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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 02-Jul-2021 02:15:14 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/2_msa/A6NKF7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/2_msa/A6NKF7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 155 taxa and 112 sites

WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_F7GYT4_F7GYT4_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_F7DEI1_F7DEI1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A286ZRH6_A0A286ZRH6_PIG_9823 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_G7PTJ3_G7PTJ3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and sp_A5D7M7_TMM88_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_L5K005_L5K005_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A096P2S2_A0A096P2S2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A0D9RFG4_A0A0D9RFG4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2K5NN59_A0A2K5NN59_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2K6D9E5_A0A2K6D9E5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2K5XB21_A0A2K5XB21_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2U3VT78_A0A2U3VT78_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2U3Y5Q4_A0A2U3Y5Q4_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2Y9DJV5_A0A2Y9DJV5_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2Y9L3M8_A0A2Y9L3M8_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2Y9PWY5_A0A2Y9PWY5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1RFA4_G1RFA4_NOMLE_61853 and tr_A0A2Y9FPM7_A0A2Y9FPM7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G3RH25_G3RH25_GORGO_9595 and tr_H2QC57_H2QC57_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RH25_G3RH25_GORGO_9595 and sp_Q6PEY1_TMM88_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RH25_G3RH25_GORGO_9595 and tr_A0A2R9B5I2_A0A2R9B5I2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1TDD3_G1TDD3_RABIT_9986 and tr_A0A091CLX8_A0A091CLX8_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_M4A3F1_M4A3F1_XIPMA_8083 and tr_A0A087XDI7_A0A087XDI7_POEFO_48698 are exactly identical!
WARNING: Sequences tr_M3WR66_M3WR66_FELCA_9685 and tr_A0A1U7TVU1_A0A1U7TVU1_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_A0A1S3RI84_A0A1S3RI84_SALSA_8030 and tr_A0A060WU87_A0A060WU87_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226N0A7_A0A226N0A7_CALSU_9009 and tr_A0A226PFD2_A0A226PFD2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5KKA2_A0A2K5KKA2_CERAT_9531 and tr_A0A2K6E7H1_A0A2K6E7H1_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.reduced.phy

Alignment comprises 1 partitions and 112 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 112 / 112
Gaps: 3.40 %
Invariant sites: 0.89 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.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 155 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 112 / 8960
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -26726.033981] Initial branch length optimization
[00:00:00 -21148.921912] Model parameter optimization (eps = 10.000000)
[00:00:04 -21128.645259] AUTODETECT spr round 1 (radius: 5)
[00:00:07 -11663.594677] AUTODETECT spr round 2 (radius: 10)
[00:00:11 -9209.709210] AUTODETECT spr round 3 (radius: 15)
[00:00:16 -8578.475248] AUTODETECT spr round 4 (radius: 20)
[00:00:22 -8496.676341] AUTODETECT spr round 5 (radius: 25)
[00:00:28 -8486.567747] SPR radius for FAST iterations: 25 (autodetect)
[00:00:28 -8486.567747] Model parameter optimization (eps = 3.000000)
[00:00:33 -8320.339743] FAST spr round 1 (radius: 25)
[00:00:38 -7963.492531] FAST spr round 2 (radius: 25)
[00:00:41 -7951.848938] FAST spr round 3 (radius: 25)
[00:00:45 -7947.773666] FAST spr round 4 (radius: 25)
[00:00:48 -7945.481594] FAST spr round 5 (radius: 25)
[00:00:51 -7937.615419] FAST spr round 6 (radius: 25)
[00:00:54 -7937.615105] Model parameter optimization (eps = 1.000000)
[00:00:55 -7936.980403] SLOW spr round 1 (radius: 5)
[00:01:01 -7935.760794] SLOW spr round 2 (radius: 5)
[00:01:06 -7935.758701] SLOW spr round 3 (radius: 10)
[00:01:11 -7935.367275] SLOW spr round 4 (radius: 5)
[00:01:20 -7934.760711] SLOW spr round 5 (radius: 5)
[00:01:26 -7934.760585] SLOW spr round 6 (radius: 10)
[00:01:32 -7934.760583] SLOW spr round 7 (radius: 15)
[00:01:38 -7934.760583] SLOW spr round 8 (radius: 20)
[00:01:47 -7934.760583] SLOW spr round 9 (radius: 25)
[00:01:56 -7934.760583] Model parameter optimization (eps = 0.100000)

