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

System: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 07-Jul-2021 19:06:35 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/2_msa/P98174_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174 --seed 2 --threads 8 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/2_msa/P98174_trimmed_msa.fasta
[00:00:00] Loaded alignment with 836 taxa and 636 sites

WARNING: Sequences sp_P52734_FGD1_MOUSE_10090 and tr_A0A1U7R7V2_A0A1U7R7V2_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G1S2D9_G1S2D9_NOMLE_61853 and tr_G3QY89_G3QY89_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1S2D9_G1S2D9_NOMLE_61853 and tr_K7BJJ0_K7BJJ0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1S2D9_G1S2D9_NOMLE_61853 and tr_A0A2R9CM84_A0A2R9CM84_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PZ11_H2PZ11_PANTR_9598 and tr_A0A2R9A9V2_A0A2R9A9V2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QSX3_H2QSX3_PANTR_9598 and sp_Q7Z6J4_FGD2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H9GZM7_H9GZM7_HORSE_9796 and tr_M3VY47_M3VY47_FELCA_9685 are exactly identical!
WARNING: Sequences tr_H9GZM7_H9GZM7_HORSE_9796 and tr_A0A2Y9IHD7_A0A2Y9IHD7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_W5P8R2_W5P8R2_SHEEP_9940 and tr_A5D7I5_A5D7I5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F7A0I9_F7A0I9_MACMU_9544 and tr_G7PJ27_G7PJ27_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7A0I9_F7A0I9_MACMU_9544 and tr_A0A2K5ZQK1_A0A2K5ZQK1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z1A3_H0Z1A3_TAEGU_59729 and tr_A0A091EXQ8_A0A091EXQ8_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0Z1A3_H0Z1A3_TAEGU_59729 and tr_A0A091J9E6_A0A091J9E6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_H0Z1A3_H0Z1A3_TAEGU_59729 and tr_A0A091GBR7_A0A091GBR7_9AVES_55661 are exactly identical!
WARNING: Sequences tr_H0Z1A3_H0Z1A3_TAEGU_59729 and tr_A0A091I4C1_A0A091I4C1_CALAN_9244 are exactly identical!
WARNING: Sequences tr_G7Q2T8_G7Q2T8_MACFA_9541 and tr_A0A096N7K7_A0A096N7K7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7Q2T8_G7Q2T8_MACFA_9541 and tr_A0A2K5MKY8_A0A2K5MKY8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7Q2T8_G7Q2T8_MACFA_9541 and tr_A0A2K6E8Y7_A0A2K6E8Y7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0V1CFE3_A0A0V1CFE3_TRIBR_45882 and tr_A0A0V1NKF5_A0A0V1NKF5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1S3H0P4_A0A1S3H0P4_LINUN_7574 and tr_A0A1S3H0R2_A0A1S3H0R2_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3H0P4_A0A1S3H0P4_LINUN_7574 and tr_A0A1S3H275_A0A1S3H275_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A2D0QT91_A0A2D0QT91_ICTPU_7998 and tr_A0A2D0QV93_A0A2D0QV93_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0R350_A0A2D0R350_ICTPU_7998 and tr_A0A2D0R3V1_A0A2D0R3V1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T3X9_A0A2D0T3X9_ICTPU_7998 and tr_A0A2D0T473_A0A2D0T473_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5NDC5_A0A2K5NDC5_CERAT_9531 and tr_A0A2K5YAJ3_A0A2K5YAJ3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4BJM5_A0A2U4BJM5_TURTR_9739 and tr_A0A2Y9NPZ1_A0A2Y9NPZ1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4BJM5_A0A2U4BJM5_TURTR_9739 and tr_A0A2Y9SBF3_A0A2Y9SBF3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9MQB0_A0A2Y9MQB0_DELLE_9749 and tr_A0A2Y9FBB8_A0A2Y9FBB8_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 28

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/P98174/3_mltree/P98174.raxml.reduced.phy

