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

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 06-Jul-2021 14:49:48 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/2_msa/Q9Y487_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487 --seed 2 --threads 8 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/2_msa/Q9Y487_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 931 sites

WARNING: Sequences tr_B6QQF8_B6QQF8_TALMQ_441960 and tr_A0A093V7N8_A0A093V7N8_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8N3B7_B8N3B7_ASPFN_332952 and tr_Q2UJS9_Q2UJS9_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8N3B7_B8N3B7_ASPFN_332952 and tr_A0A1S9DLP6_A0A1S9DLP6_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_H2Q764_H2Q764_PANTR_9598 and tr_A0A2R9BD05_A0A2R9BD05_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7AA39_K7AA39_PANTR_9598 and tr_A0A2R9B4D4_A0A2R9B4D4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A2QIZ9_A2QIZ9_ASPNC_425011 and tr_G3Y9B8_G3Y9B8_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QIZ9_A2QIZ9_ASPNC_425011 and tr_A0A319AGR7_A0A319AGR7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7N6A4_G7N6A4_MACMU_9544 and tr_A0A2K6D3V2_A0A2K6D3V2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7X810_G7X810_ASPKW_1033177 and tr_A0A146FJK4_A0A146FJK4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7X810_G7X810_ASPKW_1033177 and tr_A0A317UPU9_A0A317UPU9_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F2SXD4_F2SXD4_TRIRC_559305 and tr_A0A178F814_A0A178F814_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RPL7_B3RPL7_TRIAD_10228 and tr_A0A369SET9_A0A369SET9_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PUU9_G7PUU9_MACFA_9541 and tr_A0A2I3LMH7_A0A2I3LMH7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A226MJP3_A0A226MJP3_CALSU_9009 and tr_A0A226NTS2_A0A226NTS2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PLB1_A0A2D0PLB1_ICTPU_7998 and tr_A0A2D0PPM1_A0A2D0PPM1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PPJ3_A0A2D0PPJ3_ICTPU_7998 and tr_W5U7X1_W5U7X1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A383ZRW5_A0A383ZRW5_BALAS_310752 and tr_A0A383ZS51_A0A383ZS51_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 17

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.raxml.reduced.phy

Alignment comprises 1 partitions and 931 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 931 / 931
Gaps: 12.51 %
Invariant sites: 0.86 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.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 / 233 / 18640
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1335123.216081] Initial branch length optimization
[00:00:09 -1147907.037650] Model parameter optimization (eps = 10.000000)
[00:01:14 -1145665.069396] AUTODETECT spr round 1 (radius: 5)
[00:04:54 -769180.650460] AUTODETECT spr round 2 (radius: 10)
[00:08:55 -568380.053824] AUTODETECT spr round 3 (radius: 15)
[00:13:04 -461900.134091] AUTODETECT spr round 4 (radius: 20)
[00:17:44 -423532.058184] AUTODETECT spr round 5 (radius: 25)
[00:22:38 -419449.987595] SPR radius for FAST iterations: 25 (autodetect)
[00:22:38 -419449.987595] Model parameter optimization (eps = 3.000000)
[00:23:05 -419268.707531] FAST spr round 1 (radius: 25)
[00:26:57 -356274.876947] FAST spr round 2 (radius: 25)
[00:29:48 -354616.011986] FAST spr round 3 (radius: 25)
[00:32:21 -354484.799947] FAST spr round 4 (radius: 25)
[00:34:37 -354468.828375] FAST spr round 5 (radius: 25)
[00:36:46 -354468.828261] Model parameter optimization (eps = 1.000000)
[00:37:04 -354464.935249] SLOW spr round 1 (radius: 5)
[00:40:17 -354377.141880] SLOW spr round 2 (radius: 5)
[00:43:18 -354371.500191] SLOW spr round 3 (radius: 5)
[00:46:14 -354371.499935] SLOW spr round 4 (radius: 10)
[00:49:22 -354367.543898] SLOW spr round 5 (radius: 5)
[00:53:16 -354366.787986] SLOW spr round 6 (radius: 5)
[00:56:38 -354366.787469] SLOW spr round 7 (radius: 10)
[00:59:53 -354366.459690] SLOW spr round 8 (radius: 5)
[01:03:45 -354363.895090] SLOW spr round 9 (radius: 5)
[01:07:03 -354363.894906] SLOW spr round 10 (radius: 10)
[01:10:17 -354363.702180] SLOW spr round 11 (radius: 5)
[01:14:07 -354361.813122] SLOW spr round 12 (radius: 5)
[01:15:21] [worker #1] ML tree search #2, logLikelihood: -354349.491132
[01:17:27 -354359.172087] SLOW spr round 13 (radius: 5)
[01:20:31 -354359.171875] SLOW spr round 14 (radius: 10)
[01:23:41 -354359.171660] SLOW spr round 15 (radius: 15)
[01:28:57 -354359.171440] SLOW spr round 16 (radius: 20)
[01:37:19 -354359.171215] SLOW spr round 17 (radius: 25)
[01:47:40 -354359.170986] Model parameter optimization (eps = 0.100000)