[00:01:57] [worker #0] ML tree search #1, logLikelihood: -7934.702298

[00:01:57 -28552.417450] Initial branch length optimization
[00:01:57 -22596.608736] Model parameter optimization (eps = 10.000000)
[00:01:59] [worker #1] ML tree search #2, logLikelihood: -7939.657327
[00:02:00 -22574.528914] AUTODETECT spr round 1 (radius: 5)
[00:02:04 -12492.795685] AUTODETECT spr round 2 (radius: 10)
[00:02:08 -11151.542063] AUTODETECT spr round 3 (radius: 15)
[00:02:13 -9981.384124] AUTODETECT spr round 4 (radius: 20)
[00:02:18 -9519.694186] AUTODETECT spr round 5 (radius: 25)
[00:02:23 -9519.693648] SPR radius for FAST iterations: 20 (autodetect)
[00:02:23 -9519.693648] Model parameter optimization (eps = 3.000000)
[00:02:28 -9346.869267] FAST spr round 1 (radius: 20)
[00:02:32 -8075.270047] FAST spr round 2 (radius: 20)
[00:02:36 -7948.460075] FAST spr round 3 (radius: 20)
[00:02:39 -7942.484008] FAST spr round 4 (radius: 20)
[00:02:42 -7942.483985] Model parameter optimization (eps = 1.000000)
[00:02:44 -7941.624063] SLOW spr round 1 (radius: 5)
[00:02:49 -7939.860377] SLOW spr round 2 (radius: 5)
[00:02:54 -7939.860204] SLOW spr round 3 (radius: 10)
[00:02:59 -7939.860177] SLOW spr round 4 (radius: 15)
[00:03:06 -7939.860173] SLOW spr round 5 (radius: 20)
[00:03:14 -7939.860172] SLOW spr round 6 (radius: 25)
[00:03:21 -7939.860172] Model parameter optimization (eps = 0.100000)

[00:03:22] [worker #0] ML tree search #3, logLikelihood: -7939.837520

[00:03:22 -28054.707383] Initial branch length optimization
[00:03:22 -22422.217471] Model parameter optimization (eps = 10.000000)
[00:03:26 -22390.434073] AUTODETECT spr round 1 (radius: 5)
[00:03:29 -11590.894744] AUTODETECT spr round 2 (radius: 10)
[00:03:34 -8776.337876] AUTODETECT spr round 3 (radius: 15)
[00:03:39 -8617.226820] AUTODETECT spr round 4 (radius: 20)
[00:03:42] [worker #1] ML tree search #4, logLikelihood: -7942.488714
[00:03:44 -8613.044457] AUTODETECT spr round 5 (radius: 25)
[00:03:48 -8613.041227] SPR radius for FAST iterations: 20 (autodetect)
[00:03:48 -8613.041227] Model parameter optimization (eps = 3.000000)
[00:03:53 -8448.482508] FAST spr round 1 (radius: 20)
[00:03:58 -7970.789116] FAST spr round 2 (radius: 20)
[00:04:02 -7960.007478] FAST spr round 3 (radius: 20)
[00:04:06 -7955.281489] FAST spr round 4 (radius: 20)
[00:04:09 -7955.281434] Model parameter optimization (eps = 1.000000)
[00:04:12 -7952.437517] SLOW spr round 1 (radius: 5)
[00:04:18 -7946.839440] SLOW spr round 2 (radius: 5)
[00:04:23 -7946.081568] SLOW spr round 3 (radius: 5)
[00:04:28 -7946.081524] SLOW spr round 4 (radius: 10)
[00:04:33 -7946.081524] SLOW spr round 5 (radius: 15)
[00:04:40 -7944.527134] SLOW spr round 6 (radius: 5)
[00:04:48 -7944.477642] SLOW spr round 7 (radius: 10)
[00:04:54 -7944.477528] SLOW spr round 8 (radius: 15)
[00:05:01 -7944.477512] SLOW spr round 9 (radius: 20)
[00:05:08 -7944.477509] SLOW spr round 10 (radius: 25)
[00:05:17 -7944.477509] Model parameter optimization (eps = 0.100000)

