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 05-Jul-2021 14:08:53 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/2_msa/Q9BWH6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/2_msa/Q9BWH6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 457 taxa and 154 sites

WARNING: Sequences tr_J3KH65_J3KH65_COCIM_246410 and tr_A0A0J6Y020_A0A0J6Y020_COCIT_404692 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_F7GYP6_F7GYP6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_G7PAY9_G7PAY9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_A0A096NTP5_A0A096NTP5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_A0A0D9R627_A0A0D9R627_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_A0A2K5LNE7_A0A2K5LNE7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2NMX5_H2NMX5_PONAB_9601 and tr_A0A2K6B9U1_A0A2K6B9U1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G2XH61_G2XH61_VERDV_498257 and tr_A0A0G4N493_A0A0G4N493_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_Q7S0F6_Q7S0F6_NEUCR_367110 and tr_G4UXG3_G4UXG3_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_A0A179UUX9_A0A179UUX9_BLAGS_559298 and tr_C5GP84_C5GP84_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q983_H2Q983_PANTR_9598 and tr_A0A2R9B7W3_A0A2R9B7W3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_A0A0D2XVU3_A0A0D2XVU3_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_S0E3T7_S0E3T7_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_N4UE52_N4UE52_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_X0CT58_X0CT58_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_A0A2H3HHZ9_A0A2H3HHZ9_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9FG58_F9FG58_FUSOF_660025 and tr_A0A365N2P0_A0A365N2P0_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_E9EWY6_E9EWY6_METRA_655844 and tr_A0A0D9PH98_A0A0D9PH98_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6HQG6_C6HQG6_AJECH_544712 and tr_F0UQH1_F0UQH1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q2U558_Q2U558_ASPOR_510516 and tr_A0A1S9DIT6_A0A1S9DIT6_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_G7XFF8_G7XFF8_ASPKW_1033177 and tr_A0A146FTI8_A0A146FTI8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XFF8_G7XFF8_ASPKW_1033177 and tr_A0A317V1Z1_A0A317V1Z1_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_E5SE09_E5SE09_TRISP_6334 and tr_A0A0V0SKQ6_A0A0V0SKQ6_9BILA_6336 are exactly identical!
WARNING: Sequences tr_F2SHL0_F2SHL0_TRIRC_559305 and tr_A0A178F0I0_A0A178F0I0_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_D4ASK2_D4ASK2_ARTBC_663331 and tr_F2PLH1_F2PLH1_TRIEC_559882 are exactly identical!
WARNING: Sequences tr_G3YBZ8_G3YBZ8_ASPNA_380704 and tr_A0A319AJJ6_A0A319AJJ6_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_M2THM3_M2THM3_COCH5_701091 and tr_W6YV49_W6YV49_COCCA_930089 are exactly identical!
WARNING: Sequences tr_A0A066X2X6_A0A066X2X6_COLSU_1173701 and tr_A0A166TJ86_A0A166TJ86_9PEZI_1573173 are exactly identical!
WARNING: Sequences tr_A0A0A2KEP2_A0A0A2KEP2_PENIT_40296 and tr_A0A0A2JPY5_A0A0A2JPY5_PENEN_27334 are exactly identical!
WARNING: Sequences tr_A0A0F0IP76_A0A0F0IP76_ASPPU_1403190 and tr_A0A2G7GBC7_A0A2G7GBC7_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0G0ATJ0_A0A0G0ATJ0_TRIHA_5544 and tr_A0A2T3ZWT4_A0A2T3ZWT4_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0F8UYA1_A0A0F8UYA1_9EURO_308745 and tr_A0A2T5M0C5_A0A2T5M0C5_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0M8P0N7_A0A0M8P0N7_9EURO_229535 and tr_A0A0G4P1C8_A0A0G4P1C8_PENCA_1429867 are exactly identical!
WARNING: Sequences tr_A0A0M8P0N7_A0A0M8P0N7_9EURO_229535 and tr_A0A101MIP2_A0A101MIP2_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0M8P0N7_A0A0M8P0N7_9EURO_229535 and tr_A0A1V6NY89_A0A1V6NY89_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0V1DE54_A0A0V1DE54_TRIBR_45882 and tr_A0A0V0VM13_A0A0V0VM13_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1DE54_A0A0V1DE54_TRIBR_45882 and tr_A0A0V0TS36_A0A0V0TS36_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1A8I5_A0A0V1A8I5_9BILA_990121 and tr_A0A0V1NY59_A0A0V1NY59_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0YLV6_A0A0V0YLV6_TRIPS_6337 and tr_A0A0V1MB93_A0A0V1MB93_9BILA_268474 are exactly identical!
WARNING: Sequences tr_A0A0V0YLV6_A0A0V0YLV6_TRIPS_6337 and tr_A0A0V1H9A8_A0A0V1H9A8_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A100IPJ4_A0A100IPJ4_ASPNG_5061 and tr_A0A1L9N2Q9_A0A1L9N2Q9_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_I1RQK7_I1RQK7_GIBZE_229533 and tr_A0A2T4GML3_A0A2T4GML3_FUSCU_5516 are exactly identical!
WARNING: Duplicate sequences found: 42

