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 30-Jun-2021 17:50:12 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/2_msa/Q9UPW6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/2_msa/Q9UPW6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 367 taxa and 805 sites

WARNING: Sequences tr_M3XQP5_M3XQP5_MUSPF_9669 and tr_A0A2Y9KBS6_A0A2Y9KBS6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Y9A7_M3Y9A7_MUSPF_9669 and tr_A0A2U3VFP8_A0A2U3VFP8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y9A7_M3Y9A7_MUSPF_9669 and tr_A0A2Y9J046_A0A2Y9J046_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1R5C9_G1R5C9_NOMLE_61853 and tr_H9EQF6_H9EQF6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1R5C9_G1R5C9_NOMLE_61853 and tr_A0A2K6DWB8_A0A2K6DWB8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2J8WVE0_A0A2J8WVE0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2I3SX19_A0A2I3SX19_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and sp_Q9UPW6_SATB2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z942_A0A2I2Z942_GORGO_9595 and tr_A0A2R9CTC5_A0A2R9CTC5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QHC8_G3QHC8_GORGO_9595 and tr_A0A2I3S8J9_A0A2I3S8J9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QHC8_G3QHC8_GORGO_9595 and tr_A0A2R8ZMZ0_A0A2R8ZMZ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H0YYC4_H0YYC4_TAEGU_59729 and tr_A0A218VDS8_A0A218VDS8_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A096MRX7_A0A096MRX7_PAPAN_9555 and tr_A0A2K5KWR2_A0A2K5KWR2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MRX7_A0A096MRX7_PAPAN_9555 and tr_A0A2K5ZFE3_A0A2K5ZFE3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K5NDI1_A0A2K5NDI1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K6C8R6_A0A2K6C8R6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3NFQ6_A0A2I3NFQ6_PAPAN_9555 and tr_A0A2K5ZC07_A0A2K5ZC07_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A087RJY7_A0A087RJY7_APTFO_9233 and tr_A0A0A0AS99_A0A0A0AS99_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN1_A0A2D0PSN1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN5_A0A2D0PSN5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PSN9_A0A2D0PSN9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PR33_A0A2D0PR33_ICTPU_7998 and tr_A0A2D0PV95_A0A2D0PV95_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PUD1_A0A2D0PUD1_ICTPU_7998 and tr_W5UIY1_W5UIY1_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 23

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/Q9UPW6/3_mltree/Q9UPW6.raxml.reduced.phy

Alignment comprises 1 partitions and 804 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 805 / 804
Gaps: 34.10 %
Invariant sites: 0.25 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 367 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -299754.570471] Initial branch length optimization
[00:00:01 -218086.211733] Model parameter optimization (eps = 10.000000)
[00:00:40 -215855.207268] AUTODETECT spr round 1 (radius: 5)
[00:01:08 -140038.472377] AUTODETECT spr round 2 (radius: 10)
[00:01:45 -103100.758291] AUTODETECT spr round 3 (radius: 15)
[00:02:34 -88319.299964] AUTODETECT spr round 4 (radius: 20)
[00:03:28 -85321.025390] AUTODETECT spr round 5 (radius: 25)
[00:04:39 -85058.387419] SPR radius for FAST iterations: 25 (autodetect)
[00:04:39 -85058.387419] Model parameter optimization (eps = 3.000000)
[00:05:07 -83909.610958] FAST spr round 1 (radius: 25)
[00:05:44 -74394.265738] FAST spr round 2 (radius: 25)
[00:06:19 -73784.718683] FAST spr round 3 (radius: 25)
[00:06:51 -73758.252952] FAST spr round 4 (radius: 25)
[00:07:16 -73754.459333] FAST spr round 5 (radius: 25)
[00:07:37 -73754.458974] Model parameter optimization (eps = 1.000000)
[00:07:46 -73751.197670] SLOW spr round 1 (radius: 5)
[00:08:29 -73743.282950] SLOW spr round 2 (radius: 5)
[00:09:04 -73740.193491] SLOW spr round 3 (radius: 5)
[00:09:37 -73740.188067] SLOW spr round 4 (radius: 10)
[00:10:11 -73739.364093] SLOW spr round 5 (radius: 5)
[00:11:00 -73739.363763] SLOW spr round 6 (radius: 10)
[00:11:46 -73739.363729] SLOW spr round 7 (radius: 15)
[00:12:54 -73738.119151] SLOW spr round 8 (radius: 5)
[00:13:47 -73738.118985] SLOW spr round 9 (radius: 10)
[00:14:38 -73738.118969] SLOW spr round 10 (radius: 15)
[00:15:42 -73738.118954] SLOW spr round 11 (radius: 20)
[00:17:14 -73737.964972] SLOW spr round 12 (radius: 5)
[00:17:59 -73733.910513] SLOW spr round 13 (radius: 5)
[00:18:41 -73733.909284] SLOW spr round 14 (radius: 10)
[00:19:20 -73733.909069] SLOW spr round 15 (radius: 15)
[00:20:22 -73733.909009] SLOW spr round 16 (radius: 20)
[00:21:52 -73733.908985] SLOW spr round 17 (radius: 25)
[00:22:11] [worker #1] ML tree search #2, logLikelihood: -73738.668141
[00:23:30 -73733.908970] Model parameter optimization (eps = 0.100000)

