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 18-Jul-2021 12:29:57 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/2_msa/Q9NQX0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/2_msa/Q9NQX0_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 511 sites

WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A1V4J6C7_A0A1V4J6C7_PATFA_372326 are exactly identical!
WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A218V159_A0A218V159_9PASE_299123 are exactly identical!
WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226NP02_A0A226NP02_CALSU_9009 are exactly identical!
WARNING: Sequences tr_E1C6K0_E1C6K0_CHICK_9031 and tr_A0A226P0G4_A0A226P0G4_COLVI_9014 are exactly identical!
WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_D3ZEJ0_D3ZEJ0_RAT_10116 are exactly identical!
WARNING: Sequences sp_A2AJ77_PRD12_MOUSE_10090 and tr_A0A1U7REI9_A0A1U7REI9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3QU29_G3QU29_GORGO_9595 and tr_H2RBZ2_H2RBZ2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S2S2_G3S2S2_GORGO_9595 and sp_B4DU55_ZN879_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and sp_Q9NQX0_PRDM6_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QRE3_H2QRE3_PANTR_9598 and tr_A0A0D9RQ11_A0A0D9RQ11_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and sp_Q9H4Q4_PRD12_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_F7I4S5_F7I4S5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_F1S0X7_F1S0X7_PIG_9823 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A337SEE4_A0A337SEE4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A096P0F9_A0A096P0F9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A0D9RQI6_A0A0D9RQI6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A2K5L0P9_A0A2K5L0P9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A2K6CVC9_A0A2K6CVC9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2QY20_H2QY20_PANTR_9598 and tr_A0A2Y9J523_A0A2Y9J523_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A1D5QJK0_A0A1D5QJK0_MACMU_9544 and tr_G7PZM3_G7PZM3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091UPR0_A0A091UPR0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091V8C5_A0A091V8C5_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091H882_A0A091H882_9AVES_55661 are exactly identical!
WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A093IBH6_A0A093IBH6_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_H0Z2N4_H0Z2N4_TAEGU_59729 and tr_A0A091HRY8_A0A091HRY8_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091JR11_A0A091JR11_EGRGA_188379 and tr_A0A093I2Y2_A0A093I2Y2_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A093PSR3_A0A093PSR3_9PASS_328815 and tr_A0A093JBE6_A0A093JBE6_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A093PSR3_A0A093PSR3_9PASS_328815 and tr_A0A099YZK0_A0A099YZK0_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A093PSR3_A0A093PSR3_9PASS_328815 and tr_A0A0A0AP02_A0A0A0AP02_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1S3PRF7_A0A1S3PRF7_SALSA_8030 and tr_A0A060XNB8_A0A060XNB8_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2D0QW48_A0A2D0QW48_ICTPU_7998 and tr_A0A2D0QWG6_A0A2D0QWG6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5LQI9_A0A2K5LQI9_CERAT_9531 and tr_A0A2K6CS75_A0A2K6CS75_MACNE_9545 are exactly identical!
WARNING: Duplicate sequences found: 32

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/Q9NQX0/3_mltree/Q9NQX0.raxml.reduced.phy

Alignment comprises 1 partitions and 511 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 511 / 511
Gaps: 37.18 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.rba

