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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 03-Jul-2021 01:01:19 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/2_msa/Q9NVE5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5 --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/Q9NVE5/2_msa/Q9NVE5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1104 sites

WARNING: Sequences tr_G1N8T7_G1N8T7_MELGA_9103 and tr_U3J6C8_U3J6C8_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_H2RDB9_H2RDB9_PANTR_9598 and sp_Q96K76_UBP47_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2RDB9_H2RDB9_PANTR_9598 and tr_A0A2R8Z9H3_A0A2R8Z9H3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6S6E3_F6S6E3_MACMU_9544 and tr_A0A2I3MRL2_A0A2I3MRL2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6WNB6_F6WNB6_MACMU_9544 and tr_A0A2I3LQ04_A0A2I3LQ04_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6WNB6_F6WNB6_MACMU_9544 and tr_A0A0D9QX69_A0A0D9QX69_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6WNB6_F6WNB6_MACMU_9544 and tr_A0A2K6DZS2_A0A2K6DZS2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0Z2S9_H0Z2S9_TAEGU_59729 and tr_A0A218UFY2_A0A218UFY2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G2YMI4_G2YMI4_BOTF4_999810 and tr_M7U2Z9_M7U2Z9_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2PQA0_F2PQA0_TRIEC_559882 and tr_A0A059JA79_A0A059JA79_9EURO_1215338 are exactly identical!
WARNING: Sequences tr_L0PAX4_L0PAX4_PNEJ8_1209962 and tr_A0A0W4ZVJ4_A0A0W4ZVJ4_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_W2QWR6_W2QWR6_PHYPN_761204 and tr_A0A0W8DK02_A0A0W8DK02_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QWR6_W2QWR6_PHYPN_761204 and tr_W2K7J0_W2K7J0_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A078FMB4_A0A078FMB4_BRANA_3708 and tr_A0A0D3AHZ4_A0A0D3AHZ4_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0D9R8K0_A0A0D9R8K0_CHLSB_60711 and tr_A0A2K6DJ91_A0A2K6DJ91_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A091UTC7_A0A091UTC7_NIPNI_128390 and tr_A0A087QIG5_A0A087QIG5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091UTC7_A0A091UTC7_NIPNI_128390 and tr_A0A091FT46_A0A091FT46_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091UTC7_A0A091UTC7_NIPNI_128390 and tr_A0A0A0ABS0_A0A0A0ABS0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091UTC7_A0A091UTC7_NIPNI_128390 and tr_A0A091HST5_A0A091HST5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A165AIC8_A0A165AIC8_9HOMO_1314777 and tr_A0A166IU37_A0A166IU37_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3Z7E1_A0A1S3Z7E1_TOBAC_4097 and tr_A0A1U7X2A4_A0A1U7X2A4_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BWE1_A0A1S4BWE1_TOBAC_4097 and tr_A0A1U7X7C3_A0A1U7X7C3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4D389_A0A1S4D389_TOBAC_4097 and tr_A0A1U7YGD6_A0A1U7YGD6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2D0SZ51_A0A2D0SZ51_ICTPU_7998 and tr_A0A2D0SZJ6_A0A2D0SZJ6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5M9X9_A0A2K5M9X9_CERAT_9531 and tr_A0A2K5Y887_A0A2K5Y887_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2A3EMD4_A0A2A3EMD4_APICC_94128 and tr_A0A2A3ENZ1_A0A2A3ENZ1_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A2U4AU18_A0A2U4AU18_TURTR_9739 and tr_A0A2Y9LE83_A0A2Y9LE83_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 27

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/Q9NVE5/3_mltree/Q9NVE5.raxml.reduced.phy

