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

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 05-Jul-2021 00:07:30 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/2_msa/Q5VIY5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5 --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/Q5VIY5/2_msa/Q5VIY5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 511 sites

WARNING: Sequences tr_G3RQT6_G3RQT6_GORGO_9595 and tr_H2QH16_H2QH16_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S2S2_G3S2S2_GORGO_9595 and tr_K7EVS2_K7EVS2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3S2S2_G3S2S2_GORGO_9595 and sp_B4DU55_ZN879_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3S7T2_G3S7T2_GORGO_9595 and tr_A0A2J8JTW2_A0A2J8JTW2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3TIE9_A0A2I3TIE9_PANTR_9598 and tr_A0A2R9CGM5_A0A2R9CGM5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QG71_H2QG71_PANTR_9598 and sp_Q8NB42_ZN527_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R058_H2R058_PANTR_9598 and tr_A0A2R9APP9_A0A2R9APP9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2RDB6_H2RDB6_PANTR_9598 and tr_A0A2R9BB79_A0A2R9BB79_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QC17_A0A1D5QC17_MACMU_9544 and tr_A0A2K6BUH3_A0A2K6BUH3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QG38_A0A1D5QG38_MACMU_9544 and tr_G7PYQ6_G7PYQ6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R3C7_A0A1D5R3C7_MACMU_9544 and tr_G7PXE8_G7PXE8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R3C7_A0A1D5R3C7_MACMU_9544 and tr_A0A2K6DA83_A0A2K6DA83_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R3C7_A0A1D5R3C7_MACMU_9544 and tr_A0A2K5XDE6_A0A2K5XDE6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1D5R704_A0A1D5R704_MACMU_9544 and tr_A0A2K6B9B3_A0A2K6B9B3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6UR85_F6UR85_MACMU_9544 and tr_A0A2K6ADH3_A0A2K6ADH3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6V0U3_F6V0U3_MACMU_9544 and tr_G7PYP5_G7PYP5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A2K6BPR5_A0A2K6BPR5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GB84_F7GB84_MACMU_9544 and tr_A0A2K5LBC9_A0A2K5LBC9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GB84_F7GB84_MACMU_9544 and tr_A0A2K6BN44_A0A2K6BN44_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H5I5_F7H5I5_MACMU_9544 and tr_G7PXE5_G7PXE5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7H5I5_F7H5I5_MACMU_9544 and tr_A0A2K6AUB7_A0A2K6AUB7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7MUI1_G7MUI1_MACMU_9544 and tr_A0A2K6AN26_A0A2K6AN26_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PZB3_G7PZB3_MACFA_9541 and tr_A0A2K6BZF6_A0A2K6BZF6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5LAJ0_A0A2K5LAJ0_CERAT_9531 and tr_A0A2K5Y6G8_A0A2K5Y6G8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5NJ59_A0A2K5NJ59_CERAT_9531 and tr_A0A2K5YNA2_A0A2K5YNA2_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 27

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/Q5VIY5/3_mltree/Q5VIY5.raxml.reduced.phy

Alignment comprises 1 partitions and 511 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 511 / 511
Gaps: 12.41 %
Invariant sites: 0.98 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.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 / 256 / 20480
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -689155.828037] Initial branch length optimization
[00:00:06 -612718.851151] Model parameter optimization (eps = 10.000000)
[00:00:58 -610359.407212] AUTODETECT spr round 1 (radius: 5)
[00:05:42 -482126.120823] AUTODETECT spr round 2 (radius: 10)
[00:11:05 -308159.316538] AUTODETECT spr round 3 (radius: 15)
[00:16:43 -244798.246479] AUTODETECT spr round 4 (radius: 20)
[00:24:47 -232777.551332] AUTODETECT spr round 5 (radius: 25)
[00:35:36 -231251.132939] SPR radius for FAST iterations: 25 (autodetect)
[00:35:36 -231251.132939] Model parameter optimization (eps = 3.000000)
[00:36:34 -230962.914245] FAST spr round 1 (radius: 25)
[00:41:54 -202473.687775] FAST spr round 2 (radius: 25)
[00:45:58 -201427.383568] FAST spr round 3 (radius: 25)
[00:49:37 -201320.849713] FAST spr round 4 (radius: 25)
[00:52:54 -201306.790535] FAST spr round 5 (radius: 25)
[00:55:58 -201299.869344] FAST spr round 6 (radius: 25)
[00:58:56 -201299.636680] FAST spr round 7 (radius: 25)
[01:01:51 -201299.635996] Model parameter optimization (eps = 1.000000)
[01:02:19 -201293.448972] SLOW spr round 1 (radius: 5)
[01:06:46 -201224.531312] SLOW spr round 2 (radius: 5)
[01:11:01 -201205.068317] SLOW spr round 3 (radius: 5)
[01:15:04 -201200.828100] SLOW spr round 4 (radius: 5)
[01:18:54 -201200.827947] SLOW spr round 5 (radius: 10)
[01:23:11 -201200.758374] SLOW spr round 6 (radius: 15)
[01:32:24 -201190.930343] SLOW spr round 7 (radius: 5)
[01:37:28 -201190.091563] SLOW spr round 8 (radius: 5)
[01:41:50 -201190.091513] SLOW spr round 9 (radius: 10)
[01:46:20 -201187.079535] SLOW spr round 10 (radius: 5)
[01:51:09 -201186.905381] SLOW spr round 11 (radius: 5)
[01:55:25 -201186.905352] SLOW spr round 12 (radius: 10)
[01:56:07] [worker #1] ML tree search #2, logLikelihood: -201240.697014
[01:58:22] [worker #2] ML tree search #3, logLikelihood: -201280.687669
[01:59:52 -201186.905352] SLOW spr round 13 (radius: 15)
[02:08:42 -201186.905351] SLOW spr round 14 (radius: 20)
[02:22:47 -201186.905351] SLOW spr round 15 (radius: 25)
[02:40:02 -201186.905351] Model parameter optimization (eps = 0.100000)

