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 14-Jul-2021 08:59:01 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/2_msa/Q9BYQ6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6 --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/Q9BYQ6/2_msa/Q9BYQ6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 620 taxa and 165 sites

WARNING: Sequences tr_A0A2I3RYQ7_A0A2I3RYQ7_PANTR_9598 and tr_A0A2R9ACU5_A0A2R9ACU5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QKY2_H2QKY2_PANTR_9598 and tr_A0A2R9ARX5_A0A2R9ARX5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R3Y2_H2R3Y2_PANTR_9598 and sp_Q6PEX3_KR261_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2RGZ0_H2RGZ0_PANTR_9598 and tr_A0A2R8ZL57_A0A2R8ZL57_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5Q9A2_A0A1D5Q9A2_MACMU_9544 and tr_A0A1D5QE58_A0A1D5QE58_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A5PJJ0_A5PJJ0_BOVIN_9913 and tr_A5PJJ4_A5PJJ4_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A5PJJ0_A5PJJ0_BOVIN_9913 and tr_Q0VC31_Q0VC31_BOVIN_9913 are exactly identical!
WARNING: Duplicate sequences found: 7

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/Q9BYQ6/3_mltree/Q9BYQ6.raxml.reduced.phy

Alignment comprises 1 partitions and 165 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 165 / 165
Gaps: 21.20 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6.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 620 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 165 / 13200
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -121313.789530] Initial branch length optimization
[00:00:02 -106058.890877] Model parameter optimization (eps = 10.000000)
[00:00:37 -105183.451790] AUTODETECT spr round 1 (radius: 5)
[00:01:28 -74284.037354] AUTODETECT spr round 2 (radius: 10)
[00:02:24 -57693.309527] AUTODETECT spr round 3 (radius: 15)
[00:03:32 -50096.299503] AUTODETECT spr round 4 (radius: 20)
[00:04:54 -48875.966636] AUTODETECT spr round 5 (radius: 25)
[00:06:30 -48820.452899] SPR radius for FAST iterations: 25 (autodetect)
[00:06:30 -48820.452899] Model parameter optimization (eps = 3.000000)
[00:06:49 -48316.992735] FAST spr round 1 (radius: 25)
[00:08:00 -44318.148618] FAST spr round 2 (radius: 25)
[00:08:58 -44107.134346] FAST spr round 3 (radius: 25)
[00:09:48 -44054.266266] FAST spr round 4 (radius: 25)
[00:10:31 -44046.632508] FAST spr round 5 (radius: 25)
[00:11:12 -44046.632408] Model parameter optimization (eps = 1.000000)
[00:11:19 -44044.435896] SLOW spr round 1 (radius: 5)
[00:12:19 -44028.977420] SLOW spr round 2 (radius: 5)
[00:13:16 -44026.161146] SLOW spr round 3 (radius: 5)
[00:14:10 -44026.161129] SLOW spr round 4 (radius: 10)
[00:15:05 -44025.321092] SLOW spr round 5 (radius: 5)
[00:16:18 -44021.601021] SLOW spr round 6 (radius: 5)
[00:17:22 -44021.600838] SLOW spr round 7 (radius: 10)
[00:18:21 -44021.490171] SLOW spr round 8 (radius: 5)
[00:19:32 -44021.490150] SLOW spr round 9 (radius: 10)
[00:20:37 -44021.490150] SLOW spr round 10 (radius: 15)
[00:22:09 -44017.649164] SLOW spr round 11 (radius: 5)
[00:23:26 -44011.584985] SLOW spr round 12 (radius: 5)
[00:24:31 -44009.693417] SLOW spr round 13 (radius: 5)
[00:25:30 -44009.693402] SLOW spr round 14 (radius: 10)
[00:26:28 -44009.693402] SLOW spr round 15 (radius: 15)
[00:28:05 -44007.739559] SLOW spr round 16 (radius: 5)
[00:29:20 -44006.926920] SLOW spr round 17 (radius: 5)
[00:29:57] [worker #2] ML tree search #3, logLikelihood: -43992.769383
[00:30:26 -44006.926920] SLOW spr round 18 (radius: 10)
[00:31:27 -44006.926920] SLOW spr round 19 (radius: 15)
[00:33:02 -44005.321409] SLOW spr round 20 (radius: 5)
[00:34:16 -44005.321408] SLOW spr round 21 (radius: 10)
[00:35:26 -44005.321407] SLOW spr round 22 (radius: 15)
[00:36:57 -44005.321407] SLOW spr round 23 (radius: 20)
[00:38:53 -43993.381046] SLOW spr round 24 (radius: 5)
[00:40:14 -43981.605783] SLOW spr round 25 (radius: 5)
[00:41:20 -43981.605704] SLOW spr round 26 (radius: 10)
[00:42:01] [worker #1] ML tree search #2, logLikelihood: -43971.620048
[00:42:21 -43981.605701] SLOW spr round 27 (radius: 15)
[00:43:57 -43973.349162] SLOW spr round 28 (radius: 5)
[00:45:13 -43972.671254] SLOW spr round 29 (radius: 5)
[00:46:17 -43972.671234] SLOW spr round 30 (radius: 10)
[00:47:18 -43972.671234] SLOW spr round 31 (radius: 15)
[00:48:53 -43972.671234] SLOW spr round 32 (radius: 20)
[00:50:48 -43972.513115] SLOW spr round 33 (radius: 5)
[00:52:06 -43972.512816] SLOW spr round 34 (radius: 10)
[00:53:19 -43972.512806] SLOW spr round 35 (radius: 15)
[00:54:51 -43972.512805] SLOW spr round 36 (radius: 20)
[00:56:47 -43972.512805] SLOW spr round 37 (radius: 25)
[00:58:32] [worker #2] ML tree search #6, logLikelihood: -44031.247674
[00:59:01 -43972.512805] Model parameter optimization (eps = 0.100000)