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/Q9BWH6/3_mltree/Q9BWH6.raxml.reduced.phy

Alignment comprises 1 partitions and 154 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 154 / 154
Gaps: 3.35 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 457 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 154 / 12320
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -115712.370612] Initial branch length optimization
[00:00:01 -96333.465634] Model parameter optimization (eps = 10.000000)
[00:00:22 -96003.274508] AUTODETECT spr round 1 (radius: 5)
[00:00:58 -64280.384421] AUTODETECT spr round 2 (radius: 10)
[00:01:41 -47830.485919] AUTODETECT spr round 3 (radius: 15)
[00:02:36 -40815.530305] AUTODETECT spr round 4 (radius: 20)
[00:03:45 -39741.055624] AUTODETECT spr round 5 (radius: 25)
[00:05:04 -39473.636075] SPR radius for FAST iterations: 25 (autodetect)
[00:05:04 -39473.636075] Model parameter optimization (eps = 3.000000)
[00:05:16 -39446.634752] FAST spr round 1 (radius: 25)
[00:06:02 -36618.933182] FAST spr round 2 (radius: 25)
[00:06:41 -36507.922423] FAST spr round 3 (radius: 25)
[00:07:13 -36499.458580] FAST spr round 4 (radius: 25)
[00:07:43 -36499.458130] Model parameter optimization (eps = 1.000000)
[00:07:54 -36487.930235] SLOW spr round 1 (radius: 5)
[00:08:41 -36476.022108] SLOW spr round 2 (radius: 5)
[00:09:26 -36473.246602] SLOW spr round 3 (radius: 5)
[00:10:10 -36471.759968] SLOW spr round 4 (radius: 5)
[00:10:53 -36471.460868] SLOW spr round 5 (radius: 5)
[00:11:34 -36471.460802] SLOW spr round 6 (radius: 10)
[00:12:16 -36471.383176] SLOW spr round 7 (radius: 15)
[00:13:29 -36470.415358] SLOW spr round 8 (radius: 5)
[00:14:32 -36469.648788] SLOW spr round 9 (radius: 5)
[00:15:24 -36467.944710] SLOW spr round 10 (radius: 5)
[00:16:11 -36467.943978] SLOW spr round 11 (radius: 10)
[00:16:55 -36467.446695] SLOW spr round 12 (radius: 5)
[00:17:55 -36467.445958] SLOW spr round 13 (radius: 10)
[00:18:43 -36467.445324] SLOW spr round 14 (radius: 15)
[00:19:52 -36467.444884] SLOW spr round 15 (radius: 20)
[00:21:16 -36467.043348] SLOW spr round 16 (radius: 5)
[00:22:18 -36467.040427] SLOW spr round 17 (radius: 10)
[00:23:11 -36467.022725] SLOW spr round 18 (radius: 15)
[00:24:18 -36467.022474] SLOW spr round 19 (radius: 20)
[00:25:40 -36465.718701] SLOW spr round 20 (radius: 5)
[00:26:02] [worker #1] ML tree search #2, logLikelihood: -36460.136105
[00:26:43 -36465.649341] SLOW spr round 21 (radius: 10)
[00:27:13] [worker #2] ML tree search #3, logLikelihood: -36471.097132
[00:27:36 -36465.649167] SLOW spr round 22 (radius: 15)
[00:28:44 -36465.649095] SLOW spr round 23 (radius: 20)
[00:30:08 -36465.625132] SLOW spr round 24 (radius: 25)
[00:31:42 -36465.624399] Model parameter optimization (eps = 0.100000)

