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

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

RAxML-NG was called at 13-Jul-2021 20:03:08 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/2_msa/Q8IUR5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5 --seed 2 --threads 8 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/2_msa/Q8IUR5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 944 taxa and 641 sites

WARNING: Sequences tr_G3RAC3_G3RAC3_GORGO_9595 and tr_H2Q6K7_H2Q6K7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_K7CUJ1_K7CUJ1_PANTR_9598 and tr_A0A2R8ZUR7_A0A2R8ZUR7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6VRM2_F6VRM2_MACMU_9544 and tr_A0A2K6AM61_A0A2K6AM61_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7AG29_F7AG29_MACMU_9544 and tr_A0A2K6CNW6_A0A2K6CNW6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PIK7_G7PIK7_MACFA_9541 and tr_A0A2I3LS68_A0A2I3LS68_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PIK7_G7PIK7_MACFA_9541 and tr_A0A2K6BBM1_A0A2K6BBM1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_W2R7G1_W2R7G1_PHYPN_761204 and tr_A0A0W8B6F3_A0A0W8B6F3_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2R7G1_W2R7G1_PHYPN_761204 and tr_W2L329_W2L329_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A096NC38_A0A096NC38_PAPAN_9555 and tr_A0A2K5N2F5_A0A2K5N2F5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NC38_A0A096NC38_PAPAN_9555 and tr_A0A2K5YT37_A0A2K5YT37_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A194R052_A0A194R052_PAPMA_76193 and tr_A0A194PHJ1_A0A194PHJ1_PAPXU_66420 are exactly identical!
WARNING: Sequences tr_A0A194RH28_A0A194RH28_PAPMA_76193 and tr_A0A194PEG2_A0A194PEG2_PAPXU_66420 are exactly identical!
WARNING: Sequences tr_A0A0V1D4H5_A0A0V1D4H5_TRIBR_45882 and tr_A0A0V0TDA0_A0A0V0TDA0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2U3ZZW6_A0A2U3ZZW6_TURTR_9739 and tr_A0A2Y9SMN7_A0A2Y9SMN7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U4A671_A0A2U4A671_TURTR_9739 and tr_A0A2Y9NCA0_A0A2Y9NCA0_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 15

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.raxml.reduced.phy

Alignment comprises 1 partitions and 641 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 641 / 641
Gaps: 26.22 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.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 944 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 161 / 12880
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -949591.752121] Initial branch length optimization
[00:00:06 -781825.335804] Model parameter optimization (eps = 10.000000)
[00:01:38 -777017.751052] AUTODETECT spr round 1 (radius: 5)
[00:04:06 -559246.062405] AUTODETECT spr round 2 (radius: 10)
[00:06:43 -418925.000585] AUTODETECT spr round 3 (radius: 15)
[00:09:37 -350888.855727] AUTODETECT spr round 4 (radius: 20)
[00:12:51 -336902.682632] AUTODETECT spr round 5 (radius: 25)
[00:16:35 -321834.647589] SPR radius for FAST iterations: 25 (autodetect)
[00:16:35 -321834.647589] Model parameter optimization (eps = 3.000000)
[00:17:20 -320502.176667] FAST spr round 1 (radius: 25)
[00:21:20 -288880.795993] FAST spr round 2 (radius: 25)
[00:24:15 -287951.039974] FAST spr round 3 (radius: 25)
[00:26:45 -287858.738902] FAST spr round 4 (radius: 25)
[00:28:57 -287842.992851] FAST spr round 5 (radius: 25)
[00:30:56 -287838.206183] FAST spr round 6 (radius: 25)
[00:32:52 -287832.128947] FAST spr round 7 (radius: 25)
[00:34:44 -287832.127980] Model parameter optimization (eps = 1.000000)
[00:35:03 -287829.940807] SLOW spr round 1 (radius: 5)
[00:37:41 -287756.914303] SLOW spr round 2 (radius: 5)
[00:40:15 -287752.246191] SLOW spr round 3 (radius: 5)
[00:42:41 -287752.243877] SLOW spr round 4 (radius: 10)
[00:45:19 -287745.709674] SLOW spr round 5 (radius: 5)
[00:48:29 -287732.793482] SLOW spr round 6 (radius: 5)
[00:51:15 -287731.970377] SLOW spr round 7 (radius: 5)
[00:53:49 -287731.936649] SLOW spr round 8 (radius: 10)
[00:56:29 -287726.751012] SLOW spr round 9 (radius: 5)
[00:59:35 -287714.752035] SLOW spr round 10 (radius: 5)
[01:02:19 -287712.879488] SLOW spr round 11 (radius: 5)
[01:04:53 -287712.771513] SLOW spr round 12 (radius: 5)
[01:07:22 -287712.764896] SLOW spr round 13 (radius: 10)
[01:09:57 -287712.764202] SLOW spr round 14 (radius: 15)
[01:14:08 -287710.197126] SLOW spr round 15 (radius: 5)
[01:17:16 -287706.144086] SLOW spr round 16 (radius: 5)
[01:20:06 -287704.367972] SLOW spr round 17 (radius: 5)
[01:22:44 -287701.798012] SLOW spr round 18 (radius: 5)
[01:25:14 -287701.797795] SLOW spr round 19 (radius: 10)
[01:27:50 -287701.797765] SLOW spr round 20 (radius: 15)
[01:32:00 -287701.724256] SLOW spr round 21 (radius: 20)
[01:37:25 -287701.705845] SLOW spr round 22 (radius: 25)
[01:44:26 -287701.677843] Model parameter optimization (eps = 0.100000)