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

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 256 / 20480
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -638028.233233] Initial branch length optimization
[00:00:06 -554186.962277] Model parameter optimization (eps = 10.000000)
[00:01:00 -552938.683631] AUTODETECT spr round 1 (radius: 5)
[00:04:47 -430186.295102] AUTODETECT spr round 2 (radius: 10)
[00:08:59 -327690.454793] AUTODETECT spr round 3 (radius: 15)
[00:13:35 -288249.383653] AUTODETECT spr round 4 (radius: 20)
[00:20:09 -273481.782406] AUTODETECT spr round 5 (radius: 25)
[00:27:42 -268545.524068] SPR radius for FAST iterations: 25 (autodetect)
[00:27:42 -268545.524068] Model parameter optimization (eps = 3.000000)
[00:28:16 -268368.018419] FAST spr round 1 (radius: 25)
[00:35:35 -248463.160295] FAST spr round 2 (radius: 25)
[00:40:47 -247497.263261] FAST spr round 3 (radius: 25)
[00:45:01 -247244.831474] FAST spr round 4 (radius: 25)
[00:48:45 -247193.594580] FAST spr round 5 (radius: 25)
[00:51:57 -247187.512602] FAST spr round 6 (radius: 25)
[00:54:54 -247187.511854] Model parameter optimization (eps = 1.000000)
[00:55:17 -247183.817211] SLOW spr round 1 (radius: 5)
[00:59:15 -247100.495695] SLOW spr round 2 (radius: 5)
[01:03:11 -247087.219217] SLOW spr round 3 (radius: 5)
[01:07:04 -247073.646868] SLOW spr round 4 (radius: 5)
[01:10:58 -247054.728200] SLOW spr round 5 (radius: 5)
[01:14:46 -247048.683156] SLOW spr round 6 (radius: 5)
[01:18:28 -247048.682475] SLOW spr round 7 (radius: 10)
[01:22:33 -247039.997377] SLOW spr round 8 (radius: 5)
[01:27:02 -247031.075206] SLOW spr round 9 (radius: 5)
[01:31:10 -247026.937968] SLOW spr round 10 (radius: 5)
[01:35:00 -247026.937896] SLOW spr round 11 (radius: 10)
[01:39:03 -247026.937881] SLOW spr round 12 (radius: 15)
[01:47:02 -247023.905906] SLOW spr round 13 (radius: 5)
[01:51:36 -247022.111223] SLOW spr round 14 (radius: 5)
[01:55:39 -247022.107399] SLOW spr round 15 (radius: 10)
[01:59:55 -247022.107335] SLOW spr round 16 (radius: 15)
[02:07:48 -247022.107330] SLOW spr round 17 (radius: 20)
[02:20:34 -247019.501961] SLOW spr round 18 (radius: 5)
[02:23:47] [worker #2] ML tree search #3, logLikelihood: -247050.659404
[02:25:06 -247019.232712] SLOW spr round 19 (radius: 5)
[02:29:12 -247019.232460] SLOW spr round 20 (radius: 10)
[02:33:29 -247019.232438] SLOW spr round 21 (radius: 15)
[02:41:07 -247019.232432] SLOW spr round 22 (radius: 20)
[02:53:34 -247019.232429] SLOW spr round 23 (radius: 25)
[03:09:00 -247019.232427] Model parameter optimization (eps = 0.100000)

[03:09:15] [worker #0] ML tree search #1, logLikelihood: -247019.083600

[03:09:15 -640676.388253] Initial branch length optimization
[03:09:22 -555995.421423] Model parameter optimization (eps = 10.000000)
[03:10:15 -554634.857298] AUTODETECT spr round 1 (radius: 5)
[03:14:00 -446101.367028] AUTODETECT spr round 2 (radius: 10)
[03:18:21 -328689.165802] AUTODETECT spr round 3 (radius: 15)
[03:23:05 -287205.143413] AUTODETECT spr round 4 (radius: 20)
[03:28:27 -272064.386216] AUTODETECT spr round 5 (radius: 25)
[03:29:17] [worker #1] ML tree search #2, logLikelihood: -246991.029843
[03:34:59 -268193.983101] SPR radius for FAST iterations: 25 (autodetect)
[03:34:59 -268193.983101] Model parameter optimization (eps = 3.000000)
[03:35:33 -268042.077060] FAST spr round 1 (radius: 25)
[03:42:29 -248463.884892] FAST spr round 2 (radius: 25)
[03:47:47 -247344.283143] FAST spr round 3 (radius: 25)
[03:51:53 -247270.128235] FAST spr round 4 (radius: 25)
[03:55:30 -247252.174161] FAST spr round 5 (radius: 25)
[03:58:49 -247244.279245] FAST spr round 6 (radius: 25)
[04:01:45 -247244.278867] Model parameter optimization (eps = 1.000000)
[04:02:09 -247240.789590] SLOW spr round 1 (radius: 5)
[04:06:08 -247128.675141] SLOW spr round 2 (radius: 5)
[04:10:05 -247091.327208] SLOW spr round 3 (radius: 5)
[04:13:54 -247087.241450] SLOW spr round 4 (radius: 5)
[04:17:34 -247087.230160] SLOW spr round 5 (radius: 10)
[04:21:43 -247079.114968] SLOW spr round 6 (radius: 5)
[04:26:19 -247054.850941] SLOW spr round 7 (radius: 5)
[04:30:30 -247050.933011] SLOW spr round 8 (radius: 5)
[04:34:29 -247048.573855] SLOW spr round 9 (radius: 5)
[04:38:14 -247048.572451] SLOW spr round 10 (radius: 10)
[04:42:18 -247048.562967] SLOW spr round 11 (radius: 15)
[04:50:29 -247045.250341] SLOW spr round 12 (radius: 5)
[04:55:06 -247042.687258] SLOW spr round 13 (radius: 5)
[04:59:15 -247042.681082] SLOW spr round 14 (radius: 10)
[05:03:36 -247042.679873] SLOW spr round 15 (radius: 15)
[05:06:35] [worker #2] ML tree search #6, logLikelihood: -246978.944937
[05:11:34 -247042.679445] SLOW spr round 16 (radius: 20)
[05:24:55 -247042.679268] SLOW spr round 17 (radius: 25)
[05:40:46 -247036.222309] SLOW spr round 18 (radius: 5)
[05:45:27 -247036.073282] SLOW spr round 19 (radius: 5)
[05:49:37 -247036.071675] SLOW spr round 20 (radius: 10)
[05:54:03 -247036.071598] SLOW spr round 21 (radius: 15)
[06:02:00 -247036.071592] SLOW spr round 22 (radius: 20)
[06:15:25 -247036.071591] SLOW spr round 23 (radius: 25)
[06:31:16 -247036.071590] Model parameter optimization (eps = 0.100000)