Alignment comprises 1 partitions and 1104 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1104 / 1104
Gaps: 15.81 %
Invariant sites: 0.54 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.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 / 276 / 22080
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1907570.026116] Initial branch length optimization
[00:00:12 -1542437.580977] Model parameter optimization (eps = 10.000000)
[00:01:53 -1539208.243196] AUTODETECT spr round 1 (radius: 5)
[00:06:18 -1065946.168226] AUTODETECT spr round 2 (radius: 10)
[00:11:04 -786440.732436] AUTODETECT spr round 3 (radius: 15)
[00:16:35 -675018.905809] AUTODETECT spr round 4 (radius: 20)
[00:23:00 -610610.449272] AUTODETECT spr round 5 (radius: 25)
[00:30:51 -588040.956864] SPR radius for FAST iterations: 25 (autodetect)
[00:30:51 -588040.956864] Model parameter optimization (eps = 3.000000)
[00:31:33 -587328.830066] FAST spr round 1 (radius: 25)
[00:38:06 -504475.662013] FAST spr round 2 (radius: 25)
[00:42:31 -501388.368468] FAST spr round 3 (radius: 25)
[00:45:59 -501200.168751] FAST spr round 4 (radius: 25)
[00:48:50 -501198.958381] FAST spr round 5 (radius: 25)
[00:51:28 -501198.922309] Model parameter optimization (eps = 1.000000)
[00:51:48 -501194.169937] SLOW spr round 1 (radius: 5)
[00:55:55 -501101.734673] SLOW spr round 2 (radius: 5)
[00:59:32 -501101.733157] SLOW spr round 3 (radius: 10)
[01:03:14 -501101.733056] SLOW spr round 4 (radius: 15)
[01:10:43 -501101.733009] SLOW spr round 5 (radius: 20)
[01:19:58 -501101.732972] SLOW spr round 6 (radius: 25)
[01:30:11 -501101.732937] Model parameter optimization (eps = 0.100000)

[01:30:24] [worker #0] ML tree search #1, logLikelihood: -501101.534338

[01:30:24 -1894179.488388] Initial branch length optimization
[01:30:36 -1523416.396108] Model parameter optimization (eps = 10.000000)
[01:32:29 -1520505.471542] AUTODETECT spr round 1 (radius: 5)
[01:36:49 -1077165.418528] AUTODETECT spr round 2 (radius: 10)
[01:41:11] [worker #1] ML tree search #2, logLikelihood: -501111.448835
[01:41:27 -822957.325624] AUTODETECT spr round 3 (radius: 15)
[01:46:50 -672160.986802] AUTODETECT spr round 4 (radius: 20)
[01:52:23 -597480.049996] AUTODETECT spr round 5 (radius: 25)
[01:58:20 -582901.744835] SPR radius for FAST iterations: 25 (autodetect)
[01:58:20 -582901.744835] Model parameter optimization (eps = 3.000000)
[01:58:32 -582880.881910] FAST spr round 1 (radius: 25)
[02:04:53 -504976.627631] FAST spr round 2 (radius: 25)
[02:09:15 -501694.460795] FAST spr round 3 (radius: 25)
[02:12:37 -501524.128607] FAST spr round 4 (radius: 25)
[02:15:45 -501487.454186] FAST spr round 5 (radius: 25)
[02:18:32 -501477.912605] FAST spr round 6 (radius: 25)
[02:21:06 -501477.912547] Model parameter optimization (eps = 1.000000)
[02:21:38 -501230.137213] SLOW spr round 1 (radius: 5)
[02:25:36 -501107.621095] SLOW spr round 2 (radius: 5)
[02:29:11 -501107.617216] SLOW spr round 3 (radius: 10)
[02:32:57 -501106.694415] SLOW spr round 4 (radius: 5)
[02:37:40 -501106.692894] SLOW spr round 5 (radius: 10)
[02:41:57 -501106.692860] SLOW spr round 6 (radius: 15)
[02:48:41 -501106.692826] SLOW spr round 7 (radius: 20)
[02:58:09 -501106.692792] SLOW spr round 8 (radius: 25)
[03:08:13 -501106.692758] Model parameter optimization (eps = 0.100000)

