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 20-Jul-2021 02:50:08 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/2_msa/Q9H611_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/2_msa/Q9H611_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 443 sites

WARNING: Sequences tr_A0A0D8JVN0_A0A0D8JVN0_COCIM_246410 and tr_E9D2X4_E9D2X4_COCPS_443226 are exactly identical!
WARNING: Sequences tr_B6Q6C2_B6Q6C2_TALMQ_441960 and tr_A0A093VFG1_A0A093VFG1_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WJA7_B2WJA7_PYRTR_426418 and tr_A0A2W1ERC3_A0A2W1ERC3_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G2XJT3_G2XJT3_VERDV_498257 and tr_A0A0G4N7A9_A0A0G4N7A9_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_Q29MC1_Q29MC1_DROPS_46245 and tr_B4G9G4_B4G9G4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_K7BQX3_K7BQX3_PANTR_9598 and sp_Q9H611_PIF1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_E9ETX6_E9ETX6_METRA_655844 and tr_A0A0D9NSG7_A0A0D9NSG7_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6HKH8_C6HKH8_AJECH_544712 and tr_F0UGZ7_F0UGZ7_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J5JW44_J5JW44_BEAB2_655819 and tr_A0A0A2VRD3_A0A0A2VRD3_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_A1DDJ4_A1DDJ4_NEOFI_331117 and tr_A0A0S7DZ37_A0A0S7DZ37_9EURO_293939 are exactly identical!
WARNING: Sequences tr_G7XV26_G7XV26_ASPKW_1033177 and tr_A0A124BXK2_A0A124BXK2_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XV26_G7XV26_ASPKW_1033177 and tr_A0A146EZ32_A0A146EZ32_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2YQM1_G2YQM1_BOTF4_999810 and tr_M7TRT5_M7TRT5_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2T115_F2T115_TRIRC_559305 and tr_A0A178F7M5_A0A178F7M5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_S0E8T2_S0E8T2_GIBF5_1279085 and tr_A0A365MXJ8_A0A365MXJ8_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_N4UDB8_N4UDB8_FUSC1_1229664 and tr_A0A2H3TI31_A0A2H3TI31_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_V2Z1H8_V2Z1H8_MONRO_1381753 and tr_A0A0W0EWM1_A0A0W0EWM1_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015KD19_A0A015KD19_9GLOM_1432141 and tr_A0A2H5R7Y2_A0A2H5R7Y2_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A015N2M8_A0A015N2M8_9GLOM_1432141 and tr_A0A2H5RZR9_A0A2H5RZR9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0F4GSW0_A0A0F4GSW0_9PEZI_1047168 and tr_A0A1X7RKD9_A0A1X7RKD9_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_A0A1S3ZIZ9_A0A1S3ZIZ9_TOBAC_4097 and tr_A0A1U7VUY1_A0A1U7VUY1_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2H5RMR0_A0A2H5RMR0_RHIID_747089 and tr_A0A2H5RMR1_A0A2H5RMR1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2H5RMR0_A0A2H5RMR0_RHIID_747089 and tr_A0A2H5SVR4_A0A2H5SVR4_RHIID_747089 are exactly identical!
WARNING: Duplicate sequences found: 23

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/Q9H611/3_mltree/Q9H611.raxml.reduced.phy

Alignment comprises 1 partitions and 443 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 443 / 443
Gaps: 13.91 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 7 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 / 64 / 5120
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -696567.742416] Initial branch length optimization
[00:00:03 -592085.227983] Model parameter optimization (eps = 10.000000)
[00:00:25 -591315.742739] AUTODETECT spr round 1 (radius: 5)
[00:02:07 -500610.990181] AUTODETECT spr round 2 (radius: 10)
[00:04:06 -412081.218512] AUTODETECT spr round 3 (radius: 15)
[00:06:28 -357147.219205] AUTODETECT spr round 4 (radius: 20)
[00:09:05 -335249.169774] AUTODETECT spr round 5 (radius: 25)
[00:12:05 -330340.628840] SPR radius for FAST iterations: 25 (autodetect)
[00:12:05 -330340.628840] Model parameter optimization (eps = 3.000000)
[00:12:10 -330337.832533] FAST spr round 1 (radius: 25)
[00:16:11 -299855.968585] FAST spr round 2 (radius: 25)
[00:18:29 -298572.947113] FAST spr round 3 (radius: 25)
[00:20:33 -298452.809075] FAST spr round 4 (radius: 25)
[00:22:16 -298442.745035] FAST spr round 5 (radius: 25)
[00:23:50 -298436.301747] FAST spr round 6 (radius: 25)
[00:25:20 -298436.301176] Model parameter optimization (eps = 1.000000)
[00:25:23 -298435.903133] SLOW spr round 1 (radius: 5)
[00:27:28 -298387.019980] SLOW spr round 2 (radius: 5)
[00:29:27 -298383.868652] SLOW spr round 3 (radius: 5)
[00:31:25 -298380.734650] SLOW spr round 4 (radius: 5)
[00:33:20 -298380.286113] SLOW spr round 5 (radius: 5)
[00:35:14 -298380.150231] SLOW spr round 6 (radius: 5)
[00:37:07 -298380.149926] SLOW spr round 7 (radius: 10)
[00:39:12 -298376.137002] SLOW spr round 8 (radius: 5)
[00:41:32 -298371.095300] SLOW spr round 9 (radius: 5)
[00:43:37 -298371.095038] SLOW spr round 10 (radius: 10)
[00:45:49 -298370.574555] SLOW spr round 11 (radius: 5)
[00:48:07 -298370.573757] SLOW spr round 12 (radius: 10)
[00:50:30 -298370.573676] SLOW spr round 13 (radius: 15)
[00:54:08 -298370.573656] SLOW spr round 14 (radius: 20)
[00:59:55 -298370.573648] SLOW spr round 15 (radius: 25)
[01:07:01 -298370.573643] Model parameter optimization (eps = 0.100000)

