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 24-Jul-2021 21:02:38 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/2_msa/Q96SR6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/3_mltree/Q96SR6 --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/Q96SR6/2_msa/Q96SR6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 660 sites

WARNING: Sequences tr_A0A2I3G9N3_A0A2I3G9N3_NOMLE_61853 and tr_H2PRJ2_H2PRJ2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3S0E0_A0A2I3S0E0_PANTR_9598 and tr_A0A2R8ZDT2_A0A2R8ZDT2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SSM4_A0A2I3SSM4_PANTR_9598 and tr_A0A2R9B6G9_A0A2R9B6G9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8QIB0_A0A2J8QIB0_PANTR_9598 and sp_Q5MCW4_ZN569_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2PYV9_H2PYV9_PANTR_9598 and sp_P17025_ZN182_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_P17014_ZNF12_HUMAN_9606 and tr_A0A2R9A3E5_A0A2R9A3E5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QTH3_A0A1D5QTH3_MACMU_9544 and tr_A0A096NF04_A0A096NF04_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QTH3_A0A1D5QTH3_MACMU_9544 and tr_A0A2K5XWI3_A0A2K5XWI3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5RD30_A0A1D5RD30_MACMU_9544 and tr_A0A2K6C701_A0A2K6C701_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_G7PJI5_G7PJI5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_A0A2I3LQN8_A0A2I3LQN8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6RKW8_F6RKW8_MACMU_9544 and tr_A0A2K6AK43_A0A2K6AK43_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K5N4G8_A0A2K5N4G8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6UPX1_F6UPX1_MACMU_9544 and tr_A0A2K6D4D0_A0A2K6D4D0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6WQ38_F6WQ38_MACMU_9544 and tr_G7PRN1_G7PRN1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FTJ3_F7FTJ3_MACMU_9544 and tr_A0A2K6CFR0_A0A2K6CFR0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GF85_F7GF85_MACMU_9544 and tr_G7PXD2_G7PXD2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H9ZBV2_H9ZBV2_MACMU_9544 and tr_A0A0D9R761_A0A0D9R761_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H9ZBV2_H9ZBV2_MACMU_9544 and tr_A0A2K6DF77_A0A2K6DF77_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096N2R2_A0A096N2R2_PAPAN_9555 and tr_A0A2K5MKS5_A0A2K5MKS5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096N2R2_A0A096N2R2_PAPAN_9555 and tr_A0A2K5YQS2_A0A2K5YQS2_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 22

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/Q96SR6/3_mltree/Q96SR6.raxml.reduced.phy

Alignment comprises 1 partitions and 660 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 660 / 660
Gaps: 13.05 %
Invariant sites: 0.91 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/3_mltree/Q96SR6.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 / 165 / 13200
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -933361.911168] Initial branch length optimization
[00:00:05 -829985.812576] Model parameter optimization (eps = 10.000000)
[00:00:44 -827482.835251] AUTODETECT spr round 1 (radius: 5)
[00:03:47 -610145.890718] AUTODETECT spr round 2 (radius: 10)
[00:07:03 -379022.266603] AUTODETECT spr round 3 (radius: 15)
[00:10:17 -296600.999409] AUTODETECT spr round 4 (radius: 20)
[00:14:49 -272751.056662] AUTODETECT spr round 5 (radius: 25)
[00:20:52 -270277.598471] SPR radius for FAST iterations: 25 (autodetect)
[00:20:52 -270277.598471] Model parameter optimization (eps = 3.000000)
[00:21:15 -270213.574926] FAST spr round 1 (radius: 25)
[00:24:14 -240038.687450] FAST spr round 2 (radius: 25)
[00:26:44 -238549.392441] FAST spr round 3 (radius: 25)
[00:29:00 -238425.373782] FAST spr round 4 (radius: 25)
[00:31:09 -238398.655207] FAST spr round 5 (radius: 25)
[00:33:07 -238397.990486] FAST spr round 6 (radius: 25)
[00:35:00 -238397.990440] Model parameter optimization (eps = 1.000000)
[00:35:13 -238392.661486] SLOW spr round 1 (radius: 5)
[00:37:58 -238302.121413] SLOW spr round 2 (radius: 5)
[00:40:37 -238299.266126] SLOW spr round 3 (radius: 5)
[00:43:12 -238296.062452] SLOW spr round 4 (radius: 5)
[00:45:44 -238296.062427] SLOW spr round 5 (radius: 10)
[00:48:18 -238296.062427] SLOW spr round 6 (radius: 15)
[00:53:35 -238296.062427] SLOW spr round 7 (radius: 20)
[01:03:07 -238296.062427] SLOW spr round 8 (radius: 25)
[01:11:49] [worker #1] ML tree search #2, logLikelihood: -238294.501913
[01:15:05 -238296.062427] Model parameter optimization (eps = 0.100000)

