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 15-Jul-2021 13:44:50 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/2_msa/Q9ULD8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/3_mltree/Q9ULD8 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/2_msa/Q9ULD8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 817 sites

WARNING: Sequences tr_M3XVK2_M3XVK2_MUSPF_9669 and tr_A0A2Y9LL41_A0A2Y9LL41_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A1ZB14_A1ZB14_DROME_7227 and tr_B4HN99_B4HN99_DROSE_7238 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_G3SKG7_G3SKG7_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A2J8V6F3_A0A2J8V6F3_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_H2Q129_H2Q129_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and sp_O95259_KCNH1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_F7GL26_F7GL26_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_U3D9B5_U3D9B5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_G7NUM9_G7NUM9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A096N8P3_A0A096N8P3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A0D9RS01_A0A0D9RS01_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A2K5NA49_A0A2K5NA49_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A2K6BR64_A0A2K6BR64_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A2K5Z1C5_A0A2K5Z1C5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1QPR1_G1QPR1_NOMLE_61853 and tr_A0A2R9CDK7_A0A2R9CDK7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2ZQ14_A0A2I2ZQ14_GORGO_9595 and tr_H2QIW5_H2QIW5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZQ14_A0A2I2ZQ14_GORGO_9595 and sp_Q9NS40_KCNH7_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_H2PBC8_H2PBC8_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_A0A2I3S5Z0_A0A2I3S5Z0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and sp_Q96L42_KCNH8_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_F7GUN6_F7GUN6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_G7NY23_G7NY23_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_A0A2K5LPE3_A0A2K5LPE3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and tr_H2R9B0_H2R9B0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and sp_Q8NCM2_KCNH5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and tr_G3SVQ7_G3SVQ7_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and tr_F7E3G0_F7E3G0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and tr_A0A2R8ZTW0_A0A2R8ZTW0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and tr_A0A2Y9DAD7_A0A2Y9DAD7_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and tr_H2Q5V5_H2Q5V5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and sp_Q9ULD8_KCNH3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and tr_A0A2R9ANM2_A0A2R9ANM2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6WEE3_F6WEE3_MACMU_9544 and tr_A0A096NPA8_A0A096NPA8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6WEE3_F6WEE3_MACMU_9544 and tr_A0A0D9R378_A0A0D9R378_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6WEE3_F6WEE3_MACMU_9544 and tr_A0A2K5MTB3_A0A2K5MTB3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_G7PAH7_G7PAH7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A096NVJ8_A0A096NVJ8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A2K6DGC9_A0A2K6DGC9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A2K6A9C2_A0A2K6A9C2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_F1MP51_F1MP51_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_M3WD34_M3WD34_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_A0A2U4AFU6_A0A2U4AFU6_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_A0A2Y9MZZ0_A0A2Y9MZZ0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_A0A2Y9SBM3_A0A2Y9SBM3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G1LC41_G1LC41_AILME_9646 and tr_A0A384CX45_A0A384CX45_URSMA_29073 are exactly identical!
WARNING: Sequences tr_B3RQL4_B3RQL4_TRIAD_10228 and tr_A0A369S7P7_A0A369S7P7_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A044UED0_A0A044UED0_ONCVO_6282 and tr_A0A182E9X1_A0A182E9X1_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A096MP06_A0A096MP06_PAPAN_9555 and tr_A0A2K5LNA9_A0A2K5LNA9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MP06_A0A096MP06_PAPAN_9555 and tr_A0A2K6B3Q4_A0A2K6B3Q4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096P5S0_A0A096P5S0_PAPAN_9555 and tr_A0A0D9S245_A0A0D9S245_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096P5S0_A0A096P5S0_PAPAN_9555 and tr_A0A2K5P1L5_A0A2K5P1L5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096P5S0_A0A096P5S0_PAPAN_9555 and tr_A0A2K6CKY2_A0A2K6CKY2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MBJ1_A0A2I3MBJ1_PAPAN_9555 and tr_A0A2K6DUX8_A0A2K6DUX8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MBJ1_A0A2I3MBJ1_PAPAN_9555 and tr_A0A2K6AGR2_A0A2K6AGR2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091VUI4_A0A091VUI4_NIPNI_128390 and tr_A0A0A0A045_A0A0A0A045_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1L9D4_A0A0V1L9D4_9BILA_6335 and tr_A0A0V1NMC9_A0A0V1NMC9_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A2D0RQ54_A0A2D0RQ54_ICTPU_7998 and tr_A0A2D0RQ68_A0A2D0RQ68_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T5E0_A0A2D0T5E0_ICTPU_7998 and tr_W5UCW3_W5UCW3_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 58