[01:07:04] ML tree search #1, logLikelihood: -298370.571172

[01:07:05 -695063.081224] Initial branch length optimization
[01:07:07 -590486.083221] Model parameter optimization (eps = 10.000000)
[01:07:30 -589606.782718] AUTODETECT spr round 1 (radius: 5)
[01:09:11 -501855.595342] AUTODETECT spr round 2 (radius: 10)
[01:11:12 -403468.396984] AUTODETECT spr round 3 (radius: 15)
[01:13:34 -347266.184825] AUTODETECT spr round 4 (radius: 20)
[01:16:10 -334421.090574] AUTODETECT spr round 5 (radius: 25)
[01:19:09 -330460.060028] SPR radius for FAST iterations: 25 (autodetect)
[01:19:09 -330460.060028] Model parameter optimization (eps = 3.000000)
[01:19:30 -330274.273942] FAST spr round 1 (radius: 25)
[01:23:19 -299841.262244] FAST spr round 2 (radius: 25)
[01:25:40 -298760.750061] FAST spr round 3 (radius: 25)
[01:27:41 -298338.436758] FAST spr round 4 (radius: 25)
[01:29:26 -298293.649298] FAST spr round 5 (radius: 25)
[01:31:00 -298293.649233] Model parameter optimization (eps = 1.000000)
[01:31:13 -298282.035813] SLOW spr round 1 (radius: 5)
[01:33:19 -298218.208104] SLOW spr round 2 (radius: 5)
[01:35:19 -298207.735478] SLOW spr round 3 (radius: 5)
[01:37:14 -298206.215031] SLOW spr round 4 (radius: 5)
[01:39:08 -298206.214697] SLOW spr round 5 (radius: 10)
[01:41:13 -298206.214641] SLOW spr round 6 (radius: 15)
[01:45:02 -298206.214601] SLOW spr round 7 (radius: 20)
[01:50:26 -298205.240763] SLOW spr round 8 (radius: 5)
[01:52:52 -298200.939428] SLOW spr round 9 (radius: 5)
[01:55:00 -298200.936842] SLOW spr round 10 (radius: 10)
[01:57:12 -298200.936214] SLOW spr round 11 (radius: 15)
[02:00:51 -298200.935902] SLOW spr round 12 (radius: 20)
[02:06:20 -298200.935683] SLOW spr round 13 (radius: 25)
[02:12:56 -298200.935514] Model parameter optimization (eps = 0.100000)

[02:13:12] ML tree search #2, logLikelihood: -298198.683748

[02:13:12 -694737.516826] Initial branch length optimization
[02:13:14 -589212.972602] Model parameter optimization (eps = 10.000000)
[02:13:40 -588441.986872] AUTODETECT spr round 1 (radius: 5)
[02:15:21 -500037.023201] AUTODETECT spr round 2 (radius: 10)
[02:17:21 -386502.849815] AUTODETECT spr round 3 (radius: 15)
[02:19:43 -342491.045620] AUTODETECT spr round 4 (radius: 20)
[02:22:20 -331876.886433] AUTODETECT spr round 5 (radius: 25)
[02:25:41 -327352.548962] SPR radius for FAST iterations: 25 (autodetect)
[02:25:41 -327352.548962] Model parameter optimization (eps = 3.000000)
[02:25:46 -327350.842875] FAST spr round 1 (radius: 25)
[02:29:40 -299562.931262] FAST spr round 2 (radius: 25)
[02:32:09 -298535.272341] FAST spr round 3 (radius: 25)
[02:34:09 -298475.560741] FAST spr round 4 (radius: 25)
[02:35:53 -298459.080554] FAST spr round 5 (radius: 25)
[02:37:28 -298455.569955] FAST spr round 6 (radius: 25)
[02:38:59 -298455.568348] Model parameter optimization (eps = 1.000000)
[02:39:03 -298455.218556] SLOW spr round 1 (radius: 5)
[02:41:14 -298406.152337] SLOW spr round 2 (radius: 5)
[02:43:14 -298403.370596] SLOW spr round 3 (radius: 5)
[02:45:10 -298403.370185] SLOW spr round 4 (radius: 10)
[02:47:15 -298400.860115] SLOW spr round 5 (radius: 5)
[02:49:36 -298400.566747] SLOW spr round 6 (radius: 5)
[02:51:43 -298400.566621] SLOW spr round 7 (radius: 10)
[02:53:52 -298400.566595] SLOW spr round 8 (radius: 15)
[02:57:36 -298400.566580] SLOW spr round 9 (radius: 20)
[03:03:09 -298400.566568] SLOW spr round 10 (radius: 25)
[03:10:07 -298400.566559] Model parameter optimization (eps = 0.100000)

[03:10:10] ML tree search #3, logLikelihood: -298400.558301

[03:10:10 -693843.710174] Initial branch length optimization
[03:10:13 -589744.923974] Model parameter optimization (eps = 10.000000)
[03:10:35 -588970.011257] AUTODETECT spr round 1 (radius: 5)
[03:12:16 -493233.079450] AUTODETECT spr round 2 (radius: 10)
[03:14:15 -408231.639464] AUTODETECT spr round 3 (radius: 15)
[03:16:41 -352431.134442] AUTODETECT spr round 4 (radius: 20)
[03:19:16 -335458.384782] AUTODETECT spr round 5 (radius: 25)
[03:22:33 -333049.945000] SPR radius for FAST iterations: 25 (autodetect)
[03:22:33 -333049.945000] Model parameter optimization (eps = 3.000000)
[03:22:55 -332813.838285] FAST spr round 1 (radius: 25)
[03:26:48 -299637.940408] FAST spr round 2 (radius: 25)
[03:29:15 -298300.497338] FAST spr round 3 (radius: 25)
[03:31:17 -298249.302010] FAST spr round 4 (radius: 25)
[03:33:00 -298239.807798] FAST spr round 5 (radius: 25)
[03:34:35 -298239.806067] Model parameter optimization (eps = 1.000000)
[03:34:51 -298231.987074] SLOW spr round 1 (radius: 5)
[03:36:59 -298159.674724] SLOW spr round 2 (radius: 5)
[03:38:59 -298154.236212] SLOW spr round 3 (radius: 5)
[03:40:56 -298154.234870] SLOW spr round 4 (radius: 10)
[03:43:00 -298153.006033] SLOW spr round 5 (radius: 5)
[03:45:20 -298152.702217] SLOW spr round 6 (radius: 5)
[03:47:25 -298152.701549] SLOW spr round 7 (radius: 10)
[03:49:35 -298152.701240] SLOW spr round 8 (radius: 15)
[03:53:11 -298152.701043] SLOW spr round 9 (radius: 20)
[03:58:34 -298152.700895] SLOW spr round 10 (radius: 25)
[04:05:16 -298152.700775] Model parameter optimization (eps = 0.100000)