[02:40:21] [worker #0] ML tree search #1, logLikelihood: -201186.452791

[02:40:21 -693113.121518] Initial branch length optimization
[02:40:27 -616742.306667] Model parameter optimization (eps = 10.000000)
[02:41:23 -614202.048761] AUTODETECT spr round 1 (radius: 5)
[02:46:13 -481051.580979] AUTODETECT spr round 2 (radius: 10)
[02:51:33 -309492.459250] AUTODETECT spr round 3 (radius: 15)
[02:57:04 -247616.801734] AUTODETECT spr round 4 (radius: 20)
[03:03:17 -231964.796245] AUTODETECT spr round 5 (radius: 25)
[03:11:15 -228455.337213] SPR radius for FAST iterations: 25 (autodetect)
[03:11:15 -228455.337213] Model parameter optimization (eps = 3.000000)
[03:11:53 -228372.033545] FAST spr round 1 (radius: 25)
[03:16:51 -202987.297201] FAST spr round 2 (radius: 25)
[03:20:46 -201529.905693] FAST spr round 3 (radius: 25)
[03:24:26 -201406.303410] FAST spr round 4 (radius: 25)
[03:27:38 -201399.911999] FAST spr round 5 (radius: 25)
[03:30:38 -201399.911994] Model parameter optimization (eps = 1.000000)
[03:30:58 -201391.197475] SLOW spr round 1 (radius: 5)
[03:35:16 -201324.258846] SLOW spr round 2 (radius: 5)
[03:39:28 -201314.127480] SLOW spr round 3 (radius: 5)
[03:43:24 -201313.697956] SLOW spr round 4 (radius: 5)
[03:46:15] [worker #1] ML tree search #5, logLikelihood: -201285.195684
[03:47:05 -201313.697949] SLOW spr round 5 (radius: 10)
[03:49:27] [worker #2] ML tree search #6, logLikelihood: -201272.186942
[03:50:33 -201306.715549] SLOW spr round 6 (radius: 5)
[03:54:40 -201304.384544] SLOW spr round 7 (radius: 5)
[03:58:12 -201304.040583] SLOW spr round 8 (radius: 5)
[04:01:30 -201304.040181] SLOW spr round 9 (radius: 10)
[04:05:01 -201304.039944] SLOW spr round 10 (radius: 15)
[04:12:40 -201302.791482] SLOW spr round 11 (radius: 5)
[04:16:55 -201299.790071] SLOW spr round 12 (radius: 5)
[04:20:29 -201299.789990] SLOW spr round 13 (radius: 10)
[04:24:07 -201299.789967] SLOW spr round 14 (radius: 15)
[04:31:30 -201299.789952] SLOW spr round 15 (radius: 20)
[04:43:15 -201299.789943] SLOW spr round 16 (radius: 25)
[04:57:18 -201299.789938] Model parameter optimization (eps = 0.100000)