[06:31:40] [worker #0] ML tree search #4, logLikelihood: -247033.128670

[06:31:40 -641558.298705] Initial branch length optimization
[06:31:47 -556393.702141] Model parameter optimization (eps = 10.000000)
[06:32:52 -555076.073705] AUTODETECT spr round 1 (radius: 5)
[06:36:00] [worker #1] ML tree search #5, logLikelihood: -246986.910004
[06:36:36 -434402.449416] AUTODETECT spr round 2 (radius: 10)
[06:40:55 -323905.585650] AUTODETECT spr round 3 (radius: 15)
[06:45:34 -284765.816086] AUTODETECT spr round 4 (radius: 20)
[06:51:37 -270178.139535] AUTODETECT spr round 5 (radius: 25)
[06:58:36 -265985.087910] SPR radius for FAST iterations: 25 (autodetect)
[06:58:36 -265985.087910] Model parameter optimization (eps = 3.000000)
[06:59:10 -265854.289580] FAST spr round 1 (radius: 25)
[07:06:05 -248194.572448] FAST spr round 2 (radius: 25)
[07:10:54 -247340.762932] FAST spr round 3 (radius: 25)
[07:14:59 -247255.329083] FAST spr round 4 (radius: 25)
[07:18:35 -247228.299812] FAST spr round 5 (radius: 25)
[07:21:46 -247226.558074] FAST spr round 6 (radius: 25)
[07:24:46 -247226.557224] Model parameter optimization (eps = 1.000000)
[07:25:18 -247221.116763] SLOW spr round 1 (radius: 5)
[07:29:15 -247155.945873] SLOW spr round 2 (radius: 5)
[07:33:13 -247144.805965] SLOW spr round 3 (radius: 5)
[07:37:00 -247143.536259] SLOW spr round 4 (radius: 5)
[07:40:47 -247143.392605] SLOW spr round 5 (radius: 5)
[07:44:32 -247143.392358] SLOW spr round 6 (radius: 10)
[07:48:39 -247139.327373] SLOW spr round 7 (radius: 5)
[07:53:03 -247136.156390] SLOW spr round 8 (radius: 5)
[07:57:05 -247136.151906] SLOW spr round 9 (radius: 10)
[08:01:21 -247136.151830] SLOW spr round 10 (radius: 15)
[08:09:04 -247134.218668] SLOW spr round 11 (radius: 5)
[08:13:40 -247129.603186] SLOW spr round 12 (radius: 5)
[08:17:45 -247129.602766] SLOW spr round 13 (radius: 10)
[08:22:04 -247129.602756] SLOW spr round 14 (radius: 15)
[08:29:44 -247129.602753] SLOW spr round 15 (radius: 20)
[08:41:07 -247129.602751] SLOW spr round 16 (radius: 25)
[08:44:34] [worker #2] ML tree search #9, logLikelihood: -247007.040231
[08:54:21 -247129.602748] Model parameter optimization (eps = 0.100000)

