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 11-Jul-2021 20:23:09 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/2_msa/Q6UXI7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/2_msa/Q6UXI7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 414 sites

WARNING: Sequences tr_A0A1D5NUG9_A0A1D5NUG9_CHICK_9031 and sp_P32018_COEA1_CHICK_9031 are exactly identical!
WARNING: Sequences sp_O42163_COCH_CHICK_9031 and tr_G1NIG3_G1NIG3_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3XYD6_M3XYD6_MUSPF_9669 and tr_A0A2Y9JZ32_A0A2Y9JZ32_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1RJF0_G1RJF0_NOMLE_61853 and tr_F7AG99_F7AG99_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RJF0_G1RJF0_NOMLE_61853 and tr_A0A0D9R1F2_A0A0D9R1F2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I2YFM7_A0A2I2YFM7_GORGO_9595 and tr_A0A2R9CHZ0_A0A2R9CHZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and tr_A0A2J8QKY7_A0A2J8QKY7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and sp_O43405_COCH_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YYV4_A0A2I2YYV4_GORGO_9595 and tr_A0A2R9CAT6_A0A2R9CAT6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2ZDD6_A0A2I2ZDD6_GORGO_9595 and tr_K7BCL4_K7BCL4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZDD6_A0A2I2ZDD6_GORGO_9595 and tr_A0A2R9B2D4_A0A2R9B2D4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S125_G3S125_GORGO_9595 and tr_H2QTA4_H2QTA4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S125_G3S125_GORGO_9595 and sp_Q99715_COCA1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S125_G3S125_GORGO_9595 and tr_A0A2R9CM08_A0A2R9CM08_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QND2_H2QND2_PANTR_9598 and tr_A0A2R9BJ46_A0A2R9BJ46_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QT85_H2QT85_PANTR_9598 and tr_A0A2R9B2E7_A0A2R9B2E7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R8V5_H2R8V5_PANTR_9598 and tr_A0A2R9BC08_A0A2R9BC08_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B5AYU5_B5AYU5_CAVPO_10141 and sp_P84552_COCH_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_A0A1D5RDG7_A0A1D5RDG7_MACMU_9544 and tr_G7NY04_G7NY04_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5RDG7_A0A1D5RDG7_MACMU_9544 and tr_A0A2K6B911_A0A2K6B911_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_G7PA12_G7PA12_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_A0A2I3MEB4_A0A2I3MEB4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_A0A0D9RT87_A0A0D9RT87_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_A0A2K6BTQ0_A0A2K6BTQ0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6XMZ4_F6XMZ4_MACMU_9544 and tr_A0A2K6A2G4_A0A2K6A2G4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K6CSK8_A0A2K6CSK8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HQD8_F7HQD8_MACMU_9544 and tr_G7PCQ7_G7PCQ7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7HQD8_F7HQD8_MACMU_9544 and tr_A0A2I3M793_A0A2I3M793_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HQD8_F7HQD8_MACMU_9544 and tr_A0A2K5KXA8_A0A2K5KXA8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HQD8_F7HQD8_MACMU_9544 and tr_A0A2K6CB99_A0A2K6CB99_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HQD8_F7HQD8_MACMU_9544 and tr_A0A2K5YVX9_A0A2K5YVX9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_L5JLB6_L5JLB6_PTEAL_9402 and tr_A0A2I4B0X6_A0A2I4B0X6_9TELE_52670 are exactly identical!
WARNING: Sequences tr_L5JLB6_L5JLB6_PTEAL_9402 and tr_A0A060WW17_A0A060WW17_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_L5JLB6_L5JLB6_PTEAL_9402 and tr_A0A2U3XED9_A0A2U3XED9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A096N2S0_A0A096N2S0_PAPAN_9555 and tr_A0A2K5ZT07_A0A2K5ZT07_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N9M9_A0A096N9M9_PAPAN_9555 and tr_A0A2K5XYG8_A0A2K5XYG8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0D9RHJ3_A0A0D9RHJ3_CHLSB_60711 and tr_A0A2K6DZZ4_A0A2K6DZZ4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9RNM7_A0A0D9RNM7_CHLSB_60711 and tr_A0A2K5P5K0_A0A2K5P5K0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RNM7_A0A0D9RNM7_CHLSB_60711 and tr_A0A2K6DG14_A0A2K6DG14_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9RNM7_A0A0D9RNM7_CHLSB_60711 and tr_A0A2K5ZDS6_A0A2K5ZDS6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151NKU7_A0A151NKU7_ALLMI_8496 and tr_A0A3Q0GIR8_A0A3Q0GIR8_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2I0M632_A0A2I0M632_COLLI_8932 and tr_A0A1V4KKK5_A0A1V4KKK5_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MNW2_A0A2I0MNW2_COLLI_8932 and tr_A0A1V4KFC9_A0A1V4KFC9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2I0MXE9_A0A2I0MXE9_COLLI_8932 and tr_A0A1V4KHI2_A0A1V4KHI2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1I7TNK3_A0A1I7TNK3_9PELO_1561998 and tr_A0A1I7TNK4_A0A1I7TNK4_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A226NEU5_A0A226NEU5_CALSU_9009 and tr_A0A226PUW8_A0A226PUW8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0Q1E0_A0A2D0Q1E0_ICTPU_7998 and tr_W5UM53_W5UM53_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QEE9_A0A2D0QEE9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QFH7_A0A2D0QFH7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QGY0_A0A2D0QGY0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QGY4_A0A2D0QGY4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QGY7_A0A2D0QGY7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEE3_A0A2D0QEE3_ICTPU_7998 and tr_A0A2D0QHS1_A0A2D0QHS1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QFI0_A0A2D0QFI0_ICTPU_7998 and tr_A0A2D0QGZ0_A0A2D0QGZ0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QNL3_A0A2D0QNL3_ICTPU_7998 and tr_A0A2D0QP39_A0A2D0QP39_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QNL3_A0A2D0QNL3_ICTPU_7998 and tr_A0A2D0QQS3_A0A2D0QQS3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QNL3_A0A2D0QNL3_ICTPU_7998 and tr_A0A2D0QRG5_A0A2D0QRG5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R7E9_A0A2D0R7E9_ICTPU_7998 and tr_A0A2D0R7G8_A0A2D0R7G8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R7E9_A0A2D0R7E9_ICTPU_7998 and tr_A0A2D0R8Z6_A0A2D0R8Z6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4C285_A0A2U4C285_TURTR_9739 and tr_A0A2U4C2C5_A0A2U4C2C5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U3VWX7_A0A2U3VWX7_ODORO_9708 and tr_A0A2U3XDS2_A0A2U3XDS2_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 61