[04:57:24] [worker #0] ML tree search #4, logLikelihood: -201299.746345

[04:57:24 -691608.466144] Initial branch length optimization
[04:57:30 -615105.773086] Model parameter optimization (eps = 10.000000)
[04:58:20 -612569.220766] AUTODETECT spr round 1 (radius: 5)
[05:02:21 -482572.292120] AUTODETECT spr round 2 (radius: 10)
[05:06:38 -312183.714462] AUTODETECT spr round 3 (radius: 15)
[05:10:51 -246520.731207] AUTODETECT spr round 4 (radius: 20)
[05:15:48 -232677.919715] AUTODETECT spr round 5 (radius: 25)
[05:21:41 -230680.261558] SPR radius for FAST iterations: 25 (autodetect)
[05:21:41 -230680.261558] Model parameter optimization (eps = 3.000000)
[05:22:05 -230616.615535] FAST spr round 1 (radius: 25)
[05:25:59 -202353.012061] FAST spr round 2 (radius: 25)
[05:29:04 -201505.659670] FAST spr round 3 (radius: 25)
[05:31:43 -201442.177998] FAST spr round 4 (radius: 25)
[05:34:11 -201411.022188] FAST spr round 5 (radius: 25)
[05:36:41 -201406.298301] FAST spr round 6 (radius: 25)
[05:37:46] [worker #1] ML tree search #8, logLikelihood: -201255.585271
[05:39:08 -201406.298189] Model parameter optimization (eps = 1.000000)
[05:39:33 -201379.408883] SLOW spr round 1 (radius: 5)
[05:43:12 -201306.835136] SLOW spr round 2 (radius: 5)
[05:46:39 -201304.944076] SLOW spr round 3 (radius: 5)
[05:49:57 -201304.563828] SLOW spr round 4 (radius: 5)
[05:53:12 -201304.563814] SLOW spr round 5 (radius: 10)
[05:55:00] [worker #2] ML tree search #9, logLikelihood: -201238.776260
[05:56:57 -201294.047751] SLOW spr round 6 (radius: 5)
[06:01:06 -201292.836110] SLOW spr round 7 (radius: 5)
[06:04:45 -201292.836080] SLOW spr round 8 (radius: 10)
[06:08:31 -201292.017393] SLOW spr round 9 (radius: 5)
[06:12:42 -201282.649435] SLOW spr round 10 (radius: 5)
[06:16:18 -201282.649389] SLOW spr round 11 (radius: 10)
[06:20:06 -201282.649389] SLOW spr round 12 (radius: 15)
[06:27:45 -201282.649389] SLOW spr round 13 (radius: 20)
[06:39:52 -201282.649389] SLOW spr round 14 (radius: 25)
[06:54:14 -201282.649389] Model parameter optimization (eps = 0.100000)

[06:54:25] [worker #0] ML tree search #7, logLikelihood: -201282.449347

[06:54:25 -691783.175015] Initial branch length optimization
[06:54:30 -616561.505259] Model parameter optimization (eps = 10.000000)
[06:55:31 -614082.314398] AUTODETECT spr round 1 (radius: 5)
[06:59:32 -476602.182086] AUTODETECT spr round 2 (radius: 10)
[07:04:00 -296087.514238] AUTODETECT spr round 3 (radius: 15)
[07:08:26 -241359.343144] AUTODETECT spr round 4 (radius: 20)
[07:14:40 -231385.070613] AUTODETECT spr round 5 (radius: 25)
[07:21:39 -230422.857602] SPR radius for FAST iterations: 25 (autodetect)
[07:21:39 -230422.857602] Model parameter optimization (eps = 3.000000)
[07:22:06] [worker #1] ML tree search #11, logLikelihood: -201253.559200
[07:22:07 -230293.540904] FAST spr round 1 (radius: 25)
[07:26:33 -202932.736840] FAST spr round 2 (radius: 25)
[07:29:53 -201561.082678] FAST spr round 3 (radius: 25)
[07:32:52 -201450.887369] FAST spr round 4 (radius: 25)
[07:35:27 -201442.268329] FAST spr round 5 (radius: 25)
[07:37:55 -201442.268154] Model parameter optimization (eps = 1.000000)
[07:38:14 -201419.997611] SLOW spr round 1 (radius: 5)
[07:39:35] [worker #2] ML tree search #12, logLikelihood: -201266.654529
[07:41:52 -201363.513384] SLOW spr round 2 (radius: 5)
[07:45:24 -201353.651459] SLOW spr round 3 (radius: 5)
[07:48:42 -201353.651432] SLOW spr round 4 (radius: 10)
[07:52:23 -201344.143307] SLOW spr round 5 (radius: 5)
[07:56:40 -201335.162609] SLOW spr round 6 (radius: 5)
[08:00:22 -201334.759230] SLOW spr round 7 (radius: 5)
[08:03:49 -201334.759204] SLOW spr round 8 (radius: 10)
[08:07:30 -201334.759204] SLOW spr round 9 (radius: 15)
[08:15:24 -201334.759204] SLOW spr round 10 (radius: 20)
[08:27:33 -201334.759204] SLOW spr round 11 (radius: 25)
[08:42:23 -201334.759204] Model parameter optimization (eps = 0.100000)