[00:05:18] [worker #0] ML tree search #5, logLikelihood: -7944.151172

[00:05:18 -28438.892758] Initial branch length optimization
[00:05:19 -22003.306291] Model parameter optimization (eps = 10.000000)
[00:05:23 -21974.768405] AUTODETECT spr round 1 (radius: 5)
[00:05:26 -12795.209569] AUTODETECT spr round 2 (radius: 10)
[00:05:30 -9569.534550] AUTODETECT spr round 3 (radius: 15)
[00:05:30] [worker #1] ML tree search #6, logLikelihood: -7937.428568
[00:05:36 -8755.379924] AUTODETECT spr round 4 (radius: 20)
[00:05:42 -8671.158184] AUTODETECT spr round 5 (radius: 25)
[00:05:48 -8671.152959] SPR radius for FAST iterations: 20 (autodetect)
[00:05:48 -8671.152959] Model parameter optimization (eps = 3.000000)
[00:05:52 -8521.660184] FAST spr round 1 (radius: 20)
[00:05:56 -7954.310417] FAST spr round 2 (radius: 20)
[00:06:00 -7941.767042] FAST spr round 3 (radius: 20)
[00:06:03 -7941.004730] FAST spr round 4 (radius: 20)
[00:06:05 -7941.004626] Model parameter optimization (eps = 1.000000)
[00:06:07 -7940.112620] SLOW spr round 1 (radius: 5)
[00:06:12 -7938.654822] SLOW spr round 2 (radius: 5)
[00:06:17 -7938.653782] SLOW spr round 3 (radius: 10)
[00:06:22 -7934.422491] SLOW spr round 4 (radius: 5)
[00:06:30 -7934.422072] SLOW spr round 5 (radius: 10)
[00:06:36 -7934.422061] SLOW spr round 6 (radius: 15)
[00:06:42 -7934.422060] SLOW spr round 7 (radius: 20)
[00:06:49 -7934.422060] SLOW spr round 8 (radius: 25)
[00:06:57 -7934.422060] Model parameter optimization (eps = 0.100000)