Alignment comprises 1 partitions and 636 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 636 / 636
Gaps: 21.68 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.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 836 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 159 / 12720
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -894249.733835] Initial branch length optimization
[00:00:08 -738259.045982] Model parameter optimization (eps = 10.000000)
[00:00:48 -735410.315333] AUTODETECT spr round 1 (radius: 5)
[00:02:58 -497780.965495] AUTODETECT spr round 2 (radius: 10)
[00:05:23 -362476.102498] AUTODETECT spr round 3 (radius: 15)
[00:07:58 -289852.917183] AUTODETECT spr round 4 (radius: 20)
[00:11:02 -267307.174127] AUTODETECT spr round 5 (radius: 25)
[00:14:29 -264399.948705] SPR radius for FAST iterations: 25 (autodetect)
[00:14:29 -264399.948705] Model parameter optimization (eps = 3.000000)
[00:15:11 -263777.333031] FAST spr round 1 (radius: 25)
[00:18:04 -235131.340963] FAST spr round 2 (radius: 25)
[00:20:16 -234131.276221] FAST spr round 3 (radius: 25)
[00:22:13 -234073.586009] FAST spr round 4 (radius: 25)
[00:23:58 -234057.750700] FAST spr round 5 (radius: 25)
[00:25:32 -234057.320789] FAST spr round 6 (radius: 25)
[00:27:04 -234057.320581] Model parameter optimization (eps = 1.000000)
[00:27:21 -234055.147780] SLOW spr round 1 (radius: 5)
[00:29:31 -234025.668951] SLOW spr round 2 (radius: 5)
[00:31:34 -234025.376534] SLOW spr round 3 (radius: 5)
[00:33:34 -234025.376181] SLOW spr round 4 (radius: 10)
[00:35:37 -234025.252091] SLOW spr round 5 (radius: 5)
[00:38:12 -234025.252063] SLOW spr round 6 (radius: 10)
[00:40:33 -234025.252061] SLOW spr round 7 (radius: 15)
[00:43:51 -234025.252061] SLOW spr round 8 (radius: 20)
[00:50:07 -234025.252061] SLOW spr round 9 (radius: 25)
[00:58:15 -234025.252060] Model parameter optimization (eps = 0.100000)

[00:58:20] [worker #0] ML tree search #1, logLikelihood: -234025.240051

[00:58:20 -885035.092034] Initial branch length optimization
[00:58:26 -730501.815271] Model parameter optimization (eps = 10.000000)
[00:59:08 -727537.686534] AUTODETECT spr round 1 (radius: 5)
[01:01:12 -487521.866672] AUTODETECT spr round 2 (radius: 10)
[01:03:30 -352318.430346] AUTODETECT spr round 3 (radius: 15)
[01:05:59 -298018.201907] AUTODETECT spr round 4 (radius: 20)
[01:06:27] [worker #1] ML tree search #2, logLikelihood: -234013.798598
[01:08:56 -272004.369069] AUTODETECT spr round 5 (radius: 25)
[01:12:14 -267722.728518] SPR radius for FAST iterations: 25 (autodetect)
[01:12:14 -267722.728518] Model parameter optimization (eps = 3.000000)
[01:12:48 -267256.512032] FAST spr round 1 (radius: 25)
[01:15:53 -235636.065714] FAST spr round 2 (radius: 25)
[01:18:18 -234135.586046] FAST spr round 3 (radius: 25)
[01:20:20 -234084.636541] FAST spr round 4 (radius: 25)
[01:22:01 -234077.898603] FAST spr round 5 (radius: 25)
[01:23:38 -234077.898325] Model parameter optimization (eps = 1.000000)
[01:23:58 -234063.386641] SLOW spr round 1 (radius: 5)
[01:26:18 -234011.113737] SLOW spr round 2 (radius: 5)
[01:28:32 -234002.804911] SLOW spr round 3 (radius: 5)
[01:30:41 -234001.899198] SLOW spr round 4 (radius: 5)
[01:32:51 -234000.732418] SLOW spr round 5 (radius: 5)
[01:34:57 -234000.732005] SLOW spr round 6 (radius: 10)
[01:37:05 -233999.590266] SLOW spr round 7 (radius: 5)
[01:39:44 -233999.589811] SLOW spr round 8 (radius: 10)
[01:42:10 -233999.589802] SLOW spr round 9 (radius: 15)
[01:45:48 -233999.589802] SLOW spr round 10 (radius: 20)
[01:52:55 -233999.589802] SLOW spr round 11 (radius: 25)
[02:01:29 -233999.589802] Model parameter optimization (eps = 0.100000)