[00:23:36] [worker #0] ML tree search #1, logLikelihood: -73733.724419

[00:23:36 -303100.419519] Initial branch length optimization
[00:23:38 -219760.701836] Model parameter optimization (eps = 10.000000)
[00:24:07 -217659.399708] AUTODETECT spr round 1 (radius: 5)
[00:24:33 -140397.596084] AUTODETECT spr round 2 (radius: 10)
[00:25:06 -106789.213646] AUTODETECT spr round 3 (radius: 15)
[00:25:44 -92253.100244] AUTODETECT spr round 4 (radius: 20)
[00:26:30 -84774.072901] AUTODETECT spr round 5 (radius: 25)
[00:27:19 -84381.233369] SPR radius for FAST iterations: 25 (autodetect)
[00:27:19 -84381.233369] Model parameter optimization (eps = 3.000000)
[00:27:48 -83329.344338] FAST spr round 1 (radius: 25)
[00:28:23 -74225.212970] FAST spr round 2 (radius: 25)
[00:28:51 -73785.050534] FAST spr round 3 (radius: 25)
[00:29:17 -73761.353547] FAST spr round 4 (radius: 25)
[00:29:38 -73757.223600] FAST spr round 5 (radius: 25)
[00:29:59 -73757.196958] Model parameter optimization (eps = 1.000000)
[00:30:08 -73751.808544] SLOW spr round 1 (radius: 5)
[00:30:44 -73744.598794] SLOW spr round 2 (radius: 5)
[00:31:16 -73744.586669] SLOW spr round 3 (radius: 10)
[00:31:50 -73743.913568] SLOW spr round 4 (radius: 5)
[00:32:36 -73743.913500] SLOW spr round 5 (radius: 10)
[00:33:17 -73743.913479] SLOW spr round 6 (radius: 15)
[00:34:14 -73741.123363] SLOW spr round 7 (radius: 5)
[00:35:04 -73740.866545] SLOW spr round 8 (radius: 5)
[00:35:42 -73740.866504] SLOW spr round 9 (radius: 10)
[00:36:16 -73740.866482] SLOW spr round 10 (radius: 15)
[00:37:08 -73740.866463] SLOW spr round 11 (radius: 20)
[00:38:24 -73739.724443] SLOW spr round 12 (radius: 5)
[00:39:12 -73732.625989] SLOW spr round 13 (radius: 5)
[00:39:47 -73732.545048] SLOW spr round 14 (radius: 10)
[00:40:20 -73732.544807] SLOW spr round 15 (radius: 15)
[00:41:13 -73732.544753] SLOW spr round 16 (radius: 20)
[00:42:31 -73732.544720] SLOW spr round 17 (radius: 25)
[00:42:47] [worker #1] ML tree search #4, logLikelihood: -73734.194763
[00:43:51 -73732.544697] Model parameter optimization (eps = 0.100000)