[01:15:16] [worker #0] ML tree search #1, logLikelihood: -238295.819544

[01:15:16 -936687.831402] Initial branch length optimization
[01:15:21 -831319.333514] Model parameter optimization (eps = 10.000000)
[01:16:00 -828825.529424] AUTODETECT spr round 1 (radius: 5)
[01:19:06 -600992.379974] AUTODETECT spr round 2 (radius: 10)
[01:22:16 -382784.378029] AUTODETECT spr round 3 (radius: 15)
[01:25:37 -295121.953952] AUTODETECT spr round 4 (radius: 20)
[01:29:46 -276223.435934] AUTODETECT spr round 5 (radius: 25)
[01:35:03 -273680.059026] SPR radius for FAST iterations: 25 (autodetect)
[01:35:03 -273680.059026] Model parameter optimization (eps = 3.000000)
[01:35:22 -273625.161249] FAST spr round 1 (radius: 25)
[01:38:33 -240406.592899] FAST spr round 2 (radius: 25)
[01:41:08 -238543.054838] FAST spr round 3 (radius: 25)
[01:43:31 -238387.654753] FAST spr round 4 (radius: 25)
[01:45:36 -238367.688967] FAST spr round 5 (radius: 25)
[01:47:34 -238357.281887] FAST spr round 6 (radius: 25)
[01:49:32 -238348.673309] FAST spr round 7 (radius: 25)
[01:51:25 -238348.673283] Model parameter optimization (eps = 1.000000)
[01:51:38 -238346.282061] SLOW spr round 1 (radius: 5)
[01:54:20 -238258.673442] SLOW spr round 2 (radius: 5)
[01:57:01 -238254.342942] SLOW spr round 3 (radius: 5)
[01:59:35 -238254.342930] SLOW spr round 4 (radius: 10)
[02:02:13 -238247.552708] SLOW spr round 5 (radius: 5)
[02:05:16 -238243.526441] SLOW spr round 6 (radius: 5)
[02:08:00 -238243.335878] SLOW spr round 7 (radius: 5)
[02:10:35 -238243.335820] SLOW spr round 8 (radius: 10)
[02:13:11 -238243.335820] SLOW spr round 9 (radius: 15)
[02:18:29 -238243.335820] SLOW spr round 10 (radius: 20)
[02:27:15] [worker #1] ML tree search #4, logLikelihood: -238277.424632
[02:28:24 -238243.335820] SLOW spr round 11 (radius: 25)
[02:40:30 -238243.335820] Model parameter optimization (eps = 0.100000)