[02:01:41] [worker #0] ML tree search #3, logLikelihood: -233999.162672

[02:01:41 -889728.656318] Initial branch length optimization
[02:01:46 -731674.963323] Model parameter optimization (eps = 10.000000)
[02:02:22 -728743.893862] AUTODETECT spr round 1 (radius: 5)
[02:04:32 -488778.476186] AUTODETECT spr round 2 (radius: 10)
[02:06:55 -361864.918595] AUTODETECT spr round 3 (radius: 15)
[02:09:02] [worker #1] ML tree search #4, logLikelihood: -233999.673095
[02:09:39 -292088.944540] AUTODETECT spr round 4 (radius: 20)
[02:12:48 -263352.914611] AUTODETECT spr round 5 (radius: 25)
[02:16:25 -260609.605477] SPR radius for FAST iterations: 25 (autodetect)
[02:16:25 -260609.605477] Model parameter optimization (eps = 3.000000)
[02:16:57 -260178.312744] FAST spr round 1 (radius: 25)
[02:19:49 -235814.252447] FAST spr round 2 (radius: 25)
[02:22:00 -234161.496079] FAST spr round 3 (radius: 25)
[02:23:57 -234059.245476] FAST spr round 4 (radius: 25)
[02:25:43 -234042.072480] FAST spr round 5 (radius: 25)
[02:27:20 -234038.169786] FAST spr round 6 (radius: 25)
[02:28:55 -234038.169781] Model parameter optimization (eps = 1.000000)
[02:29:16 -234027.953612] SLOW spr round 1 (radius: 5)
[02:31:30 -234007.020942] SLOW spr round 2 (radius: 5)
[02:33:37 -234004.551779] SLOW spr round 3 (radius: 5)
[02:35:42 -234004.551521] SLOW spr round 4 (radius: 10)
[02:37:52 -234004.551258] SLOW spr round 5 (radius: 15)
[02:41:51 -234004.181228] SLOW spr round 6 (radius: 5)
[02:44:36 -234004.181200] SLOW spr round 7 (radius: 10)
[02:47:11 -234004.181195] SLOW spr round 8 (radius: 15)
[02:50:44 -234004.181195] SLOW spr round 9 (radius: 20)
[02:57:24 -234004.181195] SLOW spr round 10 (radius: 25)
[03:05:53 -234004.181195] Model parameter optimization (eps = 0.100000)

[03:05:59] [worker #0] ML tree search #5, logLikelihood: -234004.155036

[03:05:59 -891139.025304] Initial branch length optimization
[03:06:04 -734252.711036] Model parameter optimization (eps = 10.000000)
[03:06:42 -731306.755094] AUTODETECT spr round 1 (radius: 5)
[03:08:50 -494381.367400] AUTODETECT spr round 2 (radius: 10)
[03:11:15 -368836.370660] AUTODETECT spr round 3 (radius: 15)
[03:13:59 -296490.331238] AUTODETECT spr round 4 (radius: 20)
[03:17:11 -263056.708267] AUTODETECT spr round 5 (radius: 25)
[03:17:36] [worker #1] ML tree search #6, logLikelihood: -233990.364238
[03:21:12 -259835.126899] SPR radius for FAST iterations: 25 (autodetect)
[03:21:12 -259835.126899] Model parameter optimization (eps = 3.000000)
[03:21:41 -259313.075673] FAST spr round 1 (radius: 25)
[03:24:55 -235122.137953] FAST spr round 2 (radius: 25)
[03:27:17 -234131.327181] FAST spr round 3 (radius: 25)
[03:29:20 -234086.899812] FAST spr round 4 (radius: 25)
[03:31:04 -234079.711250] FAST spr round 5 (radius: 25)
[03:32:41 -234079.710503] Model parameter optimization (eps = 1.000000)
[03:33:06 -234065.844147] SLOW spr round 1 (radius: 5)
[03:35:31 -234012.571539] SLOW spr round 2 (radius: 5)
[03:37:49 -233991.928119] SLOW spr round 3 (radius: 5)
[03:39:57 -233990.377949] SLOW spr round 4 (radius: 5)
[03:42:03 -233990.377080] SLOW spr round 5 (radius: 10)
[03:44:12 -233988.985489] SLOW spr round 6 (radius: 5)
[03:46:53 -233988.985460] SLOW spr round 7 (radius: 10)
[03:49:18 -233988.985191] SLOW spr round 8 (radius: 15)
[03:52:54 -233988.616762] SLOW spr round 9 (radius: 5)
[03:55:41 -233988.615904] SLOW spr round 10 (radius: 10)
[03:58:14 -233988.615904] SLOW spr round 11 (radius: 15)
[04:01:46 -233988.615904] SLOW spr round 12 (radius: 20)
[04:08:31 -233988.615904] SLOW spr round 13 (radius: 25)
[04:16:53 -233988.615904] Model parameter optimization (eps = 0.100000)