[01:44:35] [worker #0] ML tree search #1, logLikelihood: -287701.448437

[01:44:36 -941972.096032] Initial branch length optimization
[01:44:42 -778390.367263] Model parameter optimization (eps = 10.000000)
[01:45:55 -773201.603446] AUTODETECT spr round 1 (radius: 5)
[01:48:24 -542191.615868] AUTODETECT spr round 2 (radius: 10)
[01:51:01 -419551.005862] AUTODETECT spr round 3 (radius: 15)
[01:53:57 -350809.246300] AUTODETECT spr round 4 (radius: 20)
[01:57:11 -326745.779653] AUTODETECT spr round 5 (radius: 25)
[02:00:40 -320706.540890] SPR radius for FAST iterations: 25 (autodetect)
[02:00:40 -320706.540890] Model parameter optimization (eps = 3.000000)
[02:01:19 -319383.682686] FAST spr round 1 (radius: 25)
[02:02:45] [worker #1] ML tree search #2, logLikelihood: -287692.262182
[02:05:04 -289174.374597] FAST spr round 2 (radius: 25)
[02:07:57 -287887.707463] FAST spr round 3 (radius: 25)
[02:10:25 -287776.326546] FAST spr round 4 (radius: 25)
[02:12:30 -287771.562615] FAST spr round 5 (radius: 25)
[02:14:27 -287771.561995] Model parameter optimization (eps = 1.000000)
[02:14:43 -287767.085098] SLOW spr round 1 (radius: 5)
[02:17:26 -287697.553215] SLOW spr round 2 (radius: 5)
[02:20:02 -287683.288184] SLOW spr round 3 (radius: 5)
[02:22:32 -287683.058270] SLOW spr round 4 (radius: 5)
[02:24:59 -287683.057760] SLOW spr round 5 (radius: 10)
[02:27:34 -287679.646759] SLOW spr round 6 (radius: 5)
[02:30:34 -287679.646480] SLOW spr round 7 (radius: 10)
[02:33:31 -287679.598695] SLOW spr round 8 (radius: 15)
[02:37:35 -287679.576632] SLOW spr round 9 (radius: 20)
[02:43:17 -287679.569023] SLOW spr round 10 (radius: 25)
[02:50:18 -287679.566052] Model parameter optimization (eps = 0.100000)