[08:54:29] [worker #0] ML tree search #7, logLikelihood: -247129.586384

[08:54:29 -642650.813379] Initial branch length optimization
[08:54:37 -557010.984017] Model parameter optimization (eps = 10.000000)
[08:55:21] [worker #1] ML tree search #8, logLikelihood: -247044.720204
[08:55:42 -555650.737220] AUTODETECT spr round 1 (radius: 5)
[08:59:31 -436889.632297] AUTODETECT spr round 2 (radius: 10)
[09:03:54 -334199.783863] AUTODETECT spr round 3 (radius: 15)
[09:08:40 -289845.159973] AUTODETECT spr round 4 (radius: 20)
[09:14:14 -271802.530910] AUTODETECT spr round 5 (radius: 25)
[09:20:15 -266491.424311] SPR radius for FAST iterations: 25 (autodetect)
[09:20:15 -266491.424311] Model parameter optimization (eps = 3.000000)
[09:20:52 -266385.849160] FAST spr round 1 (radius: 25)
[09:28:14 -248325.722017] FAST spr round 2 (radius: 25)
[09:33:25 -247529.568659] FAST spr round 3 (radius: 25)
[09:37:35 -247444.616583] FAST spr round 4 (radius: 25)
[09:41:11 -247424.374022] FAST spr round 5 (radius: 25)
[09:44:17 -247423.361828] FAST spr round 6 (radius: 25)
[09:47:14 -247423.361019] Model parameter optimization (eps = 1.000000)
[09:47:35 -247419.196723] SLOW spr round 1 (radius: 5)
[09:51:47 -247341.081847] SLOW spr round 2 (radius: 5)
[09:55:45 -247325.719818] SLOW spr round 3 (radius: 5)
[09:59:36 -247324.525302] SLOW spr round 4 (radius: 5)
[10:03:20 -247324.523186] SLOW spr round 5 (radius: 10)
[10:07:27 -247320.914788] SLOW spr round 6 (radius: 5)
[10:11:55 -247317.735494] SLOW spr round 7 (radius: 5)
[10:16:02 -247317.730586] SLOW spr round 8 (radius: 10)
[10:20:16 -247317.730319] SLOW spr round 9 (radius: 15)
[10:27:46 -247317.455507] SLOW spr round 10 (radius: 5)
[10:32:21 -247317.455446] SLOW spr round 11 (radius: 10)
[10:37:10 -247317.453899] SLOW spr round 12 (radius: 15)
[10:44:22 -247317.437141] SLOW spr round 13 (radius: 20)
[10:56:22 -247316.942545] SLOW spr round 14 (radius: 5)
[11:01:02 -247316.942204] SLOW spr round 15 (radius: 10)
[11:05:58 -247316.942163] SLOW spr round 16 (radius: 15)
[11:13:15 -247316.942140] SLOW spr round 17 (radius: 20)
[11:25:26 -247316.942128] SLOW spr round 18 (radius: 25)
[11:39:50 -247271.898157] SLOW spr round 19 (radius: 5)
[11:44:34 -247269.490619] SLOW spr round 20 (radius: 5)
[11:48:53 -247266.266269] SLOW spr round 21 (radius: 5)
[11:52:52 -247266.264673] SLOW spr round 22 (radius: 10)
[11:57:01 -247266.264608] SLOW spr round 23 (radius: 15)
[12:04:37 -247266.264594] SLOW spr round 24 (radius: 20)
[12:16:38 -247266.264587] SLOW spr round 25 (radius: 25)
[12:31:08 -247264.595645] SLOW spr round 26 (radius: 5)
[12:33:37] [worker #2] ML tree search #12, logLikelihood: -246994.359326
[12:35:58 -247257.966660] SLOW spr round 27 (radius: 5)
[12:40:21 -247251.986714] SLOW spr round 28 (radius: 5)
[12:44:27 -247247.762984] SLOW spr round 29 (radius: 5)
[12:48:22 -247244.231848] SLOW spr round 30 (radius: 5)
[12:52:08 -247244.230808] SLOW spr round 31 (radius: 10)
[12:56:10 -247242.874147] SLOW spr round 32 (radius: 5)
[13:00:40 -247242.392596] SLOW spr round 33 (radius: 5)
[13:04:45 -247242.391493] SLOW spr round 34 (radius: 10)
[13:08:57 -247242.391410] SLOW spr round 35 (radius: 15)
[13:16:43 -247224.644609] SLOW spr round 36 (radius: 5)
[13:21:22 -247221.040067] SLOW spr round 37 (radius: 5)
[13:25:32 -247221.039019] SLOW spr round 38 (radius: 10)
[13:29:48 -247221.038871] SLOW spr round 39 (radius: 15)
[13:37:29 -247217.691687] SLOW spr round 40 (radius: 5)
[13:42:03 -247216.135080] SLOW spr round 41 (radius: 5)
[13:46:09 -247216.133540] SLOW spr round 42 (radius: 10)
[13:50:23 -247216.133199] SLOW spr round 43 (radius: 15)
[13:57:56 -247216.133138] SLOW spr round 44 (radius: 20)
[14:10:59 -247202.781225] SLOW spr round 45 (radius: 5)
[14:15:59 -247013.996185] SLOW spr round 46 (radius: 5)
[14:20:16 -247011.227840] SLOW spr round 47 (radius: 5)
[14:24:18 -247007.157640] SLOW spr round 48 (radius: 5)
[14:28:15 -247006.567860] SLOW spr round 49 (radius: 5)
[14:32:04 -247006.567581] SLOW spr round 50 (radius: 10)
[14:36:06 -247006.567576] SLOW spr round 51 (radius: 15)
[14:37:33] [worker #1] ML tree search #11, logLikelihood: -247027.323063
[14:43:56 -247006.567576] SLOW spr round 52 (radius: 20)
[14:56:53 -247006.567576] SLOW spr round 53 (radius: 25)
[15:13:08 -247006.567576] Model parameter optimization (eps = 0.100000)

