2Y9LDZ9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XWL0_M3XWL0_MUSPF_9669 and tr_A0A2Y9IR02_A0A2Y9IR02_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_W5NRD4_W5NRD4_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_I3LX39_I3LX39_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A286XNC8_A0A286XNC8_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_G3SQW8_G3SQW8_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_G1M0I1_G1M0I1_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and sp_P02639_S10A1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_M3XA34_M3XA34_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2U3W4T9_A0A2U3W4T9_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2U3YWQ1_A0A2U3YWQ1_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9IHF9_A0A2Y9IHF9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9MD03_A0A2Y9MD03_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A2Y9FVI4_A0A2Y9FVI4_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3YA96_M3YA96_MUSPF_9669 and tr_A0A383ZU35_A0A383ZU35_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_G3RL51_G3RL51_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_I6L539_I6L539_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and sp_Q5RC36_S10A1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_H2Q035_H2Q035_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and sp_P23297_S10A1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_F7HGE0_F7HGE0_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_F6QF56_F6QF56_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_G7NUH2_G7NUH2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A096NYU6_A0A096NYU6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A0D9S5N2_A0A0D9S5N2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K5NH83_A0A2K5NH83_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K6DJR8_A0A2K6DJR8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2K5Y2G8_A0A2K5Y2G8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RHH7_G1RHH7_NOMLE_61853 and tr_A0A2R9BUH5_A0A2R9BUH5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1Q9C5_G1Q9C5_MYOLU_59463 and tr_A0A1U7T1U2_A0A1U7T1U2_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G3HC24_G3HC24_CRIGR_10029 and tr_A0A1U7R3I4_A0A1U7R3I4_MESAU_10036 are exactly identical!
WARNING: Sequences tr_B2VXF8_B2VXF8_PYRTR_426418 and tr_A0A2W1HC14_A0A2W1HC14_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_H2QP64_H2QP64_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_A0A2R8ZMX9_A0A2R8ZMX9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_Q6YNR6_S100B_RABIT_9986 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_F6RF49_F6RF49_HORSE_9796 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_P04271_S100B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_G1L2S1_G1L2S1_AILME_9646 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2I2UW07_A0A2I2UW07_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2Y9FKI7_A0A2Y9FKI7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A384DNP5_A0A384DNP5_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A383ZCB7_A0A383ZCB7_BALAS_310752 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and sp_P25815_S100P_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_F6PWQ7_F6PWQ7_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A096NZC3_A0A096NZC3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A0D9RU76_A0A0D9RU76_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5NID4_A0A2K5NID4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K6DNK8_A0A2K6DNK8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5XH25_A0A2K5XH25_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1SNF3_G1SNF3_RABIT_9986 and sp_P37709_TRHY_RABIT_9986 are exactly identical!
WARNING: Sequences tr_B8NAU1_B8NAU1_ASPFN_332952 and tr_A0A1S9DCW6_A0A1S9DCW6_ASPOZ_5062 are exactly identical!
WARNING: Sequences sp_P22793_TRHY_SHEEP_9940 and tr_W5QIV5_W5QIV5_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_G7PWM2_G7PWM2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A0D9R407_A0A0D9R407_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3VAA5_A0A2U3VAA5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3X2C1_A0A2U3X2C1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3Z3M3_A0A2U3Z3M3_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2Y9Q578_A0A2Y9Q578_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M4AK49_M4AK49_XIPMA_8083 and tr_A0A087XVD3_A0A087XVD3_POEFO_48698 are exactly identical!
WARNING: Sequences tr_I3MDN4_I3MDN4_ICTTR_43179 and tr_A0A286XTU0_A0A286XTU0_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_A0A1D5QZ82_A0A1D5QZ82_MACMU_9544 and tr_A0A2K6C482_A0A2K6C482_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6R3M7_F6R3M7_MACMU_9544 and tr_A0A0D9S5Q6_A0A0D9S5Q6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6R3M7_F6R3M7_MACMU_9544 and tr_A0A2K6BR78_A0A2K6BR78_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_G8F5R2_G8F5R2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_A0A0D9S5Q4_A0A0D9S5Q4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7FCK7_F7FCK7_MACMU_9544 and tr_A0A2K6DK96_A0A2K6DK96_MACNE_9545 are exactly identical!
WARNING: Sequences tr_B5FXV2_B5FXV2_TAEGU_59729 and tr_U3KFS2_U3KFS2_FICAL_59894 are exactly identical!
WARNING: Sequences tr_F9XN67_F9XN67_ZYMTI_336722 and tr_A0A0F4GNF2_A0A0F4GNF2_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9XN67_F9XN67_ZYMTI_336722 and tr_A0A1X7S7A8_A0A1X7S7A8_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G1LGH3_G1LGH3_AILME_9646 and tr_A0A384CHP1_A0A384CHP1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_U3K4U3_U3K4U3_FICAL_59894 and tr_A0A218V2N0_A0A218V2N0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A096MPI8_A0A096MPI8_PAPAN_9555 and tr_A0A2K5P568_A0A2K5P568_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MPI8_A0A096MPI8_PAPAN_9555 and tr_A0A2K6DRF8_A0A2K6DRF8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096MQV7_A0A096MQV7_PAPAN_9555 and tr_A0A2K5L0B3_A0A2K5L0B3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A087R9H8_A0A087R9H8_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A091V676_A0A091V676_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A2I0LXI2_A0A2I0LXI2_COLLI_8932 are exactly identical!
WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A1V4L055_A0A1V4L055_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A091VLA0_A0A091VLA0_NIPNI_128390 and tr_A0A0A0AUF7_A0A0A0AUF7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091W6Y1_A0A091W6Y1_NIPNI_128390 and tr_A0A0A0AES4_A0A0A0AES4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0M190_A0A2I0M190_COLLI_8932 and tr_A0A1V4L1H1_A0A1V4L1H1_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MMV3_A0A2I0MMV3_COLLI_8932 and tr_A0A1V4JFN9_A0A1V4JFN9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3PXA3_A0A1S3PXA3_SALSA_8030 and tr_A0A060WMA6_A0A060WMA6_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3RWW0_A0A1S3RWW0_SALSA_8030 and tr_A0A060WZ60_A0A060WZ60_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_M4UZZ7_M4UZZ7_SALSA_8030 and tr_A0A060YVE5_A0A060YVE5_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1L9MYN8_A0A1L9MYN8_ASPTU_767770 and tr_A0A317W2F7_A0A317W2F7_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A2D0QYR7_A0A2D0QYR7_ICTPU_7998 and tr_A0A2D0QYS7_A0A2D0QYS7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SZ10_A0A2D0SZ10_ICTPU_7998 and tr_A0A2D0SZ13_A0A2D0SZ13_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2I1GIE4_A0A2I1GIE4_9GLOM_588596 and tr_A0A2H5UHH8_A0A2H5UHH8_RHIID_747089 are exactly identical!
WARNING: Duplicate sequences found: 101