[00:06:59] [worker #0] ML tree search #7, logLikelihood: -7934.365290

[00:06:59 -28265.971695] Initial branch length optimization
[00:06:59 -22883.904807] Model parameter optimization (eps = 10.000000)
[00:07:02 -22863.178017] AUTODETECT spr round 1 (radius: 5)
[00:07:05 -10759.206082] AUTODETECT spr round 2 (radius: 10)
[00:07:10 -8641.406416] AUTODETECT spr round 3 (radius: 15)
[00:07:14 -8468.921301] AUTODETECT spr round 4 (radius: 20)
[00:07:19 -8468.911510] SPR radius for FAST iterations: 15 (autodetect)
[00:07:19 -8468.911510] Model parameter optimization (eps = 3.000000)
[00:07:25 -8311.071969] FAST spr round 1 (radius: 15)
[00:07:29 -7962.604126] FAST spr round 2 (radius: 15)
[00:07:33 -7954.738077] FAST spr round 3 (radius: 15)
[00:07:36 -7954.738072] Model parameter optimization (eps = 1.000000)
[00:07:37 -7954.617503] SLOW spr round 1 (radius: 5)
[00:07:43 -7950.108204] SLOW spr round 2 (radius: 5)
[00:07:49 -7949.564754] SLOW spr round 3 (radius: 5)
[00:07:53 -7949.564742] SLOW spr round 4 (radius: 10)
[00:07:58 -7949.564742] SLOW spr round 5 (radius: 15)
[00:08:05 -7949.564742] SLOW spr round 6 (radius: 20)
[00:08:12] [worker #1] ML tree search #8, logLikelihood: -8001.297925
[00:08:12 -7947.605481] SLOW spr round 7 (radius: 5)
[00:08:20 -7947.605368] SLOW spr round 8 (radius: 10)
[00:08:27 -7947.605367] SLOW spr round 9 (radius: 15)
[00:08:33 -7947.605367] SLOW spr round 10 (radius: 20)
[00:08:41 -7947.605367] SLOW spr round 11 (radius: 25)
[00:08:48 -7947.605367] Model parameter optimization (eps = 0.100000)

[00:08:49] [worker #0] ML tree search #9, logLikelihood: -7947.539791

[00:08:49 -27657.453502] Initial branch length optimization
[00:08:49 -22026.108997] Model parameter optimization (eps = 10.000000)
[00:08:53 -22007.252677] AUTODETECT spr round 1 (radius: 5)
[00:08:56 -11906.979462] AUTODETECT spr round 2 (radius: 10)
[00:09:00 -9338.193203] AUTODETECT spr round 3 (radius: 15)
[00:09:06 -8832.182508] AUTODETECT spr round 4 (radius: 20)
[00:09:11 -8633.081534] AUTODETECT spr round 5 (radius: 25)
[00:09:17 -8632.347978] SPR radius for FAST iterations: 25 (autodetect)
[00:09:17 -8632.347978] Model parameter optimization (eps = 3.000000)
[00:09:22 -8485.869351] FAST spr round 1 (radius: 25)
[00:09:27 -7976.565896] FAST spr round 2 (radius: 25)
[00:09:32 -7947.628879] FAST spr round 3 (radius: 25)
[00:09:35 -7940.336720] FAST spr round 4 (radius: 25)
[00:09:38 -7940.336718] Model parameter optimization (eps = 1.000000)
[00:09:40 -7938.854027] SLOW spr round 1 (radius: 5)
[00:09:42] [worker #1] ML tree search #10, logLikelihood: -7931.682574
[00:09:46 -7937.404318] SLOW spr round 2 (radius: 5)
[00:09:51 -7937.403512] SLOW spr round 3 (radius: 10)
[00:09:56 -7936.346659] SLOW spr round 4 (radius: 5)
[00:10:04 -7935.264606] SLOW spr round 5 (radius: 5)
[00:10:11 -7935.264529] SLOW spr round 6 (radius: 10)
[00:10:16 -7935.264517] SLOW spr round 7 (radius: 15)
[00:10:23 -7935.264515] SLOW spr round 8 (radius: 20)
[00:10:30 -7935.264515] SLOW spr round 9 (radius: 25)
[00:10:39 -7935.264515] Model parameter optimization (eps = 0.100000)

