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 30-Jul-2021 10:16:31 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/2_msa/Q562E7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/2_msa/Q562E7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 882 sites

WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2I3S7H5_A0A2I3S7H5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and sp_Q8NFP9_NBEA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_F6YF98_F6YF98_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K5LHX6_A0A2K5LHX6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QKY6_G1QKY6_NOMLE_61853 and tr_A0A2K6BCF5_A0A2K6BCF5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_E2QWB6_E2QWB6_CANLF_9615 and tr_A0A337S5P0_A0A337S5P0_FELCA_9685 are exactly identical!
WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and sp_Q8IZQ1_WDFY3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QPU0_H2QPU0_PANTR_9598 and tr_A0A2R9CBV9_A0A2R9CBV9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_G7P517_G7P517_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A096MWM6_A0A096MWM6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K5L9D9_A0A2K5L9D9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QGT9_A0A1D5QGT9_MACMU_9544 and tr_A0A2K6CVR0_A0A2K6CVR0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I1PFD6_I1PFD6_ORYGL_4538 and tr_A0A0E0P160_A0A0E0P160_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_I1PFD6_I1PFD6_ORYGL_4538 and tr_A0A0D3FNY2_A0A0D3FNY2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PFD6_I1PFD6_ORYGL_4538 and tr_A0A0D9ZD04_A0A0D9ZD04_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A287BJF5_A0A287BJF5_PIG_9823 and tr_A0A2Y9ESM2_A0A2Y9ESM2_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G7PEU3_G7PEU3_MACFA_9541 and tr_A0A2K6AMA8_A0A2K6AMA8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3VZG1_M3VZG1_FELCA_9685 and tr_A0A2Y9KMF9_A0A2Y9KMF9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3VZG1_M3VZG1_FELCA_9685 and tr_A0A384C9Q3_A0A384C9Q3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_W2PY36_W2PY36_PHYPN_761204 and tr_A0A0W8CFN5_A0A0W8CFN5_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PY36_W2PY36_PHYPN_761204 and tr_W2KUT5_W2KUT5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A0F8VV81_A0A0F8VV81_9EURO_308745 and tr_A0A2T5M9X1_A0A2T5M9X1_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A091JTD1_A0A091JTD1_EGRGA_188379 and tr_A0A087QGX7_A0A087QGX7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A087R3Z2_A0A087R3Z2_APTFO_9233 and tr_A0A0A0AXP7_A0A0A0AXP7_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 and tr_A0A0V0VEV7_A0A0V0VEV7_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 and tr_A0A0V1KYD0_A0A0V1KYD0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0WCE8_A0A0V0WCE8_9BILA_92179 and tr_A0A0V0UDH9_A0A0V0UDH9_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2G2ZXU7_A0A2G2ZXU7_CAPAN_4072 and tr_A0A2G3CTM5_A0A2G3CTM5_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2K5MPI5_A0A2K5MPI5_CERAT_9531 and tr_A0A2K6B0W8_A0A2K6B0W8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5MPI5_A0A2K5MPI5_CERAT_9531 and tr_A0A2K5Y3U6_A0A2K5Y3U6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A2Y9M8G0_A0A2Y9M8G0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4AMN7_A0A2U4AMN7_TURTR_9739 and tr_A0A384AXN8_A0A384AXN8_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 32

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/Q562E7/3_mltree/Q562E7.raxml.reduced.phy

Alignment comprises 1 partitions and 882 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 882 / 882
Gaps: 21.41 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 9 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 / 98 / 7840
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1475963.608512] Initial branch length optimization
[00:00:06 -1216144.250301] Model parameter optimization (eps = 10.000000)
[00:00:51 -1212950.692224] AUTODETECT spr round 1 (radius: 5)
[00:03:03 -835330.779194] AUTODETECT spr round 2 (radius: 10)
[00:05:21 -613568.241297] AUTODETECT spr round 3 (radius: 15)
[00:07:49 -528034.620158] AUTODETECT spr round 4 (radius: 20)
[00:10:35 -482850.370492] AUTODETECT spr round 5 (radius: 25)
[00:13:37 -451561.150750] SPR radius for FAST iterations: 25 (autodetect)
[00:13:37 -451561.150750] Model parameter optimization (eps = 3.000000)
[00:14:00 -451041.393620] FAST spr round 1 (radius: 25)
[00:16:53 -368519.177587] FAST spr round 2 (radius: 25)
[00:19:09 -364807.389881] FAST spr round 3 (radius: 25)
[00:21:13 -364609.839794] FAST spr round 4 (radius: 25)
[00:22:58 -364605.917658] FAST spr round 5 (radius: 25)
[00:24:39 -364605.917518] Model parameter optimization (eps = 1.000000)
[00:24:57 -364589.926443] SLOW spr round 1 (radius: 5)
[00:27:14 -364501.386603] SLOW spr round 2 (radius: 5)
[00:29:23 -364497.437670] SLOW spr round 3 (radius: 5)
[00:31:29 -364497.337397] SLOW spr round 4 (radius: 5)
[00:33:33 -364497.312113] SLOW spr round 5 (radius: 10)
[00:35:43 -364495.382383] SLOW spr round 6 (radius: 5)
[00:38:21 -364487.862503] SLOW spr round 7 (radius: 5)
[00:40:37 -364487.789064] SLOW spr round 8 (radius: 10)
[00:42:50 -364487.787392] SLOW spr round 9 (radius: 15)
[00:46:14 -364487.787263] SLOW spr round 10 (radius: 20)
[00:51:16 -364487.787237] SLOW spr round 11 (radius: 25)
[00:57:35 -364487.787223] Model parameter optimization (eps = 0.100000)