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.reduced.phy

Alignment comprises 1 partitions and 90 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 90 / 90
Gaps: 9.32 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.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 640 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 90 / 7200
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -103178.572502] Initial branch length optimization
[00:00:01 -83947.638013] Model parameter optimization (eps = 10.000000)
[00:00:17 -83795.188738] AUTODETECT spr round 1 (radius: 5)
[00:01:05 -55205.967876] AUTODETECT spr round 2 (radius: 10)
[00:01:56 -40685.314609] AUTODETECT spr round 3 (radius: 15)
[00:02:54 -34784.660433] AUTODETECT spr round 4 (radius: 20)
[00:04:00 -32306.401143] AUTODETECT spr round 5 (radius: 25)
[00:05:13 -30587.538282] SPR radius for FAST iterations: 25 (autodetect)
[00:05:13 -30587.538282] Model parameter optimization (eps = 3.000000)
[00:05:26 -30402.203959] FAST spr round 1 (radius: 25)
[00:06:18 -25797.958540] FAST spr round 2 (radius: 25)
[00:07:03 -25612.846413] FAST spr round 3 (radius: 25)
[00:07:46 -24996.894460] FAST spr round 4 (radius: 25)
[00:08:28 -24844.608447] FAST spr round 5 (radius: 25)
[00:09:11 -24653.493882] FAST spr round 6 (radius: 25)
[00:09:52 -24622.483200] FAST spr round 7 (radius: 25)
[00:10:30 -24619.310425] FAST spr round 8 (radius: 25)
[00:11:07 -24497.428789] FAST spr round 9 (radius: 25)
[00:11:44 -24495.529398] FAST spr round 10 (radius: 25)
[00:12:20 -24495.528494] Model parameter optimization (eps = 1.000000)
[00:12:32 -24484.329979] SLOW spr round 1 (radius: 5)
[00:13:21 -24472.446871] SLOW spr round 2 (radius: 5)
[00:14:10 -24468.929778] SLOW spr round 3 (radius: 5)
[00:14:59 -24468.929465] SLOW spr round 4 (radius: 10)
[00:15:49 -24457.213377] SLOW spr round 5 (radius: 5)
[00:16:51 -24444.669404] SLOW spr round 6 (radius: 5)
[00:17:45 -24444.029023] SLOW spr round 7 (radius: 5)
[00:18:36 -24443.813523] SLOW spr round 8 (radius: 5)
[00:19:24 -24443.813218] SLOW spr round 9 (radius: 10)
[00:20:13 -24443.813165] SLOW spr round 10 (radius: 15)
[00:21:30 -24441.052538] SLOW spr round 11 (radius: 5)
[00:22:33 -24440.212835] SLOW spr round 12 (radius: 5)
[00:23:28 -24440.212755] SLOW spr round 13 (radius: 10)
[00:24:19 -24440.212739] SLOW spr round 14 (radius: 15)
[00:25:33 -24440.212730] SLOW spr round 15 (radius: 20)
[00:27:21 -24438.795612] SLOW spr round 16 (radius: 5)
[00:28:26 -24438.674844] SLOW spr round 17 (radius: 5)
[00:29:22 -24438.674642] SLOW spr round 18 (radius: 10)
[00:30:13 -24438.674579] SLOW spr round 19 (radius: 15)
[00:31:28 -24438.674534] SLOW spr round 20 (radius: 20)
[00:33:15 -24438.674494] SLOW spr round 21 (radius: 25)
[00:35:22 -24437.960359] SLOW spr round 22 (radius: 5)
[00:36:27 -24437.949270] SLOW spr round 23 (radius: 10)
[00:37:25 -24437.949031] SLOW spr round 24 (radius: 15)
[00:38:38 -24437.948926] SLOW spr round 25 (radius: 20)
[00:40:16] [worker #1] ML tree search #2, logLikelihood: -24451.973990
[00:40:25 -24437.948859] SLOW spr round 26 (radius: 25)
[00:42:33 -24437.363458] SLOW spr round 27 (radius: 5)
[00:43:38 -24437.347204] SLOW spr round 28 (radius: 10)
[00:44:36 -24437.345528] SLOW spr round 29 (radius: 15)
[00:45:50 -24437.105379] SLOW spr round 30 (radius: 5)
[00:46:53 -24437.104135] SLOW spr round 31 (radius: 10)
[00:47:49 -24437.103727] SLOW spr round 32 (radius: 15)
[00:49:03 -24437.082830] SLOW spr round 33 (radius: 20)
[00:50:49 -24437.082236] SLOW spr round 34 (radius: 25)
[00:52:54 -24437.082123] Model parameter optimization (eps = 0.100000)

