RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 06-Jul-2021 06:54:47 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/2_msa/P47897_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897 --seed 2 --threads 8 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/2_msa/P47897_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 804 sites

WARNING: Sequences tr_J3KGB3_J3KGB3_COCIM_246410 and tr_A0A0J6XX00_A0A0J6XX00_COCIT_404692 are exactly identical!
WARNING: Sequences tr_Q7S9Z2_Q7S9Z2_NEUCR_367110 and tr_G4ULT6_G4ULT6_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_A0A179UWY6_A0A179UWY6_BLAGS_559298 and tr_C5GLP6_C5GLP6_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FRI4_F9FRI4_FUSOF_660025 and tr_A0A2H3HHG8_A0A2H3HHG8_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_M0RDR7_M0RDR7_RAT_10116 and sp_P47897_SYQ_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A2QFZ1_A2QFZ1_ASPNC_425011 and tr_G3Y890_G3Y890_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QFZ1_A2QFZ1_ASPNC_425011 and tr_A0A319A5R4_A0A319A5R4_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5QUA8_A0A1D5QUA8_MACMU_9544 and tr_G7NXU7_G7NXU7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QUA8_A0A1D5QUA8_MACMU_9544 and tr_A0A2K5MRX9_A0A2K5MRX9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QUA8_A0A1D5QUA8_MACMU_9544 and tr_A0A2K6CH70_A0A2K6CH70_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A2Y140_A2Y140_ORYSI_39946 and tr_Q65WY6_Q65WY6_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4NXW0_F4NXW0_BATDJ_684364 and tr_A0A177WLN5_A0A177WLN5_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1PT00_I1PT00_ORYGL_4538 and tr_A0A0D3G3Z5_A0A0D3G3Z5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_G2YMH1_G2YMH1_BOTF4_999810 and tr_M7UJ90_M7UJ90_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SWT9_F2SWT9_TRIRC_559305 and tr_A0A178F9L5_A0A178F9L5_TRIRU_5551 are exactly identical!
WARNING: Sequences sp_C4V819_SYQ_NOSCE_578460 and tr_A0A0F9WHM0_A0A0F9WHM0_9MICR_40302 are exactly identical!
WARNING: Sequences tr_N4UBC6_N4UBC6_FUSC1_1229664 and tr_A0A2H3SXR1_A0A2H3SXR1_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_V2X5M1_V2X5M1_MONRO_1381753 and tr_A0A0W0EZD4_A0A0W0EZD4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015I1N6_A0A015I1N6_9GLOM_1432141 and tr_A0A2H5SBK5_A0A2H5SBK5_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0D3EKG0_A0A0D3EKG0_9ORYZ_65489 and tr_A0A0D9Y4A3_A0A0D9Y4A3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0JF02_A0A0E0JF02_ORYPU_4537 and tr_A0A0E0K1R7_A0A0E0K1R7_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_A0A094EJK7_A0A094EJK7_9PEZI_1420912 and tr_A0A1B8GWS5_A0A1B8GWS5_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4UHD9_V4UHD9_9ROSI_85681 and tr_A0A2H5P5C1_A0A2H5P5C1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A1S3YF68_A0A1S3YF68_TOBAC_4097 and tr_A0A1U7YGK9_A0A1U7YGK9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1Q3DVJ6_A0A1Q3DVJ6_LENED_5353 and tr_A0A1Q3DVY8_A0A1Q3DVY8_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A2N5THL1_A0A2N5THL1_9BASI_200324 and tr_A0A2N5V5D1_A0A2N5V5D1_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 26