[01:47:49] [worker #0] ML tree search #1, logLikelihood: -354359.033010

[01:47:49 -1330919.617756] Initial branch length optimization
[01:47:57 -1146790.675799] Model parameter optimization (eps = 10.000000)
[01:48:43 -1144736.678690] AUTODETECT spr round 1 (radius: 5)
[01:52:26 -782856.535293] AUTODETECT spr round 2 (radius: 10)
[01:56:27 -581843.176456] AUTODETECT spr round 3 (radius: 15)
[02:00:31 -484818.651340] AUTODETECT spr round 4 (radius: 20)
[02:05:13 -430796.405635] AUTODETECT spr round 5 (radius: 25)
[02:10:20 -420017.849306] SPR radius for FAST iterations: 25 (autodetect)
[02:10:20 -420017.849306] Model parameter optimization (eps = 3.000000)
[02:10:46 -419840.894367] FAST spr round 1 (radius: 25)
[02:14:48 -356610.776223] FAST spr round 2 (radius: 25)
[02:17:44 -354728.416236] FAST spr round 3 (radius: 25)
[02:20:20 -354513.856816] FAST spr round 4 (radius: 25)
[02:22:38 -354504.261741] FAST spr round 5 (radius: 25)
[02:24:45 -354502.053493] FAST spr round 6 (radius: 25)
[02:26:50 -354502.053493] Model parameter optimization (eps = 1.000000)
[02:27:07 -354493.785408] SLOW spr round 1 (radius: 5)
[02:30:24 -354406.549984] SLOW spr round 2 (radius: 5)
[02:33:29 -354382.845078] SLOW spr round 3 (radius: 5)
[02:36:24 -354382.845047] SLOW spr round 4 (radius: 10)
[02:39:38 -354367.168014] SLOW spr round 5 (radius: 5)
[02:42:07] [worker #1] ML tree search #4, logLikelihood: -354366.221351
[02:43:31 -354367.167617] SLOW spr round 6 (radius: 10)
[02:47:08 -354361.521796] SLOW spr round 7 (radius: 5)
[02:51:04 -354357.312610] SLOW spr round 8 (radius: 5)
[02:54:24 -354357.312554] SLOW spr round 9 (radius: 10)
[02:57:44 -354357.312554] SLOW spr round 10 (radius: 15)
[03:02:57 -354357.312554] SLOW spr round 11 (radius: 20)
[03:11:27 -354357.312554] SLOW spr round 12 (radius: 25)
[03:22:25 -354357.312554] Model parameter optimization (eps = 0.100000)