[00:43:54] [worker #0] ML tree search #3, logLikelihood: -73732.475256

[00:43:54 -300573.206541] Initial branch length optimization
[00:43:55 -221801.451751] Model parameter optimization (eps = 10.000000)
[00:44:22 -219450.258641] AUTODETECT spr round 1 (radius: 5)
[00:44:44 -148042.261922] AUTODETECT spr round 2 (radius: 10)
[00:45:12 -105215.608135] AUTODETECT spr round 3 (radius: 15)
[00:45:44 -91198.194587] AUTODETECT spr round 4 (radius: 20)
[00:46:24 -83063.059853] AUTODETECT spr round 5 (radius: 25)
[00:47:07 -82636.789886] SPR radius for FAST iterations: 25 (autodetect)
[00:47:07 -82636.789886] Model parameter optimization (eps = 3.000000)
[00:47:39 -81536.287182] FAST spr round 1 (radius: 25)
[00:48:10 -74241.352165] FAST spr round 2 (radius: 25)
[00:48:34 -73779.816556] FAST spr round 3 (radius: 25)
[00:48:55 -73760.838377] FAST spr round 4 (radius: 25)
[00:49:13 -73751.356343] FAST spr round 5 (radius: 25)
[00:49:30 -73751.342610] Model parameter optimization (eps = 1.000000)
[00:49:37 -73747.443393] SLOW spr round 1 (radius: 5)
[00:50:07 -73734.628904] SLOW spr round 2 (radius: 5)
[00:50:34 -73734.627335] SLOW spr round 3 (radius: 10)
[00:51:03 -73734.627085] SLOW spr round 4 (radius: 15)
[00:51:59 -73734.412884] SLOW spr round 5 (radius: 5)
[00:52:42 -73734.412726] SLOW spr round 6 (radius: 10)
[00:53:20 -73734.412703] SLOW spr round 7 (radius: 15)
[00:54:12 -73734.412663] SLOW spr round 8 (radius: 20)
[00:55:38 -73734.412646] SLOW spr round 9 (radius: 25)
[00:55:50] [worker #1] ML tree search #6, logLikelihood: -73728.145026
[00:57:03 -73734.412629] Model parameter optimization (eps = 0.100000)

[00:57:06] [worker #0] ML tree search #5, logLikelihood: -73734.389305

[00:57:06 -299392.048498] Initial branch length optimization
[00:57:08 -218644.326549] Model parameter optimization (eps = 10.000000)
[00:57:55 -216457.756482] AUTODETECT spr round 1 (radius: 5)
[00:58:25 -143666.858948] AUTODETECT spr round 2 (radius: 10)
[00:59:03 -108875.787089] AUTODETECT spr round 3 (radius: 15)
[00:59:47 -93005.238701] AUTODETECT spr round 4 (radius: 20)
[01:00:39 -83084.287818] AUTODETECT spr round 5 (radius: 25)
[01:01:38 -82866.281331] SPR radius for FAST iterations: 25 (autodetect)
[01:01:38 -82866.281331] Model parameter optimization (eps = 3.000000)
[01:02:06 -81768.952552] FAST spr round 1 (radius: 25)
[01:02:47 -74211.879087] FAST spr round 2 (radius: 25)
[01:03:23 -73917.499843] FAST spr round 3 (radius: 25)
[01:03:53 -73760.952091] FAST spr round 4 (radius: 25)
[01:04:18 -73756.834400] FAST spr round 5 (radius: 25)
[01:04:41 -73756.832450] Model parameter optimization (eps = 1.000000)
[01:04:55 -73749.459137] SLOW spr round 1 (radius: 5)
[01:05:34 -73735.490312] SLOW spr round 2 (radius: 5)
[01:06:11 -73735.488412] SLOW spr round 3 (radius: 10)
[01:06:50 -73733.867087] SLOW spr round 4 (radius: 5)
[01:07:43 -73733.866721] SLOW spr round 5 (radius: 10)
[01:08:31 -73733.866684] SLOW spr round 6 (radius: 15)
[01:09:39 -73732.594258] SLOW spr round 7 (radius: 5)
[01:10:36 -73732.585975] SLOW spr round 8 (radius: 10)
[01:11:28 -73732.585566] SLOW spr round 9 (radius: 15)
[01:12:37 -73732.585462] SLOW spr round 10 (radius: 20)
[01:14:16 -73732.556720] SLOW spr round 11 (radius: 25)
[01:16:05 -73732.552577] Model parameter optimization (eps = 0.100000)