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.reduced.phy

Alignment comprises 1 partitions and 804 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 804 / 804
Gaps: 14.94 %
Invariant sites: 1.49 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.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 / 201 / 16080
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1148373.375022] Initial branch length optimization
[00:00:10 -1011233.760626] Model parameter optimization (eps = 10.000000)
[00:01:48 -1008336.161130] AUTODETECT spr round 1 (radius: 5)
[00:05:26 -712648.432080] AUTODETECT spr round 2 (radius: 10)
[00:09:05 -513487.185064] AUTODETECT spr round 3 (radius: 15)
[00:12:52 -464230.583186] AUTODETECT spr round 4 (radius: 20)
[00:17:33 -435452.696938] AUTODETECT spr round 5 (radius: 25)
[00:23:18 -433383.719317] SPR radius for FAST iterations: 25 (autodetect)
[00:23:18 -433383.719317] Model parameter optimization (eps = 3.000000)
[00:23:42 -433309.451847] FAST spr round 1 (radius: 25)
[00:28:08 -379848.830302] FAST spr round 2 (radius: 25)
[00:31:14 -378228.211985] FAST spr round 3 (radius: 25)
[00:33:56 -378142.443827] FAST spr round 4 (radius: 25)
[00:36:19 -378137.908104] FAST spr round 5 (radius: 25)
[00:38:39 -378137.908061] Model parameter optimization (eps = 1.000000)
[00:38:57 -378136.833456] SLOW spr round 1 (radius: 5)
[00:42:34 -378040.816838] SLOW spr round 2 (radius: 5)
[00:45:49 -378038.204230] SLOW spr round 3 (radius: 5)
[00:48:59 -378037.119727] SLOW spr round 4 (radius: 5)
[00:52:04 -378037.119346] SLOW spr round 5 (radius: 10)
[00:55:18 -378032.264452] SLOW spr round 6 (radius: 5)
[00:59:22 -378028.641480] SLOW spr round 7 (radius: 5)
[01:02:50 -378028.641474] SLOW spr round 8 (radius: 10)
[01:06:19 -378028.641474] SLOW spr round 9 (radius: 15)
[01:11:41 -378028.641474] SLOW spr round 10 (radius: 20)
[01:19:41 -378028.641474] SLOW spr round 11 (radius: 25)
[01:30:07 -378028.641474] Model parameter optimization (eps = 0.100000)

[01:30:19] [worker #0] ML tree search #1, logLikelihood: -378028.378726

[01:30:20 -1152907.970115] Initial branch length optimization
[01:30:26 -1013910.771092] Model parameter optimization (eps = 10.000000)
[01:31:18 -1011057.749462] AUTODETECT spr round 1 (radius: 5)
[01:35:13 -724720.179605] AUTODETECT spr round 2 (radius: 10)
[01:39:36 -522681.942861] AUTODETECT spr round 3 (radius: 15)
[01:42:13] [worker #1] ML tree search #2, logLikelihood: -378035.134361
[01:43:30 -462015.273392] AUTODETECT spr round 4 (radius: 20)
[01:48:08 -435563.136682] AUTODETECT spr round 5 (radius: 25)
[01:53:40 -431451.850150] SPR radius for FAST iterations: 25 (autodetect)
[01:53:40 -431451.850150] Model parameter optimization (eps = 3.000000)
[01:54:02 -431358.998378] FAST spr round 1 (radius: 25)
[01:58:35 -380216.612110] FAST spr round 2 (radius: 25)
[02:01:44 -378285.439131] FAST spr round 3 (radius: 25)
[02:04:23 -378159.816277] FAST spr round 4 (radius: 25)
[02:06:39 -378147.070298] FAST spr round 5 (radius: 25)
[02:08:54 -378141.491332] FAST spr round 6 (radius: 25)
[02:11:07 -378141.491310] Model parameter optimization (eps = 1.000000)
[02:11:28 -378131.365299] SLOW spr round 1 (radius: 5)
[02:15:00 -378055.276820] SLOW spr round 2 (radius: 5)
[02:18:15 -378048.850071] SLOW spr round 3 (radius: 5)
[02:21:22 -378048.011432] SLOW spr round 4 (radius: 5)
[02:24:24 -378048.011396] SLOW spr round 5 (radius: 10)
[02:27:38 -378043.455714] SLOW spr round 6 (radius: 5)
[02:31:44 -378041.587409] SLOW spr round 7 (radius: 5)
[02:35:12 -378041.587394] SLOW spr round 8 (radius: 10)
[02:38:25 -378041.587394] SLOW spr round 9 (radius: 15)
[02:43:44 -378041.587394] SLOW spr round 10 (radius: 20)
[02:51:58 -378041.587394] SLOW spr round 11 (radius: 25)
[02:54:45] [worker #1] ML tree search #4, logLikelihood: -378092.011065
[03:03:03 -378041.587394] Model parameter optimization (eps = 0.100000)

