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

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

RAxML-NG was called at 05-Jul-2021 23:19:51 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/2_msa/P07954_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/2_msa/P07954_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 454 sites

WARNING: Sequences tr_Q9W3X6_Q9W3X6_DROME_7227 and tr_B4I081_B4I081_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3G9T5_A0A2I3G9T5_NOMLE_61853 and tr_A0A2R9A8K1_A0A2R9A8K1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_B6Q2H4_B6Q2H4_TALMQ_441960 and tr_A0A093VGK3_A0A093VGK3_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3R3D3_G3R3D3_GORGO_9595 and sp_P07954_FUMH_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q7S3Z6_Q7S3Z6_NEUCR_367110 and tr_G4U936_G4U936_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B5DPI9_B5DPI9_DROPS_46245 and tr_B4GRX7_B4GRX7_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8NKG1_B8NKG1_ASPFN_332952 and tr_Q2U6Q8_Q2U6Q8_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NKG1_B8NKG1_ASPFN_332952 and tr_A0A1S9D9I7_A0A1S9D9I7_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179ULD3_A0A179ULD3_BLAGS_559298 and tr_C5GAL1_C5GAL1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A0D2XGP1_A0A0D2XGP1_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_S0E5W7_S0E5W7_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_N4TRV2_N4TRV2_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_X0CYB1_X0CYB1_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A2H3TPD6_A0A2H3TPD6_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FRB4_F9FRB4_FUSOF_660025 and tr_A0A2H3H0N6_A0A2H3H0N6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_C6HT95_C6HT95_AJECH_544712 and tr_F0UT08_F0UT08_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_I1PB46_I1PB46_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_A0A0E0D075_A0A0E0D075_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_A0A0E0NUR8_A0A0E0NUR8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GM46_A0A0E0GM46_ORYNI_4536 and tr_Q10LR5_Q10LR5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2R097_A2R097_ASPNC_425011 and tr_G3XW87_G3XW87_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R097_A2R097_ASPNC_425011 and tr_A0A318ZZ73_A0A318ZZ73_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XL65_G7XL65_ASPKW_1033177 and tr_A0A146EYW8_A0A146EYW8_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XL65_G7XL65_ASPKW_1033177 and tr_A0A317VSG9_A0A317VSG9_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F9XBL6_F9XBL6_ZYMTI_336722 and tr_A0A1X7RUS3_A0A1X7RUS3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_E3MWG9_E3MWG9_CAERE_31234 and tr_A0A261C7W2_A0A261C7W2_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_F2SDX2_F2SDX2_TRIRC_559305 and tr_A0A178EWI9_A0A178EWI9_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_M7YQ73_M7YQ73_TRIUA_4572 and tr_A0A0C4BJJ8_A0A0C4BJJ8_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_U3JHF0_U3JHF0_FICAL_59894 and tr_A0A091F0P3_A0A091F0P3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3JHF0_U3JHF0_FICAL_59894 and tr_A0A093SXW6_A0A093SXW6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3JHF0_U3JHF0_FICAL_59894 and tr_A0A218VAK2_A0A218VAK2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_U5H080_U5H080_USTV1_683840 and tr_A0A2X0MCK7_A0A2X0MCK7_9BASI_796604 are exactly identical!