[04:05:20] ML tree search #4, logLikelihood: -298152.684471

[04:05:20 -694860.982508] Initial branch length optimization
[04:05:22 -590630.175650] Model parameter optimization (eps = 10.000000)
[04:05:41 -589824.442958] AUTODETECT spr round 1 (radius: 5)
[04:07:23 -492506.316899] AUTODETECT spr round 2 (radius: 10)
[04:09:23 -393315.530293] AUTODETECT spr round 3 (radius: 15)
[04:11:53 -349576.375954] AUTODETECT spr round 4 (radius: 20)
[04:14:33 -328703.012332] AUTODETECT spr round 5 (radius: 25)
[04:18:15 -326927.091410] SPR radius for FAST iterations: 25 (autodetect)
[04:18:15 -326927.091410] Model parameter optimization (eps = 3.000000)
[04:18:20 -326924.696566] FAST spr round 1 (radius: 25)
[04:22:27 -300046.670603] FAST spr round 2 (radius: 25)
[04:24:59 -298586.321967] FAST spr round 3 (radius: 25)
[04:27:08 -298460.711790] FAST spr round 4 (radius: 25)
[04:28:53 -298444.903874] FAST spr round 5 (radius: 25)
[04:30:28 -298444.903110] Model parameter optimization (eps = 1.000000)
[04:30:32 -298444.615619] SLOW spr round 1 (radius: 5)
[04:32:48 -298389.322924] SLOW spr round 2 (radius: 5)
[04:34:58 -298375.934612] SLOW spr round 3 (radius: 5)
[04:37:01 -298374.750411] SLOW spr round 4 (radius: 5)
[04:38:59 -298374.747508] SLOW spr round 5 (radius: 10)
[04:41:07 -298373.723015] SLOW spr round 6 (radius: 5)
[04:43:30 -298373.719999] SLOW spr round 7 (radius: 10)
[04:45:54 -298373.718883] SLOW spr round 8 (radius: 15)
[04:49:33 -298373.718405] SLOW spr round 9 (radius: 20)
[04:55:18 -298373.718188] SLOW spr round 10 (radius: 25)
[05:02:38 -298373.718086] Model parameter optimization (eps = 0.100000)

[05:02:42] ML tree search #5, logLikelihood: -298373.679266

[05:02:42 -694949.176372] Initial branch length optimization
[05:02:45 -590482.635391] Model parameter optimization (eps = 10.000000)
[05:03:06 -589661.607984] AUTODETECT spr round 1 (radius: 5)
[05:04:48 -500168.084474] AUTODETECT spr round 2 (radius: 10)
[05:06:48 -400511.717446] AUTODETECT spr round 3 (radius: 15)
[05:09:12 -355077.257498] AUTODETECT spr round 4 (radius: 20)
[05:11:41 -334698.951613] AUTODETECT spr round 5 (radius: 25)
[05:14:39 -331091.947191] SPR radius for FAST iterations: 25 (autodetect)
[05:14:39 -331091.947191] Model parameter optimization (eps = 3.000000)
[05:14:58 -330832.972721] FAST spr round 1 (radius: 25)
[05:19:10 -299114.111281] FAST spr round 2 (radius: 25)
[05:21:39 -298324.505287] FAST spr round 3 (radius: 25)
[05:23:42 -298260.434465] FAST spr round 4 (radius: 25)
[05:25:23 -298247.739624] FAST spr round 5 (radius: 25)
[05:26:58 -298247.592866] FAST spr round 6 (radius: 25)
[05:28:30 -298247.209948] FAST spr round 7 (radius: 25)
[05:29:59 -298247.195796] Model parameter optimization (eps = 1.000000)
[05:30:12 -298246.035648] SLOW spr round 1 (radius: 5)
[05:32:22 -298180.040155] SLOW spr round 2 (radius: 5)
[05:34:26 -298167.873862] SLOW spr round 3 (radius: 5)
[05:36:23 -298162.428832] SLOW spr round 4 (radius: 5)
[05:38:18 -298162.427988] SLOW spr round 5 (radius: 10)
[05:40:22 -298161.208340] SLOW spr round 6 (radius: 5)
[05:42:43 -298155.527109] SLOW spr round 7 (radius: 5)
[05:44:48 -298155.526794] SLOW spr round 8 (radius: 10)
[05:46:57 -298155.421989] SLOW spr round 9 (radius: 5)
[05:49:16 -298153.221071] SLOW spr round 10 (radius: 5)
[05:51:21 -298153.220581] SLOW spr round 11 (radius: 10)
[05:53:29 -298153.220407] SLOW spr round 12 (radius: 15)
[05:57:01 -298153.220313] SLOW spr round 13 (radius: 20)
[06:02:19 -298153.220259] SLOW spr round 14 (radius: 25)
[06:09:08 -298153.220228] Model parameter optimization (eps = 0.100000)

[06:09:15] ML tree search #6, logLikelihood: -298153.053474

[06:09:15 -693755.595229] Initial branch length optimization
[06:09:17 -590576.924278] Model parameter optimization (eps = 10.000000)
[06:09:38 -589748.990749] AUTODETECT spr round 1 (radius: 5)
[06:11:21 -493840.788015] AUTODETECT spr round 2 (radius: 10)
[06:13:26 -400673.269894] AUTODETECT spr round 3 (radius: 15)
[06:15:56 -355751.002796] AUTODETECT spr round 4 (radius: 20)
[06:18:22 -336677.886244] AUTODETECT spr round 5 (radius: 25)
[06:21:18 -332399.281870] SPR radius for FAST iterations: 25 (autodetect)
[06:21:18 -332399.281870] Model parameter optimization (eps = 3.000000)
[06:21:23 -332396.594302] FAST spr round 1 (radius: 25)
[06:25:25 -299635.171604] FAST spr round 2 (radius: 25)
[06:27:54 -298548.035443] FAST spr round 3 (radius: 25)
[06:29:55 -298487.622366] FAST spr round 4 (radius: 25)
[06:31:38 -298483.628118] FAST spr round 5 (radius: 25)
[06:33:15 -298478.428370] FAST spr round 6 (radius: 25)
[06:34:47 -298478.428280] Model parameter optimization (eps = 1.000000)
[06:34:52 -298478.223235] SLOW spr round 1 (radius: 5)
[06:37:03 -298388.193680] SLOW spr round 2 (radius: 5)
[06:39:06 -298370.565657] SLOW spr round 3 (radius: 5)
[06:41:04 -298367.818732] SLOW spr round 4 (radius: 5)
[06:43:00 -298367.818645] SLOW spr round 5 (radius: 10)
[06:45:09 -298365.044602] SLOW spr round 6 (radius: 5)
[06:47:32 -298364.555807] SLOW spr round 7 (radius: 5)
[06:49:39 -298364.555503] SLOW spr round 8 (radius: 10)
[06:51:54 -298364.555436] SLOW spr round 9 (radius: 15)
[06:55:40 -298364.555384] SLOW spr round 10 (radius: 20)
[07:01:13 -298364.555333] SLOW spr round 11 (radius: 25)
[07:08:10 -298364.555283] Model parameter optimization (eps = 0.100000)