[00:10:41] [worker #0] ML tree search #11, logLikelihood: -7935.086642

[00:10:41 -28191.016522] Initial branch length optimization
[00:10:41 -22029.176634] Model parameter optimization (eps = 10.000000)
[00:10:44 -22009.505768] AUTODETECT spr round 1 (radius: 5)
[00:10:48 -12226.339394] AUTODETECT spr round 2 (radius: 10)
[00:10:52 -10368.732259] AUTODETECT spr round 3 (radius: 15)
[00:10:57 -9208.452479] AUTODETECT spr round 4 (radius: 20)
[00:11:02 -8986.391234] AUTODETECT spr round 5 (radius: 25)
[00:11:08 -8986.378635] SPR radius for FAST iterations: 20 (autodetect)
[00:11:08 -8986.378635] Model parameter optimization (eps = 3.000000)
[00:11:12 -8799.248068] FAST spr round 1 (radius: 20)
[00:11:16 -8003.510144] FAST spr round 2 (radius: 20)
[00:11:20 -7947.353686] FAST spr round 3 (radius: 20)
[00:11:23 -7945.859977] FAST spr round 4 (radius: 20)
[00:11:26 -7945.859949] Model parameter optimization (eps = 1.000000)
[00:11:28 -7944.376148] SLOW spr round 1 (radius: 5)
[00:11:33 -7941.046075] SLOW spr round 2 (radius: 5)
[00:11:38 -7941.044092] SLOW spr round 3 (radius: 10)
[00:11:43 -7941.043847] SLOW spr round 4 (radius: 15)
[00:11:49 -7941.043811] SLOW spr round 5 (radius: 20)
[00:11:56 -7941.043806] SLOW spr round 6 (radius: 25)
[00:12:05 -7941.043805] Model parameter optimization (eps = 0.100000)

[00:12:06] [worker #0] ML tree search #13, logLikelihood: -7941.022690

[00:12:06 -28393.770736] Initial branch length optimization
[00:12:06 -22240.052333] Model parameter optimization (eps = 10.000000)
[00:12:12 -22181.288907] AUTODETECT spr round 1 (radius: 5)
[00:12:14] [worker #1] ML tree search #12, logLikelihood: -7941.733044
[00:12:15 -11756.876954] AUTODETECT spr round 2 (radius: 10)
[00:12:19 -8748.374158] AUTODETECT spr round 3 (radius: 15)
[00:12:24 -8577.877670] AUTODETECT spr round 4 (radius: 20)
[00:12:30 -8577.845521] SPR radius for FAST iterations: 15 (autodetect)
[00:12:30 -8577.845521] Model parameter optimization (eps = 3.000000)
[00:12:34 -8413.649294] FAST spr round 1 (radius: 15)
[00:12:38 -7964.899828] FAST spr round 2 (radius: 15)
[00:12:42 -7946.763720] FAST spr round 3 (radius: 15)
[00:12:45 -7944.924257] FAST spr round 4 (radius: 15)
[00:12:48 -7944.924116] Model parameter optimization (eps = 1.000000)
[00:12:50 -7943.914838] SLOW spr round 1 (radius: 5)
[00:12:56 -7943.840630] SLOW spr round 2 (radius: 10)
[00:13:01 -7943.840536] SLOW spr round 3 (radius: 15)
[00:13:07 -7943.840518] SLOW spr round 4 (radius: 20)
[00:13:14 -7943.840513] SLOW spr round 5 (radius: 25)
[00:13:22 -7943.840512] Model parameter optimization (eps = 0.100000)

[00:13:23] [worker #0] ML tree search #15, logLikelihood: -7943.834667

[00:13:23 -27988.319629] Initial branch length optimization
[00:13:23 -21982.180761] Model parameter optimization (eps = 10.000000)
[00:13:27 -21915.698143] AUTODETECT spr round 1 (radius: 5)
[00:13:31 -13121.920551] AUTODETECT spr round 2 (radius: 10)
[00:13:35 -10212.036156] AUTODETECT spr round 3 (radius: 15)
[00:13:40 -9109.438886] AUTODETECT spr round 4 (radius: 20)
[00:13:46 -8885.415914] AUTODETECT spr round 5 (radius: 25)
[00:13:50 -8885.387699] SPR radius for FAST iterations: 20 (autodetect)
[00:13:50 -8885.387699] Model parameter optimization (eps = 3.000000)
[00:13:54 -8725.177692] FAST spr round 1 (radius: 20)
[00:14:00 -8053.501036] FAST spr round 2 (radius: 20)
[00:14:04 -7954.352530] FAST spr round 3 (radius: 20)
[00:14:08 -7944.056614] FAST spr round 4 (radius: 20)
[00:14:10 -7944.055797] Model parameter optimization (eps = 1.000000)
[00:14:13 -7941.239885] SLOW spr round 1 (radius: 5)
[00:14:18 -7939.213896] SLOW spr round 2 (radius: 5)
[00:14:23 -7938.831161] SLOW spr round 3 (radius: 5)
[00:14:28 -7938.830647] SLOW spr round 4 (radius: 10)
[00:14:30] [worker #1] ML tree search #14, logLikelihood: -7938.721992
[00:14:33 -7938.830524] SLOW spr round 5 (radius: 15)
[00:14:40 -7938.830482] SLOW spr round 6 (radius: 20)
[00:14:48 -7938.830467] SLOW spr round 7 (radius: 25)
[00:14:56 -7938.830461] Model parameter optimization (eps = 0.100000)