[00:59:05] [worker #0] ML tree search #1, logLikelihood: -43972.443751

[00:59:05 -120149.380649] Initial branch length optimization
[00:59:07 -104612.777613] Model parameter optimization (eps = 10.000000)
[00:59:33 -103793.498990] AUTODETECT spr round 1 (radius: 5)
[01:00:23 -74983.219990] AUTODETECT spr round 2 (radius: 10)
[01:01:22 -57522.234019] AUTODETECT spr round 3 (radius: 15)
[01:02:39 -50144.358614] AUTODETECT spr round 4 (radius: 20)
[01:04:01 -49106.611480] AUTODETECT spr round 5 (radius: 25)
[01:05:31 -48511.339700] SPR radius for FAST iterations: 25 (autodetect)
[01:05:31 -48511.339700] Model parameter optimization (eps = 3.000000)
[01:05:48 -48007.564844] FAST spr round 1 (radius: 25)
[01:07:01 -44226.311564] FAST spr round 2 (radius: 25)
[01:07:59 -44008.026087] FAST spr round 3 (radius: 25)
[01:08:50 -43982.479088] FAST spr round 4 (radius: 25)
[01:09:32 -43981.994602] FAST spr round 5 (radius: 25)
[01:10:12 -43981.994602] Model parameter optimization (eps = 1.000000)
[01:10:21 -43978.409520] SLOW spr round 1 (radius: 5)
[01:11:22 -43964.615493] SLOW spr round 2 (radius: 5)
[01:12:20 -43963.523904] SLOW spr round 3 (radius: 5)
[01:13:17 -43962.187983] SLOW spr round 4 (radius: 5)
[01:14:11 -43962.187946] SLOW spr round 5 (radius: 10)
[01:15:07 -43960.367190] SLOW spr round 6 (radius: 5)
[01:16:20 -43959.554396] SLOW spr round 7 (radius: 5)
[01:17:22 -43959.554396] SLOW spr round 8 (radius: 10)
[01:18:22 -43958.568386] SLOW spr round 9 (radius: 5)
[01:19:34 -43957.955616] SLOW spr round 10 (radius: 5)
[01:20:36 -43957.955464] SLOW spr round 11 (radius: 10)
[01:21:35 -43957.236395] SLOW spr round 12 (radius: 5)
[01:22:46 -43957.236164] SLOW spr round 13 (radius: 10)
[01:23:51 -43957.236153] SLOW spr round 14 (radius: 15)
[01:25:25 -43952.291705] SLOW spr round 15 (radius: 5)
[01:26:41 -43952.289413] SLOW spr round 16 (radius: 10)
[01:27:52 -43952.047770] SLOW spr round 17 (radius: 5)
[01:29:02 -43952.047329] SLOW spr round 18 (radius: 10)
[01:30:05 -43952.047298] SLOW spr round 19 (radius: 15)
[01:31:41 -43952.047297] SLOW spr round 20 (radius: 20)
[01:33:41 -43952.047296] SLOW spr round 21 (radius: 25)
[01:35:55 -43952.047296] Model parameter optimization (eps = 0.100000)