[07:08:13] ML tree search #7, logLikelihood: -298364.548016

[07:08:14 -691894.450878] Initial branch length optimization
[07:08:16 -588198.200893] Model parameter optimization (eps = 10.000000)
[07:08:43 -587369.629502] AUTODETECT spr round 1 (radius: 5)
[07:10:24 -500816.638764] AUTODETECT spr round 2 (radius: 10)
[07:12:19 -412069.117088] AUTODETECT spr round 3 (radius: 15)
[07:14:42 -361791.622609] AUTODETECT spr round 4 (radius: 20)
[07:17:10 -334796.273762] AUTODETECT spr round 5 (radius: 25)
[07:20:32 -330216.978435] SPR radius for FAST iterations: 25 (autodetect)
[07:20:32 -330216.978435] Model parameter optimization (eps = 3.000000)
[07:20:50 -330012.496613] FAST spr round 1 (radius: 25)
[07:24:39 -299845.793765] FAST spr round 2 (radius: 25)
[07:27:08 -298633.054731] FAST spr round 3 (radius: 25)
[07:29:11 -298273.715177] FAST spr round 4 (radius: 25)
[07:31:00 -298247.682129] FAST spr round 5 (radius: 25)
[07:32:37 -298239.120090] FAST spr round 6 (radius: 25)
[07:34:08 -298239.119920] Model parameter optimization (eps = 1.000000)
[07:34:21 -298230.132132] SLOW spr round 1 (radius: 5)
[07:36:28 -298189.764891] SLOW spr round 2 (radius: 5)
[07:38:29 -298181.442824] SLOW spr round 3 (radius: 5)
[07:40:26 -298181.278675] SLOW spr round 4 (radius: 5)
[07:42:20 -298181.277865] SLOW spr round 5 (radius: 10)
[07:44:27 -298178.004686] SLOW spr round 6 (radius: 5)
[07:46:48 -298177.335566] SLOW spr round 7 (radius: 5)
[07:48:54 -298177.230451] SLOW spr round 8 (radius: 5)
[07:50:53 -298177.230079] SLOW spr round 9 (radius: 10)
[07:53:00 -298177.229970] SLOW spr round 10 (radius: 15)
[07:56:56 -298177.229926] SLOW spr round 11 (radius: 20)
[08:02:56 -298177.229907] SLOW spr round 12 (radius: 25)
[08:10:27 -298177.229898] Model parameter optimization (eps = 0.100000)

[08:10:32] ML tree search #8, logLikelihood: -298177.221678

[08:10:32 -692886.928537] Initial branch length optimization
[08:10:35 -589581.294645] Model parameter optimization (eps = 10.000000)
[08:11:00 -588745.558959] AUTODETECT spr round 1 (radius: 5)
[08:12:39 -503803.590874] AUTODETECT spr round 2 (radius: 10)
[08:14:38 -409530.490805] AUTODETECT spr round 3 (radius: 15)
[08:17:09 -358515.881238] AUTODETECT spr round 4 (radius: 20)
[08:19:43 -333702.769944] AUTODETECT spr round 5 (radius: 25)
[08:23:15 -331682.814581] SPR radius for FAST iterations: 25 (autodetect)
[08:23:15 -331682.814581] Model parameter optimization (eps = 3.000000)
[08:23:33 -331480.737675] FAST spr round 1 (radius: 25)
[08:27:22 -299408.164413] FAST spr round 2 (radius: 25)
[08:29:44 -298523.851278] FAST spr round 3 (radius: 25)
[08:31:40 -298486.493204] FAST spr round 4 (radius: 25)
[08:33:23 -298462.866375] FAST spr round 5 (radius: 25)
[08:34:59 -298274.837232] FAST spr round 6 (radius: 25)
[08:36:30 -298274.836982] Model parameter optimization (eps = 1.000000)
[08:36:46 -298261.375658] SLOW spr round 1 (radius: 5)
[08:38:49 -298176.515602] SLOW spr round 2 (radius: 5)
[08:40:48 -298171.685437] SLOW spr round 3 (radius: 5)
[08:42:41 -298171.680611] SLOW spr round 4 (radius: 10)
[08:44:42 -298170.956945] SLOW spr round 5 (radius: 5)
[08:46:59 -298170.655342] SLOW spr round 6 (radius: 5)
[08:49:02 -298170.655266] SLOW spr round 7 (radius: 10)
[08:51:08 -298170.655239] SLOW spr round 8 (radius: 15)
[08:54:32 -298169.602541] SLOW spr round 9 (radius: 5)
[08:56:57 -298166.008806] SLOW spr round 10 (radius: 5)
[08:59:06 -298164.304683] SLOW spr round 11 (radius: 5)
[09:01:04 -298164.303739] SLOW spr round 12 (radius: 10)
[09:03:09 -298163.869452] SLOW spr round 13 (radius: 5)
[09:05:27 -298163.202990] SLOW spr round 14 (radius: 5)
[09:07:32 -298163.193400] SLOW spr round 15 (radius: 10)
[09:09:39 -298163.193386] SLOW spr round 16 (radius: 15)
[09:13:10 -298162.643355] SLOW spr round 17 (radius: 5)
[09:15:33 -298162.448877] SLOW spr round 18 (radius: 5)
[09:17:39 -298162.424901] SLOW spr round 19 (radius: 10)
[09:19:48 -298162.424344] SLOW spr round 20 (radius: 15)
[09:23:17 -298162.423887] SLOW spr round 21 (radius: 20)
[09:28:25 -298162.423513] SLOW spr round 22 (radius: 25)
[09:34:33 -298162.423206] Model parameter optimization (eps = 0.100000)