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/Q9ULD8/3_mltree/Q9ULD8.raxml.reduced.phy

Alignment comprises 1 partitions and 817 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 817 / 817
Gaps: 13.78 %
Invariant sites: 0.12 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/3_mltree/Q9ULD8.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 205 / 16400
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1088623.841168] Initial branch length optimization
[00:00:07 -916616.306325] Model parameter optimization (eps = 10.000000)
[00:01:03 -914889.075073] AUTODETECT spr round 1 (radius: 5)
[00:04:22 -522440.111595] AUTODETECT spr round 2 (radius: 10)
[00:07:51 -362252.831438] AUTODETECT spr round 3 (radius: 15)
[00:11:36 -307525.128713] AUTODETECT spr round 4 (radius: 20)
[00:15:51 -271387.626940] AUTODETECT spr round 5 (radius: 25)
[00:20:51 -253522.020281] SPR radius for FAST iterations: 25 (autodetect)
[00:20:51 -253522.020281] Model parameter optimization (eps = 3.000000)
[00:21:23 -253320.725222] FAST spr round 1 (radius: 25)
[00:25:02 -207314.548939] FAST spr round 2 (radius: 25)
[00:28:00 -203634.761259] FAST spr round 3 (radius: 25)
[00:30:37 -203361.423615] FAST spr round 4 (radius: 25)
[00:33:02 -203345.772299] FAST spr round 5 (radius: 25)
[00:35:17 -203345.771527] Model parameter optimization (eps = 1.000000)
[00:35:38 -203335.886891] SLOW spr round 1 (radius: 5)
[00:38:41 -203299.757684] SLOW spr round 2 (radius: 5)
[00:41:36 -203297.853239] SLOW spr round 3 (radius: 5)
[00:44:27 -203297.853086] SLOW spr round 4 (radius: 10)
[00:47:26 -203266.987976] SLOW spr round 5 (radius: 5)
[00:51:08 -203258.726894] SLOW spr round 6 (radius: 5)
[00:54:21 -203252.681659] SLOW spr round 7 (radius: 5)
[00:57:19 -203252.681392] SLOW spr round 8 (radius: 10)
[01:00:14 -203252.681260] SLOW spr round 9 (radius: 15)
[01:04:22 -203252.681133] SLOW spr round 10 (radius: 20)
[01:05:31] [worker #1] ML tree search #2, logLikelihood: -203271.329702
[01:10:23 -203252.681005] SLOW spr round 11 (radius: 25)
[01:17:44 -203252.680878] Model parameter optimization (eps = 0.100000)