[02:40:38] [worker #0] ML tree search #3, logLikelihood: -238243.287233

[02:40:38 -935982.775026] Initial branch length optimization
[02:40:42 -832701.011972] Model parameter optimization (eps = 10.000000)
[02:41:21 -830254.340340] AUTODETECT spr round 1 (radius: 5)
[02:44:28 -609561.181037] AUTODETECT spr round 2 (radius: 10)
[02:47:49 -366147.990944] AUTODETECT spr round 3 (radius: 15)
[02:51:14 -284584.662158] AUTODETECT spr round 4 (radius: 20)
[02:55:36 -271182.751531] AUTODETECT spr round 5 (radius: 25)
[03:01:46 -269866.467318] SPR radius for FAST iterations: 25 (autodetect)
[03:01:46 -269866.467318] Model parameter optimization (eps = 3.000000)
[03:02:05 -269794.283702] FAST spr round 1 (radius: 25)
[03:05:07 -239714.633238] FAST spr round 2 (radius: 25)
[03:07:37 -238429.586684] FAST spr round 3 (radius: 25)
[03:09:52 -238375.046051] FAST spr round 4 (radius: 25)
[03:11:54 -238370.519133] FAST spr round 5 (radius: 25)
[03:13:50 -238370.519122] Model parameter optimization (eps = 1.000000)
[03:14:06 -238363.315302] SLOW spr round 1 (radius: 5)
[03:16:57 -238305.765956] SLOW spr round 2 (radius: 5)
[03:19:34 -238300.654171] SLOW spr round 3 (radius: 5)
[03:22:09 -238300.654099] SLOW spr round 4 (radius: 10)
[03:24:48 -238293.258838] SLOW spr round 5 (radius: 5)
[03:27:53 -238289.271460] SLOW spr round 6 (radius: 5)
[03:30:39 -238287.372369] SLOW spr round 7 (radius: 5)
[03:33:17 -238287.372295] SLOW spr round 8 (radius: 10)
[03:35:55 -238285.897026] SLOW spr round 9 (radius: 5)
[03:38:59 -238274.965695] SLOW spr round 10 (radius: 5)
[03:41:42 -238273.098655] SLOW spr round 11 (radius: 5)
[03:44:18 -238269.118313] SLOW spr round 12 (radius: 5)
[03:46:50 -238267.588221] SLOW spr round 13 (radius: 5)
[03:49:22 -238267.588167] SLOW spr round 14 (radius: 10)
[03:51:58 -238258.049979] SLOW spr round 15 (radius: 5)
[03:54:57 -238257.992938] SLOW spr round 16 (radius: 10)
[03:57:46] [worker #1] ML tree search #6, logLikelihood: -238298.804865
[03:57:49 -238257.992918] SLOW spr round 17 (radius: 15)
[04:02:38 -238257.992918] SLOW spr round 18 (radius: 20)
[04:11:51 -238257.992918] SLOW spr round 19 (radius: 25)
[04:23:41 -238257.992918] Model parameter optimization (eps = 0.100000)

[04:23:51] [worker #0] ML tree search #5, logLikelihood: -238257.720401

[04:23:51 -931275.408097] Initial branch length optimization
[04:23:56 -828376.183877] Model parameter optimization (eps = 10.000000)
[04:24:41 -825915.385988] AUTODETECT spr round 1 (radius: 5)
[04:27:48 -596481.800122] AUTODETECT spr round 2 (radius: 10)
[04:31:05 -376490.574402] AUTODETECT spr round 3 (radius: 15)
[04:34:20 -288817.225551] AUTODETECT spr round 4 (radius: 20)
[04:38:40 -271590.320141] AUTODETECT spr round 5 (radius: 25)
[04:44:48 -269612.476448] SPR radius for FAST iterations: 25 (autodetect)
[04:44:48 -269612.476448] Model parameter optimization (eps = 3.000000)
[04:45:12 -269542.605286] FAST spr round 1 (radius: 25)
[04:48:18 -239555.610778] FAST spr round 2 (radius: 25)
[04:50:45 -238515.405023] FAST spr round 3 (radius: 25)
[04:53:02 -238395.098454] FAST spr round 4 (radius: 25)
[04:55:03 -238384.565838] FAST spr round 5 (radius: 25)
[04:56:59 -238382.568341] FAST spr round 6 (radius: 25)
[04:58:52 -238382.568327] Model parameter optimization (eps = 1.000000)
[04:59:07 -238371.058772] SLOW spr round 1 (radius: 5)
[05:01:52 -238297.645938] SLOW spr round 2 (radius: 5)
[05:04:30 -238294.682640] SLOW spr round 3 (radius: 5)
[05:07:05 -238293.679610] SLOW spr round 4 (radius: 5)
[05:09:45 -238292.008367] SLOW spr round 5 (radius: 5)
[05:12:25 -238274.476474] SLOW spr round 6 (radius: 5)
[05:14:57 -238274.476460] SLOW spr round 7 (radius: 10)
[05:17:33 -238274.476460] SLOW spr round 8 (radius: 15)
[05:22:47 -238274.476460] SLOW spr round 9 (radius: 20)
[05:32:34 -238274.476460] SLOW spr round 10 (radius: 25)
[05:39:09] [worker #1] ML tree search #8, logLikelihood: -238269.331090
[05:45:10 -238274.476460] Model parameter optimization (eps = 0.100000)