[09:34:40] ML tree search #9, logLikelihood: -298162.249590

[09:34:40 -693971.066044] Initial branch length optimization
[09:34:43 -588073.361652] Model parameter optimization (eps = 10.000000)
[09:35:08 -587262.992472] AUTODETECT spr round 1 (radius: 5)
[09:36:48 -494679.342207] AUTODETECT spr round 2 (radius: 10)
[09:38:46 -397268.285118] AUTODETECT spr round 3 (radius: 15)
[09:41:04 -348678.909663] AUTODETECT spr round 4 (radius: 20)
[09:43:30 -331150.173686] AUTODETECT spr round 5 (radius: 25)
[09:46:26 -328891.452025] SPR radius for FAST iterations: 25 (autodetect)
[09:46:26 -328891.452025] Model parameter optimization (eps = 3.000000)
[09:46:44 -328705.526104] FAST spr round 1 (radius: 25)
[09:50:50 -300068.707124] FAST spr round 2 (radius: 25)
[09:53:16 -298457.228364] FAST spr round 3 (radius: 25)
[09:55:19 -298276.650993] FAST spr round 4 (radius: 25)
[09:57:02 -298252.046710] FAST spr round 5 (radius: 25)
[09:58:36 -298248.887315] FAST spr round 6 (radius: 25)
[10:00:08 -298245.351209] FAST spr round 7 (radius: 25)
[10:01:37 -298240.934908] FAST spr round 8 (radius: 25)
[10:03:04 -298240.933434] Model parameter optimization (eps = 1.000000)
[10:03:19 -298235.593603] SLOW spr round 1 (radius: 5)
[10:05:23 -298169.352078] SLOW spr round 2 (radius: 5)
[10:07:22 -298160.702278] SLOW spr round 3 (radius: 5)
[10:09:17 -298160.408142] SLOW spr round 4 (radius: 5)
[10:11:10 -298160.406918] SLOW spr round 5 (radius: 10)
[10:13:11 -298160.406804] SLOW spr round 6 (radius: 15)
[10:16:46 -298160.406788] SLOW spr round 7 (radius: 20)
[10:21:59 -298160.406781] SLOW spr round 8 (radius: 25)
[10:28:31 -298160.406777] Model parameter optimization (eps = 0.100000)

[10:28:42] ML tree search #10, logLikelihood: -298159.019893

[10:28:42 -692370.739204] Initial branch length optimization
[10:28:45 -588064.900661] Model parameter optimization (eps = 10.000000)
[10:29:08 -587277.317577] AUTODETECT spr round 1 (radius: 5)
[10:30:48 -498553.095850] AUTODETECT spr round 2 (radius: 10)
[10:32:47 -407128.952780] AUTODETECT spr round 3 (radius: 15)
[10:35:13 -352807.105111] AUTODETECT spr round 4 (radius: 20)
[10:37:43 -338969.219623] AUTODETECT spr round 5 (radius: 25)
[10:40:34 -332879.358696] SPR radius for FAST iterations: 25 (autodetect)
[10:40:34 -332879.358696] Model parameter optimization (eps = 3.000000)
[10:40:51 -332673.079779] FAST spr round 1 (radius: 25)
[10:44:46 -299784.662049] FAST spr round 2 (radius: 25)
[10:47:12 -298410.912472] FAST spr round 3 (radius: 25)
[10:49:19 -298280.730247] FAST spr round 4 (radius: 25)
[10:51:09 -298258.677828] FAST spr round 5 (radius: 25)
[10:52:44 -298255.386312] FAST spr round 6 (radius: 25)
[10:54:16 -298255.372854] Model parameter optimization (eps = 1.000000)
[10:54:29 -298244.167689] SLOW spr round 1 (radius: 5)
[10:56:41 -298177.004313] SLOW spr round 2 (radius: 5)
[10:58:42 -298169.258426] SLOW spr round 3 (radius: 5)
[11:00:39 -298169.106208] SLOW spr round 4 (radius: 5)
[11:02:34 -298169.104723] SLOW spr round 5 (radius: 10)
[11:04:40 -298165.883239] SLOW spr round 6 (radius: 5)
[11:07:03 -298160.421869] SLOW spr round 7 (radius: 5)
[11:09:09 -298160.118125] SLOW spr round 8 (radius: 5)
[11:11:08 -298160.117746] SLOW spr round 9 (radius: 10)
[11:13:16 -298159.915801] SLOW spr round 10 (radius: 5)
[11:15:35 -298159.908021] SLOW spr round 11 (radius: 10)
[11:17:56 -298159.907022] SLOW spr round 12 (radius: 15)
[11:21:31 -298159.906825] SLOW spr round 13 (radius: 20)
[11:27:16 -298159.259161] SLOW spr round 14 (radius: 5)
[11:29:43 -298159.241823] SLOW spr round 15 (radius: 10)
[11:32:14 -298159.241428] SLOW spr round 16 (radius: 15)
[11:35:47 -298159.241101] SLOW spr round 17 (radius: 20)
[11:41:30 -298159.240837] SLOW spr round 18 (radius: 25)
[11:48:35 -298159.240631] Model parameter optimization (eps = 0.100000)

[11:48:42] ML tree search #11, logLikelihood: -298159.125208

[11:48:42 -696303.214734] Initial branch length optimization
[11:48:45 -591978.541399] Model parameter optimization (eps = 10.000000)
[11:49:04 -591168.070621] AUTODETECT spr round 1 (radius: 5)
[11:50:46 -500722.621838] AUTODETECT spr round 2 (radius: 10)
[11:52:48 -397309.753652] AUTODETECT spr round 3 (radius: 15)
[11:55:13 -345472.374586] AUTODETECT spr round 4 (radius: 20)
[11:58:00 -326864.128039] AUTODETECT spr round 5 (radius: 25)
[12:01:50 -324673.122674] SPR radius for FAST iterations: 25 (autodetect)
[12:01:50 -324673.122674] Model parameter optimization (eps = 3.000000)
[12:01:57 -324669.305229] FAST spr round 1 (radius: 25)
[12:06:03 -299321.531016] FAST spr round 2 (radius: 25)
[12:08:27 -298588.239811] FAST spr round 3 (radius: 25)
[12:10:31 -298475.575977] FAST spr round 4 (radius: 25)
[12:12:13 -298466.601948] FAST spr round 5 (radius: 25)
[12:13:49 -298462.472431] FAST spr round 6 (radius: 25)
[12:15:27 -298455.413585] FAST spr round 7 (radius: 25)
[12:16:56 -298455.413389] Model parameter optimization (eps = 1.000000)
[12:17:00 -298454.981556] SLOW spr round 1 (radius: 5)
[12:19:12 -298403.454806] SLOW spr round 2 (radius: 5)
[12:21:15 -298399.065935] SLOW spr round 3 (radius: 5)
[12:23:13 -298398.899188] SLOW spr round 4 (radius: 5)
[12:25:10 -298398.899163] SLOW spr round 5 (radius: 10)
[12:27:16 -298398.747317] SLOW spr round 6 (radius: 5)
[12:29:40 -298397.471451] SLOW spr round 7 (radius: 5)
[12:31:49 -298397.470321] SLOW spr round 8 (radius: 10)
[12:34:00 -298397.470207] SLOW spr round 9 (radius: 15)
[12:37:47 -298397.470185] SLOW spr round 10 (radius: 20)
[12:43:28 -298397.470181] SLOW spr round 11 (radius: 25)
[12:50:35 -298397.470180] Model parameter optimization (eps = 0.100000)