[01:17:58] [worker #0] ML tree search #1, logLikelihood: -203252.534036

[01:17:58 -1095801.430455] Initial branch length optimization
[01:18:07 -910184.657317] Model parameter optimization (eps = 10.000000)
[01:18:56 -908565.804463] AUTODETECT spr round 1 (radius: 5)
[01:22:14 -518514.855233] AUTODETECT spr round 2 (radius: 10)
[01:25:48 -356000.188074] AUTODETECT spr round 3 (radius: 15)
[01:29:32 -284736.173663] AUTODETECT spr round 4 (radius: 20)
[01:34:07 -250896.064499] AUTODETECT spr round 5 (radius: 25)
[01:38:56 -245629.249590] SPR radius for FAST iterations: 25 (autodetect)
[01:38:56 -245629.249590] Model parameter optimization (eps = 3.000000)
[01:39:30 -245413.655895] FAST spr round 1 (radius: 25)
[01:43:20 -204993.825390] FAST spr round 2 (radius: 25)
[01:46:17 -203427.110544] FAST spr round 3 (radius: 25)
[01:48:54 -203380.042095] FAST spr round 4 (radius: 25)
[01:51:22 -203374.139620] FAST spr round 5 (radius: 25)
[01:53:41 -203373.978241] FAST spr round 6 (radius: 25)
[01:55:57 -203373.977601] Model parameter optimization (eps = 1.000000)
[01:56:19 -203361.887643] SLOW spr round 1 (radius: 5)
[01:59:20 -203304.709536] SLOW spr round 2 (radius: 5)
[02:02:17 -203299.510211] SLOW spr round 3 (radius: 5)
[02:05:06 -203299.509532] SLOW spr round 4 (radius: 10)
[02:08:02 -203294.925695] SLOW spr round 5 (radius: 5)
[02:11:37 -203284.587861] SLOW spr round 6 (radius: 5)
[02:14:47 -203284.587731] SLOW spr round 7 (radius: 10)
[02:17:47 -203284.587610] SLOW spr round 8 (radius: 15)
[02:21:53 -203284.587488] SLOW spr round 9 (radius: 20)
[02:27:56 -203284.587367] SLOW spr round 10 (radius: 25)
[02:31:59] [worker #1] ML tree search #4, logLikelihood: -203249.579619
[02:35:21 -203284.587246] Model parameter optimization (eps = 0.100000)

[02:35:29] [worker #0] ML tree search #3, logLikelihood: -203284.566884

[02:35:29 -1111623.613814] Initial branch length optimization
[02:35:41 -926846.891856] Model parameter optimization (eps = 10.000000)
[02:36:24 -925156.880432] AUTODETECT spr round 1 (radius: 5)
[02:39:44 -524670.485218] AUTODETECT spr round 2 (radius: 10)
[02:43:20 -369433.909008] AUTODETECT spr round 3 (radius: 15)
[02:47:20 -298899.573283] AUTODETECT spr round 4 (radius: 20)
[02:51:49 -247412.762828] AUTODETECT spr round 5 (radius: 25)
[02:56:35 -239140.653644] SPR radius for FAST iterations: 25 (autodetect)
[02:56:35 -239140.653644] Model parameter optimization (eps = 3.000000)
[02:57:06 -238848.615616] FAST spr round 1 (radius: 25)
[03:00:46 -205478.377063] FAST spr round 2 (radius: 25)
[03:03:44 -203469.954032] FAST spr round 3 (radius: 25)
[03:06:25 -203372.382662] FAST spr round 4 (radius: 25)
[03:08:51 -203360.649466] FAST spr round 5 (radius: 25)
[03:11:07 -203357.651270] FAST spr round 6 (radius: 25)
[03:13:22 -203357.648109] Model parameter optimization (eps = 1.000000)
[03:13:42 -203353.292819] SLOW spr round 1 (radius: 5)
[03:16:48 -203307.752941] SLOW spr round 2 (radius: 5)
[03:19:46 -203306.419178] SLOW spr round 3 (radius: 5)
[03:22:37 -203304.677956] SLOW spr round 4 (radius: 5)
[03:25:25 -203304.677325] SLOW spr round 5 (radius: 10)
[03:28:20 -203303.791802] SLOW spr round 6 (radius: 5)
[03:31:55 -203303.791496] SLOW spr round 7 (radius: 10)
[03:35:12 -203303.791321] SLOW spr round 8 (radius: 15)
[03:39:18 -203303.791183] SLOW spr round 9 (radius: 20)
[03:45:33 -203303.791070] SLOW spr round 10 (radius: 25)
[03:46:35] [worker #1] ML tree search #6, logLikelihood: -203281.434353
[03:53:06 -203303.790972] Model parameter optimization (eps = 0.100000)