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/Q6UXI7/3_mltree/Q6UXI7.raxml.reduced.phy

Alignment comprises 1 partitions and 414 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 414 / 414
Gaps: 13.29 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1000 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 207 / 16560
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -757024.705757] Initial branch length optimization
[00:00:06 -631242.209065] Model parameter optimization (eps = 10.000000)
[00:01:12 -629177.188304] AUTODETECT spr round 1 (radius: 5)
[00:04:31 -400101.509259] AUTODETECT spr round 2 (radius: 10)
[00:08:00 -260638.539748] AUTODETECT spr round 3 (radius: 15)
[00:11:32 -202295.123514] AUTODETECT spr round 4 (radius: 20)
[00:16:00 -182002.765183] AUTODETECT spr round 5 (radius: 25)
[00:22:01 -171814.084189] SPR radius for FAST iterations: 25 (autodetect)
[00:22:01 -171814.084189] Model parameter optimization (eps = 3.000000)
[00:22:27 -171742.310940] FAST spr round 1 (radius: 25)
[00:25:47 -140955.520523] FAST spr round 2 (radius: 25)
[00:28:15 -139247.121129] FAST spr round 3 (radius: 25)
[00:30:36 -139160.614560] FAST spr round 4 (radius: 25)
[00:32:46 -139143.414372] FAST spr round 5 (radius: 25)
[00:34:47 -139143.414047] Model parameter optimization (eps = 1.000000)
[00:35:03 -139140.112769] SLOW spr round 1 (radius: 5)
[00:37:46 -139097.897840] SLOW spr round 2 (radius: 5)
[00:40:29 -139089.931888] SLOW spr round 3 (radius: 5)
[00:43:09 -139088.243946] SLOW spr round 4 (radius: 5)
[00:45:47 -139088.243537] SLOW spr round 5 (radius: 10)
[00:48:23 -139088.243537] SLOW spr round 6 (radius: 15)
[00:53:00 -139088.243537] SLOW spr round 7 (radius: 20)
[01:00:12 -139088.243537] SLOW spr round 8 (radius: 25)
[01:09:49 -139088.243537] Model parameter optimization (eps = 0.100000)