[00:52:58] [worker #0] ML tree search #1, logLikelihood: -24436.999444

[00:52:58 -104621.795013] Initial branch length optimization
[00:52:59 -85054.676215] Model parameter optimization (eps = 10.000000)
[00:53:22 -84913.894201] AUTODETECT spr round 1 (radius: 5)
[00:54:09 -56824.842328] AUTODETECT spr round 2 (radius: 10)
[00:55:00 -42537.061975] AUTODETECT spr round 3 (radius: 15)
[00:56:01 -35331.735506] AUTODETECT spr round 4 (radius: 20)
[00:57:12 -32651.746599] AUTODETECT spr round 5 (radius: 25)
[00:58:28 -30196.310567] SPR radius for FAST iterations: 25 (autodetect)
[00:58:28 -30196.310567] Model parameter optimization (eps = 3.000000)
[00:58:46 -30040.853891] FAST spr round 1 (radius: 25)
[00:59:39 -25349.992170] FAST spr round 2 (radius: 25)
[01:00:28 -24619.631827] FAST spr round 3 (radius: 25)
[01:01:13 -24564.164293] FAST spr round 4 (radius: 25)
[01:01:49] [worker #1] ML tree search #4, logLikelihood: -24437.054084
[01:01:53 -24558.182739] FAST spr round 5 (radius: 25)
[01:02:32 -24554.800517] FAST spr round 6 (radius: 25)
[01:03:10 -24553.123653] FAST spr round 7 (radius: 25)
[01:03:47 -24553.123487] Model parameter optimization (eps = 1.000000)
[01:03:57 -24539.766037] SLOW spr round 1 (radius: 5)
[01:04:48 -24532.051978] SLOW spr round 2 (radius: 5)
[01:05:37 -24529.340283] SLOW spr round 3 (radius: 5)
[01:06:26 -24528.883940] SLOW spr round 4 (radius: 5)
[01:07:13 -24528.196572] SLOW spr round 5 (radius: 5)
[01:08:00 -24528.196456] SLOW spr round 6 (radius: 10)
[01:08:49 -24525.599408] SLOW spr round 7 (radius: 5)
[01:09:51 -24520.240788] SLOW spr round 8 (radius: 5)
[01:10:46 -24520.240007] SLOW spr round 9 (radius: 10)
[01:11:35 -24519.834931] SLOW spr round 10 (radius: 5)
[01:12:35 -24519.205684] SLOW spr round 11 (radius: 5)
[01:13:28 -24519.204736] SLOW spr round 12 (radius: 10)
[01:14:16 -24519.204683] SLOW spr round 13 (radius: 15)
[01:15:36 -24464.494653] SLOW spr round 14 (radius: 5)
[01:16:40 -24456.748690] SLOW spr round 15 (radius: 5)
[01:17:37 -24453.201348] SLOW spr round 16 (radius: 5)
[01:18:29 -24453.190235] SLOW spr round 17 (radius: 10)
[01:19:18 -24450.904507] SLOW spr round 18 (radius: 5)
[01:20:18 -24450.135166] SLOW spr round 19 (radius: 5)
[01:21:11 -24449.958711] SLOW spr round 20 (radius: 5)
[01:22:00 -24449.956862] SLOW spr round 21 (radius: 10)
[01:22:48 -24449.956641] SLOW spr round 22 (radius: 15)
[01:24:07 -24447.607702] SLOW spr round 23 (radius: 5)
[01:25:13 -24446.810803] SLOW spr round 24 (radius: 5)
[01:26:09 -24446.408291] SLOW spr round 25 (radius: 5)
[01:26:59 -24445.848667] SLOW spr round 26 (radius: 5)
[01:27:47 -24445.848439] SLOW spr round 27 (radius: 10)
[01:28:35 -24445.848415] SLOW spr round 28 (radius: 15)
[01:29:54 -24445.492463] SLOW spr round 29 (radius: 5)
[01:30:57 -24445.466228] SLOW spr round 30 (radius: 10)
[01:31:55 -24444.200615] SLOW spr round 31 (radius: 5)
[01:32:52 -24444.200334] SLOW spr round 32 (radius: 10)
[01:33:44 -24444.200258] SLOW spr round 33 (radius: 15)
[01:35:01 -24444.200227] SLOW spr round 34 (radius: 20)
[01:36:54 -24443.386423] SLOW spr round 35 (radius: 5)
[01:38:00 -24443.381672] SLOW spr round 36 (radius: 10)
[01:38:56 -24443.381629] SLOW spr round 37 (radius: 15)
[01:40:13 -24442.818817] SLOW spr round 38 (radius: 5)
[01:41:16 -24442.817960] SLOW spr round 39 (radius: 10)
[01:42:11 -24442.817895] SLOW spr round 40 (radius: 15)
[01:43:27 -24442.817873] SLOW spr round 41 (radius: 20)
[01:45:17 -24442.817857] SLOW spr round 42 (radius: 25)
[01:47:34 -24442.410780] SLOW spr round 43 (radius: 5)
[01:47:45] [worker #1] ML tree search #6, logLikelihood: -24441.186297
[01:48:40 -24442.408762] SLOW spr round 44 (radius: 10)
[01:49:36 -24442.408669] SLOW spr round 45 (radius: 15)
[01:50:53 -24442.408647] SLOW spr round 46 (radius: 20)
[01:52:45 -24442.408632] SLOW spr round 47 (radius: 25)
[01:55:05 -24442.408618] Model parameter optimization (eps = 0.100000)