[04:17:08] [worker #0] ML tree search #7, logLikelihood: -233988.271784

[04:17:08 -891769.942637] Initial branch length optimization
[04:17:14 -736141.025302] Model parameter optimization (eps = 10.000000)
[04:17:53 -733072.038196] AUTODETECT spr round 1 (radius: 5)
[04:19:59 -492128.306683] AUTODETECT spr round 2 (radius: 10)
[04:22:18 -356396.354301] AUTODETECT spr round 3 (radius: 15)
[04:24:49 -296265.085843] AUTODETECT spr round 4 (radius: 20)
[04:25:54] [worker #1] ML tree search #8, logLikelihood: -233994.903032
[04:27:41 -277246.408214] AUTODETECT spr round 5 (radius: 25)
[04:30:43 -270373.914580] SPR radius for FAST iterations: 25 (autodetect)
[04:30:43 -270373.914580] Model parameter optimization (eps = 3.000000)
[04:31:13 -269835.992955] FAST spr round 1 (radius: 25)
[04:34:05 -236631.946589] FAST spr round 2 (radius: 25)
[04:36:17 -234275.238845] FAST spr round 3 (radius: 25)
[04:38:10 -234088.945899] FAST spr round 4 (radius: 25)
[04:39:49 -234080.843914] FAST spr round 5 (radius: 25)
[04:41:23 -234080.843414] Model parameter optimization (eps = 1.000000)
[04:41:42 -234061.403344] SLOW spr round 1 (radius: 5)
[04:43:53 -234011.673911] SLOW spr round 2 (radius: 5)
[04:46:04 -234006.452824] SLOW spr round 3 (radius: 5)
[04:48:10 -233995.582761] SLOW spr round 4 (radius: 5)
[04:50:15 -233994.126105] SLOW spr round 5 (radius: 5)
[04:52:18 -233993.720851] SLOW spr round 6 (radius: 5)
[04:54:20 -233993.720529] SLOW spr round 7 (radius: 10)
[04:56:26 -233992.329411] SLOW spr round 8 (radius: 5)
[04:59:03 -233992.085460] SLOW spr round 9 (radius: 5)
[05:01:21 -233992.084864] SLOW spr round 10 (radius: 10)
[05:03:34 -233992.084864] SLOW spr round 11 (radius: 15)
[05:07:12 -233992.084863] SLOW spr round 12 (radius: 20)
[05:14:09 -233992.084863] SLOW spr round 13 (radius: 25)
[05:23:06 -233992.084863] Model parameter optimization (eps = 0.100000)