[01:10:01] [worker #0] ML tree search #1, logLikelihood: -139088.113585

[01:10:01 -753093.116458] Initial branch length optimization
[01:10:11 -624220.173651] Model parameter optimization (eps = 10.000000)
[01:11:35 -622047.558263] AUTODETECT spr round 1 (radius: 5)
[01:14:54 -406355.182786] AUTODETECT spr round 2 (radius: 10)
[01:18:25 -271733.096404] AUTODETECT spr round 3 (radius: 15)
[01:22:06 -198280.863085] AUTODETECT spr round 4 (radius: 20)
[01:25:56 -170976.464840] AUTODETECT spr round 5 (radius: 25)
[01:29:01] [worker #1] ML tree search #2, logLikelihood: -139075.649186
[01:31:02 -165296.963396] SPR radius for FAST iterations: 25 (autodetect)
[01:31:02 -165296.963396] Model parameter optimization (eps = 3.000000)
[01:31:31 -165239.984042] FAST spr round 1 (radius: 25)
[01:34:50 -140460.629721] FAST spr round 2 (radius: 25)
[01:36:59] [worker #2] ML tree search #3, logLikelihood: -139099.364542
[01:37:28 -139266.946708] FAST spr round 3 (radius: 25)
[01:39:50 -139146.030213] FAST spr round 4 (radius: 25)
[01:42:05 -139125.155368] FAST spr round 5 (radius: 25)
[01:44:08 -139122.310861] FAST spr round 6 (radius: 25)
[01:46:09 -139122.310830] Model parameter optimization (eps = 1.000000)
[01:46:27 -139119.001586] SLOW spr round 1 (radius: 5)
[01:49:13 -139083.602403] SLOW spr round 2 (radius: 5)
[01:51:56 -139078.279297] SLOW spr round 3 (radius: 5)
[01:54:36 -139078.279103] SLOW spr round 4 (radius: 10)
[01:57:11 -139078.279088] SLOW spr round 5 (radius: 15)
[02:01:54 -139078.279079] SLOW spr round 6 (radius: 20)
[02:09:14 -139078.279073] SLOW spr round 7 (radius: 25)
[02:19:09 -139078.279069] Model parameter optimization (eps = 0.100000)

[02:19:17] [worker #0] ML tree search #4, logLikelihood: -139078.230848

[02:19:17 -751267.223609] Initial branch length optimization
[02:19:24 -625605.045466] Model parameter optimization (eps = 10.000000)
[02:20:10 -623422.107601] AUTODETECT spr round 1 (radius: 5)
[02:23:26 -405923.633717] AUTODETECT spr round 2 (radius: 10)
[02:27:00 -270233.477315] AUTODETECT spr round 3 (radius: 15)
[02:30:36 -207310.162780] AUTODETECT spr round 4 (radius: 20)
[02:35:25 -174203.089367] AUTODETECT spr round 5 (radius: 25)
[02:40:52 -167924.162471] SPR radius for FAST iterations: 25 (autodetect)
[02:40:52 -167924.162471] Model parameter optimization (eps = 3.000000)
[02:41:27 -167854.767856] FAST spr round 1 (radius: 25)
[02:44:47 -140400.014690] FAST spr round 2 (radius: 25)
[02:47:19 -139181.721019] FAST spr round 3 (radius: 25)
[02:49:35 -139129.072882] FAST spr round 4 (radius: 25)
[02:51:45 -139116.681475] FAST spr round 5 (radius: 25)
[02:53:49 -139114.322776] FAST spr round 6 (radius: 25)
[02:55:49 -139112.803648] FAST spr round 7 (radius: 25)
[02:57:47 -139112.801425] Model parameter optimization (eps = 1.000000)
[02:58:06 -139105.005547] SLOW spr round 1 (radius: 5)
[03:00:43 -139075.999561] SLOW spr round 2 (radius: 5)
[03:03:24 -139071.975641] SLOW spr round 3 (radius: 5)
[03:05:59 -139071.975461] SLOW spr round 4 (radius: 10)
[03:07:09] [worker #2] ML tree search #6, logLikelihood: -139102.063392
[03:08:36 -139070.196533] SLOW spr round 5 (radius: 5)
[03:11:57 -139070.196235] SLOW spr round 6 (radius: 10)
[03:14:53 -139070.195982] SLOW spr round 7 (radius: 15)
[03:19:16 -139070.195733] SLOW spr round 8 (radius: 20)
[03:24:46] [worker #1] ML tree search #5, logLikelihood: -139072.135524
[03:26:42 -139070.195488] SLOW spr round 9 (radius: 25)
[03:36:04 -139070.195249] Model parameter optimization (eps = 0.100000)