[03:08:24] [worker #0] ML tree search #3, logLikelihood: -501106.584841

[03:08:24 -1907341.757101] Initial branch length optimization
[03:08:35 -1535977.739612] Model parameter optimization (eps = 10.000000)
[03:10:21 -1532965.140646] AUTODETECT spr round 1 (radius: 5)
[03:14:41 -1098097.449035] AUTODETECT spr round 2 (radius: 10)
[03:14:54] [worker #1] ML tree search #4, logLikelihood: -501096.645198
[03:19:30 -808284.881927] AUTODETECT spr round 3 (radius: 15)
[03:25:11 -651652.920568] AUTODETECT spr round 4 (radius: 20)
[03:30:37 -586500.190783] AUTODETECT spr round 5 (radius: 25)
[03:36:15 -572603.641292] SPR radius for FAST iterations: 25 (autodetect)
[03:36:15 -572603.641292] Model parameter optimization (eps = 3.000000)
[03:37:00 -572083.177420] FAST spr round 1 (radius: 25)
[03:42:51 -503995.822445] FAST spr round 2 (radius: 25)
[03:46:56 -501455.385213] FAST spr round 3 (radius: 25)
[03:50:20 -501259.542308] FAST spr round 4 (radius: 25)
[03:53:12 -501248.834193] FAST spr round 5 (radius: 25)
[03:55:51 -501248.834106] Model parameter optimization (eps = 1.000000)
[03:56:12 -501241.169333] SLOW spr round 1 (radius: 5)
[04:00:13 -501116.030782] SLOW spr round 2 (radius: 5)
[04:04:00 -501109.626109] SLOW spr round 3 (radius: 5)
[04:07:34 -501109.625974] SLOW spr round 4 (radius: 10)
[04:11:15 -501109.625928] SLOW spr round 5 (radius: 15)
[04:18:41 -501109.625892] SLOW spr round 6 (radius: 20)
[04:28:01 -501109.625857] SLOW spr round 7 (radius: 25)
[04:38:18 -501109.625822] Model parameter optimization (eps = 0.100000)

[04:38:28] [worker #0] ML tree search #5, logLikelihood: -501109.428384

[04:38:29 -1914742.406961] Initial branch length optimization
[04:38:40 -1539284.534597] Model parameter optimization (eps = 10.000000)
[04:40:19 -1536177.891300] AUTODETECT spr round 1 (radius: 5)
[04:44:40 -1046762.150913] AUTODETECT spr round 2 (radius: 10)
[04:45:30] [worker #1] ML tree search #6, logLikelihood: -501112.298761
[04:49:21 -791084.688987] AUTODETECT spr round 3 (radius: 15)
[04:54:20 -672509.492885] AUTODETECT spr round 4 (radius: 20)
[05:00:00 -596541.624102] AUTODETECT spr round 5 (radius: 25)
[05:06:38 -592655.511967] SPR radius for FAST iterations: 25 (autodetect)
[05:06:38 -592655.511967] Model parameter optimization (eps = 3.000000)
[05:06:50 -592616.434769] FAST spr round 1 (radius: 25)
[05:12:49 -506382.850656] FAST spr round 2 (radius: 25)
[05:16:44 -501703.272392] FAST spr round 3 (radius: 25)
[05:20:01 -501622.392371] FAST spr round 4 (radius: 25)
[05:22:53 -501618.253489] FAST spr round 5 (radius: 25)
[05:25:34 -501618.035743] FAST spr round 6 (radius: 25)
[05:28:10 -501618.035020] Model parameter optimization (eps = 1.000000)
[05:28:46 -501253.543235] SLOW spr round 1 (radius: 5)
[05:32:42 -501105.869835] SLOW spr round 2 (radius: 5)
[05:36:17 -501103.440832] SLOW spr round 3 (radius: 5)
[05:39:48 -501103.440639] SLOW spr round 4 (radius: 10)
[05:43:31 -501103.440588] SLOW spr round 5 (radius: 15)
[05:50:56 -501103.440552] SLOW spr round 6 (radius: 20)
[06:00:14 -501103.440517] SLOW spr round 7 (radius: 25)
[06:10:36 -501103.440483] Model parameter optimization (eps = 0.100000)