[03:53:14] [worker #0] ML tree search #5, logLikelihood: -203303.754501

[03:53:14 -1099816.881346] Initial branch length optimization
[03:53:22 -916117.519979] Model parameter optimization (eps = 10.000000)
[03:54:02 -914376.177946] AUTODETECT spr round 1 (radius: 5)
[03:57:20 -530901.764112] AUTODETECT spr round 2 (radius: 10)
[04:01:01 -358046.075392] AUTODETECT spr round 3 (radius: 15)
[04:04:48 -281827.767671] AUTODETECT spr round 4 (radius: 20)
[04:08:48 -256798.421786] AUTODETECT spr round 5 (radius: 25)
[04:13:04 -243525.975786] SPR radius for FAST iterations: 25 (autodetect)
[04:13:04 -243525.975786] Model parameter optimization (eps = 3.000000)
[04:13:38 -243311.224892] FAST spr round 1 (radius: 25)
[04:17:20 -205087.099047] FAST spr round 2 (radius: 25)
[04:20:16 -203414.637180] FAST spr round 3 (radius: 25)
[04:23:03 -203338.592930] FAST spr round 4 (radius: 25)
[04:25:31 -203330.732082] FAST spr round 5 (radius: 25)
[04:27:52 -203328.863938] FAST spr round 6 (radius: 25)
[04:30:09 -203328.863226] Model parameter optimization (eps = 1.000000)
[04:30:32 -203322.246507] SLOW spr round 1 (radius: 5)
[04:33:38 -203280.315684] SLOW spr round 2 (radius: 5)
[04:36:34 -203280.311853] SLOW spr round 3 (radius: 10)
[04:39:31 -203270.998643] SLOW spr round 4 (radius: 5)
[04:43:04 -203269.446868] SLOW spr round 5 (radius: 5)
[04:46:14 -203269.446032] SLOW spr round 6 (radius: 10)
[04:49:14 -203269.445821] SLOW spr round 7 (radius: 15)
[04:53:21 -203269.445679] SLOW spr round 8 (radius: 20)
[04:59:23 -203269.445577] SLOW spr round 9 (radius: 25)
[05:04:39] [worker #1] ML tree search #8, logLikelihood: -203270.634430
[05:06:37 -203269.445501] Model parameter optimization (eps = 0.100000)

[05:06:43] [worker #0] ML tree search #7, logLikelihood: -203269.435936

[05:06:43 -1094609.709758] Initial branch length optimization
[05:06:52 -917178.610452] Model parameter optimization (eps = 10.000000)
[05:07:57 -915392.632972] AUTODETECT spr round 1 (radius: 5)
[05:11:17 -516234.329141] AUTODETECT spr round 2 (radius: 10)
[05:14:52 -361810.049407] AUTODETECT spr round 3 (radius: 15)
[05:18:33 -295653.447306] AUTODETECT spr round 4 (radius: 20)
[05:22:49 -241885.331403] AUTODETECT spr round 5 (radius: 25)
[05:27:28 -238049.777007] SPR radius for FAST iterations: 25 (autodetect)
[05:27:28 -238049.777007] Model parameter optimization (eps = 3.000000)
[05:28:02 -237902.482323] FAST spr round 1 (radius: 25)
[05:31:50 -204097.745723] FAST spr round 2 (radius: 25)
[05:34:46 -203423.131480] FAST spr round 3 (radius: 25)
[05:37:36 -203367.378431] FAST spr round 4 (radius: 25)
[05:40:02 -203363.618468] FAST spr round 5 (radius: 25)
[05:42:23 -203363.618316] Model parameter optimization (eps = 1.000000)
[05:42:46 -203348.939079] SLOW spr round 1 (radius: 5)
[05:45:59 -203294.344546] SLOW spr round 2 (radius: 5)
[05:49:04 -203283.780361] SLOW spr round 3 (radius: 5)
[05:51:58 -203283.779784] SLOW spr round 4 (radius: 10)
[05:54:53 -203283.301066] SLOW spr round 5 (radius: 5)
[05:58:27 -203283.300979] SLOW spr round 6 (radius: 10)
[06:01:42 -203283.300948] SLOW spr round 7 (radius: 15)
[06:05:47 -203283.300916] SLOW spr round 8 (radius: 20)
[06:12:09 -203283.300885] SLOW spr round 9 (radius: 25)
[06:18:24] [worker #1] ML tree search #10, logLikelihood: -203296.945499
[06:19:45 -203283.300853] Model parameter optimization (eps = 0.100000)