[08:42:46] [worker #0] ML tree search #10, logLikelihood: -201334.249822

[08:42:46 -692664.199886] Initial branch length optimization
[08:42:51 -615280.599278] Model parameter optimization (eps = 10.000000)
[08:43:42 -612563.017129] AUTODETECT spr round 1 (radius: 5)
[08:47:44 -489613.351386] AUTODETECT spr round 2 (radius: 10)
[08:48:32] [worker #1] ML tree search #14, logLikelihood: -201170.380133
[08:52:16 -303004.324238] AUTODETECT spr round 3 (radius: 15)
[08:56:45 -240530.263496] AUTODETECT spr round 4 (radius: 20)
[09:02:40 -226286.981049] AUTODETECT spr round 5 (radius: 25)
[09:09:45 -225074.315090] SPR radius for FAST iterations: 25 (autodetect)
[09:09:45 -225074.315090] Model parameter optimization (eps = 3.000000)
[09:10:13 -224909.908479] FAST spr round 1 (radius: 25)
[09:14:31 -202325.750003] FAST spr round 2 (radius: 25)
[09:17:50 -201506.404292] FAST spr round 3 (radius: 25)
[09:20:51 -201431.192214] FAST spr round 4 (radius: 25)
[09:23:31 -201418.087079] FAST spr round 5 (radius: 25)
[09:26:03 -201408.250857] FAST spr round 6 (radius: 25)
[09:28:29 -201408.250793] Model parameter optimization (eps = 1.000000)
[09:28:47 -201400.005975] SLOW spr round 1 (radius: 5)
[09:32:32 -201340.752461] SLOW spr round 2 (radius: 5)
[09:36:07 -201318.394260] SLOW spr round 3 (radius: 5)
[09:39:39 -201311.341102] SLOW spr round 4 (radius: 5)
[09:43:06 -201300.157069] SLOW spr round 5 (radius: 5)
[09:43:58] [worker #2] ML tree search #15, logLikelihood: -201253.199322
[09:46:26 -201300.010043] SLOW spr round 6 (radius: 5)
[09:49:50 -201290.028154] SLOW spr round 7 (radius: 5)
[09:53:09 -201290.028127] SLOW spr round 8 (radius: 10)
[09:56:47 -201283.166222] SLOW spr round 9 (radius: 5)
[10:01:04 -201272.181538] SLOW spr round 10 (radius: 5)
[10:04:46 -201272.181341] SLOW spr round 11 (radius: 10)
[10:08:34 -201272.181341] SLOW spr round 12 (radius: 15)
[10:16:08 -201272.181341] SLOW spr round 13 (radius: 20)
[10:28:19 -201272.181341] SLOW spr round 14 (radius: 25)
[10:43:12 -201272.181341] Model parameter optimization (eps = 0.100000)

[10:43:25] [worker #0] ML tree search #13, logLikelihood: -201272.011792

[10:43:25 -690663.939828] Initial branch length optimization
[10:43:30 -614577.205162] Model parameter optimization (eps = 10.000000)
[10:44:15 -612071.279388] AUTODETECT spr round 1 (radius: 5)
[10:48:16 -478790.320789] AUTODETECT spr round 2 (radius: 10)
[10:52:40 -306328.061328] AUTODETECT spr round 3 (radius: 15)
[10:57:07 -242497.809363] AUTODETECT spr round 4 (radius: 20)
[11:02:19 -232567.358448] AUTODETECT spr round 5 (radius: 25)
[11:09:46 -231282.430385] SPR radius for FAST iterations: 25 (autodetect)
[11:09:46 -231282.430385] Model parameter optimization (eps = 3.000000)
[11:10:17 -231126.383560] FAST spr round 1 (radius: 25)
[11:14:43 -202450.673752] FAST spr round 2 (radius: 25)
[11:17:09] [worker #1] ML tree search #17, logLikelihood: -201251.587930
[11:18:10 -201543.618406] FAST spr round 3 (radius: 25)
[11:21:12 -201380.646033] FAST spr round 4 (radius: 25)
[11:23:57 -201351.850506] FAST spr round 5 (radius: 25)
[11:26:27 -201348.313609] FAST spr round 6 (radius: 25)
[11:28:53 -201348.313461] Model parameter optimization (eps = 1.000000)
[11:29:16 -201339.004771] SLOW spr round 1 (radius: 5)
[11:32:59 -201288.445517] SLOW spr round 2 (radius: 5)
[11:36:30 -201282.478609] SLOW spr round 3 (radius: 5)
[11:38:36] [worker #2] ML tree search #18, logLikelihood: -201340.799248
[11:39:52 -201282.478285] SLOW spr round 4 (radius: 10)
[11:43:33 -201281.025990] SLOW spr round 5 (radius: 5)
[11:47:47 -201273.224595] SLOW spr round 6 (radius: 5)
[11:51:26 -201272.521279] SLOW spr round 7 (radius: 5)
[11:54:50 -201272.521223] SLOW spr round 8 (radius: 10)
[11:58:26 -201264.777828] SLOW spr round 9 (radius: 5)
[12:02:36 -201261.984293] SLOW spr round 10 (radius: 5)
[12:06:14 -201261.984278] SLOW spr round 11 (radius: 10)
[12:09:58 -201261.984278] SLOW spr round 12 (radius: 15)
[12:17:44 -201261.984278] SLOW spr round 13 (radius: 20)
[12:30:36 -201261.984278] SLOW spr round 14 (radius: 25)
[12:45:53 -201261.984278] Model parameter optimization (eps = 0.100000)