[06:10:50] [worker #0] ML tree search #7, logLikelihood: -501103.377827

[06:10:50 -1902122.047730] Initial branch length optimization
[06:11:02 -1535373.051027] Model parameter optimization (eps = 10.000000)
[06:12:32 -1532313.076424] AUTODETECT spr round 1 (radius: 5)
[06:16:52 -1052450.840725] AUTODETECT spr round 2 (radius: 10)
[06:19:13] [worker #1] ML tree search #8, logLikelihood: -501097.916546
[06:21:33 -793617.692188] AUTODETECT spr round 3 (radius: 15)
[06:27:13 -642750.036190] AUTODETECT spr round 4 (radius: 20)
[06:32:37 -599425.431589] AUTODETECT spr round 5 (radius: 25)
[06:38:52 -579703.123990] SPR radius for FAST iterations: 25 (autodetect)
[06:38:52 -579703.123990] Model parameter optimization (eps = 3.000000)
[06:39:38 -579148.311917] FAST spr round 1 (radius: 25)
[06:45:59 -504882.533938] FAST spr round 2 (radius: 25)
[06:49:53 -501397.044864] FAST spr round 3 (radius: 25)
[06:53:28 -501251.238961] FAST spr round 4 (radius: 25)
[06:56:32 -501234.515540] FAST spr round 5 (radius: 25)
[06:59:12 -501233.298578] FAST spr round 6 (radius: 25)
[07:01:49 -501233.298452] Model parameter optimization (eps = 1.000000)
[07:02:11 -501225.033801] SLOW spr round 1 (radius: 5)
[07:06:17 -501117.281557] SLOW spr round 2 (radius: 5)
[07:09:56 -501109.617039] SLOW spr round 3 (radius: 5)
[07:13:28 -501109.616812] SLOW spr round 4 (radius: 10)
[07:17:12 -501101.631265] SLOW spr round 5 (radius: 5)
[07:21:56 -501099.118262] SLOW spr round 6 (radius: 5)
[07:26:04 -501096.719160] SLOW spr round 7 (radius: 5)
[07:29:51 -501096.719032] SLOW spr round 8 (radius: 10)
[07:33:37 -501096.718998] SLOW spr round 9 (radius: 15)
[07:40:56 -501096.718963] SLOW spr round 10 (radius: 20)
[07:50:21 -501096.718929] SLOW spr round 11 (radius: 25)
[08:00:54 -501096.718895] Model parameter optimization (eps = 0.100000)

[08:01:06] [worker #0] ML tree search #9, logLikelihood: -501096.422181

[08:01:06 -1900482.917252] Initial branch length optimization
[08:01:16 -1529439.688934] Model parameter optimization (eps = 10.000000)
[08:03:00 -1526277.795140] AUTODETECT spr round 1 (radius: 5)
[08:07:22 -1066528.067744] AUTODETECT spr round 2 (radius: 10)
[08:08:35] [worker #1] ML tree search #10, logLikelihood: -501114.005361
[08:12:04 -812292.243116] AUTODETECT spr round 3 (radius: 15)
[08:17:46 -621295.543997] AUTODETECT spr round 4 (radius: 20)
[08:23:42 -595577.040952] AUTODETECT spr round 5 (radius: 25)
[08:30:16 -588181.302879] SPR radius for FAST iterations: 25 (autodetect)
[08:30:16 -588181.302879] Model parameter optimization (eps = 3.000000)
[08:30:45 -587457.460436] FAST spr round 1 (radius: 25)
[08:36:58 -504466.433822] FAST spr round 2 (radius: 25)
[08:41:12 -501459.626648] FAST spr round 3 (radius: 25)
[08:44:41 -501286.415484] FAST spr round 4 (radius: 25)
[08:47:41 -501267.212842] FAST spr round 5 (radius: 25)
[08:50:22 -501265.426068] FAST spr round 6 (radius: 25)
[08:52:58 -501265.423229] Model parameter optimization (eps = 1.000000)
[08:53:19 -501259.515310] SLOW spr round 1 (radius: 5)
[08:57:13 -501124.277034] SLOW spr round 2 (radius: 5)
[09:00:48 -501124.215970] SLOW spr round 3 (radius: 10)
[09:04:31 -501123.298656] SLOW spr round 4 (radius: 5)
[09:09:15 -501123.297252] SLOW spr round 5 (radius: 10)
[09:13:30 -501123.297217] SLOW spr round 6 (radius: 15)
[09:20:19 -501123.297182] SLOW spr round 7 (radius: 20)
[09:29:56 -501123.297147] SLOW spr round 8 (radius: 25)
[09:40:19 -501123.297112] Model parameter optimization (eps = 0.100000)