[01:16:10] [worker #0] ML tree search #7, logLikelihood: -73732.482257

[01:16:10 -298655.490834] Initial branch length optimization
[01:16:11 -217546.529633] Model parameter optimization (eps = 10.000000)
[01:16:47 -215232.566148] AUTODETECT spr round 1 (radius: 5)
[01:17:07] [worker #1] ML tree search #8, logLikelihood: -73728.319981
[01:17:17 -146912.452668] AUTODETECT spr round 2 (radius: 10)
[01:17:56 -108707.951390] AUTODETECT spr round 3 (radius: 15)
[01:18:42 -94268.632821] AUTODETECT spr round 4 (radius: 20)
[01:19:36 -90279.975795] AUTODETECT spr round 5 (radius: 25)
[01:20:41 -89852.677808] SPR radius for FAST iterations: 25 (autodetect)
[01:20:41 -89852.677808] Model parameter optimization (eps = 3.000000)
[01:21:14 -88831.429269] FAST spr round 1 (radius: 25)
[01:22:01 -77909.631598] FAST spr round 2 (radius: 25)
[01:22:41 -75489.741219] FAST spr round 3 (radius: 25)
[01:23:09 -73934.957526] FAST spr round 4 (radius: 25)
[01:23:34 -73769.796824] FAST spr round 5 (radius: 25)
[01:23:59 -73769.365753] FAST spr round 6 (radius: 25)
[01:24:22 -73769.350466] Model parameter optimization (eps = 1.000000)
[01:24:34 -73761.961726] SLOW spr round 1 (radius: 5)
[01:25:14 -73749.165408] SLOW spr round 2 (radius: 5)
[01:25:52 -73749.161858] SLOW spr round 3 (radius: 10)
[01:26:32 -73740.972841] SLOW spr round 4 (radius: 5)
[01:27:25 -73740.928629] SLOW spr round 5 (radius: 10)
[01:28:12 -73740.928152] SLOW spr round 6 (radius: 15)
[01:29:21 -73740.927963] SLOW spr round 7 (radius: 20)
[01:31:01 -73740.927864] SLOW spr round 8 (radius: 25)
[01:32:51 -73737.018752] SLOW spr round 9 (radius: 5)
[01:33:50 -73736.976067] SLOW spr round 10 (radius: 10)
[01:34:45 -73736.974047] SLOW spr round 11 (radius: 15)
[01:35:54 -73736.973407] SLOW spr round 12 (radius: 20)
[01:37:33 -73736.973207] SLOW spr round 13 (radius: 25)
[01:39:23 -73736.973145] Model parameter optimization (eps = 0.100000)