[01:55:15] [worker #0] ML tree search #3, logLikelihood: -24439.295866

[01:55:15 -104018.219008] Initial branch length optimization
[01:55:17 -84538.332201] Model parameter optimization (eps = 10.000000)
[01:55:46 -84376.860960] AUTODETECT spr round 1 (radius: 5)
[01:56:34 -56530.281064] AUTODETECT spr round 2 (radius: 10)
[01:57:27 -41048.227567] AUTODETECT spr round 3 (radius: 15)
[01:58:25 -34744.908080] AUTODETECT spr round 4 (radius: 20)
[01:59:39 -31492.849458] AUTODETECT spr round 5 (radius: 25)
[02:00:50 -30455.810929] SPR radius for FAST iterations: 25 (autodetect)
[02:00:50 -30455.810929] Model parameter optimization (eps = 3.000000)
[02:01:05 -30317.139437] FAST spr round 1 (radius: 25)
[02:02:03 -25967.925265] FAST spr round 2 (radius: 25)
[02:02:51 -25579.621794] FAST spr round 3 (radius: 25)
[02:03:40 -24879.089493] FAST spr round 4 (radius: 25)
[02:04:25 -24614.754903] FAST spr round 5 (radius: 25)
[02:05:07 -24502.482274] FAST spr round 6 (radius: 25)
[02:05:47 -24494.458357] FAST spr round 7 (radius: 25)
[02:06:25 -24467.387116] FAST spr round 8 (radius: 25)
[02:07:04 -24463.196889] FAST spr round 9 (radius: 25)
[02:07:42 -24462.998560] FAST spr round 10 (radius: 25)
[02:08:20 -24462.932471] Model parameter optimization (eps = 1.000000)
[02:08:29 -24459.327126] SLOW spr round 1 (radius: 5)
[02:09:18 -24453.400567] SLOW spr round 2 (radius: 5)
[02:10:09 -24452.882127] SLOW spr round 3 (radius: 5)
[02:10:59 -24452.879046] SLOW spr round 4 (radius: 10)
[02:11:51 -24450.576943] SLOW spr round 5 (radius: 5)
[02:12:51 -24450.576761] SLOW spr round 6 (radius: 10)
[02:13:45 -24450.576743] SLOW spr round 7 (radius: 15)
[02:14:57 -24449.588105] SLOW spr round 8 (radius: 5)
[02:16:01 -24449.587762] SLOW spr round 9 (radius: 10)
[02:16:59 -24448.842521] SLOW spr round 10 (radius: 5)
[02:18:00 -24446.727678] SLOW spr round 11 (radius: 5)
[02:18:55 -24445.715819] SLOW spr round 12 (radius: 5)
[02:19:47 -24445.552462] SLOW spr round 13 (radius: 5)
[02:20:36 -24445.552302] SLOW spr round 14 (radius: 10)
[02:21:27 -24445.552220] SLOW spr round 15 (radius: 15)
[02:22:44 -24445.421515] SLOW spr round 16 (radius: 5)
[02:23:48 -24445.420608] SLOW spr round 17 (radius: 10)
[02:24:45 -24445.420544] SLOW spr round 18 (radius: 15)
[02:25:58 -24445.420527] SLOW spr round 19 (radius: 20)
[02:27:38 -24445.296657] SLOW spr round 20 (radius: 5)
[02:28:44 -24445.287504] SLOW spr round 21 (radius: 10)
[02:29:43 -24445.286673] SLOW spr round 22 (radius: 15)
[02:30:55 -24445.286573] SLOW spr round 23 (radius: 20)
[02:32:36 -24445.286550] SLOW spr round 24 (radius: 25)
[02:34:32 -24444.598311] SLOW spr round 25 (radius: 5)
[02:35:38 -24444.587736] SLOW spr round 26 (radius: 10)
[02:36:37 -24444.585431] SLOW spr round 27 (radius: 15)
[02:37:50 -24444.065801] SLOW spr round 28 (radius: 5)
[02:38:54 -24444.046597] SLOW spr round 29 (radius: 10)
[02:39:51 -24444.046588] SLOW spr round 30 (radius: 15)
[02:41:04 -24444.046585] SLOW spr round 31 (radius: 20)
[02:41:47] [worker #1] ML tree search #8, logLikelihood: -24469.177398
[02:42:44 -24443.760584] SLOW spr round 32 (radius: 5)
[02:43:49 -24443.757354] SLOW spr round 33 (radius: 10)
[02:44:48 -24443.756889] SLOW spr round 34 (radius: 15)
[02:46:00 -24443.756814] SLOW spr round 35 (radius: 20)
[02:47:40 -24443.756799] SLOW spr round 36 (radius: 25)
[02:49:36 -24443.756793] Model parameter optimization (eps = 0.100000)

[02:49:45] [worker #0] ML tree search #5, logLikelihood: -24442.728527

[02:49:45 -105040.453854] Initial branch length optimization
[02:49:47 -85061.826629] Model parameter optimization (eps = 10.000000)
[02:50:03 -84905.822860] AUTODETECT spr round 1 (radius: 5)
[02:50:51 -55409.860384] AUTODETECT spr round 2 (radius: 10)
[02:51:44 -40963.885409] AUTODETECT spr round 3 (radius: 15)
[02:52:42 -34801.564900] AUTODETECT spr round 4 (radius: 20)
[02:53:44 -31969.585921] AUTODETECT spr round 5 (radius: 25)
[02:54:51 -31004.123111] SPR radius for FAST iterations: 25 (autodetect)
[02:54:51 -31004.123111] Model parameter optimization (eps = 3.000000)
[02:55:08 -30854.241482] FAST spr round 1 (radius: 25)
[02:56:02 -26268.767659] FAST spr round 2 (radius: 25)
[02:56:50 -24862.916822] FAST spr round 3 (radius: 25)
[02:57:33 -24636.576871] FAST spr round 4 (radius: 25)
[02:58:14 -24604.213653] FAST spr round 5 (radius: 25)
[02:58:53 -24599.807875] FAST spr round 6 (radius: 25)
[02:59:30 -24599.548951] FAST spr round 7 (radius: 25)
[03:00:08 -24599.548675] Model parameter optimization (eps = 1.000000)
[03:00:19 -24586.977564] SLOW spr round 1 (radius: 5)
[03:01:09 -24570.994903] SLOW spr round 2 (radius: 5)
[03:01:59 -24562.123696] SLOW spr round 3 (radius: 5)
[03:02:48 -24561.998783] SLOW spr round 4 (radius: 5)
[03:03:35 -24561.997737] SLOW spr round 5 (radius: 10)
[03:04:25 -24561.997299] SLOW spr round 6 (radius: 15)
[03:05:39 -24561.997019] SLOW spr round 7 (radius: 20)
[03:07:23 -24561.996840] SLOW spr round 8 (radius: 25)
[03:09:28 -24560.739849] SLOW spr round 9 (radius: 5)
[03:10:34 -24560.434027] SLOW spr round 10 (radius: 5)
[03:11:31 -24560.433009] SLOW spr round 11 (radius: 10)
[03:12:23 -24560.432924] SLOW spr round 12 (radius: 15)
[03:13:36 -24560.138576] SLOW spr round 13 (radius: 5)
[03:14:41 -24559.774853] SLOW spr round 14 (radius: 5)
[03:15:37 -24559.773063] SLOW spr round 15 (radius: 10)
[03:16:29 -24559.772004] SLOW spr round 16 (radius: 15)
[03:17:42 -24559.771375] SLOW spr round 17 (radius: 20)
[03:19:26 -24559.770995] SLOW spr round 18 (radius: 25)
[03:21:26 -24557.624947] SLOW spr round 19 (radius: 5)
[03:22:33 -24556.664863] SLOW spr round 20 (radius: 5)
[03:23:30 -24556.657010] SLOW spr round 21 (radius: 10)
[03:24:22 -24556.656278] SLOW spr round 22 (radius: 15)
[03:25:33 -24556.655992] SLOW spr round 23 (radius: 20)
[03:27:19 -24449.064038] SLOW spr round 24 (radius: 5)
[03:28:24 -24448.941419] SLOW spr round 25 (radius: 5)
[03:29:21 -24448.941148] SLOW spr round 26 (radius: 10)
[03:30:07] [worker #1] ML tree search #10, logLikelihood: -24457.142387
[03:30:12 -24448.941090] SLOW spr round 27 (radius: 15)
[03:31:24 -24448.941073] SLOW spr round 28 (radius: 20)
[03:33:08 -24448.941061] SLOW spr round 29 (radius: 25)
[03:35:10 -24447.341333] SLOW spr round 30 (radius: 5)
[03:36:17 -24445.844538] SLOW spr round 31 (radius: 5)
[03:37:14 -24445.843843] SLOW spr round 32 (radius: 10)
[03:38:05 -24445.843509] SLOW spr round 33 (radius: 15)
[03:39:18 -24445.843309] SLOW spr round 34 (radius: 20)
[03:41:02 -24445.843180] SLOW spr round 35 (radius: 25)
[03:43:04 -24445.843096] Model parameter optimization (eps = 0.100000)