[03:22:37] [worker #0] ML tree search #3, logLikelihood: -354357.154253

[03:22:37 -1329970.304277] Initial branch length optimization
[03:22:47 -1145062.923718] Model parameter optimization (eps = 10.000000)
[03:23:37 -1142862.175256] AUTODETECT spr round 1 (radius: 5)
[03:27:36 -773828.246630] AUTODETECT spr round 2 (radius: 10)
[03:32:02 -552045.414049] AUTODETECT spr round 3 (radius: 15)
[03:36:43 -447816.914857] AUTODETECT spr round 4 (radius: 20)
[03:41:20 -423384.882860] AUTODETECT spr round 5 (radius: 25)
[03:46:33 -413976.040646] SPR radius for FAST iterations: 25 (autodetect)
[03:46:33 -413976.040646] Model parameter optimization (eps = 3.000000)
[03:47:07 -413733.908514] FAST spr round 1 (radius: 25)
[03:51:20 -356597.121822] FAST spr round 2 (radius: 25)
[03:54:24 -354642.530467] FAST spr round 3 (radius: 25)
[03:57:06 -354464.628508] FAST spr round 4 (radius: 25)
[03:59:20 -354460.625686] FAST spr round 5 (radius: 25)
[04:01:29 -354459.785576] FAST spr round 6 (radius: 25)
[04:03:35 -354459.784890] Model parameter optimization (eps = 1.000000)
[04:03:47 -354458.270903] SLOW spr round 1 (radius: 5)
[04:07:03 -354400.021089] SLOW spr round 2 (radius: 5)
[04:10:04 -354399.241104] SLOW spr round 3 (radius: 5)
[04:11:30] [worker #1] ML tree search #6, logLikelihood: -354348.973938
[04:13:02 -354399.241104] SLOW spr round 4 (radius: 10)
[04:16:19 -354397.220931] SLOW spr round 5 (radius: 5)
[04:20:18 -354395.415713] SLOW spr round 6 (radius: 5)
[04:23:41 -354395.415712] SLOW spr round 7 (radius: 10)
[04:27:02 -354395.415712] SLOW spr round 8 (radius: 15)
[04:32:19 -354395.415712] SLOW spr round 9 (radius: 20)
[04:40:54 -354395.415712] SLOW spr round 10 (radius: 25)
[04:51:23 -354395.415712] Model parameter optimization (eps = 0.100000)

[04:51:33] [worker #0] ML tree search #5, logLikelihood: -354395.374156

[04:51:33 -1323118.754540] Initial branch length optimization
[04:51:40 -1140936.689620] Model parameter optimization (eps = 10.000000)
[04:52:34 -1139072.835271] AUTODETECT spr round 1 (radius: 5)
[04:56:16 -781105.816438] AUTODETECT spr round 2 (radius: 10)
[05:00:33 -567594.436886] AUTODETECT spr round 3 (radius: 15)
[05:04:32 -448530.315992] AUTODETECT spr round 4 (radius: 20)
[05:09:04 -424908.057507] AUTODETECT spr round 5 (radius: 25)
[05:15:19 -420867.327093] SPR radius for FAST iterations: 25 (autodetect)
[05:15:19 -420867.327093] Model parameter optimization (eps = 3.000000)
[05:15:46 -420673.771696] FAST spr round 1 (radius: 25)
[05:20:01 -356697.538209] FAST spr round 2 (radius: 25)
[05:23:01 -354621.221380] FAST spr round 3 (radius: 25)
[05:25:40 -354540.696006] FAST spr round 4 (radius: 25)
[05:27:59 -354527.190100] FAST spr round 5 (radius: 25)
[05:30:12 -354520.453998] FAST spr round 6 (radius: 25)
[05:32:21 -354520.453867] Model parameter optimization (eps = 1.000000)
[05:32:40 -354510.903395] SLOW spr round 1 (radius: 5)
[05:36:10 -354415.707764] SLOW spr round 2 (radius: 5)
[05:39:14 -354413.807538] SLOW spr round 3 (radius: 5)
[05:39:15] [worker #1] ML tree search #8, logLikelihood: -354369.435459
[05:42:16 -354413.807346] SLOW spr round 4 (radius: 10)
[05:45:34 -354413.807187] SLOW spr round 5 (radius: 15)
[05:51:07 -354413.807025] SLOW spr round 6 (radius: 20)
[05:59:34 -354413.806859] SLOW spr round 7 (radius: 25)
[06:10:05 -354413.806690] Model parameter optimization (eps = 0.100000)