[02:50:30] [worker #0] ML tree search #3, logLikelihood: -287679.333881

[02:50:30 -945536.800373] Initial branch length optimization
[02:50:36 -783059.810107] Model parameter optimization (eps = 10.000000)
[02:51:49 -778179.640551] AUTODETECT spr round 1 (radius: 5)
[02:54:21 -540672.415445] AUTODETECT spr round 2 (radius: 10)
[02:56:58 -420089.882941] AUTODETECT spr round 3 (radius: 15)
[02:59:43 -369989.256728] AUTODETECT spr round 4 (radius: 20)
[03:03:01 -326282.432086] AUTODETECT spr round 5 (radius: 25)
[03:06:47 -321641.098914] SPR radius for FAST iterations: 25 (autodetect)
[03:06:48 -321641.098914] Model parameter optimization (eps = 3.000000)
[03:07:22 -320165.621963] FAST spr round 1 (radius: 25)
[03:11:18 -289064.312734] FAST spr round 2 (radius: 25)
[03:14:20 -287995.168919] FAST spr round 3 (radius: 25)
[03:16:55 -287892.057692] FAST spr round 4 (radius: 25)
[03:19:20 -287789.171018] FAST spr round 5 (radius: 25)
[03:21:24 -287774.415544] FAST spr round 6 (radius: 25)
[03:23:18 -287774.141463] FAST spr round 7 (radius: 25)
[03:25:11 -287774.132402] Model parameter optimization (eps = 1.000000)
[03:25:28 -287770.483154] SLOW spr round 1 (radius: 5)
[03:28:07 -287714.688856] SLOW spr round 2 (radius: 5)
[03:30:44 -287692.831018] SLOW spr round 3 (radius: 5)
[03:33:15 -287689.845901] SLOW spr round 4 (radius: 5)
[03:35:43 -287689.387577] SLOW spr round 5 (radius: 5)
[03:38:12 -287688.912111] SLOW spr round 6 (radius: 5)
[03:40:39 -287688.665759] SLOW spr round 7 (radius: 5)
[03:43:06 -287688.665342] SLOW spr round 8 (radius: 10)
[03:45:42 -287688.665274] SLOW spr round 9 (radius: 15)
[03:49:53 -287687.780358] SLOW spr round 10 (radius: 5)
[03:52:57 -287687.780125] SLOW spr round 11 (radius: 10)
[03:54:27] [worker #1] ML tree search #4, logLikelihood: -287666.842720
[03:56:04 -287687.012643] SLOW spr round 12 (radius: 5)
[03:59:01 -287687.012617] SLOW spr round 13 (radius: 10)
[04:01:58 -287687.012597] SLOW spr round 14 (radius: 15)
[04:05:55 -287687.012579] SLOW spr round 15 (radius: 20)
[04:11:20 -287686.993337] SLOW spr round 16 (radius: 25)
[04:18:08 -287686.991896] Model parameter optimization (eps = 0.100000)

