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 30-Jun-2021 18:15:20 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/2_msa/P10696_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/2_msa/P10696_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 378 sites

WARNING: Sequences tr_B4R2C7_B4R2C7_DROSI_7240 and tr_B4HZY3_B4HZY3_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B2WJH5_B2WJH5_PYRTR_426418 and tr_A0A2W1EB81_A0A2W1EB81_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_Q28XS4_Q28XS4_DROPS_46245 and tr_B4GHH9_B4GHH9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q299F1_Q299F1_DROPS_46245 and tr_B4G540_B4G540_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q29CD2_Q29CD2_DROPS_46245 and tr_B4GN81_B4GN81_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q2LZN0_Q2LZN0_DROPS_46245 and tr_B4H3D6_B4H3D6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QJL8_H2QJL8_PANTR_9598 and tr_A0A2R9AW48_A0A2R9AW48_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7B4Y6_K7B4Y6_PANTR_9598 and tr_A0A2R9ABM8_A0A2R9ABM8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_C6H9T0_C6H9T0_AJECH_544712 and tr_F0UKP3_F0UKP3_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A5AAV2_A5AAV2_ASPNC_425011 and tr_G3XZ83_G3XZ83_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A0A1D5R5B1_A0A1D5R5B1_MACMU_9544 and tr_G7NUV3_G7NUV3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R5B1_A0A1D5R5B1_MACMU_9544 and tr_A0A096N206_A0A096N206_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R5B1_A0A1D5R5B1_MACMU_9544 and tr_A0A0D9S8B5_A0A0D9S8B5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R5B1_A0A1D5R5B1_MACMU_9544 and tr_A0A2K5MDC8_A0A2K5MDC8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R5B1_A0A1D5R5B1_MACMU_9544 and tr_A0A2K6E5Z3_A0A2K6E5Z3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XF13_G7XF13_ASPKW_1033177 and tr_A0A146F290_A0A146F290_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_Q5TSZ8_Q5TSZ8_ANOGA_7165 and tr_Q7PD92_Q7PD92_ANOGA_7165 are exactly identical!
WARNING: Sequences tr_F2SJQ0_F2SJQ0_TRIRC_559305 and tr_A0A178EQY4_A0A178EQY4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_F2SUR2_F2SUR2_TRIRC_559305 and tr_A0A178F6G4_A0A178F6G4_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_B3RR74_B3RR74_TRIAD_10228 and tr_A0A369SE50_A0A369SE50_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3RR75_B3RR75_TRIAD_10228 and tr_A0A369SEC8_A0A369SEC8_9METZ_287889 are exactly identical!
WARNING: Sequences tr_A0A151IZ22_A0A151IZ22_9HYME_471704 and tr_A0A195ATQ8_A0A195ATQ8_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A226MZL8_A0A226MZL8_CALSU_9009 and tr_A0A226PBF3_A0A226PBF3_COLVI_9014 are exactly identical!
WARNING: Duplicate sequences found: 23

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/P10696/3_mltree/P10696.raxml.reduced.phy

Alignment comprises 1 partitions and 378 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 378 / 378
Gaps: 7.90 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 189 / 15120
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -635743.530272] Initial branch length optimization
[00:00:05 -540159.775722] Model parameter optimization (eps = 10.000000)
[00:00:49 -538708.388451] AUTODETECT spr round 1 (radius: 5)
[00:04:17 -422432.262145] AUTODETECT spr round 2 (radius: 10)
[00:08:20 -325947.761184] AUTODETECT spr round 3 (radius: 15)
[00:12:58 -275436.712205] AUTODETECT spr round 4 (radius: 20)
[00:18:16 -250492.769533] AUTODETECT spr round 5 (radius: 25)
[00:25:20 -244786.930966] SPR radius for FAST iterations: 25 (autodetect)
[00:25:20 -244786.930966] Model parameter optimization (eps = 3.000000)
[00:25:54 -244542.862621] FAST spr round 1 (radius: 25)
[00:31:13 -223400.057514] FAST spr round 2 (radius: 25)
[00:35:06 -222605.578378] FAST spr round 3 (radius: 25)
[00:38:24 -222498.250277] FAST spr round 4 (radius: 25)
[00:41:18 -222466.597066] FAST spr round 5 (radius: 25)
[00:43:54 -222466.404888] FAST spr round 6 (radius: 25)
[00:46:28 -222466.404869] Model parameter optimization (eps = 1.000000)
[00:46:49 -222460.572367] SLOW spr round 1 (radius: 5)
[00:50:34 -222405.661119] SLOW spr round 2 (radius: 5)
[00:54:04 -222397.826685] SLOW spr round 3 (radius: 5)
[00:57:23 -222397.826577] SLOW spr round 4 (radius: 10)
[01:00:50 -222397.826576] SLOW spr round 5 (radius: 15)
[01:07:21 -222397.826575] SLOW spr round 6 (radius: 20)
[01:16:46 -222397.826575] SLOW spr round 7 (radius: 25)
[01:29:18 -222397.826575] Model parameter optimization (eps = 0.100000)