[05:45:21] [worker #0] ML tree search #7, logLikelihood: -238274.355248

[05:45:21 -933797.351236] Initial branch length optimization
[05:45:25 -831238.557618] Model parameter optimization (eps = 10.000000)
[05:46:09 -828719.422422] AUTODETECT spr round 1 (radius: 5)
[05:49:16 -610904.253719] AUTODETECT spr round 2 (radius: 10)
[05:52:43 -376548.266169] AUTODETECT spr round 3 (radius: 15)
[05:55:58 -290429.993005] AUTODETECT spr round 4 (radius: 20)
[05:59:59 -271588.823032] AUTODETECT spr round 5 (radius: 25)
[06:05:36 -268961.678939] SPR radius for FAST iterations: 25 (autodetect)
[06:05:36 -268961.678939] Model parameter optimization (eps = 3.000000)
[06:05:58 -268893.375502] FAST spr round 1 (radius: 25)
[06:09:04 -239604.336800] FAST spr round 2 (radius: 25)
[06:11:34 -238551.909324] FAST spr round 3 (radius: 25)
[06:13:50 -238448.704930] FAST spr round 4 (radius: 25)
[06:15:58 -238399.848924] FAST spr round 5 (radius: 25)
[06:17:59 -238379.657962] FAST spr round 6 (radius: 25)
[06:19:54 -238378.294438] FAST spr round 7 (radius: 25)
[06:21:48 -238378.294395] Model parameter optimization (eps = 1.000000)
[06:22:02 -238367.735069] SLOW spr round 1 (radius: 5)
[06:24:46 -238305.662348] SLOW spr round 2 (radius: 5)
[06:27:25 -238304.374615] SLOW spr round 3 (radius: 5)
[06:29:58 -238304.374553] SLOW spr round 4 (radius: 10)
[06:32:34 -238304.374552] SLOW spr round 5 (radius: 15)
[06:37:59 -238304.374552] SLOW spr round 6 (radius: 20)
[06:47:52 -238304.374552] SLOW spr round 7 (radius: 25)
[06:52:10] [worker #1] ML tree search #10, logLikelihood: -238249.854069
[07:00:05 -238304.374552] Model parameter optimization (eps = 0.100000)