[06:19:52] [worker #0] ML tree search #9, logLikelihood: -203283.283850

[06:19:52 -1089799.414125] Initial branch length optimization
[06:19:59 -905853.106489] Model parameter optimization (eps = 10.000000)
[06:20:40 -904049.236247] AUTODETECT spr round 1 (radius: 5)
[06:24:00 -529564.765162] AUTODETECT spr round 2 (radius: 10)
[06:27:38 -353953.763407] AUTODETECT spr round 3 (radius: 15)
[06:31:24 -293785.759979] AUTODETECT spr round 4 (radius: 20)
[06:35:39 -272158.146963] AUTODETECT spr round 5 (radius: 25)
[06:40:30 -247386.943910] SPR radius for FAST iterations: 25 (autodetect)
[06:40:30 -247386.943910] Model parameter optimization (eps = 3.000000)
[06:41:03 -247180.659439] FAST spr round 1 (radius: 25)
[06:45:04 -205729.852380] FAST spr round 2 (radius: 25)
[06:48:14 -203389.610411] FAST spr round 3 (radius: 25)
[06:50:47 -203353.366436] FAST spr round 4 (radius: 25)
[06:53:11 -203338.438522] FAST spr round 5 (radius: 25)
[06:55:35 -203315.060353] FAST spr round 6 (radius: 25)
[06:57:48 -203315.060231] Model parameter optimization (eps = 1.000000)
[06:58:12 -203297.674842] SLOW spr round 1 (radius: 5)
[07:01:11 -203253.036296] SLOW spr round 2 (radius: 5)
[07:04:06 -203250.234968] SLOW spr round 3 (radius: 5)
[07:06:57 -203250.233527] SLOW spr round 4 (radius: 10)
[07:09:53 -203250.006196] SLOW spr round 5 (radius: 5)
[07:13:27 -203249.194091] SLOW spr round 6 (radius: 5)
[07:16:37 -203249.193236] SLOW spr round 7 (radius: 10)
[07:19:40 -203248.498805] SLOW spr round 8 (radius: 5)
[07:23:07 -203248.492239] SLOW spr round 9 (radius: 10)
[07:26:17 -203248.492138] SLOW spr round 10 (radius: 15)
[07:30:19 -203248.492063] SLOW spr round 11 (radius: 20)
[07:35:02] [worker #1] ML tree search #12, logLikelihood: -203287.701616
[07:36:28 -203248.492005] SLOW spr round 12 (radius: 25)
[07:43:51 -203248.491956] Model parameter optimization (eps = 0.100000)

[07:43:58] [worker #0] ML tree search #11, logLikelihood: -203248.464441

[07:43:58 -1096561.810884] Initial branch length optimization
[07:44:07 -906978.128641] Model parameter optimization (eps = 10.000000)
[07:44:55 -905147.500680] AUTODETECT spr round 1 (radius: 5)
[07:48:15 -517499.541803] AUTODETECT spr round 2 (radius: 10)
[07:51:44 -367523.226928] AUTODETECT spr round 3 (radius: 15)
[07:55:28 -299443.956421] AUTODETECT spr round 4 (radius: 20)
[07:59:50 -267297.035426] AUTODETECT spr round 5 (radius: 25)
[08:05:04 -244808.115239] SPR radius for FAST iterations: 25 (autodetect)
[08:05:04 -244808.115239] Model parameter optimization (eps = 3.000000)
[08:05:38 -244595.551612] FAST spr round 1 (radius: 25)
[08:09:29 -204993.017256] FAST spr round 2 (radius: 25)
[08:12:33 -203383.482339] FAST spr round 3 (radius: 25)
[08:15:11 -203312.716051] FAST spr round 4 (radius: 25)
[08:17:34 -203303.088832] FAST spr round 5 (radius: 25)
[08:19:52 -203302.085366] FAST spr round 6 (radius: 25)
[08:22:07 -203302.085312] Model parameter optimization (eps = 1.000000)
[08:22:28 -203291.011069] SLOW spr round 1 (radius: 5)
[08:25:38 -203257.747430] SLOW spr round 2 (radius: 5)
[08:28:39 -203257.164188] SLOW spr round 3 (radius: 5)
[08:31:34 -203257.163949] SLOW spr round 4 (radius: 10)
[08:34:30 -203257.101832] SLOW spr round 5 (radius: 15)
[08:38:44 -203257.101774] SLOW spr round 6 (radius: 20)
[08:44:41 -203257.101728] SLOW spr round 7 (radius: 25)
[08:50:51] [worker #1] ML tree search #14, logLikelihood: -203294.780212
[08:51:56 -203257.101683] Model parameter optimization (eps = 0.100000)