[03:43:12] [worker #0] ML tree search #7, logLikelihood: -24445.130867

[03:43:12 -104114.575403] Initial branch length optimization
[03:43:14 -84875.673117] Model parameter optimization (eps = 10.000000)
[03:43:33 -84736.510072] AUTODETECT spr round 1 (radius: 5)
[03:44:20 -56190.354506] AUTODETECT spr round 2 (radius: 10)
[03:45:14 -42482.535849] AUTODETECT spr round 3 (radius: 15)
[03:46:14 -33219.670841] AUTODETECT spr round 4 (radius: 20)
[03:47:15 -30560.749974] AUTODETECT spr round 5 (radius: 25)
[03:48:28 -29132.626707] SPR radius for FAST iterations: 25 (autodetect)
[03:48:28 -29132.626707] Model parameter optimization (eps = 3.000000)
[03:48:41 -28974.836367] FAST spr round 1 (radius: 25)
[03:49:37 -24879.185974] FAST spr round 2 (radius: 25)
[03:50:27 -24604.861549] FAST spr round 3 (radius: 25)
[03:51:12 -24523.233842] FAST spr round 4 (radius: 25)
[03:51:55 -24506.062607] FAST spr round 5 (radius: 25)
[03:52:34 -24493.827771] FAST spr round 6 (radius: 25)
[03:53:12 -24492.406443] FAST spr round 7 (radius: 25)
[03:53:51 -24490.039636] FAST spr round 8 (radius: 25)
[03:54:28 -24490.037732] Model parameter optimization (eps = 1.000000)
[03:54:42 -24473.587562] SLOW spr round 1 (radius: 5)
[03:55:34 -24458.439317] SLOW spr round 2 (radius: 5)
[03:56:26 -24455.963418] SLOW spr round 3 (radius: 5)
[03:57:16 -24455.247937] SLOW spr round 4 (radius: 5)
[03:58:04 -24455.247670] SLOW spr round 5 (radius: 10)
[03:58:55 -24451.585245] SLOW spr round 6 (radius: 5)
[03:59:56 -24451.302410] SLOW spr round 7 (radius: 5)
[04:00:49 -24451.301335] SLOW spr round 8 (radius: 10)
[04:01:41 -24451.300800] SLOW spr round 9 (radius: 15)
[04:03:05 -24450.847326] SLOW spr round 10 (radius: 5)
[04:04:10 -24448.317063] SLOW spr round 11 (radius: 5)
[04:05:06 -24448.316531] SLOW spr round 12 (radius: 10)
[04:05:59 -24448.316349] SLOW spr round 13 (radius: 15)
[04:07:21 -24447.833875] SLOW spr round 14 (radius: 5)
[04:08:25 -24447.830758] SLOW spr round 15 (radius: 10)
[04:09:22 -24447.829971] SLOW spr round 16 (radius: 15)
[04:10:43 -24447.495381] SLOW spr round 17 (radius: 5)
[04:11:46 -24447.439997] SLOW spr round 18 (radius: 10)
[04:12:44 -24447.439717] SLOW spr round 19 (radius: 15)
[04:14:05 -24447.439451] SLOW spr round 20 (radius: 20)
[04:14:49] [worker #1] ML tree search #12, logLikelihood: -24441.972218
[04:16:08 -24446.446271] SLOW spr round 21 (radius: 5)
[04:17:13 -24446.415787] SLOW spr round 22 (radius: 10)
[04:18:12 -24445.274546] SLOW spr round 23 (radius: 5)
[04:19:12 -24444.858511] SLOW spr round 24 (radius: 5)
[04:20:05 -24444.857179] SLOW spr round 25 (radius: 10)
[04:20:56 -24444.856796] SLOW spr round 26 (radius: 15)
[04:22:17 -24444.699738] SLOW spr round 27 (radius: 5)
[04:23:21 -24444.679202] SLOW spr round 28 (radius: 10)
[04:24:18 -24444.677946] SLOW spr round 29 (radius: 15)
[04:25:37 -24444.677465] SLOW spr round 30 (radius: 20)
[04:27:36 -24444.280746] SLOW spr round 31 (radius: 5)
[04:28:42 -24444.276520] SLOW spr round 32 (radius: 10)
[04:29:41 -24444.275853] SLOW spr round 33 (radius: 15)
[04:31:00 -24444.275639] SLOW spr round 34 (radius: 20)
[04:32:58 -24444.275559] SLOW spr round 35 (radius: 25)
[04:35:25 -24444.275525] Model parameter optimization (eps = 0.100000)