[01:35:59] [worker #0] ML tree search #4, logLikelihood: -43951.988085

[01:35:59 -121177.418257] Initial branch length optimization
[01:36:01 -105597.940251] Model parameter optimization (eps = 10.000000)
[01:36:23 -104750.663815] AUTODETECT spr round 1 (radius: 5)
[01:37:14 -74460.780131] AUTODETECT spr round 2 (radius: 10)
[01:38:11 -57138.124392] AUTODETECT spr round 3 (radius: 15)
[01:39:23 -51038.869425] AUTODETECT spr round 4 (radius: 20)
[01:39:32] [worker #2] ML tree search #9, logLikelihood: -43982.209533
[01:40:42 -49767.272889] AUTODETECT spr round 5 (radius: 25)
[01:42:17 -48986.265157] SPR radius for FAST iterations: 25 (autodetect)
[01:42:17 -48986.265157] Model parameter optimization (eps = 3.000000)
[01:42:34 -48490.126112] FAST spr round 1 (radius: 25)
[01:43:50 -44361.174935] FAST spr round 2 (radius: 25)
[01:44:47 -44077.137092] FAST spr round 3 (radius: 25)
[01:45:38 -44025.904209] FAST spr round 4 (radius: 25)
[01:46:19 -44024.897596] FAST spr round 5 (radius: 25)
[01:47:00 -44024.897130] Model parameter optimization (eps = 1.000000)
[01:47:04 -44024.342026] SLOW spr round 1 (radius: 5)
[01:48:02 -43997.982259] SLOW spr round 2 (radius: 5)
[01:49:01 -43996.391463] SLOW spr round 3 (radius: 5)
[01:49:58 -43995.914661] SLOW spr round 4 (radius: 5)
[01:50:52 -43995.914390] SLOW spr round 5 (radius: 10)
[01:51:48 -43994.690219] SLOW spr round 6 (radius: 5)
[01:52:59 -43994.690096] SLOW spr round 7 (radius: 10)
[01:54:04 -43994.690091] SLOW spr round 8 (radius: 15)
[01:55:14] [worker #1] ML tree search #5, logLikelihood: -43947.640016
[01:55:37 -43989.938711] SLOW spr round 9 (radius: 5)
[01:56:55 -43984.720682] SLOW spr round 10 (radius: 5)
[01:58:01 -43984.657804] SLOW spr round 11 (radius: 10)
[01:59:01 -43983.923535] SLOW spr round 12 (radius: 5)
[02:00:11 -43983.768961] SLOW spr round 13 (radius: 5)
[02:01:13 -43983.768412] SLOW spr round 14 (radius: 10)
[02:02:12 -43983.201704] SLOW spr round 15 (radius: 5)
[02:03:23 -43982.589712] SLOW spr round 16 (radius: 5)
[02:04:25 -43982.589624] SLOW spr round 17 (radius: 10)
[02:05:24 -43981.861043] SLOW spr round 18 (radius: 5)
[02:06:35 -43981.861011] SLOW spr round 19 (radius: 10)
[02:07:39 -43981.861011] SLOW spr round 20 (radius: 15)
[02:09:12 -43981.861011] SLOW spr round 21 (radius: 20)
[02:11:16 -43981.861011] SLOW spr round 22 (radius: 25)
[02:13:42 -43981.861011] Model parameter optimization (eps = 0.100000)