[15:13:21] [worker #0] ML tree search #10, logLikelihood: -247006.249165

[15:13:21 -639001.390822] Initial branch length optimization
[15:13:28 -555146.136073] Model parameter optimization (eps = 10.000000)
[15:14:33 -553819.129986] AUTODETECT spr round 1 (radius: 5)
[15:18:22 -438428.758478] AUTODETECT spr round 2 (radius: 10)
[15:22:36 -337309.614410] AUTODETECT spr round 3 (radius: 15)
[15:27:21 -291947.828929] AUTODETECT spr round 4 (radius: 20)
[15:33:07 -274000.673821] AUTODETECT spr round 5 (radius: 25)
[15:40:05 -269455.669149] SPR radius for FAST iterations: 25 (autodetect)
[15:40:05 -269455.669149] Model parameter optimization (eps = 3.000000)
[15:40:43 -269342.873116] FAST spr round 1 (radius: 25)
[15:48:39 -248243.852203] FAST spr round 2 (radius: 25)
[15:54:05 -247312.196426] FAST spr round 3 (radius: 25)
[15:58:28 -247218.226020] FAST spr round 4 (radius: 25)
[16:02:01 -247206.125411] FAST spr round 5 (radius: 25)
[16:05:10 -247204.969804] FAST spr round 6 (radius: 25)
[16:08:08 -247204.969484] Model parameter optimization (eps = 1.000000)
[16:08:29 -247198.325374] SLOW spr round 1 (radius: 5)
[16:12:36 -247122.923394] SLOW spr round 2 (radius: 5)
[16:16:33 -247104.745251] SLOW spr round 3 (radius: 5)
[16:17:32] [worker #2] ML tree search #15, logLikelihood: -247013.117227
[16:20:40 -247091.571614] SLOW spr round 4 (radius: 5)
[16:24:38 -247083.066903] SLOW spr round 5 (radius: 5)
[16:28:26 -247082.038714] SLOW spr round 6 (radius: 5)
[16:32:11 -247082.038656] SLOW spr round 7 (radius: 10)
[16:36:24 -247075.605452] SLOW spr round 8 (radius: 5)
[16:41:03 -247054.339202] SLOW spr round 9 (radius: 5)
[16:45:14 -247049.430291] SLOW spr round 10 (radius: 5)
[16:46:16] [worker #1] ML tree search #14, logLikelihood: -247023.900616
[16:49:10 -247049.097742] SLOW spr round 11 (radius: 5)
[16:53:00 -247049.097709] SLOW spr round 12 (radius: 10)
[16:57:08 -247049.097708] SLOW spr round 13 (radius: 15)
[17:05:14 -247045.351670] SLOW spr round 14 (radius: 5)
[17:09:55 -247041.041719] SLOW spr round 15 (radius: 5)
[17:14:09 -247040.645782] SLOW spr round 16 (radius: 5)
[17:18:07 -247040.642014] SLOW spr round 17 (radius: 10)
[17:22:21 -247039.425577] SLOW spr round 18 (radius: 5)
[17:26:45 -247039.423823] SLOW spr round 19 (radius: 10)
[17:31:21 -247039.423596] SLOW spr round 20 (radius: 15)
[17:39:01 -247039.407246] SLOW spr round 21 (radius: 20)
[17:51:41 -247039.333387] SLOW spr round 22 (radius: 25)
[18:06:49 -247039.332873] Model parameter optimization (eps = 0.100000)