[09:40:36] [worker #0] ML tree search #11, logLikelihood: -501122.887347

[09:40:37 -1905645.185073] Initial branch length optimization
[09:40:48 -1530593.064344] Model parameter optimization (eps = 10.000000)
[09:42:16 -1527386.594673] AUTODETECT spr round 1 (radius: 5)
[09:46:38 -1085731.498796] AUTODETECT spr round 2 (radius: 10)
[09:49:51] [worker #1] ML tree search #12, logLikelihood: -501117.690260
[09:51:30 -786968.611906] AUTODETECT spr round 3 (radius: 15)
[09:56:39 -677757.422231] AUTODETECT spr round 4 (radius: 20)
[10:02:54 -593683.158452] AUTODETECT spr round 5 (radius: 25)
[10:09:10 -580570.968638] SPR radius for FAST iterations: 25 (autodetect)
[10:09:10 -580570.968638] Model parameter optimization (eps = 3.000000)
[10:09:48 -579976.327742] FAST spr round 1 (radius: 25)
[10:15:49 -503784.190773] FAST spr round 2 (radius: 25)
[10:19:59 -501387.063014] FAST spr round 3 (radius: 25)
[10:23:25 -501275.852392] FAST spr round 4 (radius: 25)
[10:26:19 -501248.326887] FAST spr round 5 (radius: 25)
[10:29:01 -501243.992406] FAST spr round 6 (radius: 25)
[10:31:37 -501243.992370] Model parameter optimization (eps = 1.000000)
[10:31:53 -501241.377827] SLOW spr round 1 (radius: 5)
[10:35:46 -501143.939460] SLOW spr round 2 (radius: 5)
[10:39:28 -501126.810929] SLOW spr round 3 (radius: 5)
[10:43:01 -501126.810874] SLOW spr round 4 (radius: 10)
[10:46:45 -501126.810840] SLOW spr round 5 (radius: 15)
[10:54:12 -501126.810806] SLOW spr round 6 (radius: 20)
[11:03:39 -501126.810772] SLOW spr round 7 (radius: 25)
[11:14:03 -501126.810737] Model parameter optimization (eps = 0.100000)

[11:14:19] [worker #0] ML tree search #13, logLikelihood: -501126.551372

[11:14:19 -1910729.382416] Initial branch length optimization
[11:14:31 -1539052.650491] Model parameter optimization (eps = 10.000000)
[11:16:26 -1536133.255337] AUTODETECT spr round 1 (radius: 5)
[11:20:47 -1055128.929934] AUTODETECT spr round 2 (radius: 10)
[11:25:25 -830268.095521] AUTODETECT spr round 3 (radius: 15)
[11:30:45 -649838.144657] AUTODETECT spr round 4 (radius: 20)
[11:31:12] [worker #1] ML tree search #14, logLikelihood: -501097.340348
[11:36:01 -581769.773068] AUTODETECT spr round 5 (radius: 25)
[11:42:19 -565856.536279] SPR radius for FAST iterations: 25 (autodetect)
[11:42:19 -565856.536279] Model parameter optimization (eps = 3.000000)
[11:43:02 -565427.960575] FAST spr round 1 (radius: 25)
[11:48:58 -504483.504839] FAST spr round 2 (radius: 25)
[11:53:02 -501473.995481] FAST spr round 3 (radius: 25)
[11:56:28 -501332.950526] FAST spr round 4 (radius: 25)
[11:59:23 -501321.274783] FAST spr round 5 (radius: 25)
[12:02:05 -501320.875454] FAST spr round 6 (radius: 25)
[12:04:41 -501320.875415] Model parameter optimization (eps = 1.000000)
[12:05:03 -501316.179238] SLOW spr round 1 (radius: 5)
[12:08:54 -501143.709652] SLOW spr round 2 (radius: 5)
[12:12:39 -501124.611414] SLOW spr round 3 (radius: 5)
[12:16:13 -501121.211437] SLOW spr round 4 (radius: 5)
[12:19:46 -501121.211383] SLOW spr round 5 (radius: 10)
[12:23:29 -501120.293963] SLOW spr round 6 (radius: 5)
[12:28:11 -501120.292561] SLOW spr round 7 (radius: 10)
[12:32:24 -501120.292523] SLOW spr round 8 (radius: 15)
[12:38:57 -501120.292484] SLOW spr round 9 (radius: 20)
[12:48:44 -501120.292446] SLOW spr round 10 (radius: 25)
[12:58:46 -501120.292408] Model parameter optimization (eps = 0.100000)