[02:13:46] [worker #0] ML tree search #7, logLikelihood: -43981.595766

[02:13:47 -121557.981403] Initial branch length optimization
[02:13:49 -106032.185345] Model parameter optimization (eps = 10.000000)
[02:14:09 -105234.555657] AUTODETECT spr round 1 (radius: 5)
[02:15:00 -74374.712369] AUTODETECT spr round 2 (radius: 10)
[02:15:56 -57451.623315] AUTODETECT spr round 3 (radius: 15)
[02:17:07 -49758.985737] AUTODETECT spr round 4 (radius: 20)
[02:18:35 -48865.692530] AUTODETECT spr round 5 (radius: 25)
[02:20:13 -48690.463010] SPR radius for FAST iterations: 25 (autodetect)
[02:20:13 -48690.463010] Model parameter optimization (eps = 3.000000)
[02:20:36 -48197.776237] FAST spr round 1 (radius: 25)
[02:21:49 -44229.554048] FAST spr round 2 (radius: 25)
[02:22:45 -44073.645039] FAST spr round 3 (radius: 25)
[02:23:33 -44059.907552] FAST spr round 4 (radius: 25)
[02:24:15 -44057.873768] FAST spr round 5 (radius: 25)
[02:24:55 -44057.873450] Model parameter optimization (eps = 1.000000)
[02:25:02 -44055.843677] SLOW spr round 1 (radius: 5)
[02:26:02 -44049.884389] SLOW spr round 2 (radius: 5)
[02:26:59 -44048.220513] SLOW spr round 3 (radius: 5)
[02:27:53 -44048.167633] SLOW spr round 4 (radius: 10)
[02:28:55 -44036.288638] SLOW spr round 5 (radius: 5)
[02:30:07 -44025.910062] SLOW spr round 6 (radius: 5)
[02:30:16] [worker #2] ML tree search #12, logLikelihood: -43952.135324
[02:31:11 -44024.956719] SLOW spr round 7 (radius: 5)
[02:32:08 -44024.955437] SLOW spr round 8 (radius: 10)
[02:32:18] [worker #1] ML tree search #8, logLikelihood: -43987.185881
[02:33:06 -44024.649885] SLOW spr round 9 (radius: 5)
[02:34:17 -44024.649300] SLOW spr round 10 (radius: 10)
[02:35:24 -44016.310962] SLOW spr round 11 (radius: 5)
[02:36:35 -44013.862843] SLOW spr round 12 (radius: 5)
[02:37:36 -44013.862814] SLOW spr round 13 (radius: 10)
[02:38:36 -44013.862814] SLOW spr round 14 (radius: 15)
[02:40:19 -44007.546895] SLOW spr round 15 (radius: 5)
[02:41:36 -44005.600469] SLOW spr round 16 (radius: 5)
[02:42:41 -44005.183842] SLOW spr round 17 (radius: 5)
[02:43:40 -44005.183456] SLOW spr round 18 (radius: 10)
[02:44:40 -44004.722164] SLOW spr round 19 (radius: 5)
[02:45:52 -44004.719389] SLOW spr round 20 (radius: 10)
[02:47:00 -44004.518631] SLOW spr round 21 (radius: 5)
[02:48:10 -44004.516972] SLOW spr round 22 (radius: 10)
[02:49:16 -44004.516706] SLOW spr round 23 (radius: 15)
[02:50:58 -44002.531579] SLOW spr round 24 (radius: 5)
[02:52:14 -44002.531567] SLOW spr round 25 (radius: 10)
[02:53:27 -44002.531562] SLOW spr round 26 (radius: 15)
[02:55:07 -44002.182366] SLOW spr round 27 (radius: 5)
[02:56:24 -44000.142056] SLOW spr round 28 (radius: 5)
[02:57:29 -44000.141563] SLOW spr round 29 (radius: 10)
[02:58:31 -44000.141520] SLOW spr round 30 (radius: 15)
[03:00:14 -44000.141516] SLOW spr round 31 (radius: 20)
[03:02:22 -44000.141516] SLOW spr round 32 (radius: 25)
[03:04:38 -43999.789312] SLOW spr round 33 (radius: 5)
[03:05:56 -43999.789113] SLOW spr round 34 (radius: 10)
[03:07:14 -43999.789096] SLOW spr round 35 (radius: 15)
[03:08:55 -43999.789094] SLOW spr round 36 (radius: 20)
[03:11:03 -43999.789094] SLOW spr round 37 (radius: 25)
[03:11:21] [worker #1] ML tree search #11, logLikelihood: -43987.428660
[03:13:17 -43999.789094] Model parameter optimization (eps = 0.100000)