[18:06:57] [worker #0] ML tree search #13, logLikelihood: -247039.319675

[18:06:58 -639368.176079] Initial branch length optimization
[18:07:05 -555679.515690] Model parameter optimization (eps = 10.000000)
[18:08:03 -554321.731517] AUTODETECT spr round 1 (radius: 5)
[18:11:50 -439391.219591] AUTODETECT spr round 2 (radius: 10)
[18:16:13 -321562.741303] AUTODETECT spr round 3 (radius: 15)
[18:20:51 -283656.400871] AUTODETECT spr round 4 (radius: 20)
[18:25:52 -275739.895905] AUTODETECT spr round 5 (radius: 25)
[18:31:58 -273666.883884] SPR radius for FAST iterations: 25 (autodetect)
[18:31:58 -273666.883884] Model parameter optimization (eps = 3.000000)
[18:32:26 -273565.979135] FAST spr round 1 (radius: 25)
[18:39:37 -253692.640013] FAST spr round 2 (radius: 25)
[18:45:13 -247691.180517] FAST spr round 3 (radius: 25)
[18:49:36 -247193.686807] FAST spr round 4 (radius: 25)
[18:53:17 -247148.545013] FAST spr round 5 (radius: 25)
[18:56:33 -247142.199028] FAST spr round 6 (radius: 25)
[18:59:32 -247142.198854] Model parameter optimization (eps = 1.000000)
[18:59:58 -247134.615097] SLOW spr round 1 (radius: 5)
[19:03:59 -247056.475152] SLOW spr round 2 (radius: 5)
[19:07:55 -247052.516044] SLOW spr round 3 (radius: 5)
[19:11:41 -247052.513557] SLOW spr round 4 (radius: 10)
[19:15:47 -247050.389667] SLOW spr round 5 (radius: 5)
[19:20:16 -247050.388439] SLOW spr round 6 (radius: 10)
[19:24:52 -247050.388328] SLOW spr round 7 (radius: 15)
[19:31:57] [worker #2] ML tree search #18, logLikelihood: -247070.997149
[19:32:27 -247049.440261] SLOW spr round 8 (radius: 5)
[19:37:02 -247047.818993] SLOW spr round 9 (radius: 5)
[19:41:10 -247047.268988] SLOW spr round 10 (radius: 5)
[19:45:04 -247047.268826] SLOW spr round 11 (radius: 10)
[19:49:14 -247047.268794] SLOW spr round 12 (radius: 15)
[19:57:15 -247044.137456] SLOW spr round 13 (radius: 5)
[20:01:59 -247029.750276] SLOW spr round 14 (radius: 5)
[20:06:09 -247028.296818] SLOW spr round 15 (radius: 5)
[20:09:03] [worker #1] ML tree search #17, logLikelihood: -247043.414965
[20:10:03 -247028.296691] SLOW spr round 16 (radius: 10)
[20:14:13 -247026.432901] SLOW spr round 17 (radius: 5)
[20:18:38 -247026.123054] SLOW spr round 18 (radius: 5)
[20:22:39 -247026.123029] SLOW spr round 19 (radius: 10)
[20:26:54 -247026.123025] SLOW spr round 20 (radius: 15)
[20:34:48 -247022.628547] SLOW spr round 21 (radius: 5)
[20:39:18 -247022.627610] SLOW spr round 22 (radius: 10)
[20:44:07 -247022.627495] SLOW spr round 23 (radius: 15)
[20:51:41 -247022.627476] SLOW spr round 24 (radius: 20)
[21:04:05 -247021.991091] SLOW spr round 25 (radius: 5)
[21:08:45 -247021.987427] SLOW spr round 26 (radius: 10)
[21:13:45 -247018.529905] SLOW spr round 27 (radius: 5)
[21:18:12 -247015.659800] SLOW spr round 28 (radius: 5)
[21:22:17 -247014.493964] SLOW spr round 29 (radius: 5)
[21:26:08 -247014.493962] SLOW spr round 30 (radius: 10)
[21:30:15 -247014.493962] SLOW spr round 31 (radius: 15)
[21:38:14 -247014.493962] SLOW spr round 32 (radius: 20)
[21:50:15 -247014.493962] SLOW spr round 33 (radius: 25)
[22:04:49 -247014.493962] Model parameter optimization (eps = 0.100000)