[01:29:31] [worker #0] ML tree search #1, logLikelihood: -222397.683474

[01:29:31 -631455.396910] Initial branch length optimization
[01:29:35 -539476.016732] Model parameter optimization (eps = 10.000000)
[01:30:33 -537993.140941] AUTODETECT spr round 1 (radius: 5)
[01:34:03 -420815.275354] AUTODETECT spr round 2 (radius: 10)
[01:38:02 -315198.412778] AUTODETECT spr round 3 (radius: 15)
[01:38:55] [worker #2] ML tree search #3, logLikelihood: -222540.836054
[01:42:24 -270197.565140] AUTODETECT spr round 4 (radius: 20)
[01:47:36 -252514.641651] AUTODETECT spr round 5 (radius: 25)
[01:54:14 -250057.114955] SPR radius for FAST iterations: 25 (autodetect)
[01:54:14 -250057.114955] Model parameter optimization (eps = 3.000000)
[01:54:25 -250053.688416] FAST spr round 1 (radius: 25)
[01:59:58 -223862.825053] FAST spr round 2 (radius: 25)
[02:04:01 -222773.535710] FAST spr round 3 (radius: 25)
[02:04:55] [worker #1] ML tree search #2, logLikelihood: -222398.093831
[02:07:31 -222678.213593] FAST spr round 4 (radius: 25)
[02:10:19 -222668.880676] FAST spr round 5 (radius: 25)
[02:12:59 -222667.294641] FAST spr round 6 (radius: 25)
[02:15:34 -222667.294081] Model parameter optimization (eps = 1.000000)
[02:15:41 -222666.757396] SLOW spr round 1 (radius: 5)
[02:19:42 -222590.714340] SLOW spr round 2 (radius: 5)
[02:23:29 -222564.364812] SLOW spr round 3 (radius: 5)
[02:26:57 -222561.561703] SLOW spr round 4 (radius: 5)
[02:30:17 -222561.561002] SLOW spr round 5 (radius: 10)
[02:33:53 -222556.896816] SLOW spr round 6 (radius: 5)
[02:38:14 -222554.746664] SLOW spr round 7 (radius: 5)
[02:42:03 -222554.746626] SLOW spr round 8 (radius: 10)
[02:45:47 -222554.701293] SLOW spr round 9 (radius: 15)
[02:52:17 -222554.701179] SLOW spr round 10 (radius: 20)
[03:02:23 -222554.701175] SLOW spr round 11 (radius: 25)
[03:15:41 -222554.701174] Model parameter optimization (eps = 0.100000)

[03:15:49] [worker #0] ML tree search #4, logLikelihood: -222554.672059

[03:15:49 -633324.258196] Initial branch length optimization
[03:15:53 -540027.145958] Model parameter optimization (eps = 10.000000)
[03:16:57 -538472.339239] AUTODETECT spr round 1 (radius: 5)
[03:20:34 -411710.337433] AUTODETECT spr round 2 (radius: 10)
[03:24:28 -320535.195629] AUTODETECT spr round 3 (radius: 15)
[03:28:52 -275735.903841] AUTODETECT spr round 4 (radius: 20)
[03:33:45 -254273.889354] AUTODETECT spr round 5 (radius: 25)
[03:39:40 -250939.030598] SPR radius for FAST iterations: 25 (autodetect)
[03:39:40 -250939.030598] Model parameter optimization (eps = 3.000000)
[03:39:51 -250935.806711] FAST spr round 1 (radius: 25)
[03:42:53] [worker #2] ML tree search #6, logLikelihood: -222401.665435
[03:45:24 -223884.445006] FAST spr round 2 (radius: 25)
[03:49:30 -222755.316597] FAST spr round 3 (radius: 25)
[03:50:49] [worker #1] ML tree search #5, logLikelihood: -222556.083790
[03:53:01 -222644.318004] FAST spr round 4 (radius: 25)
[03:55:56 -222622.356201] FAST spr round 5 (radius: 25)
[03:58:35 -222622.355681] Model parameter optimization (eps = 1.000000)
[03:59:14 -222481.250618] SLOW spr round 1 (radius: 5)
[04:03:14 -222425.306322] SLOW spr round 2 (radius: 5)
[04:06:57 -222405.989679] SLOW spr round 3 (radius: 5)
[04:10:26 -222401.970806] SLOW spr round 4 (radius: 5)
[04:13:45 -222401.735161] SLOW spr round 5 (radius: 5)
[04:17:03 -222401.734999] SLOW spr round 6 (radius: 10)
[04:20:33 -222397.424130] SLOW spr round 7 (radius: 5)
[04:24:48 -222395.787215] SLOW spr round 8 (radius: 5)
[04:28:33 -222395.787144] SLOW spr round 9 (radius: 10)
[04:32:11 -222395.787143] SLOW spr round 10 (radius: 15)
[04:38:37 -222395.787143] SLOW spr round 11 (radius: 20)
[04:48:30 -222395.787143] SLOW spr round 12 (radius: 25)
[05:00:51 -222395.787143] Model parameter optimization (eps = 0.100000)