[03:36:10] [worker #0] ML tree search #7, logLikelihood: -139070.152141

[03:36:10 -752519.054953] Initial branch length optimization
[03:36:15 -626817.666945] Model parameter optimization (eps = 10.000000)
[03:37:04 -624514.188338] AUTODETECT spr round 1 (radius: 5)
[03:40:23 -417406.278133] AUTODETECT spr round 2 (radius: 10)
[03:43:59 -268943.029628] AUTODETECT spr round 3 (radius: 15)
[03:47:47 -213984.853241] AUTODETECT spr round 4 (radius: 20)
[03:51:56 -194253.540611] AUTODETECT spr round 5 (radius: 25)
[03:57:00 -175714.057864] SPR radius for FAST iterations: 25 (autodetect)
[03:57:00 -175714.057864] Model parameter optimization (eps = 3.000000)
[03:57:27 -175657.306944] FAST spr round 1 (radius: 25)
[04:00:47 -142315.458229] FAST spr round 2 (radius: 25)
[04:03:32 -139437.907181] FAST spr round 3 (radius: 25)
[04:05:56 -139168.824370] FAST spr round 4 (radius: 25)
[04:08:10 -139120.020886] FAST spr round 5 (radius: 25)
[04:10:14 -139116.240792] FAST spr round 6 (radius: 25)
[04:12:14 -139115.881828] FAST spr round 7 (radius: 25)
[04:14:12 -139115.881672] Model parameter optimization (eps = 1.000000)
[04:14:32 -139111.648825] SLOW spr round 1 (radius: 5)
[04:17:13 -139077.518643] SLOW spr round 2 (radius: 5)
[04:19:55 -139075.316684] SLOW spr round 3 (radius: 5)
[04:22:33 -139075.316161] SLOW spr round 4 (radius: 10)
[04:25:12 -139073.353064] SLOW spr round 5 (radius: 5)
[04:28:37 -139071.198681] SLOW spr round 6 (radius: 5)
[04:31:34 -139071.198441] SLOW spr round 7 (radius: 10)
[04:34:17 -139071.198407] SLOW spr round 8 (radius: 15)
[04:38:55 -139071.198393] SLOW spr round 9 (radius: 20)
[04:39:57] [worker #1] ML tree search #8, logLikelihood: -139086.344928
[04:46:20 -139071.198384] SLOW spr round 10 (radius: 25)
[04:51:09] [worker #2] ML tree search #9, logLikelihood: -139088.430405
[04:55:58 -139071.057503] SLOW spr round 11 (radius: 5)
[04:59:36 -139071.036942] SLOW spr round 12 (radius: 10)
[05:02:57 -139071.036915] SLOW spr round 13 (radius: 15)
[05:07:23 -139071.036911] SLOW spr round 14 (radius: 20)
[05:15:02 -139071.036909] SLOW spr round 15 (radius: 25)
[05:24:36 -139071.036908] Model parameter optimization (eps = 0.100000)