[06:10:14] [worker #0] ML tree search #7, logLikelihood: -354413.662331

[06:10:15 -1322688.118586] Initial branch length optimization
[06:10:24 -1138799.057896] Model parameter optimization (eps = 10.000000)
[06:11:18 -1136726.421214] AUTODETECT spr round 1 (radius: 5)
[06:15:06 -769847.079236] AUTODETECT spr round 2 (radius: 10)
[06:19:06 -547712.135203] AUTODETECT spr round 3 (radius: 15)
[06:23:02 -475217.958040] AUTODETECT spr round 4 (radius: 20)
[06:27:24 -460697.053292] AUTODETECT spr round 5 (radius: 25)
[06:32:52 -441817.212984] SPR radius for FAST iterations: 25 (autodetect)
[06:32:52 -441817.212984] Model parameter optimization (eps = 3.000000)
[06:33:04 -441809.947791] FAST spr round 1 (radius: 25)
[06:37:26 -357405.959214] FAST spr round 2 (radius: 25)
[06:40:32 -354787.212339] FAST spr round 3 (radius: 25)
[06:43:11 -354669.985287] FAST spr round 4 (radius: 25)
[06:45:28 -354667.245867] FAST spr round 5 (radius: 25)
[06:47:39 -354664.003290] FAST spr round 6 (radius: 25)
[06:49:48 -354664.003117] Model parameter optimization (eps = 1.000000)
[06:50:10 -354468.896124] SLOW spr round 1 (radius: 5)
[06:53:36 -354366.402538] SLOW spr round 2 (radius: 5)
[06:56:38] [worker #1] ML tree search #10, logLikelihood: -354406.235956
[06:56:47 -354357.700336] SLOW spr round 3 (radius: 5)
[06:59:50 -354357.700136] SLOW spr round 4 (radius: 10)
[07:03:05 -354357.699942] SLOW spr round 5 (radius: 15)
[07:08:35 -354357.699744] SLOW spr round 6 (radius: 20)
[07:17:05 -354357.699541] SLOW spr round 7 (radius: 25)
[07:27:40 -354357.699335] Model parameter optimization (eps = 0.100000)

[07:27:46] [worker #0] ML tree search #9, logLikelihood: -354357.651136

[07:27:47 -1321762.922468] Initial branch length optimization
[07:27:55 -1136362.753327] Model parameter optimization (eps = 10.000000)
[07:28:43 -1134395.819116] AUTODETECT spr round 1 (radius: 5)
[07:32:25 -761770.434183] AUTODETECT spr round 2 (radius: 10)
[07:36:26 -566852.306243] AUTODETECT spr round 3 (radius: 15)
[07:40:33 -475529.151048] AUTODETECT spr round 4 (radius: 20)
[07:45:07 -425454.272708] AUTODETECT spr round 5 (radius: 25)
[07:49:56 -419511.994755] SPR radius for FAST iterations: 25 (autodetect)
[07:49:56 -419511.994755] Model parameter optimization (eps = 3.000000)
[07:50:24 -419283.807589] FAST spr round 1 (radius: 25)
[07:54:31 -357329.630037] FAST spr round 2 (radius: 25)
[07:57:23 -354628.803804] FAST spr round 3 (radius: 25)
[08:00:03 -354484.993430] FAST spr round 4 (radius: 25)
[08:02:20 -354472.029138] FAST spr round 5 (radius: 25)
[08:04:34 -354464.931964] FAST spr round 6 (radius: 25)
[08:06:42 -354464.931962] Model parameter optimization (eps = 1.000000)
[08:07:01 -354463.692992] SLOW spr round 1 (radius: 5)
[08:10:16 -354386.131103] SLOW spr round 2 (radius: 5)
[08:13:19 -354385.103576] SLOW spr round 3 (radius: 5)
[08:16:18 -354385.103516] SLOW spr round 4 (radius: 10)
[08:19:30 -354384.096712] SLOW spr round 5 (radius: 5)
[08:21:26] [worker #1] ML tree search #12, logLikelihood: -354355.191020
[08:23:30 -354383.684282] SLOW spr round 6 (radius: 5)
[08:26:57 -354383.684282] SLOW spr round 7 (radius: 10)
[08:30:20 -354383.684282] SLOW spr round 8 (radius: 15)
[08:35:41 -354383.684282] SLOW spr round 9 (radius: 20)
[08:44:31 -354383.684282] SLOW spr round 10 (radius: 25)
[08:55:30 -354383.684282] Model parameter optimization (eps = 0.100000)