[03:13:25] [worker #0] ML tree search #10, logLikelihood: -43999.473838

[03:13:25 -121288.328204] Initial branch length optimization
[03:13:27 -105574.302113] Model parameter optimization (eps = 10.000000)
[03:14:01 -104792.381492] AUTODETECT spr round 1 (radius: 5)
[03:14:52 -74629.816548] AUTODETECT spr round 2 (radius: 10)
[03:15:43] [worker #2] ML tree search #15, logLikelihood: -43969.777996
[03:15:50 -57321.064267] AUTODETECT spr round 3 (radius: 15)
[03:16:58 -50835.214259] AUTODETECT spr round 4 (radius: 20)
[03:18:19 -48413.524682] AUTODETECT spr round 5 (radius: 25)
[03:19:46 -48218.441464] SPR radius for FAST iterations: 25 (autodetect)
[03:19:46 -48218.441464] Model parameter optimization (eps = 3.000000)
[03:20:05 -47771.094773] FAST spr round 1 (radius: 25)
[03:21:18 -44384.768758] FAST spr round 2 (radius: 25)
[03:22:14 -44173.756896] FAST spr round 3 (radius: 25)
[03:23:03 -44112.131662] FAST spr round 4 (radius: 25)
[03:23:49 -44098.785358] FAST spr round 5 (radius: 25)
[03:24:29 -44098.785053] Model parameter optimization (eps = 1.000000)
[03:24:38 -44095.537816] SLOW spr round 1 (radius: 5)
[03:25:40 -44084.595547] SLOW spr round 2 (radius: 5)
[03:26:36 -44084.463463] SLOW spr round 3 (radius: 5)
[03:27:30 -44084.462992] SLOW spr round 4 (radius: 10)
[03:28:27 -44084.263408] SLOW spr round 5 (radius: 5)
[03:29:39 -44084.263346] SLOW spr round 6 (radius: 10)
[03:30:45 -44084.263344] SLOW spr round 7 (radius: 15)
[03:32:15 -44084.263342] SLOW spr round 8 (radius: 20)
[03:34:00 -44065.217635] SLOW spr round 9 (radius: 5)
[03:35:23 -44031.419396] SLOW spr round 10 (radius: 5)
[03:36:31 -44027.034964] SLOW spr round 11 (radius: 5)
[03:37:31 -44027.034910] SLOW spr round 12 (radius: 10)
[03:38:29 -44027.034908] SLOW spr round 13 (radius: 15)
[03:40:02 -44027.034906] SLOW spr round 14 (radius: 20)
[03:41:45 -44018.639273] SLOW spr round 15 (radius: 5)
[03:43:06 -44014.160551] SLOW spr round 16 (radius: 5)
[03:44:12 -44014.160375] SLOW spr round 17 (radius: 10)
[03:45:14 -44014.160372] SLOW spr round 18 (radius: 15)
[03:46:45 -44014.160370] SLOW spr round 19 (radius: 20)
[03:48:29 -44014.160368] SLOW spr round 20 (radius: 25)
[03:50:20 -43998.577192] SLOW spr round 21 (radius: 5)
[03:51:39 -43997.481559] SLOW spr round 22 (radius: 5)
[03:52:46 -43997.481489] SLOW spr round 23 (radius: 10)
[03:53:47 -43997.481486] SLOW spr round 24 (radius: 15)
[03:55:18 -43997.481483] SLOW spr round 25 (radius: 20)
[03:57:01 -43997.481481] SLOW spr round 26 (radius: 25)
[03:57:31] [worker #1] ML tree search #14, logLikelihood: -43975.215286
[03:58:53 -43996.102642] SLOW spr round 27 (radius: 5)
[04:00:10 -43996.102437] SLOW spr round 28 (radius: 10)
[04:01:24 -43996.102433] SLOW spr round 29 (radius: 15)
[04:02:52 -43996.102431] SLOW spr round 30 (radius: 20)
[04:04:36 -43996.102428] SLOW spr round 31 (radius: 25)
[04:06:27 -43996.102426] Model parameter optimization (eps = 0.100000)