[07:00:11] [worker #0] ML tree search #9, logLikelihood: -238304.352539

[07:00:11 -933079.892600] Initial branch length optimization
[07:00:16 -828905.564158] Model parameter optimization (eps = 10.000000)
[07:00:55 -826555.348868] AUTODETECT spr round 1 (radius: 5)
[07:03:59 -591798.214739] AUTODETECT spr round 2 (radius: 10)
[07:07:17 -379272.919507] AUTODETECT spr round 3 (radius: 15)
[07:10:29 -302287.827639] AUTODETECT spr round 4 (radius: 20)
[07:14:26 -275603.234222] AUTODETECT spr round 5 (radius: 25)
[07:20:03 -271629.348693] SPR radius for FAST iterations: 25 (autodetect)
[07:20:03 -271629.348693] Model parameter optimization (eps = 3.000000)
[07:20:24 -271550.640687] FAST spr round 1 (radius: 25)
[07:23:31 -240124.625799] FAST spr round 2 (radius: 25)
[07:25:58 -238485.400744] FAST spr round 3 (radius: 25)
[07:28:17 -238372.657858] FAST spr round 4 (radius: 25)
[07:30:21 -238361.569913] FAST spr round 5 (radius: 25)
[07:32:18 -238359.878472] FAST spr round 6 (radius: 25)
[07:34:12 -238359.878215] Model parameter optimization (eps = 1.000000)
[07:34:27 -238351.713073] SLOW spr round 1 (radius: 5)
[07:37:14 -238283.035910] SLOW spr round 2 (radius: 5)
[07:39:51 -238281.311547] SLOW spr round 3 (radius: 5)
[07:42:26 -238280.965619] SLOW spr round 4 (radius: 5)
[07:44:59 -238280.965617] SLOW spr round 5 (radius: 10)
[07:47:36 -238273.481489] SLOW spr round 6 (radius: 5)
[07:50:42 -238262.032630] SLOW spr round 7 (radius: 5)
[07:53:29 -238260.508345] SLOW spr round 8 (radius: 5)
[07:56:07 -238260.508051] SLOW spr round 9 (radius: 10)
[07:58:45 -238260.147449] SLOW spr round 10 (radius: 5)
[08:01:48 -238258.078775] SLOW spr round 11 (radius: 5)
[08:04:34 -238258.078674] SLOW spr round 12 (radius: 10)
[08:07:16 -238258.078674] SLOW spr round 13 (radius: 15)
[08:12:26 -238252.852992] SLOW spr round 14 (radius: 5)
[08:15:34 -238252.852922] SLOW spr round 15 (radius: 10)
[08:18:38 -238252.852921] SLOW spr round 16 (radius: 15)
[08:23:29 -238252.852921] SLOW spr round 17 (radius: 20)
[08:33:43 -238252.852921] SLOW spr round 18 (radius: 25)
[08:35:16] [worker #1] ML tree search #12, logLikelihood: -238265.818260
[08:45:58 -238252.852921] Model parameter optimization (eps = 0.100000)

[08:46:04] [worker #0] ML tree search #11, logLikelihood: -238252.793289

[08:46:04 -936088.029374] Initial branch length optimization
[08:46:09 -832537.200516] Model parameter optimization (eps = 10.000000)
[08:46:54 -830125.673505] AUTODETECT spr round 1 (radius: 5)
[08:50:00 -608233.550761] AUTODETECT spr round 2 (radius: 10)
[08:53:18 -373542.922316] AUTODETECT spr round 3 (radius: 15)
[08:56:31 -293973.316314] AUTODETECT spr round 4 (radius: 20)
[09:01:11 -273721.830565] AUTODETECT spr round 5 (radius: 25)
[09:06:56 -271316.021357] SPR radius for FAST iterations: 25 (autodetect)
[09:06:56 -271316.021357] Model parameter optimization (eps = 3.000000)
[09:07:18 -271248.250120] FAST spr round 1 (radius: 25)
[09:10:28 -239436.276938] FAST spr round 2 (radius: 25)
[09:13:01 -238527.441201] FAST spr round 3 (radius: 25)
[09:15:21 -238379.369467] FAST spr round 4 (radius: 25)
[09:17:31 -238341.742235] FAST spr round 5 (radius: 25)
[09:19:29 -238339.744975] FAST spr round 6 (radius: 25)
[09:21:25 -238339.744875] Model parameter optimization (eps = 1.000000)
[09:21:42 -238331.203514] SLOW spr round 1 (radius: 5)
[09:24:29 -238277.484830] SLOW spr round 2 (radius: 5)
[09:27:03 -238276.977201] SLOW spr round 3 (radius: 5)
[09:29:34 -238276.977119] SLOW spr round 4 (radius: 10)
[09:32:09 -238276.977119] SLOW spr round 5 (radius: 15)
[09:37:20 -238276.977119] SLOW spr round 6 (radius: 20)
[09:46:32 -238276.977119] SLOW spr round 7 (radius: 25)
[09:49:47] [worker #1] ML tree search #14, logLikelihood: -238272.766442
[09:58:13 -238276.977119] Model parameter optimization (eps = 0.100000)