[04:18:25] [worker #0] ML tree search #5, logLikelihood: -287686.502298

[04:18:25 -940733.895992] Initial branch length optimization
[04:18:33 -781151.806423] Model parameter optimization (eps = 10.000000)
[04:19:45 -776087.912509] AUTODETECT spr round 1 (radius: 5)
[04:22:17 -548829.449987] AUTODETECT spr round 2 (radius: 10)
[04:24:55 -424954.386208] AUTODETECT spr round 3 (radius: 15)
[04:27:46 -357740.805866] AUTODETECT spr round 4 (radius: 20)
[04:30:56 -328761.630060] AUTODETECT spr round 5 (radius: 25)
[04:34:42 -323662.593478] SPR radius for FAST iterations: 25 (autodetect)
[04:34:42 -323662.593478] Model parameter optimization (eps = 3.000000)
[04:35:34 -322324.900170] FAST spr round 1 (radius: 25)
[04:39:33 -289176.978974] FAST spr round 2 (radius: 25)
[04:42:38 -288024.577742] FAST spr round 3 (radius: 25)
[04:45:10 -287928.377469] FAST spr round 4 (radius: 25)
[04:47:27 -287914.258264] FAST spr round 5 (radius: 25)
[04:49:32 -287904.383593] FAST spr round 6 (radius: 25)
[04:51:29 -287899.797294] FAST spr round 7 (radius: 25)
[04:53:23 -287897.798392] FAST spr round 8 (radius: 25)
[04:55:18 -287876.932344] FAST spr round 9 (radius: 25)
[04:57:11 -287816.263419] FAST spr round 10 (radius: 25)
[04:59:04 -287816.059017] FAST spr round 11 (radius: 25)
[05:00:56 -287816.053358] Model parameter optimization (eps = 1.000000)
[05:01:13 -287813.891515] SLOW spr round 1 (radius: 5)
[05:03:54 -287700.207136] SLOW spr round 2 (radius: 5)
[05:06:28 -287688.473833] SLOW spr round 3 (radius: 5)
[05:09:03 -287683.995953] SLOW spr round 4 (radius: 5)
[05:11:31 -287680.807428] SLOW spr round 5 (radius: 5)
[05:14:04 -287678.419462] SLOW spr round 6 (radius: 5)
[05:16:33 -287678.298785] SLOW spr round 7 (radius: 5)
[05:19:00 -287678.297761] SLOW spr round 8 (radius: 10)
[05:21:36 -287675.057262] SLOW spr round 9 (radius: 5)
[05:24:36 -287673.524158] SLOW spr round 10 (radius: 5)
[05:27:20 -287673.523856] SLOW spr round 11 (radius: 10)
[05:30:04 -287670.644567] SLOW spr round 12 (radius: 5)
[05:33:03 -287670.644396] SLOW spr round 13 (radius: 10)
[05:35:59 -287670.644117] SLOW spr round 14 (radius: 15)
[05:40:01 -287668.665083] SLOW spr round 15 (radius: 5)
[05:43:07 -287668.368664] SLOW spr round 16 (radius: 5)
[05:45:53 -287668.367204] SLOW spr round 17 (radius: 10)
[05:48:39 -287668.366939] SLOW spr round 18 (radius: 15)
[05:52:47 -287668.366873] SLOW spr round 19 (radius: 20)
[05:58:26 -287668.366846] SLOW spr round 20 (radius: 25)
[06:05:27 -287668.366829] Model parameter optimization (eps = 0.100000)

[06:05:44] [worker #0] ML tree search #7, logLikelihood: -287667.809488

[06:05:44 -943492.154793] Initial branch length optimization
[06:05:50 -780572.381902] Model parameter optimization (eps = 10.000000)
[06:06:59 -775717.438113] AUTODETECT spr round 1 (radius: 5)
[06:09:28 -541342.813715] AUTODETECT spr round 2 (radius: 10)
[06:11:08] [worker #1] ML tree search #6, logLikelihood: -287709.747715
[06:12:05 -422358.759005] AUTODETECT spr round 3 (radius: 15)
[06:14:59 -361511.851490] AUTODETECT spr round 4 (radius: 20)
[06:18:07 -328271.739524] AUTODETECT spr round 5 (radius: 25)
[06:21:43 -323667.925064] SPR radius for FAST iterations: 25 (autodetect)
[06:21:43 -323667.925064] Model parameter optimization (eps = 3.000000)
[06:22:24 -322359.828710] FAST spr round 1 (radius: 25)
[06:26:33 -289302.071551] FAST spr round 2 (radius: 25)
[06:29:36 -287960.525979] FAST spr round 3 (radius: 25)
[06:32:12 -287819.896961] FAST spr round 4 (radius: 25)
[06:34:26 -287784.826711] FAST spr round 5 (radius: 25)
[06:36:26 -287782.630918] FAST spr round 6 (radius: 25)
[06:38:22 -287782.628530] Model parameter optimization (eps = 1.000000)
[06:38:41 -287779.325557] SLOW spr round 1 (radius: 5)
[06:41:19 -287714.210264] SLOW spr round 2 (radius: 5)
[06:43:54 -287681.622008] SLOW spr round 3 (radius: 5)
[06:46:31 -287673.008069] SLOW spr round 4 (radius: 5)
[06:49:00 -287672.514999] SLOW spr round 5 (radius: 5)
[06:51:28 -287672.513333] SLOW spr round 6 (radius: 10)
[06:54:07 -287668.592120] SLOW spr round 7 (radius: 5)
[06:57:11 -287665.792996] SLOW spr round 8 (radius: 5)
[06:59:54 -287665.792254] SLOW spr round 9 (radius: 10)
[07:02:42 -287665.792108] SLOW spr round 10 (radius: 15)
[07:06:49 -287663.661907] SLOW spr round 11 (radius: 5)
[07:09:56 -287663.407991] SLOW spr round 12 (radius: 5)
[07:12:43 -287663.406202] SLOW spr round 13 (radius: 10)
[07:15:32 -287663.406029] SLOW spr round 14 (radius: 15)
[07:19:37 -287663.406007] SLOW spr round 15 (radius: 20)
[07:25:16 -287663.405999] SLOW spr round 16 (radius: 25)
[07:32:18 -287663.405994] Model parameter optimization (eps = 0.100000)