[00:57:42] ML tree search #1, logLikelihood: -364487.636830

[00:57:42 -1478808.334288] Initial branch length optimization
[00:57:46 -1211900.238144] Model parameter optimization (eps = 10.000000)
[00:58:34 -1208736.684444] AUTODETECT spr round 1 (radius: 5)
[01:00:44 -830273.093822] AUTODETECT spr round 2 (radius: 10)
[01:03:03 -605031.582695] AUTODETECT spr round 3 (radius: 15)
[01:05:32 -463450.973320] AUTODETECT spr round 4 (radius: 20)
[01:08:07 -421052.818636] AUTODETECT spr round 5 (radius: 25)
[01:11:23 -415973.536524] SPR radius for FAST iterations: 25 (autodetect)
[01:11:23 -415973.536524] Model parameter optimization (eps = 3.000000)
[01:11:45 -415739.252521] FAST spr round 1 (radius: 25)
[01:14:33 -366601.996557] FAST spr round 2 (radius: 25)
[01:16:47 -364722.209987] FAST spr round 3 (radius: 25)
[01:18:49 -364591.092735] FAST spr round 4 (radius: 25)
[01:20:38 -364577.773141] FAST spr round 5 (radius: 25)
[01:22:20 -364577.772767] Model parameter optimization (eps = 1.000000)
[01:22:37 -364574.848300] SLOW spr round 1 (radius: 5)
[01:24:54 -364494.186904] SLOW spr round 2 (radius: 5)
[01:27:07 -364482.412114] SLOW spr round 3 (radius: 5)
[01:29:12 -364482.066089] SLOW spr round 4 (radius: 5)
[01:31:17 -364482.066066] SLOW spr round 5 (radius: 10)
[01:33:28 -364482.065599] SLOW spr round 6 (radius: 15)
[01:37:01 -364482.065587] SLOW spr round 7 (radius: 20)
[01:42:20 -364482.065575] SLOW spr round 8 (radius: 25)
[01:49:08 -364482.065563] Model parameter optimization (eps = 0.100000)

[01:49:16] ML tree search #2, logLikelihood: -364481.974317

[01:49:16 -1473969.005586] Initial branch length optimization
[01:49:21 -1211214.196475] Model parameter optimization (eps = 10.000000)
[01:50:28 -1208137.793215] AUTODETECT spr round 1 (radius: 5)
[01:52:39 -825382.913911] AUTODETECT spr round 2 (radius: 10)
[01:54:56 -619518.419157] AUTODETECT spr round 3 (radius: 15)
[01:57:25 -506309.699952] AUTODETECT spr round 4 (radius: 20)
[02:00:08 -441826.495172] AUTODETECT spr round 5 (radius: 25)
[02:03:15 -429082.424915] SPR radius for FAST iterations: 25 (autodetect)
[02:03:15 -429082.424915] Model parameter optimization (eps = 3.000000)
[02:03:39 -428810.303531] FAST spr round 1 (radius: 25)
[02:06:35 -367402.369138] FAST spr round 2 (radius: 25)
[02:08:52 -364768.748264] FAST spr round 3 (radius: 25)
[02:10:51 -364606.520626] FAST spr round 4 (radius: 25)
[02:12:42 -364566.613045] FAST spr round 5 (radius: 25)
[02:14:25 -364551.731614] FAST spr round 6 (radius: 25)
[02:16:06 -364551.731386] Model parameter optimization (eps = 1.000000)
[02:16:23 -364541.244710] SLOW spr round 1 (radius: 5)
[02:18:35 -364487.201869] SLOW spr round 2 (radius: 5)
[02:20:45 -364472.226951] SLOW spr round 3 (radius: 5)
[02:22:53 -364465.728434] SLOW spr round 4 (radius: 5)
[02:25:00 -364462.337259] SLOW spr round 5 (radius: 5)
[02:27:04 -364462.337064] SLOW spr round 6 (radius: 10)
[02:29:13 -364461.984077] SLOW spr round 7 (radius: 5)
[02:31:45 -364461.616874] SLOW spr round 8 (radius: 5)
[02:34:03 -364461.616585] SLOW spr round 9 (radius: 10)
[02:36:17 -364461.616392] SLOW spr round 10 (radius: 15)
[02:39:40 -364461.616198] SLOW spr round 11 (radius: 20)
[02:44:45 -364461.616003] SLOW spr round 12 (radius: 25)
[02:51:15 -364461.615808] Model parameter optimization (eps = 0.100000)

[02:51:20] ML tree search #3, logLikelihood: -364461.583911

[02:51:20 -1473044.800135] Initial branch length optimization
[02:51:26 -1206678.843276] Model parameter optimization (eps = 10.000000)
[02:52:25 -1203810.902905] AUTODETECT spr round 1 (radius: 5)
[02:54:37 -823364.624589] AUTODETECT spr round 2 (radius: 10)
[02:56:57 -617044.986601] AUTODETECT spr round 3 (radius: 15)
[02:59:34 -475760.447837] AUTODETECT spr round 4 (radius: 20)
[03:02:26 -424486.634715] AUTODETECT spr round 5 (radius: 25)
[03:05:29 -417792.591799] SPR radius for FAST iterations: 25 (autodetect)
[03:05:29 -417792.591799] Model parameter optimization (eps = 3.000000)
[03:05:51 -417578.163154] FAST spr round 1 (radius: 25)
[03:08:46 -366524.115309] FAST spr round 2 (radius: 25)
[03:11:05 -364801.999282] FAST spr round 3 (radius: 25)
[03:13:08 -364666.878803] FAST spr round 4 (radius: 25)
[03:14:55 -364631.266278] FAST spr round 5 (radius: 25)
[03:16:38 -364614.935398] FAST spr round 6 (radius: 25)
[03:18:19 -364614.932342] Model parameter optimization (eps = 1.000000)
[03:18:33 -364601.777588] SLOW spr round 1 (radius: 5)
[03:20:48 -364521.358396] SLOW spr round 2 (radius: 5)
[03:22:59 -364510.681421] SLOW spr round 3 (radius: 5)
[03:25:05 -364509.149171] SLOW spr round 4 (radius: 5)
[03:27:10 -364509.111749] SLOW spr round 5 (radius: 10)
[03:29:20 -364509.098338] SLOW spr round 6 (radius: 15)
[03:32:50 -364509.096522] SLOW spr round 7 (radius: 20)
[03:38:00 -364509.094878] SLOW spr round 8 (radius: 25)
[03:44:46 -364509.094166] Model parameter optimization (eps = 0.100000)