[00:31:50] [worker #0] ML tree search #1, logLikelihood: -36465.012855

[00:31:50 -117531.921226] Initial branch length optimization
[00:31:52 -98501.187027] Model parameter optimization (eps = 10.000000)
[00:32:10 -98186.225324] AUTODETECT spr round 1 (radius: 5)
[00:32:46 -66854.565426] AUTODETECT spr round 2 (radius: 10)
[00:33:29 -52941.420321] AUTODETECT spr round 3 (radius: 15)
[00:34:23 -45636.510893] AUTODETECT spr round 4 (radius: 20)
[00:35:17 -43568.515047] AUTODETECT spr round 5 (radius: 25)
[00:36:17 -42444.161934] SPR radius for FAST iterations: 25 (autodetect)
[00:36:17 -42444.161934] Model parameter optimization (eps = 3.000000)
[00:36:28 -42408.605756] FAST spr round 1 (radius: 25)
[00:37:16 -36866.861367] FAST spr round 2 (radius: 25)
[00:37:58 -36523.845379] FAST spr round 3 (radius: 25)
[00:38:35 -36501.005114] FAST spr round 4 (radius: 25)
[00:39:03 -36500.767615] FAST spr round 5 (radius: 25)
[00:39:32 -36500.767608] Model parameter optimization (eps = 1.000000)
[00:39:41 -36489.683315] SLOW spr round 1 (radius: 5)
[00:40:28 -36474.365220] SLOW spr round 2 (radius: 5)
[00:41:11 -36472.620872] SLOW spr round 3 (radius: 5)
[00:41:52 -36472.265310] SLOW spr round 4 (radius: 5)
[00:42:33 -36472.264900] SLOW spr round 5 (radius: 10)
[00:43:16 -36472.264890] SLOW spr round 6 (radius: 15)
[00:44:27 -36470.961002] SLOW spr round 7 (radius: 5)
[00:45:29 -36470.960577] SLOW spr round 8 (radius: 10)
[00:46:19 -36470.960495] SLOW spr round 9 (radius: 15)
[00:47:25 -36470.960456] SLOW spr round 10 (radius: 20)
[00:48:56 -36470.026863] SLOW spr round 11 (radius: 5)
[00:49:23] [worker #2] ML tree search #6, logLikelihood: -36448.455900
[00:49:25] [worker #1] ML tree search #5, logLikelihood: -36469.786189
[00:49:58 -36470.026718] SLOW spr round 12 (radius: 10)
[00:50:50 -36470.026715] SLOW spr round 13 (radius: 15)
[00:51:56 -36470.026714] SLOW spr round 14 (radius: 20)
[00:53:26 -36470.026714] SLOW spr round 15 (radius: 25)
[00:55:02 -36470.026714] Model parameter optimization (eps = 0.100000)

[00:55:06] [worker #0] ML tree search #4, logLikelihood: -36469.813049

[00:55:06 -117580.458989] Initial branch length optimization
[00:55:08 -98059.789055] Model parameter optimization (eps = 10.000000)
[00:55:25 -97703.039853] AUTODETECT spr round 1 (radius: 5)
[00:56:03 -64716.606601] AUTODETECT spr round 2 (radius: 10)
[00:56:45 -48611.692063] AUTODETECT spr round 3 (radius: 15)
[00:57:37 -41951.468613] AUTODETECT spr round 4 (radius: 20)
[00:58:41 -40885.411980] AUTODETECT spr round 5 (radius: 25)
[00:59:53 -40694.102150] SPR radius for FAST iterations: 25 (autodetect)
[00:59:53 -40694.102150] Model parameter optimization (eps = 3.000000)
[01:00:09 -40658.030744] FAST spr round 1 (radius: 25)
[01:00:57 -36950.678286] FAST spr round 2 (radius: 25)
[01:01:33 -36674.400243] FAST spr round 3 (radius: 25)
[01:02:08 -36551.161101] FAST spr round 4 (radius: 25)
[01:02:39 -36488.304707] FAST spr round 5 (radius: 25)
[01:03:09 -36474.733969] FAST spr round 6 (radius: 25)
[01:03:36 -36474.731172] Model parameter optimization (eps = 1.000000)
[01:03:47 -36470.365446] SLOW spr round 1 (radius: 5)
[01:04:29 -36460.703444] SLOW spr round 2 (radius: 5)
[01:05:13 -36458.550773] SLOW spr round 3 (radius: 5)
[01:05:53 -36458.549454] SLOW spr round 4 (radius: 10)
[01:06:37 -36457.775699] SLOW spr round 5 (radius: 5)
[01:07:36 -36457.775266] SLOW spr round 6 (radius: 10)
[01:08:24 -36457.051471] SLOW spr round 7 (radius: 5)
[01:09:20 -36457.050643] SLOW spr round 8 (radius: 10)
[01:10:08 -36457.050434] SLOW spr round 9 (radius: 15)
[01:11:16 -36456.357255] SLOW spr round 10 (radius: 5)
[01:12:17 -36454.737742] SLOW spr round 11 (radius: 5)
[01:13:08 -36454.737701] SLOW spr round 12 (radius: 10)
[01:13:41] [worker #2] ML tree search #9, logLikelihood: -36459.670215
[01:13:52 -36454.737698] SLOW spr round 13 (radius: 15)
[01:14:25] [worker #1] ML tree search #8, logLikelihood: -36474.855770
[01:15:00 -36454.737698] SLOW spr round 14 (radius: 20)
[01:16:28 -36454.737697] SLOW spr round 15 (radius: 25)
[01:18:03 -36454.737697] Model parameter optimization (eps = 0.100000)