[12:59:04] [worker #0] ML tree search #15, logLikelihood: -501118.075223

[12:59:04 -1912942.705658] Initial branch length optimization
[12:59:15 -1541974.134494] Model parameter optimization (eps = 10.000000)
[13:00:51 -1539060.754355] AUTODETECT spr round 1 (radius: 5)
[13:02:43] [worker #1] ML tree search #16, logLikelihood: -501122.640067
[13:05:16 -1075265.307355] AUTODETECT spr round 2 (radius: 10)
[13:10:00 -810156.977209] AUTODETECT spr round 3 (radius: 15)
[13:15:22 -652419.868789] AUTODETECT spr round 4 (radius: 20)
[13:20:54 -593617.684614] AUTODETECT spr round 5 (radius: 25)
[13:28:04 -583314.985693] SPR radius for FAST iterations: 25 (autodetect)
[13:28:04 -583314.985693] Model parameter optimization (eps = 3.000000)
[13:28:46 -582690.291277] FAST spr round 1 (radius: 25)
[13:34:51 -504524.665889] FAST spr round 2 (radius: 25)
[13:39:03 -501301.301258] FAST spr round 3 (radius: 25)
[13:42:27 -501231.889489] FAST spr round 4 (radius: 25)
[13:45:15 -501231.889139] Model parameter optimization (eps = 1.000000)
[13:45:34 -501227.196733] SLOW spr round 1 (radius: 5)
[13:49:42 -501113.457001] SLOW spr round 2 (radius: 5)
[13:53:31 -501105.530491] SLOW spr round 3 (radius: 5)
[13:57:05 -501103.860936] SLOW spr round 4 (radius: 5)
[14:00:37 -501103.860725] SLOW spr round 5 (radius: 10)
[14:04:19 -501102.942473] SLOW spr round 6 (radius: 5)
[14:09:01 -501102.942085] SLOW spr round 7 (radius: 10)
[14:13:15 -501102.942050] SLOW spr round 8 (radius: 15)
[14:20:08 -501102.942016] SLOW spr round 9 (radius: 20)
[14:29:46 -501102.941981] SLOW spr round 10 (radius: 25)
[14:34:14] [worker #1] ML tree search #18, logLikelihood: -501103.973016
[14:40:22 -501102.941947] Model parameter optimization (eps = 0.100000)

[14:40:32] [worker #0] ML tree search #17, logLikelihood: -501102.799297

[14:40:33 -1887282.210890] Initial branch length optimization
[14:40:46 -1525121.571249] Model parameter optimization (eps = 10.000000)
[14:42:14 -1521911.625766] AUTODETECT spr round 1 (radius: 5)
[14:46:44 -1053808.369881] AUTODETECT spr round 2 (radius: 10)
[14:51:27 -784150.234121] AUTODETECT spr round 3 (radius: 15)
[14:56:57 -665610.462203] AUTODETECT spr round 4 (radius: 20)
[15:03:06 -594916.743084] AUTODETECT spr round 5 (radius: 25)
[15:10:19 -584710.573848] SPR radius for FAST iterations: 25 (autodetect)
[15:10:19 -584710.573848] Model parameter optimization (eps = 3.000000)
[15:10:57 -584075.195255] FAST spr round 1 (radius: 25)
[15:17:08 -506989.972476] FAST spr round 2 (radius: 25)
[15:21:25 -501573.968949] FAST spr round 3 (radius: 25)
[15:24:46 -501305.647871] FAST spr round 4 (radius: 25)
[15:27:42 -501237.226059] FAST spr round 5 (radius: 25)
[15:30:23 -501230.568393] FAST spr round 6 (radius: 25)
[15:33:00 -501229.309154] FAST spr round 7 (radius: 25)
[15:35:34 -501229.309011] Model parameter optimization (eps = 1.000000)
[15:35:53 -501226.031780] SLOW spr round 1 (radius: 5)
[15:39:43 -501127.858880] SLOW spr round 2 (radius: 5)
[15:43:20 -501121.767897] SLOW spr round 3 (radius: 5)
[15:46:50 -501121.767522] SLOW spr round 4 (radius: 10)
[15:50:34 -501121.767411] SLOW spr round 5 (radius: 15)
[15:57:52 -501121.767354] SLOW spr round 6 (radius: 20)
[16:06:33] [worker #1] ML tree search #20, logLikelihood: -501100.552655
[16:07:24 -501121.767311] SLOW spr round 7 (radius: 25)
[16:17:48 -501121.767272] Model parameter optimization (eps = 0.100000)

[16:17:51] [worker #0] ML tree search #19, logLikelihood: -501121.767248


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.151571,0.286124) (0.175981,0.498929) (0.367546,0.878453) (0.304902,1.790603) 
   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: -501096.422181

AIC score: 1006202.844361 / AICc score: 9050262.844361 / BIC score: 1016241.268291
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1104).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 68 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVE5/3_mltree/Q9NVE5.raxml.log

Analysis started: 03-Jul-2021 01:01:19 / finished: 03-Jul-2021 17:19:10

Elapsed time: 58671.356 seconds

Consumed energy: 4207.072 Wh (= 21 km in an electric car, or 105 km with an e-scooter!)