[03:44:51] ML tree search #4, logLikelihood: -364509.014888

[03:44:51 -1478271.921592] Initial branch length optimization
[03:44:56 -1209101.887931] Model parameter optimization (eps = 10.000000)
[03:45:42 -1205964.386405] AUTODETECT spr round 1 (radius: 5)
[03:47:56 -839162.270046] AUTODETECT spr round 2 (radius: 10)
[03:50:16 -618586.881198] AUTODETECT spr round 3 (radius: 15)
[03:52:49 -551054.500156] AUTODETECT spr round 4 (radius: 20)
[03:55:33 -505884.472718] AUTODETECT spr round 5 (radius: 25)
[03:58:39 -463149.831388] SPR radius for FAST iterations: 25 (autodetect)
[03:58:39 -463149.831388] Model parameter optimization (eps = 3.000000)
[03:59:01 -462744.929529] FAST spr round 1 (radius: 25)
[04:01:55 -369387.982051] FAST spr round 2 (radius: 25)
[04:04:17 -364743.756561] FAST spr round 3 (radius: 25)
[04:06:20 -364636.382545] FAST spr round 4 (radius: 25)
[04:08:12 -364603.349344] FAST spr round 5 (radius: 25)
[04:09:55 -364601.713614] FAST spr round 6 (radius: 25)
[04:11:37 -364601.712143] Model parameter optimization (eps = 1.000000)
[04:11:52 -364598.486957] SLOW spr round 1 (radius: 5)
[04:14:04 -364526.486478] SLOW spr round 2 (radius: 5)
[04:16:16 -364516.386074] SLOW spr round 3 (radius: 5)
[04:18:22 -364516.315487] SLOW spr round 4 (radius: 10)
[04:20:35 -364503.175612] SLOW spr round 5 (radius: 5)
[04:23:10 -364499.768242] SLOW spr round 6 (radius: 5)
[04:25:30 -364497.997520] SLOW spr round 7 (radius: 5)
[04:27:41 -364497.997278] SLOW spr round 8 (radius: 10)
[04:29:54 -364497.997115] SLOW spr round 9 (radius: 15)
[04:33:27 -364485.205048] SLOW spr round 10 (radius: 5)
[04:36:07 -364477.818332] SLOW spr round 11 (radius: 5)
[04:38:28 -364477.817104] SLOW spr round 12 (radius: 10)
[04:40:46 -364477.816921] SLOW spr round 13 (radius: 15)
[04:44:10 -364477.816820] SLOW spr round 14 (radius: 20)
[04:49:24 -364477.816748] SLOW spr round 15 (radius: 25)
[04:55:57 -364477.816695] Model parameter optimization (eps = 0.100000)

[04:56:16] ML tree search #5, logLikelihood: -364474.964204

[04:56:16 -1476382.950838] Initial branch length optimization
[04:56:20 -1212408.119292] Model parameter optimization (eps = 10.000000)
[04:56:54 -1209453.058612] AUTODETECT spr round 1 (radius: 5)
[04:59:07 -855364.981315] AUTODETECT spr round 2 (radius: 10)
[05:01:28 -631032.329984] AUTODETECT spr round 3 (radius: 15)
[05:04:01 -511941.475471] AUTODETECT spr round 4 (radius: 20)
[05:06:53 -428904.036863] AUTODETECT spr round 5 (radius: 25)
[05:09:57 -413148.311221] SPR radius for FAST iterations: 25 (autodetect)
[05:09:57 -413148.311221] Model parameter optimization (eps = 3.000000)
[05:10:22 -412875.247760] FAST spr round 1 (radius: 25)
[05:13:13 -366963.926238] FAST spr round 2 (radius: 25)
[05:15:32 -364735.179736] FAST spr round 3 (radius: 25)
[05:17:29 -364643.672891] FAST spr round 4 (radius: 25)
[05:19:20 -364579.900853] FAST spr round 5 (radius: 25)
[05:21:05 -364552.862718] FAST spr round 6 (radius: 25)
[05:22:46 -364552.861153] Model parameter optimization (eps = 1.000000)
[05:23:01 -364539.199908] SLOW spr round 1 (radius: 5)
[05:25:11 -364484.509763] SLOW spr round 2 (radius: 5)
[05:27:20 -364481.226165] SLOW spr round 3 (radius: 5)
[05:29:28 -364480.366097] SLOW spr round 4 (radius: 5)
[05:31:33 -364480.365518] SLOW spr round 5 (radius: 10)
[05:33:43 -364480.365496] SLOW spr round 6 (radius: 15)
[05:37:10 -364480.365482] SLOW spr round 7 (radius: 20)
[05:42:09 -364480.365470] SLOW spr round 8 (radius: 25)
[05:48:32 -364480.365460] Model parameter optimization (eps = 0.100000)

[05:48:39] ML tree search #6, logLikelihood: -364480.339163

[05:48:39 -1483921.289079] Initial branch length optimization
[05:48:43 -1212399.870930] Model parameter optimization (eps = 10.000000)
[05:49:18 -1209102.953015] AUTODETECT spr round 1 (radius: 5)
[05:51:32 -830367.166859] AUTODETECT spr round 2 (radius: 10)
[05:53:52 -604281.269679] AUTODETECT spr round 3 (radius: 15)
[05:56:23 -493730.373090] AUTODETECT spr round 4 (radius: 20)
[05:59:21 -438003.764167] AUTODETECT spr round 5 (radius: 25)
[06:02:54 -415926.909656] SPR radius for FAST iterations: 25 (autodetect)
[06:02:54 -415926.909656] Model parameter optimization (eps = 3.000000)
[06:03:15 -415553.772905] FAST spr round 1 (radius: 25)
[06:06:03 -367011.854908] FAST spr round 2 (radius: 25)
[06:08:18 -364764.647851] FAST spr round 3 (radius: 25)
[06:10:18 -364625.147100] FAST spr round 4 (radius: 25)
[06:12:05 -364609.655866] FAST spr round 5 (radius: 25)
[06:13:46 -364609.653573] Model parameter optimization (eps = 1.000000)
[06:14:02 -364586.097834] SLOW spr round 1 (radius: 5)
[06:16:13 -364495.104658] SLOW spr round 2 (radius: 5)
[06:18:23 -364492.476511] SLOW spr round 3 (radius: 5)
[06:20:30 -364492.416834] SLOW spr round 4 (radius: 10)
[06:22:44 -364484.264899] SLOW spr round 5 (radius: 5)
[06:25:18 -364479.890808] SLOW spr round 6 (radius: 5)
[06:27:36 -364478.813654] SLOW spr round 7 (radius: 5)
[06:29:46 -364478.812637] SLOW spr round 8 (radius: 10)
[06:31:58 -364478.812588] SLOW spr round 9 (radius: 15)
[06:35:34 -364478.510512] SLOW spr round 10 (radius: 5)
[06:38:13 -364478.148043] SLOW spr round 11 (radius: 5)
[06:40:36 -364478.147988] SLOW spr round 12 (radius: 10)
[06:42:54 -364478.147959] SLOW spr round 13 (radius: 15)
[06:46:23 -364478.147932] SLOW spr round 14 (radius: 20)
[06:51:54 -364478.147906] SLOW spr round 15 (radius: 25)
[06:58:48 -364478.147880] Model parameter optimization (eps = 0.100000)