[00:14:58] [worker #0] ML tree search #17, logLikelihood: -7938.794889

[00:14:58 -28226.199872] Initial branch length optimization
[00:14:58 -22432.477589] Model parameter optimization (eps = 10.000000)
[00:15:02 -22415.650070] AUTODETECT spr round 1 (radius: 5)
[00:15:05 -12815.365128] AUTODETECT spr round 2 (radius: 10)
[00:15:10 -9713.191637] AUTODETECT spr round 3 (radius: 15)
[00:15:14 -8915.266057] AUTODETECT spr round 4 (radius: 20)
[00:15:21 -8839.286139] AUTODETECT spr round 5 (radius: 25)
[00:15:27 -8839.283303] SPR radius for FAST iterations: 20 (autodetect)
[00:15:27 -8839.283303] Model parameter optimization (eps = 3.000000)
[00:15:31 -8684.081078] FAST spr round 1 (radius: 20)
[00:15:35 -7981.212912] FAST spr round 2 (radius: 20)
[00:15:38 -7949.968411] FAST spr round 3 (radius: 20)
[00:15:42 -7947.572916] FAST spr round 4 (radius: 20)
[00:15:45 -7944.332924] FAST spr round 5 (radius: 20)
[00:15:48 -7942.726812] FAST spr round 6 (radius: 20)
[00:15:51 -7939.673800] FAST spr round 7 (radius: 20)
[00:15:54 -7939.672924] Model parameter optimization (eps = 1.000000)
[00:15:57 -7937.443458] SLOW spr round 1 (radius: 5)
[00:16:02 -7937.167902] SLOW spr round 2 (radius: 5)
[00:16:07 -7937.167238] SLOW spr round 3 (radius: 10)
[00:16:12 -7937.167138] SLOW spr round 4 (radius: 15)
[00:16:18 -7937.167120] SLOW spr round 5 (radius: 20)
[00:16:26 -7937.167117] SLOW spr round 6 (radius: 25)
[00:16:35 -7937.167117] Model parameter optimization (eps = 0.100000)

[00:16:35] [worker #0] ML tree search #19, logLikelihood: -7937.151471

[00:17:05] [worker #1] ML tree search #16, logLikelihood: -7933.660922
[00:18:39] [worker #1] ML tree search #18, logLikelihood: -7939.633389
[00:20:08] [worker #1] ML tree search #20, logLikelihood: -7937.908515

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.428416,0.808440) (0.165952,1.111247) (0.354872,0.955267) (0.050760,2.565804) 
   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: -7931.682574

AIC score: 16489.365148 / AICc score: 213053.365148 / BIC score: 17340.255295
Free parameters (model + branch lengths): 313

WARNING: Number of free parameters (K=313) is larger than alignment size (n=112).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 45 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKF7/3_mltree/A6NKF7.raxml.log

Analysis started: 02-Jul-2021 02:15:14 / finished: 02-Jul-2021 02:35:23

Elapsed time: 1208.657 seconds

Consumed energy: 99.001 Wh