[05:00:58] [worker #0] ML tree search #7, logLikelihood: -222395.709422

[05:00:58 -633200.372720] Initial branch length optimization
[05:01:02 -537715.297949] Model parameter optimization (eps = 10.000000)
[05:01:53 -536158.863137] AUTODETECT spr round 1 (radius: 5)
[05:05:22 -412451.448913] AUTODETECT spr round 2 (radius: 10)
[05:09:19 -314195.479187] AUTODETECT spr round 3 (radius: 15)
[05:13:39 -287067.266362] AUTODETECT spr round 4 (radius: 20)
[05:16:05] [worker #2] ML tree search #9, logLikelihood: -222405.805404
[05:19:39 -258674.126219] AUTODETECT spr round 5 (radius: 25)
[05:27:05 -254584.082819] SPR radius for FAST iterations: 25 (autodetect)
[05:27:05 -254584.082819] Model parameter optimization (eps = 3.000000)
[05:27:35 -254363.179277] FAST spr round 1 (radius: 25)
[05:33:26 -223905.537107] FAST spr round 2 (radius: 25)
[05:37:27 -222574.730176] FAST spr round 3 (radius: 25)
[05:40:51 -222484.951016] FAST spr round 4 (radius: 25)
[05:43:38 -222479.951632] FAST spr round 5 (radius: 25)
[05:46:07] [worker #1] ML tree search #8, logLikelihood: -222406.119896
[05:46:15 -222476.583585] FAST spr round 6 (radius: 25)
[05:48:49 -222476.583548] Model parameter optimization (eps = 1.000000)
[05:49:16 -222474.543683] SLOW spr round 1 (radius: 5)
[05:53:11 -222433.044747] SLOW spr round 2 (radius: 5)
[05:56:50 -222421.264273] SLOW spr round 3 (radius: 5)
[06:00:19 -222414.739825] SLOW spr round 4 (radius: 5)
[06:03:42 -222413.838413] SLOW spr round 5 (radius: 5)
[06:07:04 -222405.100017] SLOW spr round 6 (radius: 5)
[06:10:20 -222405.099456] SLOW spr round 7 (radius: 10)
[06:13:51 -222402.651968] SLOW spr round 8 (radius: 5)
[06:18:18 -222387.603716] SLOW spr round 9 (radius: 5)
[06:22:04 -222385.678861] SLOW spr round 10 (radius: 5)
[06:25:31 -222385.366829] SLOW spr round 11 (radius: 5)
[06:28:51 -222385.366814] SLOW spr round 12 (radius: 10)
[06:32:19 -222385.010279] SLOW spr round 13 (radius: 5)
[06:36:32 -222382.325214] SLOW spr round 14 (radius: 5)
[06:40:14 -222382.105854] SLOW spr round 15 (radius: 5)
[06:43:42 -222381.046863] SLOW spr round 16 (radius: 5)
[06:47:02 -222381.046776] SLOW spr round 17 (radius: 10)
[06:50:31 -222380.695038] SLOW spr round 18 (radius: 5)
[06:54:43 -222380.248903] SLOW spr round 19 (radius: 5)
[06:58:24 -222380.248887] SLOW spr round 20 (radius: 10)
[07:02:02 -222380.248884] SLOW spr round 21 (radius: 15)
[07:08:26 -222380.248882] SLOW spr round 22 (radius: 20)
[07:18:51 -222380.248880] SLOW spr round 23 (radius: 25)
[07:25:38] [worker #2] ML tree search #12, logLikelihood: -222440.689551
[07:31:33 -222380.248878] Model parameter optimization (eps = 0.100000)