[07:32:28] [worker #0] ML tree search #9, logLikelihood: -287663.102512

[07:32:28 -941252.135330] Initial branch length optimization
[07:32:35 -780352.435247] Model parameter optimization (eps = 10.000000)
[07:33:20] [worker #1] ML tree search #8, logLikelihood: -287702.402114
[07:33:51 -775746.229618] AUTODETECT spr round 1 (radius: 5)
[07:36:22 -544304.206380] AUTODETECT spr round 2 (radius: 10)
[07:38:58 -411999.396015] AUTODETECT spr round 3 (radius: 15)
[07:41:52 -349496.515277] AUTODETECT spr round 4 (radius: 20)
[07:45:05 -327860.249923] AUTODETECT spr round 5 (radius: 25)
[07:48:43 -321821.788423] SPR radius for FAST iterations: 25 (autodetect)
[07:48:43 -321821.788423] Model parameter optimization (eps = 3.000000)
[07:49:27 -320202.072742] FAST spr round 1 (radius: 25)
[07:53:15 -289375.744105] FAST spr round 2 (radius: 25)
[07:56:13 -287885.567710] FAST spr round 3 (radius: 25)
[07:58:49 -287807.210228] FAST spr round 4 (radius: 25)
[08:01:05 -287793.230467] FAST spr round 5 (radius: 25)
[08:03:10 -287786.309935] FAST spr round 6 (radius: 25)
[08:05:05 -287786.309658] Model parameter optimization (eps = 1.000000)
[08:05:24 -287775.933756] SLOW spr round 1 (radius: 5)
[08:08:07 -287704.590235] SLOW spr round 2 (radius: 5)
[08:10:47 -287691.310066] SLOW spr round 3 (radius: 5)
[08:13:21 -287689.486988] SLOW spr round 4 (radius: 5)
[08:15:49 -287689.390707] SLOW spr round 5 (radius: 10)
[08:18:27 -287686.072758] SLOW spr round 6 (radius: 5)
[08:21:31 -287685.358185] SLOW spr round 7 (radius: 5)
[08:24:15 -287685.356195] SLOW spr round 8 (radius: 10)
[08:27:01 -287684.982726] SLOW spr round 9 (radius: 5)
[08:30:03 -287681.509982] SLOW spr round 10 (radius: 5)
[08:32:46 -287681.507958] SLOW spr round 11 (radius: 10)
[08:35:30 -287681.507598] SLOW spr round 12 (radius: 15)
[08:39:39 -287680.156835] SLOW spr round 13 (radius: 5)
[08:42:44 -287680.147734] SLOW spr round 14 (radius: 10)
[08:45:51 -287678.181523] SLOW spr round 15 (radius: 5)
[08:48:50 -287677.781152] SLOW spr round 16 (radius: 5)
[08:51:30 -287677.780297] SLOW spr round 17 (radius: 10)
[08:54:15 -287677.780199] SLOW spr round 18 (radius: 15)
[08:58:25 -287677.780176] SLOW spr round 19 (radius: 20)
[09:04:01 -287677.780167] SLOW spr round 20 (radius: 25)
[09:11:06 -287677.780161] Model parameter optimization (eps = 0.100000)