[03:03:10] [worker #0] ML tree search #3, logLikelihood: -378041.526201

[03:03:10 -1148564.236819] Initial branch length optimization
[03:03:17 -1009014.141452] Model parameter optimization (eps = 10.000000)
[03:04:11 -1006098.371624] AUTODETECT spr round 1 (radius: 5)
[03:07:33 -703117.085168] AUTODETECT spr round 2 (radius: 10)
[03:11:16 -491711.035798] AUTODETECT spr round 3 (radius: 15)
[03:15:18 -425074.675244] AUTODETECT spr round 4 (radius: 20)
[03:20:32 -417896.191174] AUTODETECT spr round 5 (radius: 25)
[03:27:08 -416759.222675] SPR radius for FAST iterations: 25 (autodetect)
[03:27:08 -416759.222675] Model parameter optimization (eps = 3.000000)
[03:27:33 -416648.661061] FAST spr round 1 (radius: 25)
[03:31:51 -379068.583439] FAST spr round 2 (radius: 25)
[03:34:58 -378302.336687] FAST spr round 3 (radius: 25)
[03:37:40 -378222.791556] FAST spr round 4 (radius: 25)
[03:40:00 -378214.577589] FAST spr round 5 (radius: 25)
[03:42:09 -378214.576479] Model parameter optimization (eps = 1.000000)
[03:42:28 -378204.513839] SLOW spr round 1 (radius: 5)
[03:46:06 -378060.598680] SLOW spr round 2 (radius: 5)
[03:49:18 -378053.053807] SLOW spr round 3 (radius: 5)
[03:52:20 -378053.053315] SLOW spr round 4 (radius: 10)
[03:55:28 -378044.954872] SLOW spr round 5 (radius: 5)
[03:59:33 -378038.705146] SLOW spr round 6 (radius: 5)
[04:02:55 -378038.705111] SLOW spr round 7 (radius: 10)
[04:06:04 -378038.705110] SLOW spr round 8 (radius: 15)
[04:11:34 -378032.719702] SLOW spr round 9 (radius: 5)
[04:15:41 -378032.719518] SLOW spr round 10 (radius: 10)
[04:19:16 -378032.719505] SLOW spr round 11 (radius: 15)
[04:21:04] [worker #1] ML tree search #6, logLikelihood: -378015.692400
[04:24:45 -378032.719504] SLOW spr round 12 (radius: 20)
[04:34:16 -378032.719504] SLOW spr round 13 (radius: 25)
[04:46:11 -378032.719504] Model parameter optimization (eps = 0.100000)

[04:46:24] [worker #0] ML tree search #5, logLikelihood: -378031.915253

[04:46:24 -1144845.288615] Initial branch length optimization
[04:46:31 -1007053.638858] Model parameter optimization (eps = 10.000000)
[04:47:23 -1004265.038998] AUTODETECT spr round 1 (radius: 5)
[04:50:31 -713557.827542] AUTODETECT spr round 2 (radius: 10)
[04:53:54 -531544.604110] AUTODETECT spr round 3 (radius: 15)
[04:57:43 -452319.075475] AUTODETECT spr round 4 (radius: 20)
[05:02:05 -431467.339392] AUTODETECT spr round 5 (radius: 25)
[05:06:55 -429526.163484] SPR radius for FAST iterations: 25 (autodetect)
[05:06:55 -429526.163484] Model parameter optimization (eps = 3.000000)
[05:07:14 -429431.314518] FAST spr round 1 (radius: 25)
[05:11:04 -379372.251196] FAST spr round 2 (radius: 25)
[05:13:49 -378151.809309] FAST spr round 3 (radius: 25)
[05:16:11 -378094.070900] FAST spr round 4 (radius: 25)
[05:18:13 -378091.945864] FAST spr round 5 (radius: 25)
[05:20:11 -378091.945862] Model parameter optimization (eps = 1.000000)
[05:20:34 -378086.990345] SLOW spr round 1 (radius: 5)
[05:23:33 -378022.869724] SLOW spr round 2 (radius: 5)
[05:26:28 -378021.538458] SLOW spr round 3 (radius: 5)
[05:29:17 -378021.538188] SLOW spr round 4 (radius: 10)
[05:32:00 -378020.889445] SLOW spr round 5 (radius: 5)
[05:35:37] [worker #1] ML tree search #8, logLikelihood: -378020.214544
[05:35:47 -378020.198440] SLOW spr round 6 (radius: 5)
[05:38:59 -378020.198411] SLOW spr round 7 (radius: 10)
[05:41:49 -378020.198411] SLOW spr round 8 (radius: 15)
[05:46:34 -378020.198411] SLOW spr round 9 (radius: 20)
[05:53:34 -378020.198411] SLOW spr round 10 (radius: 25)
[06:02:52 -378020.198411] Model parameter optimization (eps = 0.100000)