[01:39:30] [worker #0] ML tree search #9, logLikelihood: -73736.522835

[01:39:30 -297707.636692] Initial branch length optimization
[01:39:32 -217917.247201] Model parameter optimization (eps = 10.000000)
[01:40:09 -215679.306235] AUTODETECT spr round 1 (radius: 5)
[01:40:38 -143210.270246] AUTODETECT spr round 2 (radius: 10)
[01:41:02] [worker #1] ML tree search #10, logLikelihood: -73726.759647
[01:41:15 -108070.227944] AUTODETECT spr round 3 (radius: 15)
[01:42:00 -87329.796347] AUTODETECT spr round 4 (radius: 20)
[01:42:51 -82384.443159] AUTODETECT spr round 5 (radius: 25)
[01:43:59 -82334.960253] SPR radius for FAST iterations: 25 (autodetect)
[01:43:59 -82334.960253] Model parameter optimization (eps = 3.000000)
[01:44:33 -81367.159297] FAST spr round 1 (radius: 25)
[01:45:12 -74143.221994] FAST spr round 2 (radius: 25)
[01:45:43 -73796.116370] FAST spr round 3 (radius: 25)
[01:46:12 -73772.664151] FAST spr round 4 (radius: 25)
[01:46:37 -73769.448263] FAST spr round 5 (radius: 25)
[01:47:01 -73769.246714] FAST spr round 6 (radius: 25)
[01:47:24 -73769.246318] Model parameter optimization (eps = 1.000000)
[01:47:36 -73758.514848] SLOW spr round 1 (radius: 5)
[01:48:15 -73743.626151] SLOW spr round 2 (radius: 5)
[01:48:53 -73743.625390] SLOW spr round 3 (radius: 10)
[01:49:33 -73742.307563] SLOW spr round 4 (radius: 5)
[01:50:26 -73742.307126] SLOW spr round 5 (radius: 10)
[01:51:14 -73742.307079] SLOW spr round 6 (radius: 15)
[01:52:27 -73739.794196] SLOW spr round 7 (radius: 5)
[01:53:23 -73739.792786] SLOW spr round 8 (radius: 10)
[01:54:15 -73739.792686] SLOW spr round 9 (radius: 15)
[01:55:25 -73738.519000] SLOW spr round 10 (radius: 5)
[01:56:21 -73736.735137] SLOW spr round 11 (radius: 5)
[01:57:08 -73736.735102] SLOW spr round 12 (radius: 10)
[01:57:51 -73736.735076] SLOW spr round 13 (radius: 15)
[01:59:03 -73736.735053] SLOW spr round 14 (radius: 20)
[02:00:45 -73735.488593] SLOW spr round 15 (radius: 5)
[02:01:43 -73735.477224] SLOW spr round 16 (radius: 10)
[02:02:37 -73735.476741] SLOW spr round 17 (radius: 15)
[02:03:47 -73735.476620] SLOW spr round 18 (radius: 20)
[02:05:30 -73735.476574] SLOW spr round 19 (radius: 25)
[02:07:24 -73731.136555] SLOW spr round 20 (radius: 5)
[02:07:34] [worker #1] ML tree search #12, logLikelihood: -73736.186269
[02:08:23 -73731.111265] SLOW spr round 21 (radius: 10)
[02:09:19 -73731.109163] SLOW spr round 22 (radius: 15)
[02:10:30 -73731.108486] SLOW spr round 23 (radius: 20)
[02:12:14 -73731.108266] SLOW spr round 24 (radius: 25)
[02:14:10 -73731.108188] Model parameter optimization (eps = 0.100000)

[02:14:18] [worker #0] ML tree search #11, logLikelihood: -73730.796958

[02:14:18 -300500.728225] Initial branch length optimization
[02:14:19 -218714.721528] Model parameter optimization (eps = 10.000000)
[02:14:58 -216634.868985] AUTODETECT spr round 1 (radius: 5)
[02:15:27 -144309.699585] AUTODETECT spr round 2 (radius: 10)
[02:16:04 -106520.667114] AUTODETECT spr round 3 (radius: 15)
[02:16:50 -95421.385127] AUTODETECT spr round 4 (radius: 20)
[02:17:48 -88810.912678] AUTODETECT spr round 5 (radius: 25)
[02:18:47 -85050.070372] SPR radius for FAST iterations: 25 (autodetect)
[02:18:47 -85050.070372] Model parameter optimization (eps = 3.000000)
[02:19:34 -83962.231700] FAST spr round 1 (radius: 25)
[02:20:13 -74079.680292] FAST spr round 2 (radius: 25)
[02:20:46 -73807.856167] FAST spr round 3 (radius: 25)
[02:21:16 -73764.888523] FAST spr round 4 (radius: 25)
[02:21:41 -73764.887533] Model parameter optimization (eps = 1.000000)
[02:21:55 -73737.209290] SLOW spr round 1 (radius: 5)
[02:22:37 -73729.881102] SLOW spr round 2 (radius: 5)
[02:23:15 -73729.400850] SLOW spr round 3 (radius: 5)
[02:23:52 -73729.400463] SLOW spr round 4 (radius: 10)
[02:24:31 -73727.888402] SLOW spr round 5 (radius: 5)
[02:25:23 -73727.888220] SLOW spr round 6 (radius: 10)
[02:26:11 -73727.888115] SLOW spr round 7 (radius: 15)
[02:27:20 -73727.888038] SLOW spr round 8 (radius: 20)
[02:29:01 -73727.887977] SLOW spr round 9 (radius: 25)
[02:30:51 -73727.887924] Model parameter optimization (eps = 0.100000)