[09:11:12] [worker #0] ML tree search #11, logLikelihood: -287677.718333

[09:11:12 -944554.182390] Initial branch length optimization
[09:11:19 -778869.805330] Model parameter optimization (eps = 10.000000)
[09:12:23 -774157.483398] AUTODETECT spr round 1 (radius: 5)
[09:14:52 -538551.110095] AUTODETECT spr round 2 (radius: 10)
[09:16:12] [worker #1] ML tree search #10, logLikelihood: -287668.709214
[09:17:29 -404315.650802] AUTODETECT spr round 3 (radius: 15)
[09:20:19 -363971.040130] AUTODETECT spr round 4 (radius: 20)
[09:23:34 -326117.875060] AUTODETECT spr round 5 (radius: 25)
[09:27:12 -322770.494958] SPR radius for FAST iterations: 25 (autodetect)
[09:27:12 -322770.494958] Model parameter optimization (eps = 3.000000)
[09:27:51 -321309.075460] FAST spr round 1 (radius: 25)
[09:31:55 -289354.896745] FAST spr round 2 (radius: 25)
[09:35:03 -287906.070822] FAST spr round 3 (radius: 25)
[09:37:36 -287796.126215] FAST spr round 4 (radius: 25)
[09:39:49 -287778.620973] FAST spr round 5 (radius: 25)
[09:41:51 -287776.953906] FAST spr round 6 (radius: 25)
[09:43:46 -287776.951615] Model parameter optimization (eps = 1.000000)
[09:44:01 -287774.003994] SLOW spr round 1 (radius: 5)
[09:46:42 -287715.271524] SLOW spr round 2 (radius: 5)
[09:49:17 -287709.561673] SLOW spr round 3 (radius: 5)
[09:51:50 -287709.276856] SLOW spr round 4 (radius: 5)
[09:54:19 -287709.275032] SLOW spr round 5 (radius: 10)
[09:57:00 -287700.485879] SLOW spr round 6 (radius: 5)
[10:00:06 -287695.008113] SLOW spr round 7 (radius: 5)
[10:02:56 -287686.368056] SLOW spr round 8 (radius: 5)
[10:05:37 -287683.012655] SLOW spr round 9 (radius: 5)
[10:08:12 -287680.266448] SLOW spr round 10 (radius: 5)
[10:10:42 -287680.264162] SLOW spr round 11 (radius: 10)
[10:13:20 -287675.347450] SLOW spr round 12 (radius: 5)
[10:16:21 -287673.948733] SLOW spr round 13 (radius: 5)
[10:19:04 -287673.944975] SLOW spr round 14 (radius: 10)
[10:21:50 -287673.904179] SLOW spr round 15 (radius: 15)
[10:25:51 -287673.902279] SLOW spr round 16 (radius: 20)
[10:31:15 -287669.739357] SLOW spr round 17 (radius: 5)
[10:34:29 -287666.541546] SLOW spr round 18 (radius: 5)
[10:37:18 -287666.540784] SLOW spr round 19 (radius: 10)
[10:40:08 -287666.136835] SLOW spr round 20 (radius: 5)
[10:43:07 -287665.758630] SLOW spr round 21 (radius: 5)
[10:45:49 -287665.755948] SLOW spr round 22 (radius: 10)
[10:48:33 -287665.755526] SLOW spr round 23 (radius: 15)
[10:52:36 -287665.755414] SLOW spr round 24 (radius: 20)
[10:57:57 -287665.755375] SLOW spr round 25 (radius: 25)
[11:04:47 -287665.755356] Model parameter optimization (eps = 0.100000)