[08:55:37] [worker #0] ML tree search #11, logLikelihood: -354383.646558

[08:55:37 -1329529.277346] Initial branch length optimization
[08:55:47 -1145522.760224] Model parameter optimization (eps = 10.000000)
[08:56:45 -1143657.269186] AUTODETECT spr round 1 (radius: 5)
[09:00:31 -773886.681198] AUTODETECT spr round 2 (radius: 10)
[09:04:31 -573103.852429] AUTODETECT spr round 3 (radius: 15)
[09:08:45 -479473.948773] AUTODETECT spr round 4 (radius: 20)
[09:13:23 -424786.913879] AUTODETECT spr round 5 (radius: 25)
[09:19:02 -418887.823515] SPR radius for FAST iterations: 25 (autodetect)
[09:19:02 -418887.823515] Model parameter optimization (eps = 3.000000)
[09:19:29 -418686.584694] FAST spr round 1 (radius: 25)
[09:23:25 -357530.308428] FAST spr round 2 (radius: 25)
[09:26:23 -354640.674713] FAST spr round 3 (radius: 25)
[09:28:57 -354549.812436] FAST spr round 4 (radius: 25)
[09:31:14 -354545.279995] FAST spr round 5 (radius: 25)
[09:33:25 -354544.381785] FAST spr round 6 (radius: 25)
[09:35:33 -354544.381644] Model parameter optimization (eps = 1.000000)
[09:35:48 -354541.331649] SLOW spr round 1 (radius: 5)
[09:39:04 -354437.087493] SLOW spr round 2 (radius: 5)
[09:42:15 -354416.633781] SLOW spr round 3 (radius: 5)
[09:45:15 -354416.633525] SLOW spr round 4 (radius: 10)
[09:48:30 -354416.633348] SLOW spr round 5 (radius: 15)
[09:52:25] [worker #1] ML tree search #14, logLikelihood: -354399.306912
[09:53:58 -354416.633171] SLOW spr round 6 (radius: 20)
[10:02:22 -354416.632989] SLOW spr round 7 (radius: 25)
[10:12:34 -354416.632804] Model parameter optimization (eps = 0.100000)