[05:23:15] [worker #0] ML tree search #9, logLikelihood: -233991.852126

[05:23:15 -881613.052554] Initial branch length optimization
[05:23:22 -729102.784772] Model parameter optimization (eps = 10.000000)
[05:23:23] [worker #1] ML tree search #10, logLikelihood: -233999.160785
[05:24:20 -726179.200150] AUTODETECT spr round 1 (radius: 5)
[05:26:33 -484277.658834] AUTODETECT spr round 2 (radius: 10)
[05:28:57 -354574.936666] AUTODETECT spr round 3 (radius: 15)
[05:31:27 -311913.100770] AUTODETECT spr round 4 (radius: 20)
[05:34:35 -283420.193041] AUTODETECT spr round 5 (radius: 25)
[05:38:18 -269061.968813] SPR radius for FAST iterations: 25 (autodetect)
[05:38:18 -269061.968813] Model parameter optimization (eps = 3.000000)
[05:38:49 -268499.282866] FAST spr round 1 (radius: 25)
[05:41:51 -235620.729075] FAST spr round 2 (radius: 25)
[05:44:08 -234186.102094] FAST spr round 3 (radius: 25)
[05:46:11 -234112.147366] FAST spr round 4 (radius: 25)
[05:48:02 -234101.541243] FAST spr round 5 (radius: 25)
[05:49:49 -234094.692500] FAST spr round 6 (radius: 25)
[05:51:26 -234093.414607] FAST spr round 7 (radius: 25)
[05:53:01 -234093.414463] Model parameter optimization (eps = 1.000000)
[05:53:19 -234082.591407] SLOW spr round 1 (radius: 5)
[05:55:37 -234037.748153] SLOW spr round 2 (radius: 5)
[05:57:52 -234024.792683] SLOW spr round 3 (radius: 5)
[06:00:05 -234011.354615] SLOW spr round 4 (radius: 5)
[06:02:12 -234009.673639] SLOW spr round 5 (radius: 5)
[06:04:16 -234009.672315] SLOW spr round 6 (radius: 10)
[06:06:22 -234008.421583] SLOW spr round 7 (radius: 5)
[06:09:03 -234005.689426] SLOW spr round 8 (radius: 5)
[06:11:24 -234005.689398] SLOW spr round 9 (radius: 10)
[06:13:37 -234005.689398] SLOW spr round 10 (radius: 15)
[06:17:24 -234005.689397] SLOW spr round 11 (radius: 20)
[06:24:20 -234005.689397] SLOW spr round 12 (radius: 25)
[06:33:09] [worker #1] ML tree search #12, logLikelihood: -234012.775845
[06:33:13 -234005.689397] Model parameter optimization (eps = 0.100000)

[06:33:30] [worker #0] ML tree search #11, logLikelihood: -234004.170021

[06:33:30 -895980.006556] Initial branch length optimization
[06:33:35 -737713.465858] Model parameter optimization (eps = 10.000000)
[06:34:20 -734928.946931] AUTODETECT spr round 1 (radius: 5)
[06:36:31 -488378.884989] AUTODETECT spr round 2 (radius: 10)
[06:38:56 -361921.127260] AUTODETECT spr round 3 (radius: 15)
[06:41:32 -305408.575980] AUTODETECT spr round 4 (radius: 20)
[06:44:52 -262732.469810] AUTODETECT spr round 5 (radius: 25)
[06:49:04 -259445.166871] SPR radius for FAST iterations: 25 (autodetect)
[06:49:04 -259445.166871] Model parameter optimization (eps = 3.000000)
[06:49:35 -258915.341802] FAST spr round 1 (radius: 25)
[06:52:45 -235356.841297] FAST spr round 2 (radius: 25)
[06:54:56 -234132.993612] FAST spr round 3 (radius: 25)
[06:56:53 -234056.118820] FAST spr round 4 (radius: 25)
[06:58:35 -234053.296140] FAST spr round 5 (radius: 25)
[07:00:13 -234053.295650] Model parameter optimization (eps = 1.000000)
[07:00:39 -234040.787416] SLOW spr round 1 (radius: 5)
[07:02:51 -234005.659942] SLOW spr round 2 (radius: 5)
[07:05:02 -234003.776251] SLOW spr round 3 (radius: 5)
[07:07:08 -234003.775715] SLOW spr round 4 (radius: 10)
[07:09:17 -234003.565755] SLOW spr round 5 (radius: 5)
[07:11:57 -234003.565717] SLOW spr round 6 (radius: 10)
[07:14:23 -234003.565717] SLOW spr round 7 (radius: 15)
[07:17:59 -234003.565716] SLOW spr round 8 (radius: 20)
[07:25:05 -234003.565716] SLOW spr round 9 (radius: 25)
[07:33:53 -234003.565716] Model parameter optimization (eps = 0.100000)