[11:05:01] [worker #0] ML tree search #13, logLikelihood: -287665.506206

[11:05:01 -943815.676346] Initial branch length optimization
[11:05:08 -782338.323911] Model parameter optimization (eps = 10.000000)
[11:06:13 -777001.108937] AUTODETECT spr round 1 (radius: 5)
[11:08:42 -547133.917305] AUTODETECT spr round 2 (radius: 10)
[11:11:19 -412779.755101] AUTODETECT spr round 3 (radius: 15)
[11:14:07 -336263.233412] AUTODETECT spr round 4 (radius: 20)
[11:17:24 -315880.697453] AUTODETECT spr round 5 (radius: 25)
[11:21:20 -314411.180757] SPR radius for FAST iterations: 25 (autodetect)
[11:21:20 -314411.180757] Model parameter optimization (eps = 3.000000)
[11:22:08 -313086.496307] FAST spr round 1 (radius: 25)
[11:26:14 -288845.938400] FAST spr round 2 (radius: 25)
[11:29:22 -287862.771911] FAST spr round 3 (radius: 25)
[11:31:53 -287766.999032] FAST spr round 4 (radius: 25)
[11:32:40] [worker #1] ML tree search #12, logLikelihood: -287676.102840
[11:34:01 -287754.058070] FAST spr round 5 (radius: 25)
[11:36:01 -287748.264359] FAST spr round 6 (radius: 25)
[11:37:57 -287748.262633] Model parameter optimization (eps = 1.000000)
[11:38:16 -287742.574016] SLOW spr round 1 (radius: 5)
[11:41:02 -287692.197545] SLOW spr round 2 (radius: 5)
[11:43:37 -287687.499447] SLOW spr round 3 (radius: 5)
[11:46:09 -287682.088937] SLOW spr round 4 (radius: 5)
[11:48:42 -287679.104945] SLOW spr round 5 (radius: 5)
[11:51:10 -287678.110328] SLOW spr round 6 (radius: 5)
[11:53:39 -287677.738857] SLOW spr round 7 (radius: 5)
[11:56:06 -287677.738517] SLOW spr round 8 (radius: 10)
[11:58:42 -287674.884194] SLOW spr round 9 (radius: 5)
[12:01:42 -287674.883976] SLOW spr round 10 (radius: 10)
[12:04:43 -287674.844338] SLOW spr round 11 (radius: 15)
[12:08:42 -287674.841887] SLOW spr round 12 (radius: 20)
[12:14:16 -287674.841612] SLOW spr round 13 (radius: 25)
[12:21:04 -287674.841568] Model parameter optimization (eps = 0.100000)

[12:21:12] [worker #0] ML tree search #15, logLikelihood: -287674.746303

[12:21:12 -938465.786888] Initial branch length optimization
[12:21:18 -775400.246569] Model parameter optimization (eps = 10.000000)
[12:22:28 -770348.403124] AUTODETECT spr round 1 (radius: 5)
[12:24:58 -561886.117581] AUTODETECT spr round 2 (radius: 10)
[12:27:36 -441392.377920] AUTODETECT spr round 3 (radius: 15)
[12:30:28 -356893.258929] AUTODETECT spr round 4 (radius: 20)
[12:33:30 -341298.568393] AUTODETECT spr round 5 (radius: 25)
[12:37:43 -323024.438009] SPR radius for FAST iterations: 25 (autodetect)
[12:37:43 -323024.438009] Model parameter optimization (eps = 3.000000)
[12:38:18 -321565.130373] FAST spr round 1 (radius: 25)
[12:42:37 -289393.698100] FAST spr round 2 (radius: 25)
[12:45:44 -287905.480363] FAST spr round 3 (radius: 25)
[12:48:17 -287770.901825] FAST spr round 4 (radius: 25)
[12:50:28 -287737.498867] FAST spr round 5 (radius: 25)
[12:52:26 -287735.534486] FAST spr round 6 (radius: 25)
[12:54:19 -287735.534340] Model parameter optimization (eps = 1.000000)
[12:54:34 -287733.851817] SLOW spr round 1 (radius: 5)
[12:57:18 -287685.695130] SLOW spr round 2 (radius: 5)
[12:59:55 -287678.277761] SLOW spr round 3 (radius: 5)
[13:02:25 -287677.137014] SLOW spr round 4 (radius: 5)
[13:04:53 -287677.090258] SLOW spr round 5 (radius: 10)
[13:07:30 -287676.572515] SLOW spr round 6 (radius: 5)
[13:08:24] [worker #1] ML tree search #14, logLikelihood: -287666.860511
[13:10:33 -287675.587243] SLOW spr round 7 (radius: 5)
[13:13:17 -287675.561093] SLOW spr round 8 (radius: 10)
[13:16:03 -287675.560627] SLOW spr round 9 (radius: 15)
[13:20:11 -287675.560516] SLOW spr round 10 (radius: 20)
[13:25:41 -287675.560480] SLOW spr round 11 (radius: 25)
[13:32:32 -287675.560459] Model parameter optimization (eps = 0.100000)