[06:58:57] ML tree search #7, logLikelihood: -364478.014417

[06:58:57 -1480726.764133] Initial branch length optimization
[06:59:01 -1215484.201464] Model parameter optimization (eps = 10.000000)
[06:59:53 -1212371.223036] AUTODETECT spr round 1 (radius: 5)
[07:02:07 -850101.936088] AUTODETECT spr round 2 (radius: 10)
[07:04:27 -626972.916501] AUTODETECT spr round 3 (radius: 15)
[07:06:56 -515662.082205] AUTODETECT spr round 4 (radius: 20)
[07:09:38 -459802.215999] AUTODETECT spr round 5 (radius: 25)
[07:12:29 -438384.783607] SPR radius for FAST iterations: 25 (autodetect)
[07:12:29 -438384.783607] Model parameter optimization (eps = 3.000000)
[07:12:52 -438094.374715] FAST spr round 1 (radius: 25)
[07:15:42 -368417.539087] FAST spr round 2 (radius: 25)
[07:17:58 -364923.261271] FAST spr round 3 (radius: 25)
[07:19:56 -364639.837024] FAST spr round 4 (radius: 25)
[07:21:46 -364576.032810] FAST spr round 5 (radius: 25)
[07:23:28 -364572.317801] FAST spr round 6 (radius: 25)
[07:25:09 -364572.317566] Model parameter optimization (eps = 1.000000)
[07:25:26 -364567.700141] SLOW spr round 1 (radius: 5)
[07:27:38 -364488.242280] SLOW spr round 2 (radius: 5)
[07:29:47 -364487.378918] SLOW spr round 3 (radius: 5)
[07:31:53 -364487.377896] SLOW spr round 4 (radius: 10)
[07:34:03 -364487.377280] SLOW spr round 5 (radius: 15)
[07:37:30 -364487.377242] SLOW spr round 6 (radius: 20)
[07:42:24 -364487.377223] SLOW spr round 7 (radius: 25)
[07:48:27 -364487.377208] Model parameter optimization (eps = 0.100000)

[07:48:32] ML tree search #8, logLikelihood: -364487.362562

[07:48:32 -1477334.001853] Initial branch length optimization
[07:48:36 -1207013.115140] Model parameter optimization (eps = 10.000000)
[07:49:07 -1203852.898060] AUTODETECT spr round 1 (radius: 5)
[07:51:17 -848724.851992] AUTODETECT spr round 2 (radius: 10)
[07:53:36 -635877.544646] AUTODETECT spr round 3 (radius: 15)
[07:56:11 -522673.014781] AUTODETECT spr round 4 (radius: 20)
[07:58:59 -464489.951952] AUTODETECT spr round 5 (radius: 25)
[08:02:26 -433116.024096] SPR radius for FAST iterations: 25 (autodetect)
[08:02:26 -433116.024096] Model parameter optimization (eps = 3.000000)
[08:02:49 -432729.847110] FAST spr round 1 (radius: 25)
[08:05:45 -367490.233281] FAST spr round 2 (radius: 25)
[08:08:08 -364784.322940] FAST spr round 3 (radius: 25)
[08:10:13 -364602.477116] FAST spr round 4 (radius: 25)
[08:12:00 -364572.328964] FAST spr round 5 (radius: 25)
[08:13:43 -364572.326685] Model parameter optimization (eps = 1.000000)
[08:13:58 -364561.738124] SLOW spr round 1 (radius: 5)
[08:16:14 -364482.302898] SLOW spr round 2 (radius: 5)
[08:18:26 -364475.487251] SLOW spr round 3 (radius: 5)
[08:20:33 -364475.487019] SLOW spr round 4 (radius: 10)
[08:22:44 -364475.486509] SLOW spr round 5 (radius: 15)
[08:26:07 -364475.486454] SLOW spr round 6 (radius: 20)
[08:31:00 -364475.486408] SLOW spr round 7 (radius: 25)
[08:37:14 -364475.486368] Model parameter optimization (eps = 0.100000)