WARNING: Sequences tr_W2Q158_W2Q158_PHYPN_761204 and tr_A0A0W8D095_A0A0W8D095_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q158_W2Q158_PHYPN_761204 and tr_W2IPS7_W2IPS7_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A010QVN6_A0A010QVN6_9PEZI_1445577 and tr_A0A135UKN0_A0A135UKN0_9PEZI_1209931 are exactly identical!
WARNING: Sequences tr_A0A010QVN6_A0A010QVN6_9PEZI_1445577 and tr_A0A1G4B5C7_A0A1G4B5C7_9PEZI_1209926 are exactly identical!
WARNING: Sequences tr_A0A015JFC3_A0A015JFC3_9GLOM_1432141 and tr_A0A2H5T0N7_A0A2H5T0N7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067HGD8_A0A067HGD8_CITSI_2711 and tr_V4VWH7_V4VWH7_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A078GQ98_A0A078GQ98_BRANA_3708 and tr_A0A0D3C6Q7_A0A0D3C6Q7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094GDC5_A0A094GDC5_9PEZI_1420912 and tr_A0A1B8GDP3_A0A1B8GDP3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0B4I4R3_A0A0B4I4R3_METMF_1276143 and tr_A0A0D9NPK1_A0A0D9NPK1_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A0F8X4G0_A0A0F8X4G0_9EURO_308745 and tr_A0A2T5LRI6_A0A2T5LRI6_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0L1IM95_A0A0L1IM95_ASPNO_1509407 and tr_A0A1F8A9C2_A0A1F8A9C2_9EURO_109264 are exactly identical!
WARNING: Sequences tr_A0A0V0SNM5_A0A0V0SNM5_9BILA_6336 and tr_A0A0V1DDM5_A0A0V1DDM5_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0SNM5_A0A0V0SNM5_9BILA_6336 and tr_A0A0V0VTS2_A0A0V0VTS2_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0SNM5_A0A0V0SNM5_9BILA_6336 and tr_A0A0V1AF06_A0A0V1AF06_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0SNM5_A0A0V0SNM5_9BILA_6336 and tr_A0A0V1PFF7_A0A0V1PFF7_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0SNM5_A0A0V0SNM5_9BILA_6336 and tr_A0A0V0UG90_A0A0V0UG90_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0X6T1_A0A0V0X6T1_9BILA_92179 and tr_A0A0V1LTE2_A0A0V1LTE2_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A100IQV6_A0A100IQV6_ASPNG_5061 and tr_A0A1L9MTC8_A0A1L9MTC8_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A164XJ72_A0A164XJ72_9HOMO_1314777 and tr_A0A166JDZ2_A0A166JDZ2_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3DLZ8_A0A1S3DLZ8_DIACI_121845 and tr_A0A3Q0JIY5_A0A3Q0JIY5_DIACI_121845 are exactly identical!
WARNING: Sequences tr_A0A1S3YK19_A0A1S3YK19_TOBAC_4097 and tr_A0A1U7YIG2_A0A1U7YIG2_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1V8SD28_A0A1V8SD28_9PEZI_1507870 and tr_A0A1V8T6F5_A0A1V8T6F5_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A226NFE8_A0A226NFE8_CALSU_9009 and tr_A0A226P9U8_A0A226P9U8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2K5P5A0_A0A2K5P5A0_CERAT_9531 and tr_A0A2K5YQ02_A0A2K5YQ02_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2S7NSM0_A0A2S7NSM0_9HELO_2070414 and tr_A0A2S7QT00_A0A2S7QT00_9HELO_2070412 are exactly identical!
WARNING: Duplicate sequences found: 57