[13:32:39] [worker #0] ML tree search #17, logLikelihood: -287675.465682

[13:32:39 -939432.866921] Initial branch length optimization
[13:32:46 -773103.206012] Model parameter optimization (eps = 10.000000)
[13:33:52 -767702.744054] AUTODETECT spr round 1 (radius: 5)
[13:36:23 -543768.894425] AUTODETECT spr round 2 (radius: 10)
[13:39:02 -431412.861711] AUTODETECT spr round 3 (radius: 15)
[13:41:58 -360838.050327] AUTODETECT spr round 4 (radius: 20)
[13:45:04 -339314.701711] AUTODETECT spr round 5 (radius: 25)
[13:48:50 -325055.575567] SPR radius for FAST iterations: 25 (autodetect)
[13:48:50 -325055.575567] Model parameter optimization (eps = 3.000000)
[13:49:34 -323785.098044] FAST spr round 1 (radius: 25)
[13:53:32 -289498.982745] FAST spr round 2 (radius: 25)
[13:56:28 -287907.393197] FAST spr round 3 (radius: 25)
[13:58:57 -287765.117448] FAST spr round 4 (radius: 25)
[14:01:06 -287752.785795] FAST spr round 5 (radius: 25)
[14:03:05 -287751.746071] FAST spr round 6 (radius: 25)
[14:04:59 -287751.743329] Model parameter optimization (eps = 1.000000)
[14:05:15 -287747.911888] SLOW spr round 1 (radius: 5)
[14:07:53 -287693.310343] SLOW spr round 2 (radius: 5)
[14:10:30 -287681.619261] SLOW spr round 3 (radius: 5)
[14:13:02 -287679.344753] SLOW spr round 4 (radius: 5)
[14:15:33 -287677.689506] SLOW spr round 5 (radius: 5)
[14:18:03 -287677.091074] SLOW spr round 6 (radius: 5)
[14:20:30 -287677.089125] SLOW spr round 7 (radius: 10)
[14:23:06 -287676.251448] SLOW spr round 8 (radius: 5)
[14:26:07 -287676.042592] SLOW spr round 9 (radius: 5)
[14:28:51 -287676.042216] SLOW spr round 10 (radius: 10)
[14:31:36 -287675.881192] SLOW spr round 11 (radius: 5)
[14:34:36 -287673.492087] SLOW spr round 12 (radius: 5)
[14:37:20 -287668.592564] SLOW spr round 13 (radius: 5)
[14:39:54 -287668.592550] SLOW spr round 14 (radius: 10)
[14:42:33 -287668.592538] SLOW spr round 15 (radius: 15)
[14:46:38 -287668.557374] SLOW spr round 16 (radius: 20)
[14:51:57 -287668.556018] SLOW spr round 17 (radius: 25)
[14:58:39 -287668.555817] Model parameter optimization (eps = 0.100000)

[14:58:55] [worker #0] ML tree search #19, logLikelihood: -287667.998490

[15:08:45] [worker #1] ML tree search #16, logLikelihood: -287684.777590
[16:40:27] [worker #1] ML tree search #18, logLikelihood: -287688.212729
[18:13:32] [worker #1] ML tree search #20, logLikelihood: -287679.344674

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.234887,0.659089) (0.165613,1.443623) (0.425224,0.751792) (0.174276,1.643520) 
   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: -287663.102512

AIC score: 579108.205023 / AICc score: 7734652.205023 / BIC score: 587547.793726
Free parameters (model + branch lengths): 1891

WARNING: Number of free parameters (K=1891) is larger than alignment size (n=641).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q8IUR5/3_mltree/Q8IUR5.raxml.log

Analysis started: 13-Jul-2021 20:03:08 / finished: 14-Jul-2021 14:16:40

Elapsed time: 65612.383 seconds