[09:58:18] [worker #0] ML tree search #13, logLikelihood: -238276.963498

[09:58:18 -936601.069217] Initial branch length optimization
[09:58:23 -833062.298213] Model parameter optimization (eps = 10.000000)
[09:59:04 -830612.715312] AUTODETECT spr round 1 (radius: 5)
[10:02:11 -614716.232772] AUTODETECT spr round 2 (radius: 10)
[10:05:37 -377626.823837] AUTODETECT spr round 3 (radius: 15)
[10:08:51 -295964.593565] AUTODETECT spr round 4 (radius: 20)
[10:13:21 -268843.199367] AUTODETECT spr round 5 (radius: 25)
[10:18:58 -268032.615417] SPR radius for FAST iterations: 25 (autodetect)
[10:18:58 -268032.615417] Model parameter optimization (eps = 3.000000)
[10:19:20 -267966.833574] FAST spr round 1 (radius: 25)
[10:22:25 -239416.675637] FAST spr round 2 (radius: 25)
[10:24:54 -238522.453039] FAST spr round 3 (radius: 25)
[10:27:08 -238390.402411] FAST spr round 4 (radius: 25)
[10:29:09 -238381.646546] FAST spr round 5 (radius: 25)
[10:31:05 -238380.962496] FAST spr round 6 (radius: 25)
[10:32:59 -238380.962487] Model parameter optimization (eps = 1.000000)
[10:33:13 -238370.822237] SLOW spr round 1 (radius: 5)
[10:35:58 -238296.841082] SLOW spr round 2 (radius: 5)
[10:38:39 -238289.137435] SLOW spr round 3 (radius: 5)
[10:41:15 -238281.459004] SLOW spr round 4 (radius: 5)
[10:43:46 -238281.458918] SLOW spr round 5 (radius: 10)
[10:46:23 -238277.745112] SLOW spr round 6 (radius: 5)
[10:49:23 -238273.923521] SLOW spr round 7 (radius: 5)
[10:52:09 -238271.027265] SLOW spr round 8 (radius: 5)
[10:54:44 -238271.026811] SLOW spr round 9 (radius: 10)
[10:57:21 -238271.026809] SLOW spr round 10 (radius: 15)
[11:02:41 -238271.026809] SLOW spr round 11 (radius: 20)
[11:04:16] [worker #1] ML tree search #16, logLikelihood: -238264.753753
[11:13:05 -238271.026809] SLOW spr round 12 (radius: 25)
[11:25:48 -238271.026809] Model parameter optimization (eps = 0.100000)

[11:25:54] [worker #0] ML tree search #15, logLikelihood: -238270.996232

[11:25:54 -927982.712917] Initial branch length optimization
[11:25:59 -825412.287378] Model parameter optimization (eps = 10.000000)
[11:27:05 -823022.498251] AUTODETECT spr round 1 (radius: 5)
[11:30:10 -596551.135557] AUTODETECT spr round 2 (radius: 10)
[11:33:23 -366877.621862] AUTODETECT spr round 3 (radius: 15)
[11:36:36 -295693.259365] AUTODETECT spr round 4 (radius: 20)
[11:40:45 -269422.959930] AUTODETECT spr round 5 (radius: 25)
[11:46:31 -267674.060105] SPR radius for FAST iterations: 25 (autodetect)
[11:46:31 -267674.060105] Model parameter optimization (eps = 3.000000)
[11:46:55 -267621.805183] FAST spr round 1 (radius: 25)
[11:49:54 -239541.476433] FAST spr round 2 (radius: 25)
[11:52:22 -238458.515088] FAST spr round 3 (radius: 25)
[11:54:36 -238412.872410] FAST spr round 4 (radius: 25)
[11:56:39 -238409.304824] FAST spr round 5 (radius: 25)
[11:58:37 -238394.634587] FAST spr round 6 (radius: 25)
[12:00:31 -238394.634580] Model parameter optimization (eps = 1.000000)
[12:00:45 -238391.929034] SLOW spr round 1 (radius: 5)
[12:03:33 -238290.993469] SLOW spr round 2 (radius: 5)
[12:06:18 -238264.473749] SLOW spr round 3 (radius: 5)
[12:08:54 -238257.225627] SLOW spr round 4 (radius: 5)
[12:11:26 -238257.225610] SLOW spr round 5 (radius: 10)
[12:14:02 -238257.055007] SLOW spr round 6 (radius: 5)
[12:17:02 -238257.055004] SLOW spr round 7 (radius: 10)
[12:19:53 -238257.055004] SLOW spr round 8 (radius: 15)
[12:24:16] [worker #1] ML tree search #18, logLikelihood: -238262.865827
[12:24:52 -238257.055004] SLOW spr round 9 (radius: 20)
[12:34:39 -238257.055004] SLOW spr round 10 (radius: 25)
[12:46:44 -238257.055004] Model parameter optimization (eps = 0.100000)