[04:35:31] [worker #0] ML tree search #9, logLikelihood: -24443.522089

[04:35:31 -104264.076724] Initial branch length optimization
[04:35:33 -84362.565936] Model parameter optimization (eps = 10.000000)
[04:36:03 -84164.226056] AUTODETECT spr round 1 (radius: 5)
[04:36:51 -56752.124759] AUTODETECT spr round 2 (radius: 10)
[04:37:43 -40442.109261] AUTODETECT spr round 3 (radius: 15)
[04:38:42 -35053.510966] AUTODETECT spr round 4 (radius: 20)
[04:39:47 -32660.963018] AUTODETECT spr round 5 (radius: 25)
[04:41:03 -31749.203182] SPR radius for FAST iterations: 25 (autodetect)
[04:41:03 -31749.203182] Model parameter optimization (eps = 3.000000)
[04:41:20 -31605.583282] FAST spr round 1 (radius: 25)
[04:42:14 -25410.900383] FAST spr round 2 (radius: 25)
[04:43:03 -24683.529305] FAST spr round 3 (radius: 25)
[04:43:45 -24506.348369] FAST spr round 4 (radius: 25)
[04:44:26 -24479.461100] FAST spr round 5 (radius: 25)
[04:45:04 -24478.971487] FAST spr round 6 (radius: 25)
[04:45:42 -24478.970814] Model parameter optimization (eps = 1.000000)
[04:45:52 -24465.750675] SLOW spr round 1 (radius: 5)
[04:46:42 -24458.100321] SLOW spr round 2 (radius: 5)
[04:47:32 -24457.108358] SLOW spr round 3 (radius: 5)
[04:48:20 -24456.900215] SLOW spr round 4 (radius: 5)
[04:49:07 -24456.898916] SLOW spr round 5 (radius: 10)
[04:49:56 -24456.340247] SLOW spr round 6 (radius: 5)
[04:50:56 -24456.339518] SLOW spr round 7 (radius: 10)
[04:51:49 -24456.339375] SLOW spr round 8 (radius: 15)
[04:53:03 -24447.000930] SLOW spr round 9 (radius: 5)
[04:54:10 -24442.876847] SLOW spr round 10 (radius: 5)
[04:55:07 -24440.188536] SLOW spr round 11 (radius: 5)
[04:55:58 -24440.188275] SLOW spr round 12 (radius: 10)
[04:56:47 -24439.235698] SLOW spr round 13 (radius: 5)
[04:57:47 -24439.233913] SLOW spr round 14 (radius: 10)
[04:58:08] [worker #1] ML tree search #14, logLikelihood: -24459.659916
[04:58:40 -24439.233721] SLOW spr round 15 (radius: 15)
[04:59:51 -24439.233686] SLOW spr round 16 (radius: 20)
[05:01:30 -24436.472852] SLOW spr round 17 (radius: 5)
[05:02:35 -24436.471695] SLOW spr round 18 (radius: 10)
[05:03:32 -24436.471664] SLOW spr round 19 (radius: 15)
[05:04:43 -24436.471654] SLOW spr round 20 (radius: 20)
[05:06:23 -24435.836616] SLOW spr round 21 (radius: 5)
[05:07:28 -24435.822774] SLOW spr round 22 (radius: 10)
[05:08:25 -24435.820437] SLOW spr round 23 (radius: 15)
[05:09:36 -24435.819750] SLOW spr round 24 (radius: 20)
[05:11:15 -24435.819516] SLOW spr round 25 (radius: 25)
[05:13:13 -24433.106615] SLOW spr round 26 (radius: 5)
[05:14:20 -24432.644165] SLOW spr round 27 (radius: 5)
[05:15:17 -24432.643627] SLOW spr round 28 (radius: 10)
[05:16:08 -24432.643602] SLOW spr round 29 (radius: 15)
[05:17:21 -24431.124936] SLOW spr round 30 (radius: 5)
[05:18:27 -24430.436346] SLOW spr round 31 (radius: 5)
[05:19:23 -24430.434988] SLOW spr round 32 (radius: 10)
[05:20:14 -24430.434870] SLOW spr round 33 (radius: 15)
[05:21:25 -24430.434854] SLOW spr round 34 (radius: 20)
[05:23:05 -24430.434847] SLOW spr round 35 (radius: 25)
[05:25:06 -24430.434840] Model parameter optimization (eps = 0.100000)