[12:46:03] [worker #0] ML tree search #16, logLikelihood: -201261.931612

[12:46:04 -692502.760492] Initial branch length optimization
[12:46:11 -615939.726937] Model parameter optimization (eps = 10.000000)
[12:47:00 -613479.340331] AUTODETECT spr round 1 (radius: 5)
[12:50:57 -478269.610630] AUTODETECT spr round 2 (radius: 10)
[12:55:12 -307934.976004] AUTODETECT spr round 3 (radius: 15)
[12:59:43 -243877.383964] AUTODETECT spr round 4 (radius: 20)
[13:05:47 -229448.767443] AUTODETECT spr round 5 (radius: 25)
[13:12:57 -228651.324805] SPR radius for FAST iterations: 25 (autodetect)
[13:12:57 -228651.324805] Model parameter optimization (eps = 3.000000)
[13:13:27 -228549.847642] FAST spr round 1 (radius: 25)
[13:17:49 -202804.091716] FAST spr round 2 (radius: 25)
[13:21:17 -201502.768814] FAST spr round 3 (radius: 25)
[13:24:08 -201398.991452] FAST spr round 4 (radius: 25)
[13:26:28] [worker #1] ML tree search #20, logLikelihood: -201248.880652
[13:26:44 -201368.031281] FAST spr round 5 (radius: 25)
[13:29:09 -201368.031234] Model parameter optimization (eps = 1.000000)
[13:29:26 -201362.164534] SLOW spr round 1 (radius: 5)
[13:33:04 -201291.615574] SLOW spr round 2 (radius: 5)
[13:36:33 -201268.510442] SLOW spr round 3 (radius: 5)
[13:40:02 -201255.457771] SLOW spr round 4 (radius: 5)
[13:43:18 -201255.456988] SLOW spr round 5 (radius: 10)
[13:46:55 -201254.304683] SLOW spr round 6 (radius: 5)
[13:51:06 -201254.304483] SLOW spr round 7 (radius: 10)
[13:55:16 -201254.304480] SLOW spr round 8 (radius: 15)
[14:02:26 -201253.918664] SLOW spr round 9 (radius: 5)
[14:06:50 -201252.908322] SLOW spr round 10 (radius: 5)
[14:10:35 -201252.908312] SLOW spr round 11 (radius: 10)
[14:14:24 -201252.908312] SLOW spr round 12 (radius: 15)
[14:21:55 -201252.908312] SLOW spr round 13 (radius: 20)
[14:34:20 -201252.908312] SLOW spr round 14 (radius: 25)
[14:48:44 -201252.908312] Model parameter optimization (eps = 0.100000)

[14:48:49] [worker #0] ML tree search #19, logLikelihood: -201252.903342


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.168380,0.169325) (0.115291,0.438058) (0.384830,0.885427) (0.331499,1.750372) 
   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: -201170.380133

AIC score: 406350.760265 / AICc score: 8450410.760265 / BIC score: 414844.681293
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=511).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 116 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VIY5/3_mltree/Q5VIY5.raxml.log

Analysis started: 05-Jul-2021 00:07:30 / finished: 05-Jul-2021 14:56:21

Elapsed time: 53330.211 seconds

Consumed energy: 4878.986 Wh (= 24 km in an electric car, or 122 km with an e-scooter!)