[07:31:42] [worker #0] ML tree search #10, logLikelihood: -222380.187533

[07:31:43 -634552.278091] Initial branch length optimization
[07:31:47 -539381.668522] Model parameter optimization (eps = 10.000000)
[07:32:37 -537946.748860] AUTODETECT spr round 1 (radius: 5)
[07:36:01 -420582.460118] AUTODETECT spr round 2 (radius: 10)
[07:39:54 -322951.742958] AUTODETECT spr round 3 (radius: 15)
[07:44:17 -268510.233234] AUTODETECT spr round 4 (radius: 20)
[07:49:15 -255600.984798] AUTODETECT spr round 5 (radius: 25)
[07:49:36] [worker #1] ML tree search #11, logLikelihood: -222538.938729
[07:56:17 -251971.243326] SPR radius for FAST iterations: 25 (autodetect)
[07:56:17 -251971.243326] Model parameter optimization (eps = 3.000000)
[07:56:50 -251684.227206] FAST spr round 1 (radius: 25)
[08:02:10 -224128.690152] FAST spr round 2 (radius: 25)
[08:06:07 -222612.175092] FAST spr round 3 (radius: 25)
[08:09:24 -222518.087513] FAST spr round 4 (radius: 25)
[08:12:09 -222515.767102] FAST spr round 5 (radius: 25)
[08:14:44 -222515.762936] Model parameter optimization (eps = 1.000000)
[08:15:16 -222509.163296] SLOW spr round 1 (radius: 5)
[08:19:07 -222455.997811] SLOW spr round 2 (radius: 5)
[08:22:41 -222446.652030] SLOW spr round 3 (radius: 5)
[08:26:01 -222446.120712] SLOW spr round 4 (radius: 5)
[08:29:18 -222446.120553] SLOW spr round 5 (radius: 10)
[08:32:46 -222442.762526] SLOW spr round 6 (radius: 5)
[08:37:08 -222434.804981] SLOW spr round 7 (radius: 5)
[08:40:54 -222432.208979] SLOW spr round 8 (radius: 5)
[08:44:23 -222432.208721] SLOW spr round 9 (radius: 10)
[08:47:54 -222431.774849] SLOW spr round 10 (radius: 5)
[08:52:09 -222425.489987] SLOW spr round 11 (radius: 5)
[08:55:53 -222424.609435] SLOW spr round 12 (radius: 5)
[08:59:19 -222424.608742] SLOW spr round 13 (radius: 10)
[09:02:49 -222424.608719] SLOW spr round 14 (radius: 15)
[09:09:30 -222424.608717] SLOW spr round 15 (radius: 20)
[09:13:01] [worker #2] ML tree search #15, logLikelihood: -222384.127561
[09:19:34 -222424.608716] SLOW spr round 16 (radius: 25)
[09:32:48 -222423.846405] SLOW spr round 17 (radius: 5)
[09:37:19 -222423.798418] SLOW spr round 18 (radius: 10)
[09:41:46 -222423.796273] SLOW spr round 19 (radius: 15)
[09:47:52 -222423.794700] SLOW spr round 20 (radius: 20)
[09:58:22 -222423.793544] SLOW spr round 21 (radius: 25)
[10:11:29 -222423.792691] Model parameter optimization (eps = 0.100000)