[05:25:15] [worker #0] ML tree search #11, logLikelihood: -24429.779644

[05:25:15 -104242.857661] Initial branch length optimization
[05:25:16 -84171.229503] Model parameter optimization (eps = 10.000000)
[05:25:31 -84050.797348] AUTODETECT spr round 1 (radius: 5)
[05:26:19 -57039.703437] AUTODETECT spr round 2 (radius: 10)
[05:27:10 -43291.772615] AUTODETECT spr round 3 (radius: 15)
[05:28:08 -36467.544840] AUTODETECT spr round 4 (radius: 20)
[05:29:19 -31129.539856] AUTODETECT spr round 5 (radius: 25)
[05:30:25 -29098.334600] SPR radius for FAST iterations: 25 (autodetect)
[05:30:25 -29098.334600] Model parameter optimization (eps = 3.000000)
[05:30:38 -28979.665604] FAST spr round 1 (radius: 25)
[05:31:32 -24923.426485] FAST spr round 2 (radius: 25)
[05:32:18 -24557.409704] FAST spr round 3 (radius: 25)
[05:33:00 -24531.813679] FAST spr round 4 (radius: 25)
[05:33:40 -24523.133617] FAST spr round 5 (radius: 25)
[05:34:18 -24523.132027] Model parameter optimization (eps = 1.000000)
[05:34:29 -24510.915819] SLOW spr round 1 (radius: 5)
[05:35:19 -24476.961487] SLOW spr round 2 (radius: 5)
[05:36:10 -24476.457846] SLOW spr round 3 (radius: 5)
[05:36:59 -24476.325925] SLOW spr round 4 (radius: 5)
[05:37:48 -24476.325564] SLOW spr round 5 (radius: 10)
[05:38:40 -24469.299876] SLOW spr round 6 (radius: 5)
[05:39:41 -24468.965545] SLOW spr round 7 (radius: 5)
[05:40:36 -24468.950011] SLOW spr round 8 (radius: 10)
[05:41:27 -24468.947781] SLOW spr round 9 (radius: 15)
[05:42:36 -24468.947147] SLOW spr round 10 (radius: 20)
[05:44:07 -24467.027611] SLOW spr round 11 (radius: 5)
[05:45:15 -24464.793018] SLOW spr round 12 (radius: 5)
[05:46:14 -24464.401495] SLOW spr round 13 (radius: 5)
[05:47:07 -24463.835206] SLOW spr round 14 (radius: 5)
[05:47:57 -24463.835074] SLOW spr round 15 (radius: 10)
[05:48:46 -24463.835035] SLOW spr round 16 (radius: 15)
[05:49:57 -24463.835013] SLOW spr round 17 (radius: 20)
[05:51:28 -24463.210397] SLOW spr round 18 (radius: 5)
[05:52:34 -24463.203653] SLOW spr round 19 (radius: 10)
[05:53:32 -24463.201488] SLOW spr round 20 (radius: 15)
[05:54:40 -24463.200708] SLOW spr round 21 (radius: 20)
[05:55:46] [worker #1] ML tree search #16, logLikelihood: -24490.521584
[05:56:11 -24463.200410] SLOW spr round 22 (radius: 25)
[05:57:52 -24461.059910] SLOW spr round 23 (radius: 5)
[05:59:01 -24459.431741] SLOW spr round 24 (radius: 5)
[05:59:58 -24459.429598] SLOW spr round 25 (radius: 10)
[06:00:50 -24459.429447] SLOW spr round 26 (radius: 15)
[06:02:00 -24459.429424] SLOW spr round 27 (radius: 20)
[06:03:31 -24459.279714] SLOW spr round 28 (radius: 5)
[06:04:37 -24459.278049] SLOW spr round 29 (radius: 10)
[06:05:36 -24458.478722] SLOW spr round 30 (radius: 5)
[06:06:35 -24458.478005] SLOW spr round 31 (radius: 10)
[06:07:28 -24458.477876] SLOW spr round 32 (radius: 15)
[06:08:37 -24458.477822] SLOW spr round 33 (radius: 20)
[06:10:08 -24458.477795] SLOW spr round 34 (radius: 25)
[06:11:47 -24458.477777] Model parameter optimization (eps = 0.100000)

[06:11:56] [worker #0] ML tree search #13, logLikelihood: -24457.358853

[06:11:56 -102652.351184] Initial branch length optimization
[06:11:57 -83283.081605] Model parameter optimization (eps = 10.000000)
[06:12:24 -83115.758155] AUTODETECT spr round 1 (radius: 5)
[06:13:13 -56752.539051] AUTODETECT spr round 2 (radius: 10)
[06:14:05 -42007.817274] AUTODETECT spr round 3 (radius: 15)
[06:15:07 -35841.538542] AUTODETECT spr round 4 (radius: 20)
[06:16:20 -30509.049143] AUTODETECT spr round 5 (radius: 25)
[06:17:38 -29723.715373] SPR radius for FAST iterations: 25 (autodetect)
[06:17:38 -29723.715373] Model parameter optimization (eps = 3.000000)
[06:17:54 -29565.342882] FAST spr round 1 (radius: 25)
[06:18:50 -24752.001114] FAST spr round 2 (radius: 25)
[06:19:38 -24512.727070] FAST spr round 3 (radius: 25)
[06:20:21 -24477.698603] FAST spr round 4 (radius: 25)
[06:21:01 -24472.064321] FAST spr round 5 (radius: 25)
[06:21:40 -24467.732938] FAST spr round 6 (radius: 25)
[06:22:17 -24467.471592] FAST spr round 7 (radius: 25)
[06:22:54 -24467.470943] Model parameter optimization (eps = 1.000000)
[06:23:05 -24461.528386] SLOW spr round 1 (radius: 5)
[06:23:54 -24450.748567] SLOW spr round 2 (radius: 5)
[06:24:44 -24449.564220] SLOW spr round 3 (radius: 5)
[06:25:32 -24449.359388] SLOW spr round 4 (radius: 5)
[06:26:19 -24449.358782] SLOW spr round 5 (radius: 10)
[06:27:08 -24447.276311] SLOW spr round 6 (radius: 5)
[06:28:10 -24445.985573] SLOW spr round 7 (radius: 5)
[06:29:03 -24445.984304] SLOW spr round 8 (radius: 10)
[06:29:52 -24445.984266] SLOW spr round 9 (radius: 15)
[06:31:04 -24444.881716] SLOW spr round 10 (radius: 5)
[06:32:09 -24444.799404] SLOW spr round 11 (radius: 10)
[06:33:04 -24444.797198] SLOW spr round 12 (radius: 15)
[06:34:15 -24444.796679] SLOW spr round 13 (radius: 20)
[06:35:56 -24444.796545] SLOW spr round 14 (radius: 25)
[06:37:56 -24444.796503] Model parameter optimization (eps = 0.100000)