[06:03:06] [worker #0] ML tree search #7, logLikelihood: -378019.933661

[06:03:06 -1148295.171129] Initial branch length optimization
[06:03:14 -1011280.149997] Model parameter optimization (eps = 10.000000)
[06:04:06 -1008534.601058] AUTODETECT spr round 1 (radius: 5)
[06:07:04 -729038.042647] AUTODETECT spr round 2 (radius: 10)
[06:10:23 -535985.624572] AUTODETECT spr round 3 (radius: 15)
[06:14:05 -458362.773025] AUTODETECT spr round 4 (radius: 20)
[06:18:27 -433621.926783] AUTODETECT spr round 5 (radius: 25)
[06:22:54 -428205.004428] SPR radius for FAST iterations: 25 (autodetect)
[06:22:54 -428205.004428] Model parameter optimization (eps = 3.000000)
[06:23:13 -428097.050663] FAST spr round 1 (radius: 25)
[06:26:45 -380608.336857] FAST spr round 2 (radius: 25)
[06:29:25 -378305.636585] FAST spr round 3 (radius: 25)
[06:31:46 -378195.699561] FAST spr round 4 (radius: 25)
[06:34:10 -378173.875406] FAST spr round 5 (radius: 25)
[06:36:08 -378149.078606] FAST spr round 6 (radius: 25)
[06:37:58 -378148.359862] FAST spr round 7 (radius: 25)
[06:39:45 -378148.359858] Model parameter optimization (eps = 1.000000)
[06:39:59 -378144.434344] SLOW spr round 1 (radius: 5)
[06:42:55 -378055.896238] SLOW spr round 2 (radius: 5)
[06:43:32] [worker #1] ML tree search #10, logLikelihood: -378122.651675
[06:45:40 -378037.996647] SLOW spr round 3 (radius: 5)
[06:48:17 -378036.102803] SLOW spr round 4 (radius: 5)
[06:50:53 -378035.902344] SLOW spr round 5 (radius: 5)
[06:53:28 -378035.902343] SLOW spr round 6 (radius: 10)
[06:56:10 -378035.829054] SLOW spr round 7 (radius: 15)
[07:00:59 -378035.828941] SLOW spr round 8 (radius: 20)
[07:08:03 -378035.828939] SLOW spr round 9 (radius: 25)
[07:17:03 -378035.828939] Model parameter optimization (eps = 0.100000)