[04:06:32] [worker #0] ML tree search #13, logLikelihood: -43995.992739

[04:06:32 -121043.785665] Initial branch length optimization
[04:06:35 -105519.736956] Model parameter optimization (eps = 10.000000)
[04:07:18 -104583.031156] AUTODETECT spr round 1 (radius: 5)
[04:08:09 -71435.634497] AUTODETECT spr round 2 (radius: 10)
[04:09:07 -55128.767883] AUTODETECT spr round 3 (radius: 15)
[04:10:20 -50380.274763] AUTODETECT spr round 4 (radius: 20)
[04:11:45 -49369.495905] AUTODETECT spr round 5 (radius: 25)
[04:11:51] [worker #2] ML tree search #18, logLikelihood: -43957.340957
[04:13:19 -48820.855843] SPR radius for FAST iterations: 25 (autodetect)
[04:13:19 -48820.855843] Model parameter optimization (eps = 3.000000)
[04:13:37 -48361.282785] FAST spr round 1 (radius: 25)
[04:14:51 -44302.312990] FAST spr round 2 (radius: 25)
[04:15:49 -44052.739818] FAST spr round 3 (radius: 25)
[04:16:39 -44016.009629] FAST spr round 4 (radius: 25)
[04:17:22 -43997.900338] FAST spr round 5 (radius: 25)
[04:18:02 -43997.025757] FAST spr round 6 (radius: 25)
[04:18:41 -43997.024238] Model parameter optimization (eps = 1.000000)
[04:18:50 -43994.683373] SLOW spr round 1 (radius: 5)
[04:19:48 -43989.642207] SLOW spr round 2 (radius: 5)
[04:20:45 -43988.470133] SLOW spr round 3 (radius: 5)
[04:21:38 -43988.469382] SLOW spr round 4 (radius: 10)
[04:22:33 -43988.469273] SLOW spr round 5 (radius: 15)
[04:24:11 -43987.519079] SLOW spr round 6 (radius: 5)
[04:25:27 -43986.273755] SLOW spr round 7 (radius: 5)
[04:26:31 -43986.273515] SLOW spr round 8 (radius: 10)
[04:27:29 -43986.273509] SLOW spr round 9 (radius: 15)
[04:29:02 -43985.354767] SLOW spr round 10 (radius: 5)
[04:30:17 -43984.984800] SLOW spr round 11 (radius: 5)
[04:31:21 -43984.983728] SLOW spr round 12 (radius: 10)
[04:32:20 -43984.983457] SLOW spr round 13 (radius: 15)
[04:33:52 -43984.768360] SLOW spr round 14 (radius: 5)
[04:35:07 -43982.554476] SLOW spr round 15 (radius: 5)
[04:36:10 -43982.553639] SLOW spr round 16 (radius: 10)
[04:37:08 -43982.553483] SLOW spr round 17 (radius: 15)
[04:38:39 -43982.553452] SLOW spr round 18 (radius: 20)
[04:40:32 -43981.724758] SLOW spr round 19 (radius: 5)
[04:41:49 -43981.528526] SLOW spr round 20 (radius: 5)
[04:42:54 -43981.527838] SLOW spr round 21 (radius: 10)
[04:43:54 -43981.527766] SLOW spr round 22 (radius: 15)
[04:45:24 -43981.527746] SLOW spr round 23 (radius: 20)
[04:47:16 -43981.527738] SLOW spr round 24 (radius: 25)
[04:49:31 -43981.527735] Model parameter optimization (eps = 0.100000)