[05:24:45] [worker #0] ML tree search #10, logLikelihood: -139070.950463

[05:24:45 -749411.517178] Initial branch length optimization
[05:24:52 -624543.377832] Model parameter optimization (eps = 10.000000)
[05:26:01 -622481.631251] AUTODETECT spr round 1 (radius: 5)
[05:29:22 -405464.797045] AUTODETECT spr round 2 (radius: 10)
[05:32:49 -261720.880296] AUTODETECT spr round 3 (radius: 15)
[05:36:21 -196529.960825] AUTODETECT spr round 4 (radius: 20)
[05:40:45 -178276.191860] AUTODETECT spr round 5 (radius: 25)
[05:46:11 -167249.574592] SPR radius for FAST iterations: 25 (autodetect)
[05:46:11 -167249.574592] Model parameter optimization (eps = 3.000000)
[05:46:36 -167169.294080] FAST spr round 1 (radius: 25)
[05:49:48 -140526.123591] FAST spr round 2 (radius: 25)
[05:52:24 -139234.301813] FAST spr round 3 (radius: 25)
[05:53:29] [worker #1] ML tree search #11, logLikelihood: -139084.305539
[05:54:44 -139154.254747] FAST spr round 4 (radius: 25)
[05:56:51 -139148.725066] FAST spr round 5 (radius: 25)
[05:58:53 -139148.724674] Model parameter optimization (eps = 1.000000)
[05:59:10 -139144.740776] SLOW spr round 1 (radius: 5)
[05:59:41] [worker #2] ML tree search #12, logLikelihood: -139105.774642
[06:01:56 -139094.306474] SLOW spr round 2 (radius: 5)
[06:04:41 -139088.394428] SLOW spr round 3 (radius: 5)
[06:07:23 -139087.807492] SLOW spr round 4 (radius: 5)
[06:10:02 -139087.806918] SLOW spr round 5 (radius: 10)
[06:12:40 -139086.860042] SLOW spr round 6 (radius: 5)
[06:16:03 -139086.859625] SLOW spr round 7 (radius: 10)
[06:19:03 -139085.994335] SLOW spr round 8 (radius: 5)
[06:22:21 -139085.991408] SLOW spr round 9 (radius: 10)
[06:25:15 -139085.730558] SLOW spr round 10 (radius: 5)
[06:28:33 -139085.709761] SLOW spr round 11 (radius: 10)
[06:31:26 -139085.709745] SLOW spr round 12 (radius: 15)
[06:35:36 -139081.812603] SLOW spr round 13 (radius: 5)
[06:39:09 -139081.576783] SLOW spr round 14 (radius: 5)
[06:42:14 -139081.576755] SLOW spr round 15 (radius: 10)
[06:44:59 -139081.576754] SLOW spr round 16 (radius: 15)
[06:49:15 -139081.576754] SLOW spr round 17 (radius: 20)
[06:55:55 -139080.111482] SLOW spr round 18 (radius: 5)
[06:59:28 -139080.110216] SLOW spr round 19 (radius: 10)
[07:02:42 -139080.110182] SLOW spr round 20 (radius: 15)
[07:06:54 -139080.110181] SLOW spr round 21 (radius: 20)
[07:07:13] [worker #1] ML tree search #14, logLikelihood: -139070.503087
[07:13:59 -139080.110181] SLOW spr round 22 (radius: 25)
[07:22:51 -139080.110181] Model parameter optimization (eps = 0.100000)

[07:23:06] [worker #0] ML tree search #13, logLikelihood: -139079.469238

[07:23:06 -749736.892157] Initial branch length optimization
[07:23:13 -624126.371131] Model parameter optimization (eps = 10.000000)
[07:24:07 -622006.423947] AUTODETECT spr round 1 (radius: 5)
[07:27:24 -389662.013616] AUTODETECT spr round 2 (radius: 10)
[07:30:53 -276270.463877] AUTODETECT spr round 3 (radius: 15)
[07:34:33 -206272.651512] AUTODETECT spr round 4 (radius: 20)
[07:38:56 -170030.030075] AUTODETECT spr round 5 (radius: 25)
[07:43:48] [worker #2] ML tree search #15, logLikelihood: -139068.466647
[07:43:59 -165863.143468] SPR radius for FAST iterations: 25 (autodetect)
[07:43:59 -165863.143468] Model parameter optimization (eps = 3.000000)
[07:44:28 -165762.941528] FAST spr round 1 (radius: 25)
[07:48:04 -140791.541435] FAST spr round 2 (radius: 25)
[07:50:54 -139266.024124] FAST spr round 3 (radius: 25)
[07:53:16 -139153.500677] FAST spr round 4 (radius: 25)
[07:55:29 -139142.872477] FAST spr round 5 (radius: 25)
[07:57:33 -139142.871564] Model parameter optimization (eps = 1.000000)
[07:57:53 -139135.749340] SLOW spr round 1 (radius: 5)
[08:00:39 -139105.148728] SLOW spr round 2 (radius: 5)
[08:03:25 -139093.908576] SLOW spr round 3 (radius: 5)
[08:06:07 -139093.898406] SLOW spr round 4 (radius: 10)
[08:08:46 -139091.634192] SLOW spr round 5 (radius: 5)
[08:12:14 -139085.072211] SLOW spr round 6 (radius: 5)
[08:15:17 -139083.908254] SLOW spr round 7 (radius: 5)
[08:18:06 -139083.543846] SLOW spr round 8 (radius: 5)
[08:19:35] [worker #1] ML tree search #17, logLikelihood: -139094.826910
[08:20:47 -139083.543842] SLOW spr round 9 (radius: 10)
[08:23:25 -139083.543842] SLOW spr round 10 (radius: 15)
[08:28:09 -139082.987286] SLOW spr round 11 (radius: 5)
[08:31:48 -139079.023603] SLOW spr round 12 (radius: 5)
[08:34:54 -139078.988752] SLOW spr round 13 (radius: 10)
[08:37:41 -139078.988603] SLOW spr round 14 (radius: 15)
[08:42:15 -139078.988599] SLOW spr round 15 (radius: 20)
[08:49:37 -139078.988599] SLOW spr round 16 (radius: 25)
[08:56:43] [worker #2] ML tree search #18, logLikelihood: -139089.595328
[08:59:21 -139078.988599] Model parameter optimization (eps = 0.100000)