[07:17:16] [worker #0] ML tree search #9, logLikelihood: -378034.202804

[07:17:16 -1149449.393979] Initial branch length optimization
[07:17:21 -1008299.729345] Model parameter optimization (eps = 10.000000)
[07:18:00 -1005466.192750] AUTODETECT spr round 1 (radius: 5)
[07:20:47 -714627.124485] AUTODETECT spr round 2 (radius: 10)
[07:23:52 -522848.600158] AUTODETECT spr round 3 (radius: 15)
[07:27:03 -467031.851958] AUTODETECT spr round 4 (radius: 20)
[07:30:54 -434774.259745] AUTODETECT spr round 5 (radius: 25)
[07:35:26 -433007.694625] SPR radius for FAST iterations: 25 (autodetect)
[07:35:26 -433007.694625] Model parameter optimization (eps = 3.000000)
[07:35:36 -433004.563752] FAST spr round 1 (radius: 25)
[07:39:14 -379920.533470] FAST spr round 2 (radius: 25)
[07:41:51 -378375.457206] FAST spr round 3 (radius: 25)
[07:44:12 -378243.952129] FAST spr round 4 (radius: 25)
[07:46:08 -378231.505597] FAST spr round 5 (radius: 25)
[07:47:59 -378231.505559] Model parameter optimization (eps = 1.000000)
[07:48:04 -378231.303146] SLOW spr round 1 (radius: 5)
[07:51:06 -378120.424348] SLOW spr round 2 (radius: 5)
[07:53:54 -378103.943540] SLOW spr round 3 (radius: 5)
[07:56:32 -378101.738314] SLOW spr round 4 (radius: 5)
[07:59:01 -378101.735321] SLOW spr round 5 (radius: 10)
[08:01:38 -378097.311854] SLOW spr round 6 (radius: 5)
[08:03:55] [worker #1] ML tree search #12, logLikelihood: -378053.018659
[08:05:01 -378095.181076] SLOW spr round 7 (radius: 5)
[08:07:54 -378095.181073] SLOW spr round 8 (radius: 10)
[08:10:37 -378095.181073] SLOW spr round 9 (radius: 15)
[08:15:07 -378089.399608] SLOW spr round 10 (radius: 5)
[08:18:41 -378089.399444] SLOW spr round 11 (radius: 10)
[08:21:42 -378089.399435] SLOW spr round 12 (radius: 15)
[08:25:56 -378089.399434] SLOW spr round 13 (radius: 20)
[08:33:06 -378089.399434] SLOW spr round 14 (radius: 25)
[08:42:15 -378089.399434] Model parameter optimization (eps = 0.100000)

[08:42:17] [worker #0] ML tree search #11, logLikelihood: -378089.398628

[08:42:17 -1151481.623895] Initial branch length optimization
[08:42:24 -1011850.406323] Model parameter optimization (eps = 10.000000)
[08:43:13 -1009191.998227] AUTODETECT spr round 1 (radius: 5)
[08:46:00 -712709.688616] AUTODETECT spr round 2 (radius: 10)
[08:49:03 -531593.319526] AUTODETECT spr round 3 (radius: 15)
[08:52:24 -463082.563710] AUTODETECT spr round 4 (radius: 20)
[08:56:19 -432917.243916] AUTODETECT spr round 5 (radius: 25)
[09:01:18 -430167.640906] SPR radius for FAST iterations: 25 (autodetect)
[09:01:18 -430167.640906] Model parameter optimization (eps = 3.000000)
[09:01:37 -430084.092054] FAST spr round 1 (radius: 25)
[09:05:11 -379629.071257] FAST spr round 2 (radius: 25)
[09:07:41 -378199.721924] FAST spr round 3 (radius: 25)
[09:08:31] [worker #1] ML tree search #14, logLikelihood: -378030.548267
[09:09:52 -378150.817336] FAST spr round 4 (radius: 25)
[09:11:51 -378141.188581] FAST spr round 5 (radius: 25)
[09:13:42 -378141.188553] Model parameter optimization (eps = 1.000000)
[09:13:57 -378138.088888] SLOW spr round 1 (radius: 5)
[09:16:57 -378054.123656] SLOW spr round 2 (radius: 5)
[09:19:42 -378036.256294] SLOW spr round 3 (radius: 5)
[09:22:18 -378035.201960] SLOW spr round 4 (radius: 5)
[09:24:50 -378033.699860] SLOW spr round 5 (radius: 5)
[09:27:20 -378033.699793] SLOW spr round 6 (radius: 10)
[09:30:00 -378033.699746] SLOW spr round 7 (radius: 15)
[09:34:41 -378033.699700] SLOW spr round 8 (radius: 20)
[09:41:25 -378033.699654] SLOW spr round 9 (radius: 25)
[09:50:05 -378033.699608] Model parameter optimization (eps = 0.100000)