[08:37:25] ML tree search #9, logLikelihood: -364475.168998

[08:37:25 -1480282.903135] Initial branch length optimization
[08:37:30 -1217163.909658] Model parameter optimization (eps = 10.000000)
[08:38:09 -1213880.724290] AUTODETECT spr round 1 (radius: 5)
[08:40:21 -824426.484255] AUTODETECT spr round 2 (radius: 10)
[08:42:40 -618786.157256] AUTODETECT spr round 3 (radius: 15)
[08:45:07 -500469.616139] AUTODETECT spr round 4 (radius: 20)
[08:47:43 -442908.823620] AUTODETECT spr round 5 (radius: 25)
[08:50:33 -429515.345477] SPR radius for FAST iterations: 25 (autodetect)
[08:50:33 -429515.345477] Model parameter optimization (eps = 3.000000)
[08:50:58 -429225.982035] FAST spr round 1 (radius: 25)
[08:53:59 -367111.507195] FAST spr round 2 (radius: 25)
[08:56:19 -364859.851922] FAST spr round 3 (radius: 25)
[08:58:22 -364632.296766] FAST spr round 4 (radius: 25)
[09:00:11 -364615.203563] FAST spr round 5 (radius: 25)
[09:01:54 -364604.920697] FAST spr round 6 (radius: 25)
[09:03:34 -364604.919834] Model parameter optimization (eps = 1.000000)
[09:03:48 -364603.068005] SLOW spr round 1 (radius: 5)
[09:06:00 -364523.876218] SLOW spr round 2 (radius: 5)
[09:08:10 -364513.279992] SLOW spr round 3 (radius: 5)
[09:10:20 -364507.710701] SLOW spr round 4 (radius: 5)
[09:12:25 -364507.709035] SLOW spr round 5 (radius: 10)
[09:14:35 -364507.708839] SLOW spr round 6 (radius: 15)
[09:18:08 -364507.511636] SLOW spr round 7 (radius: 5)
[09:20:47 -364502.871431] SLOW spr round 8 (radius: 5)
[09:23:08 -364502.871414] SLOW spr round 9 (radius: 10)
[09:25:30 -364483.066259] SLOW spr round 10 (radius: 5)
[09:28:02 -364478.770867] SLOW spr round 11 (radius: 5)
[09:30:19 -364478.770688] SLOW spr round 12 (radius: 10)
[09:32:34 -364478.770676] SLOW spr round 13 (radius: 15)
[09:35:58 -364478.770665] SLOW spr round 14 (radius: 20)
[09:41:03 -364478.770656] SLOW spr round 15 (radius: 25)
[09:47:29 -364478.770646] Model parameter optimization (eps = 0.100000)

[09:47:42] ML tree search #10, logLikelihood: -364475.253801

[09:47:42 -1470572.951539] Initial branch length optimization
[09:47:46 -1198195.232278] Model parameter optimization (eps = 10.000000)
[09:48:42 -1194857.183987] AUTODETECT spr round 1 (radius: 5)
[09:50:55 -845555.583547] AUTODETECT spr round 2 (radius: 10)
[09:53:15 -617913.127725] AUTODETECT spr round 3 (radius: 15)
[09:55:45 -500995.281939] AUTODETECT spr round 4 (radius: 20)
[09:58:29 -445732.486364] AUTODETECT spr round 5 (radius: 25)
[10:01:42 -427400.646818] SPR radius for FAST iterations: 25 (autodetect)
[10:01:42 -427400.646818] Model parameter optimization (eps = 3.000000)
[10:02:04 -427025.046926] FAST spr round 1 (radius: 25)
[10:04:59 -367026.346000] FAST spr round 2 (radius: 25)
[10:07:22 -364723.274776] FAST spr round 3 (radius: 25)
[10:09:20 -364549.769590] FAST spr round 4 (radius: 25)
[10:11:06 -364545.909348] FAST spr round 5 (radius: 25)
[10:12:48 -364545.904940] Model parameter optimization (eps = 1.000000)
[10:13:01 -364544.121540] SLOW spr round 1 (radius: 5)
[10:15:16 -364492.325013] SLOW spr round 2 (radius: 5)
[10:17:27 -364475.353977] SLOW spr round 3 (radius: 5)
[10:19:36 -364473.737684] SLOW spr round 4 (radius: 5)
[10:21:41 -364473.688963] SLOW spr round 5 (radius: 10)
[10:23:51 -364473.685643] SLOW spr round 6 (radius: 15)
[10:27:16 -364473.683008] SLOW spr round 7 (radius: 20)
[10:32:04 -364473.680595] SLOW spr round 8 (radius: 25)
[10:38:17 -364473.678483] Model parameter optimization (eps = 0.100000)

[10:38:26] ML tree search #11, logLikelihood: -364473.072800

[10:38:26 -1474271.029004] Initial branch length optimization
[10:38:30 -1207874.123849] Model parameter optimization (eps = 10.000000)
[10:39:17 -1204769.688150] AUTODETECT spr round 1 (radius: 5)
[10:41:29 -826117.898178] AUTODETECT spr round 2 (radius: 10)
[10:43:51 -639176.445302] AUTODETECT spr round 3 (radius: 15)
[10:46:21 -514852.302575] AUTODETECT spr round 4 (radius: 20)
[10:49:05 -451564.728624] AUTODETECT spr round 5 (radius: 25)
[10:52:03 -429486.593188] SPR radius for FAST iterations: 25 (autodetect)
[10:52:03 -429486.593188] Model parameter optimization (eps = 3.000000)
[10:52:24 -429127.755097] FAST spr round 1 (radius: 25)
[10:55:25 -368238.926638] FAST spr round 2 (radius: 25)
[10:57:45 -364853.989520] FAST spr round 3 (radius: 25)
[10:59:51 -364625.993710] FAST spr round 4 (radius: 25)
[11:01:45 -364595.775518] FAST spr round 5 (radius: 25)
[11:03:29 -364587.952926] FAST spr round 6 (radius: 25)
[11:05:12 -364582.311317] FAST spr round 7 (radius: 25)
[11:06:51 -364582.310714] Model parameter optimization (eps = 1.000000)
[11:07:12 -364571.850236] SLOW spr round 1 (radius: 5)
[11:09:26 -364484.945214] SLOW spr round 2 (radius: 5)
[11:11:36 -364480.064654] SLOW spr round 3 (radius: 5)
[11:13:41 -364479.953306] SLOW spr round 4 (radius: 5)
[11:15:46 -364479.953162] SLOW spr round 5 (radius: 10)
[11:17:56 -364479.953074] SLOW spr round 6 (radius: 15)
[11:21:26 -364479.953015] SLOW spr round 7 (radius: 20)
[11:26:27 -364479.952973] SLOW spr round 8 (radius: 25)
[11:32:56 -364479.952943] Model parameter optimization (eps = 0.100000)