[08:59:30] [worker #0] ML tree search #16, logLikelihood: -139078.904974

[08:59:30 -753117.897224] Initial branch length optimization
[08:59:37 -625779.227993] Model parameter optimization (eps = 10.000000)
[09:00:45 -623663.545139] AUTODETECT spr round 1 (radius: 5)
[09:04:02 -397308.846459] AUTODETECT spr round 2 (radius: 10)
[09:07:32 -269823.796698] AUTODETECT spr round 3 (radius: 15)
[09:11:15 -206284.777350] AUTODETECT spr round 4 (radius: 20)
[09:15:23 -172782.859101] AUTODETECT spr round 5 (radius: 25)
[09:20:15 -166008.467207] SPR radius for FAST iterations: 25 (autodetect)
[09:20:15 -166008.467207] Model parameter optimization (eps = 3.000000)
[09:20:43 -165938.063001] FAST spr round 1 (radius: 25)
[09:24:12 -141155.358328] FAST spr round 2 (radius: 25)
[09:26:55 -139262.687389] FAST spr round 3 (radius: 25)
[09:29:12 -139157.441561] FAST spr round 4 (radius: 25)
[09:30:30] [worker #1] ML tree search #20, logLikelihood: -139096.763283
[09:31:19 -139140.594223] FAST spr round 5 (radius: 25)
[09:33:18 -139140.593885] Model parameter optimization (eps = 1.000000)
[09:33:39 -139137.079039] SLOW spr round 1 (radius: 5)
[09:36:22 -139092.722260] SLOW spr round 2 (radius: 5)
[09:39:11 -139085.893934] SLOW spr round 3 (radius: 5)
[09:41:47 -139085.893355] SLOW spr round 4 (radius: 10)
[09:44:22 -139085.467838] SLOW spr round 5 (radius: 5)
[09:47:41 -139085.467809] SLOW spr round 6 (radius: 10)
[09:50:38 -139085.294527] SLOW spr round 7 (radius: 5)
[09:53:56 -139084.300241] SLOW spr round 8 (radius: 5)
[09:56:49 -139084.288807] SLOW spr round 9 (radius: 10)
[09:59:28 -139084.286725] SLOW spr round 10 (radius: 15)
[10:03:53 -139080.017604] SLOW spr round 11 (radius: 5)
[10:07:27 -139079.302699] SLOW spr round 12 (radius: 5)
[10:10:29 -139079.302231] SLOW spr round 13 (radius: 10)
[10:13:12 -139079.302219] SLOW spr round 14 (radius: 15)
[10:17:34 -139079.302219] SLOW spr round 15 (radius: 20)
[10:24:43 -139076.149816] SLOW spr round 16 (radius: 5)
[10:28:16 -139075.645823] SLOW spr round 17 (radius: 5)
[10:31:20 -139075.645507] SLOW spr round 18 (radius: 10)
[10:34:04 -139075.645474] SLOW spr round 19 (radius: 15)
[10:38:24 -139075.645474] SLOW spr round 20 (radius: 20)
[10:45:32 -139075.645473] SLOW spr round 21 (radius: 25)
[10:54:54 -139075.645473] Model parameter optimization (eps = 0.100000)

[10:55:07] [worker #0] ML tree search #19, logLikelihood: -139075.010244


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.123677,0.383248) (0.199497,0.428386) (0.310244,0.785091) (0.366582,1.701039) 
   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: -139068.466647

AIC score: 282142.933294 / AICc score: 8310166.933294 / BIC score: 290206.742840
Free parameters (model + branch lengths): 2003

WARNING: Number of free parameters (K=2003) is larger than alignment size (n=414).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6UXI7/3_mltree/Q6UXI7.raxml.log

Analysis started: 11-Jul-2021 20:23:09 / finished: 12-Jul-2021 07:18:17

Elapsed time: 39307.749 seconds