[09:50:14] [worker #0] ML tree search #13, logLikelihood: -378033.563746

[09:50:14 -1145442.866543] Initial branch length optimization
[09:50:19 -1011563.098046] Model parameter optimization (eps = 10.000000)
[09:51:09 -1008697.879966] AUTODETECT spr round 1 (radius: 5)
[09:53:56 -718932.036608] AUTODETECT spr round 2 (radius: 10)
[09:56:56 -528877.247125] AUTODETECT spr round 3 (radius: 15)
[10:00:12 -441369.076659] AUTODETECT spr round 4 (radius: 20)
[10:04:00 -422019.634098] AUTODETECT spr round 5 (radius: 25)
[10:08:13 -421635.158314] SPR radius for FAST iterations: 25 (autodetect)
[10:08:13 -421635.158314] Model parameter optimization (eps = 3.000000)
[10:08:36 -421551.749251] FAST spr round 1 (radius: 25)
[10:11:56 -379367.718530] FAST spr round 2 (radius: 25)
[10:14:27 -378233.778528] FAST spr round 3 (radius: 25)
[10:16:42 -378150.305269] FAST spr round 4 (radius: 25)
[10:18:46 -378131.796939] FAST spr round 5 (radius: 25)
[10:20:34 -378131.517397] FAST spr round 6 (radius: 25)
[10:22:21 -378131.517373] Model parameter optimization (eps = 1.000000)
[10:22:39 -378125.476059] SLOW spr round 1 (radius: 5)
[10:24:52] [worker #1] ML tree search #16, logLikelihood: -378022.920028
[10:25:37 -378048.410597] SLOW spr round 2 (radius: 5)
[10:28:23 -378042.386394] SLOW spr round 3 (radius: 5)
[10:30:57 -378041.879238] SLOW spr round 4 (radius: 5)
[10:33:30 -378041.879229] SLOW spr round 5 (radius: 10)
[10:36:10 -378041.879229] SLOW spr round 6 (radius: 15)
[10:40:52 -378041.879229] SLOW spr round 7 (radius: 20)
[10:48:02 -378041.879229] SLOW spr round 8 (radius: 25)
[10:57:48 -378041.879229] Model parameter optimization (eps = 0.100000)

[10:58:05] [worker #0] ML tree search #15, logLikelihood: -378040.814137

[10:58:05 -1149037.124036] Initial branch length optimization
[10:58:11 -1009643.343737] Model parameter optimization (eps = 10.000000)
[10:59:08 -1006824.599088] AUTODETECT spr round 1 (radius: 5)
[11:02:01 -712089.184262] AUTODETECT spr round 2 (radius: 10)
[11:05:11 -511941.659869] AUTODETECT spr round 3 (radius: 15)
[11:08:20 -443202.028664] AUTODETECT spr round 4 (radius: 20)
[11:12:01 -429601.522479] AUTODETECT spr round 5 (radius: 25)
[11:17:03 -425273.558691] SPR radius for FAST iterations: 25 (autodetect)
[11:17:03 -425273.558691] Model parameter optimization (eps = 3.000000)
[11:17:11 -425270.492791] FAST spr round 1 (radius: 25)
[11:20:45 -380400.863887] FAST spr round 2 (radius: 25)
[11:23:25 -378453.336225] FAST spr round 3 (radius: 25)
[11:25:41 -378261.556563] FAST spr round 4 (radius: 25)
[11:27:44 -378225.251087] FAST spr round 5 (radius: 25)
[11:29:35 -378220.159875] FAST spr round 6 (radius: 25)
[11:31:25 -378220.159859] Model parameter optimization (eps = 1.000000)
[11:31:45 -378166.571572] SLOW spr round 1 (radius: 5)
[11:34:37 -378049.511716] SLOW spr round 2 (radius: 5)
[11:37:20 -378034.524151] SLOW spr round 3 (radius: 5)
[11:39:54 -378028.743059] SLOW spr round 4 (radius: 5)
[11:42:26 -378028.342341] SLOW spr round 5 (radius: 5)
[11:44:56 -378028.341981] SLOW spr round 6 (radius: 10)
[11:46:24] [worker #1] ML tree search #18, logLikelihood: -378115.134743
[11:47:36 -378027.427297] SLOW spr round 7 (radius: 5)
[11:51:00 -378026.945675] SLOW spr round 8 (radius: 5)
[11:53:56 -378026.945320] SLOW spr round 9 (radius: 10)
[11:56:43 -378026.944993] SLOW spr round 10 (radius: 15)
[12:01:17 -378021.807713] SLOW spr round 11 (radius: 5)
[12:04:50 -378021.807206] SLOW spr round 12 (radius: 10)
[12:07:59 -378021.806880] SLOW spr round 13 (radius: 15)
[12:12:21 -378021.806565] SLOW spr round 14 (radius: 20)
[12:19:30 -378021.806252] SLOW spr round 15 (radius: 25)
[12:28:12 -378021.805940] Model parameter optimization (eps = 0.100000)