[12:50:38] ML tree search #12, logLikelihood: -298397.464990

[12:50:39 -692809.010758] Initial branch length optimization
[12:50:41 -587895.602012] Model parameter optimization (eps = 10.000000)
[12:51:21 -587118.386474] AUTODETECT spr round 1 (radius: 5)
[12:53:03 -498336.599284] AUTODETECT spr round 2 (radius: 10)
[12:55:00 -403106.413780] AUTODETECT spr round 3 (radius: 15)
[12:57:34 -356476.919696] AUTODETECT spr round 4 (radius: 20)
[13:00:07 -338515.407528] AUTODETECT spr round 5 (radius: 25)
[13:03:20 -332342.130128] SPR radius for FAST iterations: 25 (autodetect)
[13:03:20 -332342.130128] Model parameter optimization (eps = 3.000000)
[13:03:37 -332093.451951] FAST spr round 1 (radius: 25)
[13:07:54 -299489.043905] FAST spr round 2 (radius: 25)
[13:10:19 -298323.652383] FAST spr round 3 (radius: 25)
[13:12:20 -298282.273166] FAST spr round 4 (radius: 25)
[13:14:02 -298277.442684] FAST spr round 5 (radius: 25)
[13:15:37 -298277.141188] FAST spr round 6 (radius: 25)
[13:17:10 -298277.140879] Model parameter optimization (eps = 1.000000)
[13:17:14 -298276.563954] SLOW spr round 1 (radius: 5)
[13:19:26 -298206.326299] SLOW spr round 2 (radius: 5)
[13:21:30 -298201.625280] SLOW spr round 3 (radius: 5)
[13:23:28 -298200.639311] SLOW spr round 4 (radius: 5)
[13:25:25 -298200.637753] SLOW spr round 5 (radius: 10)
[13:27:31 -298198.692439] SLOW spr round 6 (radius: 5)
[13:29:54 -298197.409301] SLOW spr round 7 (radius: 5)
[13:32:00 -298197.404938] SLOW spr round 8 (radius: 10)
[13:34:09 -298197.404343] SLOW spr round 9 (radius: 15)
[13:37:51 -298197.404218] SLOW spr round 10 (radius: 20)
[13:43:22 -298197.404183] SLOW spr round 11 (radius: 25)
[13:50:20 -298197.404171] Model parameter optimization (eps = 0.100000)

[13:50:24] ML tree search #13, logLikelihood: -298197.395294

[13:50:24 -694860.866674] Initial branch length optimization
[13:50:26 -589686.556749] Model parameter optimization (eps = 10.000000)
[13:50:48 -588896.396439] AUTODETECT spr round 1 (radius: 5)
[13:52:31 -498049.953834] AUTODETECT spr round 2 (radius: 10)
[13:54:37 -399386.734250] AUTODETECT spr round 3 (radius: 15)
[13:57:10 -360938.314237] AUTODETECT spr round 4 (radius: 20)
[13:59:48 -335901.706029] AUTODETECT spr round 5 (radius: 25)
[14:03:08 -331791.948129] SPR radius for FAST iterations: 25 (autodetect)
[14:03:08 -331791.948129] Model parameter optimization (eps = 3.000000)
[14:03:13 -331789.185998] FAST spr round 1 (radius: 25)
[14:07:17 -299674.378422] FAST spr round 2 (radius: 25)
[14:09:51 -298499.337091] FAST spr round 3 (radius: 25)
[14:11:58 -298443.868311] FAST spr round 4 (radius: 25)
[14:13:46 -298430.802732] FAST spr round 5 (radius: 25)
[14:15:22 -298428.786272] FAST spr round 6 (radius: 25)
[14:16:53 -298428.785914] Model parameter optimization (eps = 1.000000)
[14:17:11 -298252.820383] SLOW spr round 1 (radius: 5)
[14:19:21 -298185.416682] SLOW spr round 2 (radius: 5)
[14:21:20 -298184.803717] SLOW spr round 3 (radius: 5)
[14:23:15 -298184.787306] SLOW spr round 4 (radius: 10)
[14:25:20 -298179.951118] SLOW spr round 5 (radius: 5)
[14:27:45 -298171.579690] SLOW spr round 6 (radius: 5)
[14:29:59 -298164.704928] SLOW spr round 7 (radius: 5)
[14:31:58 -298164.703940] SLOW spr round 8 (radius: 10)
[14:34:05 -298164.703808] SLOW spr round 9 (radius: 15)
[14:37:59 -298164.703736] SLOW spr round 10 (radius: 20)
[14:43:47 -298164.703688] SLOW spr round 11 (radius: 25)
[14:51:08 -298164.703653] Model parameter optimization (eps = 0.100000)

[14:51:15] ML tree search #14, logLikelihood: -298164.238085

[14:51:15 -696015.771020] Initial branch length optimization
[14:51:20 -590968.715143] Model parameter optimization (eps = 10.000000)
[14:51:46 -590154.837146] AUTODETECT spr round 1 (radius: 5)
[14:53:28 -497151.536290] AUTODETECT spr round 2 (radius: 10)
[14:55:31 -406077.655046] AUTODETECT spr round 3 (radius: 15)
[14:57:54 -362030.322711] AUTODETECT spr round 4 (radius: 20)
[15:00:29 -341729.527279] AUTODETECT spr round 5 (radius: 25)
[15:03:22 -335052.449286] SPR radius for FAST iterations: 25 (autodetect)
[15:03:22 -335052.449286] Model parameter optimization (eps = 3.000000)
[15:03:40 -334809.410371] FAST spr round 1 (radius: 25)
[15:07:41 -299806.756262] FAST spr round 2 (radius: 25)
[15:10:04 -298381.036965] FAST spr round 3 (radius: 25)
[15:12:02 -298308.279754] FAST spr round 4 (radius: 25)
[15:13:46 -298289.053263] FAST spr round 5 (radius: 25)
[15:15:22 -298285.187725] FAST spr round 6 (radius: 25)
[15:16:56 -298281.891000] FAST spr round 7 (radius: 25)
[15:18:26 -298281.719484] FAST spr round 8 (radius: 25)
[15:19:54 -298281.717441] Model parameter optimization (eps = 1.000000)
[15:20:12 -298274.528753] SLOW spr round 1 (radius: 5)
[15:22:18 -298202.916760] SLOW spr round 2 (radius: 5)
[15:24:17 -298192.551011] SLOW spr round 3 (radius: 5)
[15:26:10 -298192.550614] SLOW spr round 4 (radius: 10)
[15:28:13 -298192.409201] SLOW spr round 5 (radius: 5)
[15:30:32 -298192.402238] SLOW spr round 6 (radius: 10)
[15:32:51 -298192.401308] SLOW spr round 7 (radius: 15)
[15:36:31 -298190.286475] SLOW spr round 8 (radius: 5)
[15:38:56 -298188.396829] SLOW spr round 9 (radius: 5)
[15:41:05 -298184.599405] SLOW spr round 10 (radius: 5)
[15:43:05 -298184.544826] SLOW spr round 11 (radius: 10)
[15:45:10 -298184.544785] SLOW spr round 12 (radius: 15)
[15:48:59 -298184.544780] SLOW spr round 13 (radius: 20)
[15:54:37 -298184.544779] SLOW spr round 14 (radius: 25)
[16:01:45 -298184.544779] Model parameter optimization (eps = 0.100000)