[07:34:01] [worker #0] ML tree search #13, logLikelihood: -234003.315693

[07:34:01 -890488.428686] Initial branch length optimization
[07:34:07 -733681.528990] Model parameter optimization (eps = 10.000000)
[07:35:07 -730710.239863] AUTODETECT spr round 1 (radius: 5)
[07:37:17 -493511.756402] AUTODETECT spr round 2 (radius: 10)
[07:37:22] [worker #1] ML tree search #14, logLikelihood: -233990.783871
[07:39:44 -368567.050932] AUTODETECT spr round 3 (radius: 15)
[07:42:27 -297599.617782] AUTODETECT spr round 4 (radius: 20)
[07:45:17 -267713.268420] AUTODETECT spr round 5 (radius: 25)
[07:48:50 -261909.520809] SPR radius for FAST iterations: 25 (autodetect)
[07:48:50 -261909.520809] Model parameter optimization (eps = 3.000000)
[07:49:19 -261366.943952] FAST spr round 1 (radius: 25)
[07:52:15 -235505.680449] FAST spr round 2 (radius: 25)
[07:54:37 -234171.382683] FAST spr round 3 (radius: 25)
[07:56:42 -234081.089087] FAST spr round 4 (radius: 25)
[07:58:35 -234072.903950] FAST spr round 5 (radius: 25)
[08:00:17 -234071.282559] FAST spr round 6 (radius: 25)
[08:01:53 -234071.282558] Model parameter optimization (eps = 1.000000)
[08:02:22 -234054.133084] SLOW spr round 1 (radius: 5)
[08:04:47 -234014.700492] SLOW spr round 2 (radius: 5)
[08:07:03 -234008.255314] SLOW spr round 3 (radius: 5)
[08:09:08 -234008.254615] SLOW spr round 4 (radius: 10)
[08:11:17 -234008.254533] SLOW spr round 5 (radius: 15)
[08:15:15 -234008.254523] SLOW spr round 6 (radius: 20)
[08:22:04 -234008.254522] SLOW spr round 7 (radius: 25)
[08:30:50 -234008.254521] Model parameter optimization (eps = 0.100000)

[08:31:06] [worker #0] ML tree search #15, logLikelihood: -234008.037189

[08:31:06 -885007.904477] Initial branch length optimization
[08:31:13 -726884.670207] Model parameter optimization (eps = 10.000000)
[08:32:12 -724225.797451] AUTODETECT spr round 1 (radius: 5)
[08:34:21 -492882.681408] AUTODETECT spr round 2 (radius: 10)
[08:36:49 -346103.660207] AUTODETECT spr round 3 (radius: 15)
[08:39:40 -283688.943268] AUTODETECT spr round 4 (radius: 20)
[08:43:03 -266513.821687] AUTODETECT spr round 5 (radius: 25)
[08:47:24] [worker #1] ML tree search #16, logLikelihood: -233999.780968
[08:47:36 -261809.998817] SPR radius for FAST iterations: 25 (autodetect)
[08:47:36 -261809.998817] Model parameter optimization (eps = 3.000000)
[08:48:19 -261338.552247] FAST spr round 1 (radius: 25)
[08:51:27 -234736.561966] FAST spr round 2 (radius: 25)
[08:53:37 -234104.927809] FAST spr round 3 (radius: 25)
[08:55:34 -234048.189342] FAST spr round 4 (radius: 25)
[08:57:16 -234044.079511] FAST spr round 5 (radius: 25)
[08:58:52 -234044.079045] Model parameter optimization (eps = 1.000000)
[08:59:14 -234030.195530] SLOW spr round 1 (radius: 5)
[09:01:30 -233997.956856] SLOW spr round 2 (radius: 5)
[09:03:42 -233995.320266] SLOW spr round 3 (radius: 5)
[09:05:48 -233995.317439] SLOW spr round 4 (radius: 10)
[09:07:58 -233993.779872] SLOW spr round 5 (radius: 5)
[09:10:40 -233991.682398] SLOW spr round 6 (radius: 5)
[09:13:07 -233987.683507] SLOW spr round 7 (radius: 5)
[09:15:20 -233987.683392] SLOW spr round 8 (radius: 10)
[09:17:30 -233987.683367] SLOW spr round 9 (radius: 15)
[09:21:22 -233987.683365] SLOW spr round 10 (radius: 20)
[09:28:17 -233987.683364] SLOW spr round 11 (radius: 25)
[09:37:09 -233987.683364] Model parameter optimization (eps = 0.100000)