[12:28:25] [worker #0] ML tree search #17, logLikelihood: -378020.617388

[12:28:25 -1146733.703669] Initial branch length optimization
[12:28:30 -1009145.709372] Model parameter optimization (eps = 10.000000)
[12:29:12 -1006307.220775] AUTODETECT spr round 1 (radius: 5)
[12:32:02 -713274.857239] AUTODETECT spr round 2 (radius: 10)
[12:35:06 -554497.729855] AUTODETECT spr round 3 (radius: 15)
[12:38:36 -498851.241296] AUTODETECT spr round 4 (radius: 20)
[12:42:42 -444660.239386] AUTODETECT spr round 5 (radius: 25)
[12:47:48 -440182.791262] SPR radius for FAST iterations: 25 (autodetect)
[12:47:48 -440182.791262] Model parameter optimization (eps = 3.000000)
[12:48:07 -440076.374317] FAST spr round 1 (radius: 25)
[12:50:26] [worker #1] ML tree search #20, logLikelihood: -378091.270242
[12:51:52 -379921.214526] FAST spr round 2 (radius: 25)
[12:54:29 -378212.147837] FAST spr round 3 (radius: 25)
[12:56:46 -378128.875490] FAST spr round 4 (radius: 25)
[12:58:42 -378109.304682] FAST spr round 5 (radius: 25)
[13:00:32 -378108.476218] FAST spr round 6 (radius: 25)
[13:02:18 -378108.476180] Model parameter optimization (eps = 1.000000)
[13:02:42 -378104.864397] SLOW spr round 1 (radius: 5)
[13:07:18 -378034.268234] SLOW spr round 2 (radius: 5)
[13:10:32 -378025.578351] SLOW spr round 3 (radius: 5)
[13:13:02 -378024.728432] SLOW spr round 4 (radius: 5)
[13:15:32 -378024.101095] SLOW spr round 5 (radius: 5)
[13:17:59 -378024.101083] SLOW spr round 6 (radius: 10)
[13:20:33 -378023.856213] SLOW spr round 7 (radius: 5)
[13:23:49 -378023.000710] SLOW spr round 8 (radius: 5)
[13:26:37 -378023.000668] SLOW spr round 9 (radius: 10)
[13:29:17 -378023.000667] SLOW spr round 10 (radius: 15)
[13:33:43 -378023.000667] SLOW spr round 11 (radius: 20)
[13:40:21 -378023.000667] SLOW spr round 12 (radius: 25)
[13:48:44 -378023.000667] Model parameter optimization (eps = 0.100000)

[13:48:58] [worker #0] ML tree search #19, logLikelihood: -378020.800442


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.193619,0.252100) (0.227410,0.442978) (0.279124,0.927122) (0.299847,1.973236) 
   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: -378015.692400

AIC score: 760041.384800 / AICc score: 8804101.384800 / BIC score: 769444.031335
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=804).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 21 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P47897/3_mltree/P47897.raxml.log

Analysis started: 06-Jul-2021 06:54:47 / finished: 06-Jul-2021 20:43:46

Elapsed time: 49739.013 seconds

Consumed energy: 4545.547 Wh (= 23 km in an electric car, or 114 km with an e-scooter!)