[10:12:41] [worker #0] ML tree search #13, logLikelihood: -354416.613834

[10:12:41 -1323447.143848] Initial branch length optimization
[10:12:49 -1145171.867533] Model parameter optimization (eps = 10.000000)
[10:13:56 -1143052.006874] AUTODETECT spr round 1 (radius: 5)
[10:17:43 -766061.266339] AUTODETECT spr round 2 (radius: 10)
[10:21:49 -556547.975383] AUTODETECT spr round 3 (radius: 15)
[10:26:37 -456409.597702] AUTODETECT spr round 4 (radius: 20)
[10:31:13 -426167.494864] AUTODETECT spr round 5 (radius: 25)
[10:36:36 -420584.517546] SPR radius for FAST iterations: 25 (autodetect)
[10:36:36 -420584.517546] Model parameter optimization (eps = 3.000000)
[10:36:49 -420580.709079] FAST spr round 1 (radius: 25)
[10:40:44 -357456.957398] FAST spr round 2 (radius: 25)
[10:43:47 -354901.735697] FAST spr round 3 (radius: 25)
[10:46:35 -354699.150177] FAST spr round 4 (radius: 25)
[10:48:55 -354674.168067] FAST spr round 5 (radius: 25)
[10:51:06 -354674.166296] Model parameter optimization (eps = 1.000000)
[10:51:27 -354483.698677] SLOW spr round 1 (radius: 5)
[10:54:54 -354399.980994] SLOW spr round 2 (radius: 5)
[10:58:15 -354382.810324] SLOW spr round 3 (radius: 5)
[11:01:23 -354378.924244] SLOW spr round 4 (radius: 5)
[11:04:21 -354378.924088] SLOW spr round 5 (radius: 10)
[11:07:37 -354360.512695] SLOW spr round 6 (radius: 5)
[11:11:41 -354355.547662] SLOW spr round 7 (radius: 5)
[11:15:08 -354355.547395] SLOW spr round 8 (radius: 10)
[11:18:31 -354355.386957] SLOW spr round 9 (radius: 5)
[11:22:28 -354353.544762] SLOW spr round 10 (radius: 5)
[11:25:53 -354350.922052] SLOW spr round 11 (radius: 5)
[11:29:01 -354350.921895] SLOW spr round 12 (radius: 10)
[11:32:18 -354350.921735] SLOW spr round 13 (radius: 15)
[11:32:33] [worker #1] ML tree search #16, logLikelihood: -354402.352419
[11:37:44 -354350.921572] SLOW spr round 14 (radius: 20)
[11:46:15 -354350.921405] SLOW spr round 15 (radius: 25)
[11:56:43 -354350.921235] Model parameter optimization (eps = 0.100000)

[11:56:56] [worker #0] ML tree search #15, logLikelihood: -354350.633850

[11:56:56 -1322266.012738] Initial branch length optimization
[11:57:06 -1140422.350092] Model parameter optimization (eps = 10.000000)
[11:57:56 -1138461.273154] AUTODETECT spr round 1 (radius: 5)
[12:01:39 -773772.936606] AUTODETECT spr round 2 (radius: 10)
[12:05:57 -556126.434921] AUTODETECT spr round 3 (radius: 15)
[12:10:28 -450489.512296] AUTODETECT spr round 4 (radius: 20)
[12:15:23 -407623.414636] AUTODETECT spr round 5 (radius: 25)
[12:20:50 -405877.997830] SPR radius for FAST iterations: 25 (autodetect)
[12:20:50 -405877.997830] Model parameter optimization (eps = 3.000000)
[12:21:18 -405699.043902] FAST spr round 1 (radius: 25)
[12:25:05 -356533.816571] FAST spr round 2 (radius: 25)
[12:27:59 -354670.726558] FAST spr round 3 (radius: 25)
[12:30:34 -354548.695924] FAST spr round 4 (radius: 25)
[12:32:52 -354540.140607] FAST spr round 5 (radius: 25)
[12:35:05 -354537.676048] FAST spr round 6 (radius: 25)
[12:37:19 -354525.681831] FAST spr round 7 (radius: 25)
[12:39:35 -354507.624817] FAST spr round 8 (radius: 25)
[12:41:48 -354505.344467] FAST spr round 9 (radius: 25)
[12:43:57 -354505.344218] Model parameter optimization (eps = 1.000000)
[12:44:11 -354503.008468] SLOW spr round 1 (radius: 5)
[12:47:36 -354379.757609] SLOW spr round 2 (radius: 5)
[12:48:17] [worker #1] ML tree search #18, logLikelihood: -354361.568734
[12:50:49 -354372.571712] SLOW spr round 3 (radius: 5)
[12:53:52 -354372.066998] SLOW spr round 4 (radius: 5)
[12:56:53 -354372.066983] SLOW spr round 5 (radius: 10)
[13:00:12 -354361.956145] SLOW spr round 6 (radius: 5)
[13:04:18 -354354.821392] SLOW spr round 7 (radius: 5)
[13:07:46 -354349.827299] SLOW spr round 8 (radius: 5)
[13:10:58 -354349.827236] SLOW spr round 9 (radius: 10)
[13:14:18 -354349.827236] SLOW spr round 10 (radius: 15)
[13:19:48 -354349.827236] SLOW spr round 11 (radius: 20)
[13:28:20 -354349.827236] SLOW spr round 12 (radius: 25)
[13:38:43 -354349.827236] Model parameter optimization (eps = 0.100000)