[10:11:41] [worker #0] ML tree search #13, logLikelihood: -222423.679679

[10:11:41 -632199.068860] Initial branch length optimization
[10:11:46 -535620.663232] Model parameter optimization (eps = 10.000000)
[10:12:40 -534077.211603] AUTODETECT spr round 1 (radius: 5)
[10:16:04 -421300.802019] AUTODETECT spr round 2 (radius: 10)
[10:20:01 -332882.527963] AUTODETECT spr round 3 (radius: 15)
[10:24:24 -285572.989291] AUTODETECT spr round 4 (radius: 20)
[10:29:31 -258372.492532] AUTODETECT spr round 5 (radius: 25)
[10:36:48 -252224.355192] SPR radius for FAST iterations: 25 (autodetect)
[10:36:48 -252224.355192] Model parameter optimization (eps = 3.000000)
[10:37:27 -252017.234680] FAST spr round 1 (radius: 25)
[10:42:51 -223539.164436] FAST spr round 2 (radius: 25)
[10:46:39 -222598.457862] FAST spr round 3 (radius: 25)
[10:49:50 -222521.137603] FAST spr round 4 (radius: 25)
[10:52:38 -222510.296917] FAST spr round 5 (radius: 25)
[10:55:12 -222509.808283] FAST spr round 6 (radius: 25)
[10:57:40 -222509.808129] Model parameter optimization (eps = 1.000000)
[10:58:00 -222505.269090] SLOW spr round 1 (radius: 5)
[11:00:37] [worker #2] ML tree search #18, logLikelihood: -222420.145755
[11:01:40 -222444.047880] SLOW spr round 2 (radius: 5)
[11:02:45] [worker #1] ML tree search #14, logLikelihood: -222398.917360
[11:05:13 -222421.922852] SLOW spr round 3 (radius: 5)
[11:08:34 -222419.300942] SLOW spr round 4 (radius: 5)
[11:11:48 -222419.300849] SLOW spr round 5 (radius: 10)
[11:15:13 -222419.300848] SLOW spr round 6 (radius: 15)
[11:21:53 -222419.300848] SLOW spr round 7 (radius: 20)
[11:31:35 -222419.300848] SLOW spr round 8 (radius: 25)
[11:43:57 -222419.300848] Model parameter optimization (eps = 0.100000)

[11:44:12] [worker #0] ML tree search #16, logLikelihood: -222418.402083

[11:44:12 -633499.465720] Initial branch length optimization
[11:44:17 -539499.660128] Model parameter optimization (eps = 10.000000)
[11:45:15 -538096.733424] AUTODETECT spr round 1 (radius: 5)
[11:48:37 -422369.996338] AUTODETECT spr round 2 (radius: 10)
[11:52:34 -316271.637968] AUTODETECT spr round 3 (radius: 15)
[11:57:03 -272217.392481] AUTODETECT spr round 4 (radius: 20)
[12:02:29 -258259.200034] AUTODETECT spr round 5 (radius: 25)
[12:09:07 -253338.018817] SPR radius for FAST iterations: 25 (autodetect)
[12:09:07 -253338.018817] Model parameter optimization (eps = 3.000000)
[12:09:16 -253336.130388] FAST spr round 1 (radius: 25)
[12:14:43 -223524.383327] FAST spr round 2 (radius: 25)
[12:18:50 -222700.504279] FAST spr round 3 (radius: 25)
[12:22:12 -222643.575536] FAST spr round 4 (radius: 25)
[12:24:55 -222641.054935] FAST spr round 5 (radius: 25)
[12:27:29 -222640.555830] FAST spr round 6 (radius: 25)
[12:29:57 -222640.555829] Model parameter optimization (eps = 1.000000)
[12:30:04 -222639.559890] SLOW spr round 1 (radius: 5)
[12:33:47 -222572.224093] SLOW spr round 2 (radius: 5)
[12:37:22 -222560.623726] SLOW spr round 3 (radius: 5)
[12:40:44 -222557.013288] SLOW spr round 4 (radius: 5)
[12:44:03 -222556.027586] SLOW spr round 5 (radius: 5)
[12:47:16 -222556.027487] SLOW spr round 6 (radius: 10)
[12:50:47 -222556.027486] SLOW spr round 7 (radius: 15)
[12:58:05 -222556.027486] SLOW spr round 8 (radius: 20)
[13:09:18 -222556.027485] SLOW spr round 9 (radius: 25)
[13:14:20] [worker #1] ML tree search #17, logLikelihood: -222402.060690
[13:23:35 -222556.027485] Model parameter optimization (eps = 0.100000)

[13:23:40] [worker #0] ML tree search #19, logLikelihood: -222556.019079

[14:58:44] [worker #1] ML tree search #20, logLikelihood: -222427.731465

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.220370,0.366045) (0.249203,0.501027) (0.342203,1.011682) (0.188224,2.381614) 
   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: -222380.187533

AIC score: 448770.375065 / AICc score: 8492830.375065 / BIC score: 456659.837928
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=378).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 33 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P10696/3_mltree/P10696.raxml.log

Analysis started: 30-Jun-2021 18:15:20 / finished: 01-Jul-2021 09:14:05

Elapsed time: 53924.715 seconds

Consumed energy: 3455.498 Wh (= 17 km in an electric car, or 86 km with an e-scooter!)