[11:33:04] ML tree search #12, logLikelihood: -364479.876978

[11:33:04 -1468461.930619] Initial branch length optimization
[11:33:09 -1203176.919273] Model parameter optimization (eps = 10.000000)
[11:33:55 -1200168.185705] AUTODETECT spr round 1 (radius: 5)
[11:36:06 -835713.922526] AUTODETECT spr round 2 (radius: 10)
[11:38:25 -620050.263373] AUTODETECT spr round 3 (radius: 15)
[11:40:55 -495729.944650] AUTODETECT spr round 4 (radius: 20)
[11:43:36 -432828.393425] AUTODETECT spr round 5 (radius: 25)
[11:46:27 -415908.194471] SPR radius for FAST iterations: 25 (autodetect)
[11:46:27 -415908.194471] Model parameter optimization (eps = 3.000000)
[11:46:50 -415546.824938] FAST spr round 1 (radius: 25)
[11:49:42 -366919.438367] FAST spr round 2 (radius: 25)
[11:52:00 -364750.351587] FAST spr round 3 (radius: 25)
[11:54:00 -364611.267700] FAST spr round 4 (radius: 25)
[11:55:49 -364597.823674] FAST spr round 5 (radius: 25)
[11:57:33 -364595.941441] FAST spr round 6 (radius: 25)
[11:59:14 -364595.940340] Model parameter optimization (eps = 1.000000)
[11:59:31 -364589.355027] SLOW spr round 1 (radius: 5)
[12:01:41 -364504.386435] SLOW spr round 2 (radius: 5)
[12:03:51 -364501.990852] SLOW spr round 3 (radius: 5)
[12:05:58 -364501.990122] SLOW spr round 4 (radius: 10)
[12:08:07 -364501.989424] SLOW spr round 5 (radius: 15)
[12:11:32 -364501.989276] SLOW spr round 6 (radius: 20)
[12:16:26 -364501.989175] SLOW spr round 7 (radius: 25)
[12:22:40 -364501.989103] Model parameter optimization (eps = 0.100000)

[12:22:49] ML tree search #13, logLikelihood: -364501.681509

[12:22:49 -1478903.999297] Initial branch length optimization
[12:22:54 -1203587.331863] Model parameter optimization (eps = 10.000000)
[12:23:30 -1200617.564280] AUTODETECT spr round 1 (radius: 5)
[12:25:43 -848402.871849] AUTODETECT spr round 2 (radius: 10)
[12:28:04 -614546.876568] AUTODETECT spr round 3 (radius: 15)
[12:30:37 -517004.207553] AUTODETECT spr round 4 (radius: 20)
[12:33:21 -460034.016912] AUTODETECT spr round 5 (radius: 25)
[12:36:28 -430067.677085] SPR radius for FAST iterations: 25 (autodetect)
[12:36:28 -430067.677085] Model parameter optimization (eps = 3.000000)
[12:36:55 -429702.028278] FAST spr round 1 (radius: 25)
[12:39:53 -367233.612048] FAST spr round 2 (radius: 25)
[12:42:10 -364681.621847] FAST spr round 3 (radius: 25)
[12:44:13 -364598.111989] FAST spr round 4 (radius: 25)
[12:46:04 -364581.412183] FAST spr round 5 (radius: 25)
[12:47:48 -364578.611120] FAST spr round 6 (radius: 25)
[12:49:30 -364578.610518] Model parameter optimization (eps = 1.000000)
[12:49:43 -364575.009646] SLOW spr round 1 (radius: 5)
[12:52:00 -364524.085953] SLOW spr round 2 (radius: 5)
[12:54:14 -364516.533703] SLOW spr round 3 (radius: 5)
[12:56:21 -364513.757321] SLOW spr round 4 (radius: 5)
[12:58:27 -364513.755791] SLOW spr round 5 (radius: 10)
[13:00:43 -364495.131537] SLOW spr round 6 (radius: 5)
[13:03:20 -364476.784669] SLOW spr round 7 (radius: 5)
[13:05:43 -364471.668483] SLOW spr round 8 (radius: 5)
[13:07:56 -364470.749958] SLOW spr round 9 (radius: 5)
[13:10:03 -364470.749765] SLOW spr round 10 (radius: 10)
[13:12:14 -364470.749660] SLOW spr round 11 (radius: 15)
[13:15:37 -364470.749592] SLOW spr round 12 (radius: 20)
[13:20:23 -364470.749546] SLOW spr round 13 (radius: 25)
[13:26:28 -364470.749514] Model parameter optimization (eps = 0.100000)

[13:26:41] ML tree search #14, logLikelihood: -364465.467183

[13:26:42 -1467726.906344] Initial branch length optimization
[13:26:46 -1209463.841499] Model parameter optimization (eps = 10.000000)
[13:27:34 -1206268.227635] AUTODETECT spr round 1 (radius: 5)
[13:29:47 -840964.821800] AUTODETECT spr round 2 (radius: 10)
[13:32:08 -637742.479257] AUTODETECT spr round 3 (radius: 15)
[13:34:40 -513406.202426] AUTODETECT spr round 4 (radius: 20)
[13:37:32 -439953.957865] AUTODETECT spr round 5 (radius: 25)
[13:40:34 -421371.293180] SPR radius for FAST iterations: 25 (autodetect)
[13:40:34 -421371.293180] Model parameter optimization (eps = 3.000000)
[13:41:00 -421040.358723] FAST spr round 1 (radius: 25)
[13:43:57 -367521.985358] FAST spr round 2 (radius: 25)
[13:46:20 -364745.872969] FAST spr round 3 (radius: 25)
[13:48:17 -364602.536474] FAST spr round 4 (radius: 25)
[13:50:05 -364593.542880] FAST spr round 5 (radius: 25)
[13:51:49 -364588.062695] FAST spr round 6 (radius: 25)
[13:53:30 -364588.051640] Model parameter optimization (eps = 1.000000)
[13:53:45 -364574.763565] SLOW spr round 1 (radius: 5)
[13:55:59 -364491.665245] SLOW spr round 2 (radius: 5)
[13:58:10 -364486.325874] SLOW spr round 3 (radius: 5)
[14:00:19 -364483.501408] SLOW spr round 4 (radius: 5)
[14:02:24 -364483.500813] SLOW spr round 5 (radius: 10)
[14:04:36 -364483.348454] SLOW spr round 6 (radius: 5)
[14:07:08 -364483.348159] SLOW spr round 7 (radius: 10)
[14:09:35 -364483.348143] SLOW spr round 8 (radius: 15)
[14:12:55 -364483.348127] SLOW spr round 9 (radius: 20)
[14:18:21 -364483.348113] SLOW spr round 10 (radius: 25)
[14:25:11 -364483.348099] Model parameter optimization (eps = 0.100000)