[12:46:50] [worker #0] ML tree search #17, logLikelihood: -238257.035920

[12:46:50 -932187.799093] Initial branch length optimization
[12:46:55 -828168.574847] Model parameter optimization (eps = 10.000000)
[12:47:35 -825711.878754] AUTODETECT spr round 1 (radius: 5)
[12:50:42 -608836.944060] AUTODETECT spr round 2 (radius: 10)
[12:54:02 -377858.558234] AUTODETECT spr round 3 (radius: 15)
[12:57:20 -291157.930376] AUTODETECT spr round 4 (radius: 20)
[13:01:34 -273823.283924] AUTODETECT spr round 5 (radius: 25)
[13:06:39 -271481.275632] SPR radius for FAST iterations: 25 (autodetect)
[13:06:39 -271481.275632] Model parameter optimization (eps = 3.000000)
[13:07:02 -271416.789698] FAST spr round 1 (radius: 25)
[13:10:15 -240186.831643] FAST spr round 2 (radius: 25)
[13:12:52 -238461.026350] FAST spr round 3 (radius: 25)
[13:15:13 -238378.788579] FAST spr round 4 (radius: 25)
[13:17:20 -238351.140377] FAST spr round 5 (radius: 25)
[13:19:16 -238351.140113] Model parameter optimization (eps = 1.000000)
[13:19:34 -238342.091917] SLOW spr round 1 (radius: 5)
[13:22:27 -238267.691298] SLOW spr round 2 (radius: 5)
[13:25:12 -238258.579252] SLOW spr round 3 (radius: 5)
[13:27:48 -238257.185407] SLOW spr round 4 (radius: 5)
[13:30:22 -238257.185340] SLOW spr round 5 (radius: 10)
[13:33:01 -238254.271631] SLOW spr round 6 (radius: 5)
[13:36:04 -238252.286627] SLOW spr round 7 (radius: 5)
[13:38:49 -238252.286622] SLOW spr round 8 (radius: 10)
[13:41:29 -238252.286622] SLOW spr round 9 (radius: 15)
[13:46:38 -238252.286622] SLOW spr round 10 (radius: 20)
[13:56:14 -238252.286622] SLOW spr round 11 (radius: 25)
[14:01:08] [worker #1] ML tree search #20, logLikelihood: -238294.670661
[14:08:06 -238252.286622] Model parameter optimization (eps = 0.100000)

[14:08:13] [worker #0] ML tree search #19, logLikelihood: -238252.258295


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.155512,0.230884) (0.156685,0.546812) (0.415587,0.912602) (0.272216,1.833661) 
   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: -238243.287233

AIC score: 480496.574466 / AICc score: 8524556.574466 / BIC score: 489503.515335
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=660).
         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/Q96SR6/3_mltree/Q96SR6.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/3_mltree/Q96SR6.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/3_mltree/Q96SR6.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96SR6/3_mltree/Q96SR6.raxml.log

Analysis started: 24-Jul-2021 21:02:38 / finished: 25-Jul-2021 11:10:52

Elapsed time: 50893.447 seconds