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.reduced.phy

Alignment comprises 1 partitions and 454 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 454 / 454
Gaps: 0.76 %
Invariant sites: 1.32 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.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 / 65 / 5200
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -428017.378045] Initial branch length optimization
[00:00:03 -378670.738871] Model parameter optimization (eps = 10.000000)
[00:00:21 -378605.329185] AUTODETECT spr round 1 (radius: 5)
[00:02:02 -256023.782448] AUTODETECT spr round 2 (radius: 10)
[00:04:10 -187324.394298] AUTODETECT spr round 3 (radius: 15)
[00:06:09 -156135.557425] AUTODETECT spr round 4 (radius: 20)
[00:08:28 -152026.500876] AUTODETECT spr round 5 (radius: 25)
[00:11:14 -151869.993631] SPR radius for FAST iterations: 25 (autodetect)
[00:11:14 -151869.993631] Model parameter optimization (eps = 3.000000)
[00:11:32 -151693.803511] FAST spr round 1 (radius: 25)
[00:13:37 -136822.214640] FAST spr round 2 (radius: 25)
[00:15:14 -136006.959571] FAST spr round 3 (radius: 25)
[00:16:42 -135942.236061] FAST spr round 4 (radius: 25)
[00:18:03 -135935.881793] FAST spr round 5 (radius: 25)
[00:19:20 -135934.784569] FAST spr round 6 (radius: 25)
[00:20:36 -135933.366648] FAST spr round 7 (radius: 25)
[00:21:53 -135931.143494] FAST spr round 8 (radius: 25)
[00:23:08 -135931.143309] Model parameter optimization (eps = 1.000000)
[00:23:20 -135915.023742] SLOW spr round 1 (radius: 5)
[00:25:05 -135857.947301] SLOW spr round 2 (radius: 5)
[00:26:47 -135841.435951] SLOW spr round 3 (radius: 5)
[00:28:25 -135838.362849] SLOW spr round 4 (radius: 5)
[00:30:00 -135838.362847] SLOW spr round 5 (radius: 10)
[00:31:36 -135838.362847] SLOW spr round 6 (radius: 15)
[00:34:08 -135838.362847] SLOW spr round 7 (radius: 20)
[00:37:26 -135838.362847] SLOW spr round 8 (radius: 25)
[00:41:38 -135838.362847] Model parameter optimization (eps = 0.100000)

[00:41:44] ML tree search #1, logLikelihood: -135838.118843

[00:41:45 -427235.054437] Initial branch length optimization
[00:41:47 -377279.483022] Model parameter optimization (eps = 10.000000)
[00:42:06 -377215.129528] AUTODETECT spr round 1 (radius: 5)
[00:43:46 -260797.809000] AUTODETECT spr round 2 (radius: 10)
[00:45:56 -194247.908225] AUTODETECT spr round 3 (radius: 15)
[00:47:51 -159755.628562] AUTODETECT spr round 4 (radius: 20)
[00:50:07 -150717.850820] AUTODETECT spr round 5 (radius: 25)
[00:52:48 -150274.103257] SPR radius for FAST iterations: 25 (autodetect)
[00:52:48 -150274.103257] Model parameter optimization (eps = 3.000000)
[00:53:07 -150099.996419] FAST spr round 1 (radius: 25)
[00:55:08 -136441.829814] FAST spr round 2 (radius: 25)
[00:56:47 -135944.591408] FAST spr round 3 (radius: 25)
[00:58:19 -135894.556942] FAST spr round 4 (radius: 25)
[00:59:43 -135878.901063] FAST spr round 5 (radius: 25)
[01:01:00 -135877.486105] FAST spr round 6 (radius: 25)
[01:02:15 -135875.670754] FAST spr round 7 (radius: 25)
[01:03:31 -135875.670753] Model parameter optimization (eps = 1.000000)
[01:03:34 -135875.602301] SLOW spr round 1 (radius: 5)
[01:05:31 -135841.735980] SLOW spr round 2 (radius: 5)
[01:07:14 -135840.548856] SLOW spr round 3 (radius: 5)
[01:08:50 -135840.548822] SLOW spr round 4 (radius: 10)
[01:10:31 -135840.548822] SLOW spr round 5 (radius: 15)
[01:13:04 -135840.548822] SLOW spr round 6 (radius: 20)
[01:16:23 -135840.548822] SLOW spr round 7 (radius: 25)
[01:20:41 -135840.548822] Model parameter optimization (eps = 0.100000)