[06:37:59] [worker #0] ML tree search #15, logLikelihood: -24444.769811

[06:37:59 -103930.512425] Initial branch length optimization
[06:38:01 -84235.731694] Model parameter optimization (eps = 10.000000)
[06:38:15 -84078.058729] AUTODETECT spr round 1 (radius: 5)
[06:39:04 -58139.993826] AUTODETECT spr round 2 (radius: 10)
[06:39:57 -41217.204503] AUTODETECT spr round 3 (radius: 15)
[06:40:55 -34629.635604] AUTODETECT spr round 4 (radius: 20)
[06:42:01 -32149.435192] AUTODETECT spr round 5 (radius: 25)
[06:42:43] [worker #1] ML tree search #18, logLikelihood: -24463.163783
[06:43:10 -32089.252628] SPR radius for FAST iterations: 25 (autodetect)
[06:43:10 -32089.252628] Model parameter optimization (eps = 3.000000)
[06:43:29 -31921.858732] FAST spr round 1 (radius: 25)
[06:44:22 -26982.706726] FAST spr round 2 (radius: 25)
[06:45:10 -25121.415561] FAST spr round 3 (radius: 25)
[06:45:55 -24709.638016] FAST spr round 4 (radius: 25)
[06:46:38 -24490.014860] FAST spr round 5 (radius: 25)
[06:47:18 -24481.839080] FAST spr round 6 (radius: 25)
[06:47:56 -24481.838693] Model parameter optimization (eps = 1.000000)
[06:48:08 -24467.102902] SLOW spr round 1 (radius: 5)
[06:48:58 -24460.532902] SLOW spr round 2 (radius: 5)
[06:49:48 -24456.425990] SLOW spr round 3 (radius: 5)
[06:50:38 -24455.517943] SLOW spr round 4 (radius: 5)
[06:51:28 -24455.492793] SLOW spr round 5 (radius: 10)
[06:52:17 -24455.492682] SLOW spr round 6 (radius: 15)
[06:53:35 -24455.492656] SLOW spr round 7 (radius: 20)
[06:55:33 -24455.395132] SLOW spr round 8 (radius: 25)
[06:57:59 -24454.971078] SLOW spr round 9 (radius: 5)
[06:59:04 -24454.969881] SLOW spr round 10 (radius: 10)
[07:00:03 -24453.733167] SLOW spr round 11 (radius: 5)
[07:01:03 -24452.215349] SLOW spr round 12 (radius: 5)
[07:01:56 -24452.215191] SLOW spr round 13 (radius: 10)
[07:02:46 -24452.215161] SLOW spr round 14 (radius: 15)
[07:04:05 -24452.215151] SLOW spr round 15 (radius: 20)
[07:06:05 -24452.119026] SLOW spr round 16 (radius: 25)
[07:08:33 -24452.117363] Model parameter optimization (eps = 0.100000)

[07:08:37] [worker #0] ML tree search #17, logLikelihood: -24452.054992

[07:08:37 -103629.766538] Initial branch length optimization
[07:08:38 -84101.631070] Model parameter optimization (eps = 10.000000)
[07:08:53 -83962.798795] AUTODETECT spr round 1 (radius: 5)
[07:09:41 -57556.562859] AUTODETECT spr round 2 (radius: 10)
[07:10:34 -40478.290894] AUTODETECT spr round 3 (radius: 15)
[07:11:35 -33176.109506] AUTODETECT spr round 4 (radius: 20)
[07:12:45 -29639.903955] AUTODETECT spr round 5 (radius: 25)
[07:14:03 -28833.502195] SPR radius for FAST iterations: 25 (autodetect)
[07:14:03 -28833.502195] Model parameter optimization (eps = 3.000000)
[07:14:33 -28713.889626] FAST spr round 1 (radius: 25)
[07:15:26 -24912.127144] FAST spr round 2 (radius: 25)
[07:16:12 -24634.251806] FAST spr round 3 (radius: 25)
[07:16:55 -24597.159843] FAST spr round 4 (radius: 25)
[07:17:36 -24579.697378] FAST spr round 5 (radius: 25)
[07:18:15 -24577.463591] FAST spr round 6 (radius: 25)
[07:18:53 -24577.463257] Model parameter optimization (eps = 1.000000)
[07:19:03 -24574.213945] SLOW spr round 1 (radius: 5)
[07:19:53 -24566.208426] SLOW spr round 2 (radius: 5)
[07:20:43 -24565.397350] SLOW spr round 3 (radius: 5)
[07:21:31 -24565.396956] SLOW spr round 4 (radius: 10)
[07:22:21 -24563.622923] SLOW spr round 5 (radius: 5)
[07:23:21 -24563.622598] SLOW spr round 6 (radius: 10)
[07:24:16 -24563.475869] SLOW spr round 7 (radius: 5)
[07:25:15 -24563.475194] SLOW spr round 8 (radius: 10)
[07:26:08 -24563.474850] SLOW spr round 9 (radius: 15)
[07:27:23 -24563.474533] SLOW spr round 10 (radius: 20)
[07:29:08 -24562.733644] SLOW spr round 11 (radius: 5)
[07:30:14 -24562.583332] SLOW spr round 12 (radius: 5)
[07:30:39] [worker #1] ML tree search #20, logLikelihood: -24429.049737
[07:31:11 -24562.551746] SLOW spr round 13 (radius: 10)
[07:32:02 -24562.551432] SLOW spr round 14 (radius: 15)
[07:33:17 -24562.551402] SLOW spr round 15 (radius: 20)
[07:35:00 -24562.068513] SLOW spr round 16 (radius: 5)
[07:36:05 -24562.054959] SLOW spr round 17 (radius: 10)
[07:37:03 -24562.054122] SLOW spr round 18 (radius: 15)
[07:38:15 -24562.054083] SLOW spr round 19 (radius: 20)
[07:39:57 -24562.054074] SLOW spr round 20 (radius: 25)
[07:41:52 -24562.054066] Model parameter optimization (eps = 0.100000)

[07:41:55] [worker #0] ML tree search #19, logLikelihood: -24561.955085


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.171169,0.600746) (0.051682,0.420229) (0.481120,0.744484) (0.296029,1.747349) 
   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: -24429.049737

AIC score: 51424.099474 / AICc score: 3346168.099474 / BIC score: 54631.355281
Free parameters (model + branch lengths): 1283

WARNING: Number of free parameters (K=1283) is larger than alignment size (n=90).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q5D862/3_mltree/Q5D862.raxml.log

Analysis started: 17-Jun-2021 23:45:27 / finished: 18-Jun-2021 07:27:23

Elapsed time: 27716.016 seconds