[22:05:08] [worker #0] ML tree search #16, logLikelihood: -247014.315695

[22:05:08 -640228.167286] Initial branch length optimization
[22:05:15 -555849.624960] Model parameter optimization (eps = 10.000000)
[22:06:12 -554435.277746] AUTODETECT spr round 1 (radius: 5)
[22:09:56 -437753.715381] AUTODETECT spr round 2 (radius: 10)
[22:14:10 -331643.775548] AUTODETECT spr round 3 (radius: 15)
[22:19:07 -277604.687328] AUTODETECT spr round 4 (radius: 20)
[22:24:09 -266722.514321] AUTODETECT spr round 5 (radius: 25)
[22:30:39 -264222.420624] SPR radius for FAST iterations: 25 (autodetect)
[22:30:39 -264222.420624] Model parameter optimization (eps = 3.000000)
[22:31:12 -264102.271382] FAST spr round 1 (radius: 25)
[22:37:56 -248591.291769] FAST spr round 2 (radius: 25)
[22:43:08 -247468.587808] FAST spr round 3 (radius: 25)
[22:47:23 -247226.671510] FAST spr round 4 (radius: 25)
[22:50:57 -247211.779434] FAST spr round 5 (radius: 25)
[22:54:07 -247210.220181] FAST spr round 6 (radius: 25)
[22:57:06 -247199.991335] FAST spr round 7 (radius: 25)
[23:00:01 -247187.262943] FAST spr round 8 (radius: 25)
[23:02:52 -247185.853987] FAST spr round 9 (radius: 25)
[23:05:39 -247185.853612] Model parameter optimization (eps = 1.000000)
[23:06:04 -247180.048161] SLOW spr round 1 (radius: 5)
[23:09:59 -247110.582753] SLOW spr round 2 (radius: 5)
[23:13:50 -247106.470993] SLOW spr round 3 (radius: 5)
[23:17:36 -247106.149478] SLOW spr round 4 (radius: 5)
[23:21:20 -247106.148707] SLOW spr round 5 (radius: 10)
[23:25:37 -247095.770488] SLOW spr round 6 (radius: 5)
[23:30:11 -247084.424678] SLOW spr round 7 (radius: 5)
[23:34:14 -247084.372193] SLOW spr round 8 (radius: 10)
[23:38:32 -247084.372179] SLOW spr round 9 (radius: 15)
[23:41:31] [worker #1] ML tree search #20, logLikelihood: -246980.295273
[23:46:41 -247080.803095] SLOW spr round 10 (radius: 5)
[23:51:15 -247080.733585] SLOW spr round 11 (radius: 10)
[23:56:08 -247080.733269] SLOW spr round 12 (radius: 15)
[24:03:58 -247080.733209] SLOW spr round 13 (radius: 20)
[24:17:23 -247076.009006] SLOW spr round 14 (radius: 5)
[24:22:08 -247071.625343] SLOW spr round 15 (radius: 5)
[24:26:20 -247069.703344] SLOW spr round 16 (radius: 5)
[24:30:15 -247069.702887] SLOW spr round 17 (radius: 10)
[24:34:26 -247069.702876] SLOW spr round 18 (radius: 15)
[24:42:47 -247069.702854] SLOW spr round 19 (radius: 20)
[24:56:17 -247069.702814] SLOW spr round 20 (radius: 25)
[25:12:16 -247069.702813] Model parameter optimization (eps = 0.100000)

[25:12:25] [worker #0] ML tree search #19, logLikelihood: -247069.654684


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.122806,0.239897) (0.059161,0.486009) (0.431816,0.802693) (0.386217,1.541027) 
   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: -246978.944937

AIC score: 497967.889875 / AICc score: 8542027.889875 / BIC score: 506461.810903
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=511).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 2 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9NQX0/3_mltree/Q9NQX0.raxml.log

Analysis started: 18-Jul-2021 12:29:57 / finished: 19-Jul-2021 13:42:22

Elapsed time: 90745.563 seconds