[01:18:06] [worker #0] ML tree search #7, logLikelihood: -36454.706572

[01:18:06 -118095.223265] Initial branch length optimization
[01:18:08 -98539.294381] Model parameter optimization (eps = 10.000000)
[01:18:28 -98187.901439] AUTODETECT spr round 1 (radius: 5)
[01:19:04 -63462.217970] AUTODETECT spr round 2 (radius: 10)
[01:19:45 -51070.686017] AUTODETECT spr round 3 (radius: 15)
[01:20:34 -42189.290305] AUTODETECT spr round 4 (radius: 20)
[01:21:30 -41177.900636] AUTODETECT spr round 5 (radius: 25)
[01:22:45 -40823.980492] SPR radius for FAST iterations: 25 (autodetect)
[01:22:45 -40823.980492] Model parameter optimization (eps = 3.000000)
[01:23:00 -40789.452673] FAST spr round 1 (radius: 25)
[01:23:47 -36713.671660] FAST spr round 2 (radius: 25)
[01:24:22 -36503.312909] FAST spr round 3 (radius: 25)
[01:24:54 -36490.365902] FAST spr round 4 (radius: 25)
[01:25:22 -36490.129863] FAST spr round 5 (radius: 25)
[01:25:50 -36490.129822] Model parameter optimization (eps = 1.000000)
[01:25:58 -36484.898763] SLOW spr round 1 (radius: 5)
[01:26:43 -36467.431582] SLOW spr round 2 (radius: 5)
[01:27:28 -36465.192872] SLOW spr round 3 (radius: 5)
[01:28:11 -36462.920690] SLOW spr round 4 (radius: 5)
[01:28:52 -36462.920581] SLOW spr round 5 (radius: 10)
[01:29:32 -36462.071931] SLOW spr round 6 (radius: 5)
[01:30:32 -36462.070766] SLOW spr round 7 (radius: 10)
[01:31:21 -36462.070705] SLOW spr round 8 (radius: 15)
[01:32:28 -36460.185119] SLOW spr round 9 (radius: 5)
[01:33:29 -36460.145540] SLOW spr round 10 (radius: 10)
[01:34:19 -36460.144321] SLOW spr round 11 (radius: 15)
[01:35:26 -36460.143732] SLOW spr round 12 (radius: 20)
[01:36:49 -36458.657901] SLOW spr round 13 (radius: 5)
[01:37:54 -36458.276766] SLOW spr round 14 (radius: 5)
[01:38:48 -36458.273937] SLOW spr round 15 (radius: 10)
[01:39:15] [worker #2] ML tree search #12, logLikelihood: -36453.822607
[01:39:33 -36458.273429] SLOW spr round 16 (radius: 15)
[01:40:41 -36458.273327] SLOW spr round 17 (radius: 20)
[01:42:08 -36458.273303] SLOW spr round 18 (radius: 25)
[01:43:39 -36457.752492] SLOW spr round 19 (radius: 5)
[01:44:43 -36457.752227] SLOW spr round 20 (radius: 10)
[01:45:36 -36457.752214] SLOW spr round 21 (radius: 15)
[01:46:43 -36457.752209] SLOW spr round 22 (radius: 20)
[01:48:08 -36457.752208] SLOW spr round 23 (radius: 25)
[01:49:42 -36457.752207] Model parameter optimization (eps = 0.100000)