[16:01:59] ML tree search #15, logLikelihood: -298183.694940

[16:02:00 -690253.038863] Initial branch length optimization
[16:02:03 -586735.251447] Model parameter optimization (eps = 10.000000)
[16:02:24 -585900.771605] AUTODETECT spr round 1 (radius: 5)
[16:04:05 -494901.390455] AUTODETECT spr round 2 (radius: 10)
[16:06:04 -398711.587200] AUTODETECT spr round 3 (radius: 15)
[16:08:38 -340587.846884] AUTODETECT spr round 4 (radius: 20)
[16:11:14 -325589.507908] AUTODETECT spr round 5 (radius: 25)
[16:14:46 -323990.054657] SPR radius for FAST iterations: 25 (autodetect)
[16:14:46 -323990.054657] Model parameter optimization (eps = 3.000000)
[16:15:05 -323792.569385] FAST spr round 1 (radius: 25)
[16:19:11 -299289.015732] FAST spr round 2 (radius: 25)
[16:21:38 -298521.192115] FAST spr round 3 (radius: 25)
[16:23:45 -298297.423802] FAST spr round 4 (radius: 25)
[16:25:35 -298280.657367] FAST spr round 5 (radius: 25)
[16:27:12 -298271.793172] FAST spr round 6 (radius: 25)
[16:28:44 -298258.872036] FAST spr round 7 (radius: 25)
[16:30:15 -298256.880013] FAST spr round 8 (radius: 25)
[16:31:44 -298255.092893] FAST spr round 9 (radius: 25)
[16:33:12 -298255.090711] Model parameter optimization (eps = 1.000000)
[16:33:28 -298243.834706] SLOW spr round 1 (radius: 5)
[16:35:32 -298187.923940] SLOW spr round 2 (radius: 5)
[16:37:29 -298179.545986] SLOW spr round 3 (radius: 5)
[16:39:26 -298164.450122] SLOW spr round 4 (radius: 5)
[16:41:20 -298164.449364] SLOW spr round 5 (radius: 10)
[16:43:24 -298164.449044] SLOW spr round 6 (radius: 15)
[16:47:07 -298164.448807] SLOW spr round 7 (radius: 20)
[16:52:45 -298164.448624] SLOW spr round 8 (radius: 25)
[16:59:48 -298164.448482] Model parameter optimization (eps = 0.100000)

[16:59:54] ML tree search #16, logLikelihood: -298164.333119

[16:59:54 -691666.263208] Initial branch length optimization
[16:59:57 -588802.174331] Model parameter optimization (eps = 10.000000)
[17:00:18 -587992.452951] AUTODETECT spr round 1 (radius: 5)
[17:02:00 -499840.764865] AUTODETECT spr round 2 (radius: 10)
[17:03:57 -402806.276257] AUTODETECT spr round 3 (radius: 15)
[17:06:22 -356422.642941] AUTODETECT spr round 4 (radius: 20)
[17:08:48 -335598.177993] AUTODETECT spr round 5 (radius: 25)
[17:11:53 -329777.025129] SPR radius for FAST iterations: 25 (autodetect)
[17:11:53 -329777.025129] Model parameter optimization (eps = 3.000000)
[17:12:10 -329561.111464] FAST spr round 1 (radius: 25)
[17:16:00 -299303.542641] FAST spr round 2 (radius: 25)
[17:18:18 -298356.056025] FAST spr round 3 (radius: 25)
[17:20:17 -298297.742008] FAST spr round 4 (radius: 25)
[17:22:00 -298288.697018] FAST spr round 5 (radius: 25)
[17:23:34 -298288.696186] Model parameter optimization (eps = 1.000000)
[17:23:49 -298274.241894] SLOW spr round 1 (radius: 5)
[17:25:57 -298202.026010] SLOW spr round 2 (radius: 5)
[17:28:00 -298186.087686] SLOW spr round 3 (radius: 5)
[17:29:56 -298185.840210] SLOW spr round 4 (radius: 5)
[17:31:50 -298185.840036] SLOW spr round 5 (radius: 10)
[17:33:52 -298185.840010] SLOW spr round 6 (radius: 15)
[17:37:43 -298185.721215] SLOW spr round 7 (radius: 5)
[17:40:05 -298185.525913] SLOW spr round 8 (radius: 5)
[17:42:11 -298185.501287] SLOW spr round 9 (radius: 10)
[17:44:20 -298185.500542] SLOW spr round 10 (radius: 15)
[17:48:01 -298185.499927] SLOW spr round 11 (radius: 20)
[17:53:28 -298185.499420] SLOW spr round 12 (radius: 25)
[18:00:18 -298185.499002] Model parameter optimization (eps = 0.100000)

[18:00:26] ML tree search #17, logLikelihood: -298185.385443

[18:00:26 -696222.555907] Initial branch length optimization
[18:00:28 -592477.996709] Model parameter optimization (eps = 10.000000)
[18:00:49 -591674.584018] AUTODETECT spr round 1 (radius: 5)
[18:02:31 -499040.378167] AUTODETECT spr round 2 (radius: 10)
[18:04:35 -398394.588318] AUTODETECT spr round 3 (radius: 15)
[18:07:16 -343797.075501] AUTODETECT spr round 4 (radius: 20)
[18:10:00 -330237.433533] AUTODETECT spr round 5 (radius: 25)
[18:13:50 -328730.769569] SPR radius for FAST iterations: 25 (autodetect)
[18:13:50 -328730.769569] Model parameter optimization (eps = 3.000000)
[18:14:07 -328590.210577] FAST spr round 1 (radius: 25)
[18:17:55 -299542.578725] FAST spr round 2 (radius: 25)
[18:20:22 -298336.456500] FAST spr round 3 (radius: 25)
[18:22:27 -298276.298472] FAST spr round 4 (radius: 25)
[18:24:15 -298267.594642] FAST spr round 5 (radius: 25)
[18:25:51 -298265.679833] FAST spr round 6 (radius: 25)
[18:27:24 -298265.323605] FAST spr round 7 (radius: 25)
[18:28:54 -298265.322315] Model parameter optimization (eps = 1.000000)
[18:29:10 -298245.827082] SLOW spr round 1 (radius: 5)
[18:31:17 -298181.399825] SLOW spr round 2 (radius: 5)
[18:33:15 -298180.398241] SLOW spr round 3 (radius: 5)
[18:35:09 -298180.375715] SLOW spr round 4 (radius: 10)
[18:37:13 -298179.658587] SLOW spr round 5 (radius: 5)
[18:39:33 -298179.205806] SLOW spr round 6 (radius: 5)
[18:41:38 -298179.204503] SLOW spr round 7 (radius: 10)
[18:43:52 -298179.044439] SLOW spr round 8 (radius: 5)
[18:46:12 -298178.459779] SLOW spr round 9 (radius: 5)
[18:48:16 -298178.459454] SLOW spr round 10 (radius: 10)
[18:50:24 -298178.459160] SLOW spr round 11 (radius: 15)
[18:53:59 -298178.458887] SLOW spr round 12 (radius: 20)
[18:59:08 -298178.458633] SLOW spr round 13 (radius: 25)
[19:05:19 -298178.458425] Model parameter optimization (eps = 0.100000)