[13:38:50] [worker #0] ML tree search #17, logLikelihood: -354349.732454

[13:38:50 -1329758.781569] Initial branch length optimization
[13:38:58 -1146535.075371] Model parameter optimization (eps = 10.000000)
[13:39:47 -1144513.856334] AUTODETECT spr round 1 (radius: 5)
[13:43:38 -779193.003653] AUTODETECT spr round 2 (radius: 10)
[13:47:49 -564713.817411] AUTODETECT spr round 3 (radius: 15)
[13:51:54 -460195.471538] AUTODETECT spr round 4 (radius: 20)
[13:56:11 -423362.162210] AUTODETECT spr round 5 (radius: 25)
[14:01:27 -418975.303386] SPR radius for FAST iterations: 25 (autodetect)
[14:01:27 -418975.303386] Model parameter optimization (eps = 3.000000)
[14:01:53 -418827.830644] FAST spr round 1 (radius: 25)
[14:05:55 -357411.246005] FAST spr round 2 (radius: 25)
[14:08:50 -354645.435898] FAST spr round 3 (radius: 25)
[14:11:31 -354512.877358] FAST spr round 4 (radius: 25)
[14:13:46 -354506.663725] FAST spr round 5 (radius: 25)
[14:13:57] [worker #1] ML tree search #20, logLikelihood: -354360.280756
[14:15:55 -354506.663515] Model parameter optimization (eps = 1.000000)
[14:16:14 -354485.504487] SLOW spr round 1 (radius: 5)
[14:19:33 -354394.798396] SLOW spr round 2 (radius: 5)
[14:22:37 -354388.903627] SLOW spr round 3 (radius: 5)
[14:25:33 -354388.903359] SLOW spr round 4 (radius: 10)
[14:28:46 -354374.798660] SLOW spr round 5 (radius: 5)
[14:32:39 -354374.701544] SLOW spr round 6 (radius: 10)
[14:36:13 -354369.775734] SLOW spr round 7 (radius: 5)
[14:40:03 -354366.016243] SLOW spr round 8 (radius: 5)
[14:43:21 -354366.015987] SLOW spr round 9 (radius: 10)
[14:46:38 -354366.015743] SLOW spr round 10 (radius: 15)
[14:51:54 -354366.015494] SLOW spr round 11 (radius: 20)
[15:00:17 -354366.015240] SLOW spr round 12 (radius: 25)
[15:10:30 -354366.014981] Model parameter optimization (eps = 0.100000)

[15:10:40] [worker #0] ML tree search #19, logLikelihood: -354365.792501


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.199945,0.241474) (0.271762,0.366253) (0.300287,1.104409) (0.228006,2.283037) 
   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: -354348.973938

AIC score: 712707.947877 / AICc score: 8756767.947877 / BIC score: 722404.647728
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=931).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9Y487/3_mltree/Q9Y487.raxml.log

Analysis started: 06-Jul-2021 14:49:48 / finished: 07-Jul-2021 06:00:29

Elapsed time: 54640.837 seconds