[01:49:49] [worker #0] ML tree search #10, logLikelihood: -36456.669099

[01:49:49 -116500.494210] Initial branch length optimization
[01:49:50 -96797.912032] Model parameter optimization (eps = 10.000000)
[01:50:07 -96473.910324] AUTODETECT spr round 1 (radius: 5)
[01:50:43 -63738.677084] AUTODETECT spr round 2 (radius: 10)
[01:51:27 -49158.103922] AUTODETECT spr round 3 (radius: 15)
[01:52:24 -41958.447905] AUTODETECT spr round 4 (radius: 20)
[01:53:23 -40138.544110] AUTODETECT spr round 5 (radius: 25)
[01:54:38 -39974.324254] SPR radius for FAST iterations: 25 (autodetect)
[01:54:38 -39974.324254] Model parameter optimization (eps = 3.000000)
[01:54:49 -39936.123779] FAST spr round 1 (radius: 25)
[01:55:39 -36784.041944] FAST spr round 2 (radius: 25)
[01:56:20 -36529.266236] FAST spr round 3 (radius: 25)
[01:56:55 -36483.013934] FAST spr round 4 (radius: 25)
[01:57:26 -36476.700997] FAST spr round 5 (radius: 25)
[01:57:55 -36476.700662] Model parameter optimization (eps = 1.000000)
[01:58:05 -36472.348002] SLOW spr round 1 (radius: 5)
[01:58:50 -36462.375471] SLOW spr round 2 (radius: 5)
[01:59:32 -36460.434576] SLOW spr round 3 (radius: 5)
[02:00:12 -36460.434269] SLOW spr round 4 (radius: 10)
[02:00:55 -36460.373905] SLOW spr round 5 (radius: 15)
[02:01:14] [worker #1] ML tree search #11, logLikelihood: -36452.580789
[02:02:07 -36459.759179] SLOW spr round 6 (radius: 5)
[02:03:08 -36459.748537] SLOW spr round 7 (radius: 10)
[02:03:58 -36459.746877] SLOW spr round 8 (radius: 15)
[02:05:05 -36459.746338] SLOW spr round 9 (radius: 20)
[02:06:29 -36459.746159] SLOW spr round 10 (radius: 25)
[02:08:02 -36459.746099] Model parameter optimization (eps = 0.100000)

[02:08:07] [worker #0] ML tree search #13, logLikelihood: -36459.635390

[02:08:07 -116203.410757] Initial branch length optimization
[02:08:08 -97463.151373] Model parameter optimization (eps = 10.000000)
[02:08:24 -97123.242174] AUTODETECT spr round 1 (radius: 5)
[02:09:01 -65129.047352] AUTODETECT spr round 2 (radius: 10)
[02:09:44 -47634.523764] AUTODETECT spr round 3 (radius: 15)
[02:10:36 -41883.843494] AUTODETECT spr round 4 (radius: 20)
[02:11:12] [worker #2] ML tree search #15, logLikelihood: -36464.046002
[02:11:42 -40712.067622] AUTODETECT spr round 5 (radius: 25)
[02:12:57 -40370.967092] SPR radius for FAST iterations: 25 (autodetect)
[02:12:57 -40370.967092] Model parameter optimization (eps = 3.000000)
[02:13:09 -40353.201018] FAST spr round 1 (radius: 25)
[02:13:55 -36878.581839] FAST spr round 2 (radius: 25)
[02:14:30 -36558.391575] FAST spr round 3 (radius: 25)
[02:15:04 -36503.918700] FAST spr round 4 (radius: 25)
[02:15:35 -36492.343095] FAST spr round 5 (radius: 25)
[02:16:05 -36490.282224] FAST spr round 6 (radius: 25)
[02:16:32 -36490.210155] Model parameter optimization (eps = 1.000000)
[02:16:42 -36481.570805] SLOW spr round 1 (radius: 5)
[02:17:26 -36473.667451] SLOW spr round 2 (radius: 5)
[02:18:10 -36471.484303] SLOW spr round 3 (radius: 5)
[02:18:50 -36471.483765] SLOW spr round 4 (radius: 10)
[02:19:31 -36471.389945] SLOW spr round 5 (radius: 15)
[02:20:40 -36470.280061] SLOW spr round 6 (radius: 5)
[02:21:42 -36470.239879] SLOW spr round 7 (radius: 10)
[02:22:32 -36468.500733] SLOW spr round 8 (radius: 5)
[02:23:29 -36468.500422] SLOW spr round 9 (radius: 10)
[02:24:15 -36468.500400] SLOW spr round 10 (radius: 15)
[02:25:20 -36468.500390] SLOW spr round 11 (radius: 20)
[02:26:42 -36468.248585] SLOW spr round 12 (radius: 5)
[02:27:45 -36468.165985] SLOW spr round 13 (radius: 10)
[02:28:36 -36468.165861] SLOW spr round 14 (radius: 15)
[02:29:39 -36468.165859] SLOW spr round 15 (radius: 20)
[02:31:02 -36468.165859] SLOW spr round 16 (radius: 25)
[02:32:32 -36468.067950] Model parameter optimization (eps = 0.100000)