[02:30:54] [worker #0] ML tree search #13, logLikelihood: -73727.843460

[02:30:54 -302352.977559] Initial branch length optimization
[02:30:56 -218248.204487] Model parameter optimization (eps = 10.000000)
[02:31:28 -216169.582649] AUTODETECT spr round 1 (radius: 5)
[02:31:58 -151016.591125] AUTODETECT spr round 2 (radius: 10)
[02:32:36 -113346.211460] AUTODETECT spr round 3 (radius: 15)
[02:33:15] [worker #1] ML tree search #14, logLikelihood: -73728.982492
[02:33:23 -96487.502404] AUTODETECT spr round 4 (radius: 20)
[02:34:18 -84616.449551] AUTODETECT spr round 5 (radius: 25)
[02:35:19 -84075.531279] SPR radius for FAST iterations: 25 (autodetect)
[02:35:19 -84075.531279] Model parameter optimization (eps = 3.000000)
[02:35:55 -83085.945771] FAST spr round 1 (radius: 25)
[02:36:38 -74216.849855] FAST spr round 2 (radius: 25)
[02:37:10 -73900.886888] FAST spr round 3 (radius: 25)
[02:37:39 -73786.391112] FAST spr round 4 (radius: 25)
[02:38:07 -73766.696608] FAST spr round 5 (radius: 25)
[02:38:32 -73761.025045] FAST spr round 6 (radius: 25)
[02:38:55 -73761.023806] Model parameter optimization (eps = 1.000000)
[02:39:07 -73750.836304] SLOW spr round 1 (radius: 5)
[02:39:47 -73737.323804] SLOW spr round 2 (radius: 5)
[02:40:25 -73737.308339] SLOW spr round 3 (radius: 10)
[02:41:05 -73729.374666] SLOW spr round 4 (radius: 5)
[02:41:58 -73729.326815] SLOW spr round 5 (radius: 10)
[02:42:45 -73729.325569] SLOW spr round 6 (radius: 15)
[02:43:54 -73729.325115] SLOW spr round 7 (radius: 20)
[02:45:34 -73729.324884] SLOW spr round 8 (radius: 25)
[02:47:19 -73729.324745] Model parameter optimization (eps = 0.100000)

[02:47:28] [worker #0] ML tree search #15, logLikelihood: -73728.806793

[02:47:28 -299977.939196] Initial branch length optimization
[02:47:29 -218591.274615] Model parameter optimization (eps = 10.000000)
[02:48:08 -216416.058768] AUTODETECT spr round 1 (radius: 5)
[02:48:37 -145975.434657] AUTODETECT spr round 2 (radius: 10)
[02:49:16 -106623.506293] AUTODETECT spr round 3 (radius: 15)
[02:50:00 -86659.594682] AUTODETECT spr round 4 (radius: 20)
[02:50:21] [worker #1] ML tree search #16, logLikelihood: -73736.391404
[02:50:57 -83897.080113] AUTODETECT spr round 5 (radius: 25)
[02:52:01 -83878.157109] SPR radius for FAST iterations: 25 (autodetect)
[02:52:01 -83878.157109] Model parameter optimization (eps = 3.000000)
[02:52:29 -82889.923721] FAST spr round 1 (radius: 25)
[02:53:11 -74026.480093] FAST spr round 2 (radius: 25)
[02:53:42 -73795.208575] FAST spr round 3 (radius: 25)
[02:54:14 -73770.317464] FAST spr round 4 (radius: 25)
[02:54:39 -73770.273935] Model parameter optimization (eps = 1.000000)
[02:54:52 -73756.742452] SLOW spr round 1 (radius: 5)
[02:55:34 -73747.850057] SLOW spr round 2 (radius: 5)
[02:56:12 -73743.943531] SLOW spr round 3 (radius: 5)
[02:56:49 -73743.943221] SLOW spr round 4 (radius: 10)
[02:57:29 -73737.835698] SLOW spr round 5 (radius: 5)
[02:58:21 -73737.834338] SLOW spr round 6 (radius: 10)
[02:59:08 -73737.834117] SLOW spr round 7 (radius: 15)
[03:00:17 -73736.667751] SLOW spr round 8 (radius: 5)
[03:01:12 -73736.627823] SLOW spr round 9 (radius: 10)
[03:02:03 -73736.627061] SLOW spr round 10 (radius: 15)
[03:03:12 -73736.626889] SLOW spr round 11 (radius: 20)
[03:04:53 -73736.626804] SLOW spr round 12 (radius: 25)
[03:06:46 -73732.529517] SLOW spr round 13 (radius: 5)
[03:07:44 -73732.518235] SLOW spr round 14 (radius: 10)
[03:08:02] [worker #1] ML tree search #18, logLikelihood: -73734.214421
[03:08:40 -73732.514535] SLOW spr round 15 (radius: 15)
[03:09:52 -73732.513311] SLOW spr round 16 (radius: 20)
[03:11:36 -73732.512894] SLOW spr round 17 (radius: 25)
[03:13:31 -73732.512733] Model parameter optimization (eps = 0.100000)