[14:25:20] ML tree search #15, logLikelihood: -364483.108106

[14:25:20 -1476535.552101] Initial branch length optimization
[14:25:25 -1207271.519838] Model parameter optimization (eps = 10.000000)
[14:26:16 -1204164.640244] AUTODETECT spr round 1 (radius: 5)
[14:28:28 -837766.069351] AUTODETECT spr round 2 (radius: 10)
[14:30:50 -605550.083596] AUTODETECT spr round 3 (radius: 15)
[14:33:25 -507049.444156] AUTODETECT spr round 4 (radius: 20)
[14:36:13 -473273.036337] AUTODETECT spr round 5 (radius: 25)
[14:39:24 -430860.837138] SPR radius for FAST iterations: 25 (autodetect)
[14:39:24 -430860.837138] Model parameter optimization (eps = 3.000000)
[14:39:39 -430588.977717] FAST spr round 1 (radius: 25)
[14:42:37 -367029.811633] FAST spr round 2 (radius: 25)
[14:44:51 -364783.384762] FAST spr round 3 (radius: 25)
[14:46:48 -364646.015799] FAST spr round 4 (radius: 25)
[14:48:37 -364611.629424] FAST spr round 5 (radius: 25)
[14:50:21 -364610.630065] FAST spr round 6 (radius: 25)
[14:52:04 -364610.512122] FAST spr round 7 (radius: 25)
[14:53:45 -364610.454744] Model parameter optimization (eps = 1.000000)
[14:54:02 -364601.674884] SLOW spr round 1 (radius: 5)
[14:56:13 -364487.717699] SLOW spr round 2 (radius: 5)
[14:58:23 -364482.246737] SLOW spr round 3 (radius: 5)
[15:00:30 -364481.941707] SLOW spr round 4 (radius: 5)
[15:02:35 -364481.940865] SLOW spr round 5 (radius: 10)
[15:04:46 -364481.940376] SLOW spr round 6 (radius: 15)
[15:08:19 -364481.940346] SLOW spr round 7 (radius: 20)
[15:13:28 -364481.940320] SLOW spr round 8 (radius: 25)
[15:20:09 -364481.940295] Model parameter optimization (eps = 0.100000)

[15:20:17] ML tree search #16, logLikelihood: -364481.727111

[15:20:17 -1468363.022580] Initial branch length optimization
[15:20:21 -1195257.855899] Model parameter optimization (eps = 10.000000)
[15:20:56 -1192130.741401] AUTODETECT spr round 1 (radius: 5)
[15:23:10 -836240.749351] AUTODETECT spr round 2 (radius: 10)
[15:25:29 -631360.557986] AUTODETECT spr round 3 (radius: 15)
[15:28:03 -491918.477176] AUTODETECT spr round 4 (radius: 20)
[15:30:51 -462297.834828] AUTODETECT spr round 5 (radius: 25)
[15:34:12 -436833.692443] SPR radius for FAST iterations: 25 (autodetect)
[15:34:12 -436833.692443] Model parameter optimization (eps = 3.000000)
[15:34:42 -436542.110646] FAST spr round 1 (radius: 25)
[15:37:52 -367696.620381] FAST spr round 2 (radius: 25)
[15:40:15 -364803.490569] FAST spr round 3 (radius: 25)
[15:42:18 -364632.432349] FAST spr round 4 (radius: 25)
[15:44:07 -364611.135895] FAST spr round 5 (radius: 25)
[15:45:51 -364601.653464] FAST spr round 6 (radius: 25)
[15:47:33 -364601.651329] Model parameter optimization (eps = 1.000000)
[15:47:48 -364594.514014] SLOW spr round 1 (radius: 5)
[15:50:03 -364526.643742] SLOW spr round 2 (radius: 5)
[15:52:14 -364524.451329] SLOW spr round 3 (radius: 5)
[15:54:23 -364522.459336] SLOW spr round 4 (radius: 5)
[15:56:30 -364522.456972] SLOW spr round 5 (radius: 10)
[15:58:42 -364515.578085] SLOW spr round 6 (radius: 5)
[16:01:17 -364496.502228] SLOW spr round 7 (radius: 5)
[16:03:39 -364477.733054] SLOW spr round 8 (radius: 5)
[16:05:50 -364477.731826] SLOW spr round 9 (radius: 10)
[16:08:02 -364477.730648] SLOW spr round 10 (radius: 15)
[16:11:24 -364477.729509] SLOW spr round 11 (radius: 20)
[16:16:20 -364477.728402] SLOW spr round 12 (radius: 25)
[16:22:42 -364477.727325] Model parameter optimization (eps = 0.100000)

[16:22:48] ML tree search #17, logLikelihood: -364477.666360

[16:22:48 -1483662.101648] Initial branch length optimization
[16:22:52 -1210641.644902] Model parameter optimization (eps = 10.000000)
[16:23:30 -1207384.523714] AUTODETECT spr round 1 (radius: 5)
[16:25:43 -851612.736779] AUTODETECT spr round 2 (radius: 10)
[16:28:01 -644023.736114] AUTODETECT spr round 3 (radius: 15)
[16:30:29 -532710.159327] AUTODETECT spr round 4 (radius: 20)
[16:33:09 -453610.495736] AUTODETECT spr round 5 (radius: 25)
[16:36:17 -429431.854509] SPR radius for FAST iterations: 25 (autodetect)
[16:36:17 -429431.854509] Model parameter optimization (eps = 3.000000)
[16:36:41 -429073.111973] FAST spr round 1 (radius: 25)
[16:39:36 -366983.840458] FAST spr round 2 (radius: 25)
[16:41:53 -364782.730879] FAST spr round 3 (radius: 25)
[16:43:55 -364645.485633] FAST spr round 4 (radius: 25)
[16:45:44 -364604.333743] FAST spr round 5 (radius: 25)
[16:47:26 -364604.333695] Model parameter optimization (eps = 1.000000)
[16:47:40 -364597.541047] SLOW spr round 1 (radius: 5)
[16:49:56 -364527.216403] SLOW spr round 2 (radius: 5)
[16:52:08 -364517.605069] SLOW spr round 3 (radius: 5)
[16:54:17 -364516.631024] SLOW spr round 4 (radius: 5)
[16:56:23 -364516.630741] SLOW spr round 5 (radius: 10)
[16:58:34 -364516.630604] SLOW spr round 6 (radius: 15)
[17:02:04 -364516.630495] SLOW spr round 7 (radius: 20)
[17:07:09 -364516.630403] SLOW spr round 8 (radius: 25)
[17:13:44 -364516.630325] Model parameter optimization (eps = 0.100000)