[08:52:02] [worker #0] ML tree search #13, logLikelihood: -203257.094736

[08:52:02 -1084419.312096] Initial branch length optimization
[08:52:09 -903699.900695] Model parameter optimization (eps = 10.000000)
[08:52:58 -902070.695575] AUTODETECT spr round 1 (radius: 5)
[08:56:11 -510356.329586] AUTODETECT spr round 2 (radius: 10)
[08:59:38 -355892.947271] AUTODETECT spr round 3 (radius: 15)
[09:03:33 -272449.705076] AUTODETECT spr round 4 (radius: 20)
[09:08:07 -242178.172526] AUTODETECT spr round 5 (radius: 25)
[09:13:46 -235279.332697] SPR radius for FAST iterations: 25 (autodetect)
[09:13:46 -235279.332697] Model parameter optimization (eps = 3.000000)
[09:14:13 -235048.764519] FAST spr round 1 (radius: 25)
[09:17:48 -204582.300592] FAST spr round 2 (radius: 25)
[09:20:47 -203474.188074] FAST spr round 3 (radius: 25)
[09:23:19 -203386.059163] FAST spr round 4 (radius: 25)
[09:25:43 -203343.548768] FAST spr round 5 (radius: 25)
[09:27:58 -203343.547755] Model parameter optimization (eps = 1.000000)
[09:28:21 -203332.058407] SLOW spr round 1 (radius: 5)
[09:31:23 -203282.003017] SLOW spr round 2 (radius: 5)
[09:34:19 -203277.444556] SLOW spr round 3 (radius: 5)
[09:37:09 -203276.922210] SLOW spr round 4 (radius: 5)
[09:39:58 -203276.922144] SLOW spr round 5 (radius: 10)
[09:42:53 -203268.278382] SLOW spr round 6 (radius: 5)
[09:46:23 -203268.278272] SLOW spr round 7 (radius: 10)
[09:49:37 -203268.278229] SLOW spr round 8 (radius: 15)
[09:53:33 -203268.278188] SLOW spr round 9 (radius: 20)
[09:59:37 -203268.278148] SLOW spr round 10 (radius: 25)
[10:01:43] [worker #1] ML tree search #16, logLikelihood: -203272.245344
[10:06:42 -203268.278108] Model parameter optimization (eps = 0.100000)

[10:06:49] [worker #0] ML tree search #15, logLikelihood: -203268.255742

[10:06:49 -1097600.517805] Initial branch length optimization
[10:06:59 -911993.762871] Model parameter optimization (eps = 10.000000)
[10:07:44 -910085.728715] AUTODETECT spr round 1 (radius: 5)
[10:11:01 -523620.641807] AUTODETECT spr round 2 (radius: 10)
[10:14:30 -355322.817017] AUTODETECT spr round 3 (radius: 15)
[10:18:08 -267196.364939] AUTODETECT spr round 4 (radius: 20)
[10:22:07 -244097.206656] AUTODETECT spr round 5 (radius: 25)
[10:26:44 -241761.113478] SPR radius for FAST iterations: 25 (autodetect)
[10:26:44 -241761.113478] Model parameter optimization (eps = 3.000000)
[10:27:19 -241593.585899] FAST spr round 1 (radius: 25)
[10:30:46 -212763.306875] FAST spr round 2 (radius: 25)
[10:33:39 -204377.962597] FAST spr round 3 (radius: 25)
[10:36:11 -203399.000451] FAST spr round 4 (radius: 25)
[10:38:37 -203360.660088] FAST spr round 5 (radius: 25)
[10:40:54 -203357.128899] FAST spr round 6 (radius: 25)
[10:43:06 -203357.128879] Model parameter optimization (eps = 1.000000)
[10:43:28 -203348.882472] SLOW spr round 1 (radius: 5)
[10:46:27 -203306.201880] SLOW spr round 2 (radius: 5)
[10:49:19 -203305.460268] SLOW spr round 3 (radius: 5)
[10:52:08 -203305.460058] SLOW spr round 4 (radius: 10)
[10:55:02 -203305.459911] SLOW spr round 5 (radius: 15)
[10:59:15 -203305.459813] SLOW spr round 6 (radius: 20)
[11:05:23 -203305.459739] SLOW spr round 7 (radius: 25)
[11:11:48] [worker #1] ML tree search #18, logLikelihood: -203273.335442
[11:12:52 -203305.459681] Model parameter optimization (eps = 0.100000)