[03:13:41] [worker #0] ML tree search #17, logLikelihood: -73731.117624

[03:13:41 -295767.281977] Initial branch length optimization
[03:13:42 -214599.029223] Model parameter optimization (eps = 10.000000)
[03:14:31 -212584.809032] AUTODETECT spr round 1 (radius: 5)
[03:15:01 -145346.023232] AUTODETECT spr round 2 (radius: 10)
[03:15:39 -110912.319817] AUTODETECT spr round 3 (radius: 15)
[03:16:24 -93249.820059] AUTODETECT spr round 4 (radius: 20)
[03:17:24 -86078.761195] AUTODETECT spr round 5 (radius: 25)
[03:18:26 -85957.383451] SPR radius for FAST iterations: 25 (autodetect)
[03:18:26 -85957.383451] Model parameter optimization (eps = 3.000000)
[03:18:55 -85063.058731] FAST spr round 1 (radius: 25)
[03:19:37 -74305.945499] FAST spr round 2 (radius: 25)
[03:20:09 -73788.232171] FAST spr round 3 (radius: 25)
[03:20:38 -73752.615716] FAST spr round 4 (radius: 25)
[03:21:02 -73750.798833] FAST spr round 5 (radius: 25)
[03:21:25 -73750.797070] Model parameter optimization (eps = 1.000000)
[03:21:37 -73743.442145] SLOW spr round 1 (radius: 5)
[03:22:17 -73735.062833] SLOW spr round 2 (radius: 5)
[03:22:53 -73735.061441] SLOW spr round 3 (radius: 10)
[03:23:32 -73731.927220] SLOW spr round 4 (radius: 5)
[03:24:24 -73731.921534] SLOW spr round 5 (radius: 10)
[03:25:12 -73731.921176] SLOW spr round 6 (radius: 15)
[03:26:09] [worker #1] ML tree search #20, logLikelihood: -73730.754417
[03:26:20 -73731.794897] SLOW spr round 7 (radius: 5)
[03:27:17 -73731.740598] SLOW spr round 8 (radius: 10)
[03:28:08 -73731.740195] SLOW spr round 9 (radius: 15)
[03:29:15 -73731.739901] SLOW spr round 10 (radius: 20)
[03:30:56 -73730.227402] SLOW spr round 11 (radius: 5)
[03:31:54 -73730.226234] SLOW spr round 12 (radius: 10)
[03:32:47 -73730.225820] SLOW spr round 13 (radius: 15)
[03:33:55 -73730.225716] SLOW spr round 14 (radius: 20)
[03:35:36 -73730.225648] SLOW spr round 15 (radius: 25)
[03:37:24 -73730.134236] Model parameter optimization (eps = 0.100000)

[03:37:28] [worker #0] ML tree search #19, logLikelihood: -73730.067163


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.227477,0.635058) (0.125893,1.493306) (0.344738,0.522023) (0.301892,1.615086) 
   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: -73726.759647

AIC score: 148927.519294 / AICc score: 165163.519294 / BIC score: 152384.670052
Free parameters (model + branch lengths): 737

WARNING: Best ML tree contains 71 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW6/3_mltree/Q9UPW6.raxml.log

Analysis started: 30-Jun-2021 17:50:12 / finished: 30-Jun-2021 21:27:41

Elapsed time: 13049.063 seconds

Consumed energy: 1173.536 Wh (= 6 km in an electric car, or 29 km with an e-scooter!)