[17:13:54] ML tree search #18, logLikelihood: -364516.474706

[17:13:54 -1479311.220140] Initial branch length optimization
[17:13:58 -1209174.941836] Model parameter optimization (eps = 10.000000)
[17:14:47 -1206160.909796] AUTODETECT spr round 1 (radius: 5)
[17:17:01 -848020.882679] AUTODETECT spr round 2 (radius: 10)
[17:19:23 -614606.041288] AUTODETECT spr round 3 (radius: 15)
[17:21:58 -486958.572178] AUTODETECT spr round 4 (radius: 20)
[17:24:43 -431952.148725] AUTODETECT spr round 5 (radius: 25)
[17:27:53 -418886.138675] SPR radius for FAST iterations: 25 (autodetect)
[17:27:53 -418886.138675] Model parameter optimization (eps = 3.000000)
[17:28:14 -418501.552672] FAST spr round 1 (radius: 25)
[17:31:11 -367410.321259] FAST spr round 2 (radius: 25)
[17:33:33 -364686.170227] FAST spr round 3 (radius: 25)
[17:35:38 -364598.296891] FAST spr round 4 (radius: 25)
[17:37:26 -364585.758790] FAST spr round 5 (radius: 25)
[17:39:10 -364584.687940] FAST spr round 6 (radius: 25)
[17:40:51 -364584.683371] Model parameter optimization (eps = 1.000000)
[17:41:07 -364576.515938] SLOW spr round 1 (radius: 5)
[17:43:24 -364492.546151] SLOW spr round 2 (radius: 5)
[17:45:35 -364489.032468] SLOW spr round 3 (radius: 5)
[17:47:44 -364485.906501] SLOW spr round 4 (radius: 5)
[17:49:51 -364485.871969] SLOW spr round 5 (radius: 10)
[17:52:02 -364484.300021] SLOW spr round 6 (radius: 5)
[17:54:34 -364484.299337] SLOW spr round 7 (radius: 10)
[17:57:00 -364484.299284] SLOW spr round 8 (radius: 15)
[18:00:15 -364484.299260] SLOW spr round 9 (radius: 20)
[18:05:26 -364484.299243] SLOW spr round 10 (radius: 25)
[18:11:52 -364484.299229] Model parameter optimization (eps = 0.100000)

[18:12:02] ML tree search #19, logLikelihood: -364484.069024

[18:12:03 -1475028.476712] Initial branch length optimization
[18:12:07 -1206285.206425] Model parameter optimization (eps = 10.000000)
[18:12:47 -1203235.263757] AUTODETECT spr round 1 (radius: 5)
[18:15:00 -842862.517582] AUTODETECT spr round 2 (radius: 10)
[18:17:20 -625701.447380] AUTODETECT spr round 3 (radius: 15)
[18:19:51 -491227.965505] AUTODETECT spr round 4 (radius: 20)
[18:22:38 -435794.813419] AUTODETECT spr round 5 (radius: 25)
[18:25:36 -422845.471539] SPR radius for FAST iterations: 25 (autodetect)
[18:25:36 -422845.471539] Model parameter optimization (eps = 3.000000)
[18:25:58 -422463.227589] FAST spr round 1 (radius: 25)
[18:28:57 -367298.149218] FAST spr round 2 (radius: 25)
[18:31:18 -364882.778720] FAST spr round 3 (radius: 25)
[18:33:23 -364649.717692] FAST spr round 4 (radius: 25)
[18:35:19 -364589.231611] FAST spr round 5 (radius: 25)
[18:37:01 -364587.144877] FAST spr round 6 (radius: 25)
[18:38:42 -364587.144455] Model parameter optimization (eps = 1.000000)
[18:38:58 -364579.727480] SLOW spr round 1 (radius: 5)
[18:41:15 -364524.687953] SLOW spr round 2 (radius: 5)
[18:43:27 -364521.590163] SLOW spr round 3 (radius: 5)
[18:45:33 -364521.488677] SLOW spr round 4 (radius: 5)
[18:47:39 -364521.454549] SLOW spr round 5 (radius: 10)
[18:49:48 -364521.442920] SLOW spr round 6 (radius: 15)
[18:53:15 -364509.850581] SLOW spr round 7 (radius: 5)
[18:55:54 -364509.848466] SLOW spr round 8 (radius: 10)
[18:58:25 -364509.847537] SLOW spr round 9 (radius: 15)
[19:01:35 -364509.846942] SLOW spr round 10 (radius: 20)
[19:06:44 -364509.846555] SLOW spr round 11 (radius: 25)
[19:13:06 -364509.846301] Model parameter optimization (eps = 0.100000)

[19:13:13] ML tree search #20, logLikelihood: -364509.741982


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.108119,0.352610) (0.180181,0.621131) (0.439385,0.918450) (0.272314,1.639307) 
   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: -364461.583911

AIC score: 732933.167823 / AICc score: 8776993.167823 / BIC score: 742521.462895
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=882).
         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/Q562E7/3_mltree/Q562E7.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q562E7/3_mltree/Q562E7.raxml.log

Analysis started: 30-Jul-2021 10:16:31 / finished: 31-Jul-2021 05:29:45

Elapsed time: 69194.075 seconds