[04:49:34] [worker #0] ML tree search #16, logLikelihood: -43981.498226

[04:49:34 -120961.481867] Initial branch length optimization
[04:49:36 -105115.675379] Model parameter optimization (eps = 10.000000)
[04:50:10 -104255.813719] AUTODETECT spr round 1 (radius: 5)
[04:50:20] [worker #1] ML tree search #17, logLikelihood: -43966.836846
[04:51:02 -75909.265566] AUTODETECT spr round 2 (radius: 10)
[04:52:09 -58123.351474] AUTODETECT spr round 3 (radius: 15)
[04:53:19 -51780.719680] AUTODETECT spr round 4 (radius: 20)
[04:54:56 -49238.451651] AUTODETECT spr round 5 (radius: 25)
[04:56:39 -49144.120794] SPR radius for FAST iterations: 25 (autodetect)
[04:56:39 -49144.120794] Model parameter optimization (eps = 3.000000)
[04:57:02 -48751.979837] FAST spr round 1 (radius: 25)
[04:58:19 -44281.059473] FAST spr round 2 (radius: 25)
[04:59:16 -44094.171501] FAST spr round 3 (radius: 25)
[05:00:08 -44060.790673] FAST spr round 4 (radius: 25)
[05:00:53 -44046.452267] FAST spr round 5 (radius: 25)
[05:01:34 -44043.880791] FAST spr round 6 (radius: 25)
[05:02:13 -44043.879668] Model parameter optimization (eps = 1.000000)
[05:02:20 -44042.119778] SLOW spr round 1 (radius: 5)
[05:03:20 -44026.421851] SLOW spr round 2 (radius: 5)
[05:04:18 -44019.980502] SLOW spr round 3 (radius: 5)
[05:05:14 -44015.663437] SLOW spr round 4 (radius: 5)
[05:06:08 -44015.601883] SLOW spr round 5 (radius: 10)
[05:07:04 -44011.953293] SLOW spr round 6 (radius: 5)
[05:08:17 -44007.708651] SLOW spr round 7 (radius: 5)
[05:09:18 -44007.708542] SLOW spr round 8 (radius: 10)
[05:10:17 -44006.189462] SLOW spr round 9 (radius: 5)
[05:11:27 -44006.113980] SLOW spr round 10 (radius: 10)
[05:12:30 -44005.889486] SLOW spr round 11 (radius: 5)
[05:13:39 -44005.889264] SLOW spr round 12 (radius: 10)
[05:14:41 -44005.742822] SLOW spr round 13 (radius: 5)
[05:15:52 -44004.743420] SLOW spr round 14 (radius: 5)
[05:16:55 -44004.483326] SLOW spr round 15 (radius: 5)
[05:17:51 -44004.483286] SLOW spr round 16 (radius: 10)
[05:18:47 -44004.316065] SLOW spr round 17 (radius: 5)
[05:19:57 -44004.315989] SLOW spr round 18 (radius: 10)
[05:21:01 -44004.315985] SLOW spr round 19 (radius: 15)
[05:22:35 -43994.565742] SLOW spr round 20 (radius: 5)
[05:23:49 -43994.565699] SLOW spr round 21 (radius: 10)
[05:24:58 -43993.921750] SLOW spr round 22 (radius: 5)
[05:26:06 -43993.904375] SLOW spr round 23 (radius: 10)
[05:27:08 -43993.904370] SLOW spr round 24 (radius: 15)
[05:28:41 -43993.904369] SLOW spr round 25 (radius: 20)
[05:30:49 -43985.047213] SLOW spr round 26 (radius: 5)
[05:32:05 -43985.044093] SLOW spr round 27 (radius: 10)
[05:33:17 -43985.043931] SLOW spr round 28 (radius: 15)
[05:34:48 -43985.043920] SLOW spr round 29 (radius: 20)
[05:36:56 -43985.043918] SLOW spr round 30 (radius: 25)
[05:39:21 -43985.043917] Model parameter optimization (eps = 0.100000)

[05:39:29] [worker #0] ML tree search #19, logLikelihood: -43984.793883

[05:52:23] [worker #1] ML tree search #20, logLikelihood: -43983.166528

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.474439,0.677429) (0.012125,1.487320) (0.253502,1.168878) (0.259934,1.401336) 
   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: -43947.640016

AIC score: 90381.280032 / AICc score: 3182965.280032 / BIC score: 94241.970256
Free parameters (model + branch lengths): 1243

WARNING: Number of free parameters (K=1243) is larger than alignment size (n=165).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BYQ6/3_mltree/Q9BYQ6.raxml.log

Analysis started: 14-Jul-2021 08:59:01 / finished: 14-Jul-2021 14:51:24

Elapsed time: 21143.148 seconds

Consumed energy: 1497.865 Wh (= 7 km in an electric car, or 37 km with an e-scooter!)