[09:37:27] [worker #0] ML tree search #17, logLikelihood: -233987.418680

[09:37:28 -889839.407065] Initial branch length optimization
[09:37:33 -732756.992022] Model parameter optimization (eps = 10.000000)
[09:38:11 -729847.929313] AUTODETECT spr round 1 (radius: 5)
[09:40:21 -485786.257442] AUTODETECT spr round 2 (radius: 10)
[09:42:42 -358622.149112] AUTODETECT spr round 3 (radius: 15)
[09:45:25 -297900.904666] AUTODETECT spr round 4 (radius: 20)
[09:48:40 -267808.831430] AUTODETECT spr round 5 (radius: 25)
[09:53:05 -259650.992288] SPR radius for FAST iterations: 25 (autodetect)
[09:53:05 -259650.992288] Model parameter optimization (eps = 3.000000)
[09:53:44 -259196.890949] FAST spr round 1 (radius: 25)
[09:56:36 -235746.839257] FAST spr round 2 (radius: 25)
[09:58:55 -234186.644432] FAST spr round 3 (radius: 25)
[10:00:53 -234093.666475] FAST spr round 4 (radius: 25)
[10:02:34 -234077.952207] FAST spr round 5 (radius: 25)
[10:04:11 -234077.492299] FAST spr round 6 (radius: 25)
[10:05:34] [worker #1] ML tree search #18, logLikelihood: -234002.040988
[10:05:45 -234076.183648] FAST spr round 7 (radius: 25)
[10:07:21 -234076.183399] Model parameter optimization (eps = 1.000000)
[10:07:45 -234054.057783] SLOW spr round 1 (radius: 5)
[10:10:03 -234006.504705] SLOW spr round 2 (radius: 5)
[10:12:14 -234003.433241] SLOW spr round 3 (radius: 5)
[10:14:22 -234003.432957] SLOW spr round 4 (radius: 10)
[10:16:30 -233996.916306] SLOW spr round 5 (radius: 5)
[10:19:11 -233996.915195] SLOW spr round 6 (radius: 10)
[10:21:38 -233996.915047] SLOW spr round 7 (radius: 15)
[10:25:18 -233995.143163] SLOW spr round 8 (radius: 5)
[10:28:07 -233995.143146] SLOW spr round 9 (radius: 10)
[10:30:46 -233995.143140] SLOW spr round 10 (radius: 15)
[10:34:21 -233995.143139] SLOW spr round 11 (radius: 20)
[10:41:35 -233995.143139] SLOW spr round 12 (radius: 25)
[10:50:52 -233995.143139] Model parameter optimization (eps = 0.100000)

[10:50:58] [worker #0] ML tree search #19, logLikelihood: -233995.123475

[11:09:34] [worker #1] ML tree search #20, logLikelihood: -233996.567667

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.163386,0.534090) (0.095701,0.510769) (0.411376,0.722766) (0.329537,1.719162) 
   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: -233987.418680

AIC score: 471324.837359 / AICc score: 6085924.837359 / BIC score: 478787.294953
Free parameters (model + branch lengths): 1675

WARNING: Number of free parameters (K=1675) is larger than alignment size (n=636).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 91 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98174/3_mltree/P98174.raxml.log

Analysis started: 07-Jul-2021 19:06:35 / finished: 08-Jul-2021 06:16:09

Elapsed time: 40174.326 seconds

Consumed energy: 3162.714 Wh (= 16 km in an electric car, or 79 km with an e-scooter!)