[19:05:28] ML tree search #18, logLikelihood: -298178.297588

[19:05:28 -694996.620725] Initial branch length optimization
[19:05:30 -592367.234867] Model parameter optimization (eps = 10.000000)
[19:05:56 -591510.707361] AUTODETECT spr round 1 (radius: 5)
[19:07:38 -500820.882653] AUTODETECT spr round 2 (radius: 10)
[19:09:35 -408255.750521] AUTODETECT spr round 3 (radius: 15)
[19:12:17 -341848.337083] AUTODETECT spr round 4 (radius: 20)
[19:15:12 -326813.232595] AUTODETECT spr round 5 (radius: 25)
[19:19:24 -325535.780659] SPR radius for FAST iterations: 25 (autodetect)
[19:19:24 -325535.780659] Model parameter optimization (eps = 3.000000)
[19:19:43 -325371.928226] FAST spr round 1 (radius: 25)
[19:23:33 -299578.574832] FAST spr round 2 (radius: 25)
[19:26:01 -298347.542813] FAST spr round 3 (radius: 25)
[19:28:00 -298284.990380] FAST spr round 4 (radius: 25)
[19:29:41 -298273.013409] FAST spr round 5 (radius: 25)
[19:31:15 -298271.762148] FAST spr round 6 (radius: 25)
[19:32:46 -298271.761888] Model parameter optimization (eps = 1.000000)
[19:32:50 -298271.546785] SLOW spr round 1 (radius: 5)
[19:34:59 -298217.842949] SLOW spr round 2 (radius: 5)
[19:37:02 -298210.206182] SLOW spr round 3 (radius: 5)
[19:39:00 -298206.939839] SLOW spr round 4 (radius: 5)
[19:40:59 -298201.982173] SLOW spr round 5 (radius: 5)
[19:42:54 -298201.971466] SLOW spr round 6 (radius: 10)
[19:45:00 -298201.857491] SLOW spr round 7 (radius: 5)
[19:47:21 -298200.239172] SLOW spr round 8 (radius: 5)
[19:49:27 -298199.892559] SLOW spr round 9 (radius: 5)
[19:51:27 -298199.853414] SLOW spr round 10 (radius: 10)
[19:53:34 -298199.851959] SLOW spr round 11 (radius: 15)
[19:57:16 -298199.357001] SLOW spr round 12 (radius: 5)
[19:59:41 -298199.313295] SLOW spr round 13 (radius: 10)
[20:02:07 -298199.311246] SLOW spr round 14 (radius: 15)
[20:05:35 -298199.311085] SLOW spr round 15 (radius: 20)
[20:10:58 -298199.311066] SLOW spr round 16 (radius: 25)
[20:17:21 -298199.311062] Model parameter optimization (eps = 0.100000)

[20:17:35] ML tree search #19, logLikelihood: -298175.945753

[20:17:35 -697722.039164] Initial branch length optimization
[20:17:37 -590836.495780] Model parameter optimization (eps = 10.000000)
[20:17:59 -590055.404524] AUTODETECT spr round 1 (radius: 5)
[20:19:42 -504920.788493] AUTODETECT spr round 2 (radius: 10)
[20:21:43 -404552.269763] AUTODETECT spr round 3 (radius: 15)
[20:24:14 -356105.327956] AUTODETECT spr round 4 (radius: 20)
[20:26:45 -333749.593834] AUTODETECT spr round 5 (radius: 25)
[20:29:51 -329106.237350] SPR radius for FAST iterations: 25 (autodetect)
[20:29:51 -329106.237350] Model parameter optimization (eps = 3.000000)
[20:30:15 -328808.769647] FAST spr round 1 (radius: 25)
[20:34:14 -299256.713873] FAST spr round 2 (radius: 25)
[20:36:36 -298322.317820] FAST spr round 3 (radius: 25)
[20:38:36 -298264.692235] FAST spr round 4 (radius: 25)
[20:40:19 -298254.447931] FAST spr round 5 (radius: 25)
[20:41:56 -298239.005916] FAST spr round 6 (radius: 25)
[20:43:29 -298237.975546] FAST spr round 7 (radius: 25)
[20:44:59 -298237.975421] Model parameter optimization (eps = 1.000000)
[20:45:17 -298232.657157] SLOW spr round 1 (radius: 5)
[20:47:23 -298192.817771] SLOW spr round 2 (radius: 5)
[20:49:23 -298184.814060] SLOW spr round 3 (radius: 5)
[20:51:21 -298180.301769] SLOW spr round 4 (radius: 5)
[20:53:17 -298178.401239] SLOW spr round 5 (radius: 5)
[20:55:12 -298178.401194] SLOW spr round 6 (radius: 10)
[20:57:17 -298177.842373] SLOW spr round 7 (radius: 5)
[20:59:36 -298177.841021] SLOW spr round 8 (radius: 10)
[21:01:55 -298177.840746] SLOW spr round 9 (radius: 15)
[21:05:25 -298177.840665] SLOW spr round 10 (radius: 20)
[21:10:45 -298177.840633] SLOW spr round 11 (radius: 25)
[21:17:09 -298177.840618] Model parameter optimization (eps = 0.100000)

[21:17:18] ML tree search #20, logLikelihood: -298177.647297


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.196383,0.293766) (0.218014,0.356699) (0.256830,0.831056) (0.328773,1.980407) 
   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: -298152.684471

AIC score: 600315.368941 / AICc score: 8644375.368941 / BIC score: 608522.976330
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=443).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 19 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9H611/3_mltree/Q9H611.raxml.log

Analysis started: 20-Jul-2021 02:50:08 / finished: 21-Jul-2021 00:07:27

Elapsed time: 76638.442 seconds