[11:12:58] [worker #0] ML tree search #17, logLikelihood: -203305.449740

[11:12:58 -1102627.766077] Initial branch length optimization
[11:13:06 -918371.835846] Model parameter optimization (eps = 10.000000)
[11:13:59 -916595.669223] AUTODETECT spr round 1 (radius: 5)
[11:17:18 -515126.142785] AUTODETECT spr round 2 (radius: 10)
[11:20:50 -343185.040074] AUTODETECT spr round 3 (radius: 15)
[11:24:36 -260631.325296] AUTODETECT spr round 4 (radius: 20)
[11:28:39 -232478.418737] AUTODETECT spr round 5 (radius: 25)
[11:33:35 -229595.305589] SPR radius for FAST iterations: 25 (autodetect)
[11:33:35 -229595.305589] Model parameter optimization (eps = 3.000000)
[11:34:04 -229388.232369] FAST spr round 1 (radius: 25)
[11:37:36 -204173.613963] FAST spr round 2 (radius: 25)
[11:40:18 -203426.112795] FAST spr round 3 (radius: 25)
[11:42:48 -203342.929689] FAST spr round 4 (radius: 25)
[11:45:10 -203336.765374] FAST spr round 5 (radius: 25)
[11:47:24 -203335.751025] FAST spr round 6 (radius: 25)
[11:49:35 -203335.750303] Model parameter optimization (eps = 1.000000)
[11:49:49 -203334.054804] SLOW spr round 1 (radius: 5)
[11:52:52 -203288.700798] SLOW spr round 2 (radius: 5)
[11:55:44 -203283.271735] SLOW spr round 3 (radius: 5)
[11:58:33 -203283.269763] SLOW spr round 4 (radius: 10)
[12:01:27 -203279.945642] SLOW spr round 5 (radius: 5)
[12:04:57 -203278.631875] SLOW spr round 6 (radius: 5)
[12:08:05 -203278.631514] SLOW spr round 7 (radius: 10)
[12:11:05 -203277.920977] SLOW spr round 8 (radius: 5)
[12:14:32 -203276.885172] SLOW spr round 9 (radius: 5)
[12:17:38 -203276.885072] SLOW spr round 10 (radius: 10)
[12:20:35 -203276.884990] SLOW spr round 11 (radius: 15)
[12:24:43 -203276.884921] SLOW spr round 12 (radius: 20)
[12:27:39] [worker #1] ML tree search #20, logLikelihood: -203292.236131
[12:30:48 -203276.884859] SLOW spr round 13 (radius: 25)
[12:38:21 -203276.884802] Model parameter optimization (eps = 0.100000)

[12:38:30] [worker #0] ML tree search #19, logLikelihood: -203276.812794


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.258804,0.325336) (0.223922,0.368342) (0.299107,0.936638) (0.218167,2.535522) 
   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: -203248.464441

AIC score: 410506.928882 / AICc score: 8454566.928882 / BIC score: 419941.735267
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=817).
         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/Q9ULD8/3_mltree/Q9ULD8.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/3_mltree/Q9ULD8.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/3_mltree/Q9ULD8.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9ULD8/3_mltree/Q9ULD8.raxml.log

Analysis started: 15-Jul-2021 13:44:50 / finished: 16-Jul-2021 02:23:20

Elapsed time: 45510.679 seconds