[02:32:36] [worker #0] ML tree search #16, logLikelihood: -36467.915533

[02:32:36 -116455.508876] Initial branch length optimization
[02:32:37 -97421.594791] Model parameter optimization (eps = 10.000000)
[02:32:57 -97093.471318] AUTODETECT spr round 1 (radius: 5)
[02:33:33 -64060.407676] AUTODETECT spr round 2 (radius: 10)
[02:34:15 -49127.413213] AUTODETECT spr round 3 (radius: 15)
[02:35:05 -43690.653214] AUTODETECT spr round 4 (radius: 20)
[02:36:12 -41027.589190] AUTODETECT spr round 5 (radius: 25)
[02:37:26 -40590.713625] SPR radius for FAST iterations: 25 (autodetect)
[02:37:26 -40590.713625] Model parameter optimization (eps = 3.000000)
[02:37:40 -40553.882328] FAST spr round 1 (radius: 25)
[02:38:25 -36794.063825] FAST spr round 2 (radius: 25)
[02:39:04 -36539.846210] FAST spr round 3 (radius: 25)
[02:39:37 -36506.848659] FAST spr round 4 (radius: 25)
[02:40:07 -36502.658933] FAST spr round 5 (radius: 25)
[02:40:36 -36502.658512] Model parameter optimization (eps = 1.000000)
[02:40:42 -36498.001796] SLOW spr round 1 (radius: 5)
[02:40:43] [worker #1] ML tree search #14, logLikelihood: -36456.834898
[02:41:28 -36488.426885] SLOW spr round 2 (radius: 5)
[02:42:14 -36480.357769] SLOW spr round 3 (radius: 5)
[02:42:38] [worker #2] ML tree search #18, logLikelihood: -36455.135046
[02:42:56 -36479.865053] SLOW spr round 4 (radius: 5)
[02:43:37 -36479.864911] SLOW spr round 5 (radius: 10)
[02:44:18 -36479.471857] SLOW spr round 6 (radius: 5)
[02:45:16 -36479.471839] SLOW spr round 7 (radius: 10)
[02:46:03 -36479.471834] SLOW spr round 8 (radius: 15)
[02:47:11 -36478.930404] SLOW spr round 9 (radius: 5)
[02:48:12 -36478.913034] SLOW spr round 10 (radius: 10)
[02:49:01 -36478.913032] SLOW spr round 11 (radius: 15)
[02:50:08 -36478.913031] SLOW spr round 12 (radius: 20)
[02:51:31 -36478.913031] SLOW spr round 13 (radius: 25)
[02:53:05 -36468.804410] SLOW spr round 14 (radius: 5)
[02:54:09 -36468.804323] SLOW spr round 15 (radius: 10)
[02:55:00 -36468.804315] SLOW spr round 16 (radius: 15)
[02:56:06 -36468.804311] SLOW spr round 17 (radius: 20)
[02:57:30 -36468.804309] SLOW spr round 18 (radius: 25)
[02:59:03 -36468.804308] Model parameter optimization (eps = 0.100000)

[02:59:11] [worker #0] ML tree search #19, logLikelihood: -36468.059154

[03:06:43] [worker #1] ML tree search #17, logLikelihood: -36455.119584
[03:34:34] [worker #1] ML tree search #20, logLikelihood: -36469.161339

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.123904,0.421360) (0.256547,0.570315) (0.326181,0.872688) (0.293368,1.761694) 
   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: -36448.455900

AIC score: 74730.911800 / AICc score: 1758342.911800 / BIC score: 77515.797337
Free parameters (model + branch lengths): 917

WARNING: Number of free parameters (K=917) is larger than alignment size (n=154).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 61 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BWH6/3_mltree/Q9BWH6.raxml.log

Analysis started: 05-Jul-2021 14:08:53 / finished: 05-Jul-2021 17:43:28

Elapsed time: 12874.860 seconds

Consumed energy: 1010.134 Wh (= 5 km in an electric car, or 25 km with an e-scooter!)