[01:20:55] ML tree search #2, logLikelihood: -135836.617544

[01:20:55 -426337.598384] Initial branch length optimization
[01:20:58 -377525.741962] Model parameter optimization (eps = 10.000000)
[01:21:26 -377456.016357] AUTODETECT spr round 1 (radius: 5)
[01:23:06 -262631.391801] AUTODETECT spr round 2 (radius: 10)
[01:25:18 -195041.356229] AUTODETECT spr round 3 (radius: 15)
[01:27:09 -169721.984178] AUTODETECT spr round 4 (radius: 20)
[01:29:23 -157467.202548] AUTODETECT spr round 5 (radius: 25)
[01:31:57 -154338.597032] SPR radius for FAST iterations: 25 (autodetect)
[01:31:57 -154338.597032] Model parameter optimization (eps = 3.000000)
[01:32:14 -154135.032428] FAST spr round 1 (radius: 25)
[01:34:20 -136580.379010] FAST spr round 2 (radius: 25)
[01:35:59 -135990.064733] FAST spr round 3 (radius: 25)
[01:37:30 -135894.158096] FAST spr round 4 (radius: 25)
[01:38:51 -135886.025048] FAST spr round 5 (radius: 25)
[01:40:09 -135885.236214] FAST spr round 6 (radius: 25)
[01:41:26 -135884.935025] FAST spr round 7 (radius: 25)
[01:42:43 -135884.934811] Model parameter optimization (eps = 1.000000)
[01:42:59 -135873.313709] SLOW spr round 1 (radius: 5)
[01:44:40 -135854.753653] SLOW spr round 2 (radius: 5)
[01:46:20 -135854.684729] SLOW spr round 3 (radius: 10)
[01:48:01 -135854.684721] SLOW spr round 4 (radius: 15)
[01:50:29 -135853.866540] SLOW spr round 5 (radius: 5)
[01:52:32 -135852.252570] SLOW spr round 6 (radius: 5)
[01:54:21 -135852.252493] SLOW spr round 7 (radius: 10)
[01:56:04 -135852.252493] SLOW spr round 8 (radius: 15)
[01:58:28 -135852.252493] SLOW spr round 9 (radius: 20)
[02:01:37 -135852.252493] SLOW spr round 10 (radius: 25)
[02:05:32 -135852.252493] Model parameter optimization (eps = 0.100000)

[02:05:38] ML tree search #3, logLikelihood: -135852.205532

[02:05:38 -427765.640358] Initial branch length optimization
[02:05:41 -379533.666876] Model parameter optimization (eps = 10.000000)
[02:06:00 -379453.102352] AUTODETECT spr round 1 (radius: 5)
[02:07:43 -262459.291518] AUTODETECT spr round 2 (radius: 10)
[02:09:53 -196369.480252] AUTODETECT spr round 3 (radius: 15)
[02:11:44 -162800.388472] AUTODETECT spr round 4 (radius: 20)
[02:14:00 -153882.081695] AUTODETECT spr round 5 (radius: 25)
[02:16:25 -153051.423047] SPR radius for FAST iterations: 25 (autodetect)
[02:16:25 -153051.423047] Model parameter optimization (eps = 3.000000)
[02:16:41 -152856.190261] FAST spr round 1 (radius: 25)
[02:18:52 -136668.643463] FAST spr round 2 (radius: 25)
[02:20:33 -136007.993212] FAST spr round 3 (radius: 25)
[02:22:06 -135935.929584] FAST spr round 4 (radius: 25)
[02:23:30 -135921.330778] FAST spr round 5 (radius: 25)
[02:24:47 -135921.330776] Model parameter optimization (eps = 1.000000)
[02:24:50 -135921.235992] SLOW spr round 1 (radius: 5)
[02:26:40 -135902.719418] SLOW spr round 2 (radius: 5)
[02:28:22 -135899.547279] SLOW spr round 3 (radius: 5)
[02:30:01 -135899.547236] SLOW spr round 4 (radius: 10)
[02:31:42 -135889.480380] SLOW spr round 5 (radius: 5)
[02:33:45 -135876.897432] SLOW spr round 6 (radius: 5)
[02:35:37 -135866.535587] SLOW spr round 7 (radius: 5)
[02:37:20 -135865.160596] SLOW spr round 8 (radius: 5)
[02:39:00 -135865.160589] SLOW spr round 9 (radius: 10)
[02:40:39 -135865.160589] SLOW spr round 10 (radius: 15)
[02:43:15 -135865.160589] SLOW spr round 11 (radius: 20)
[02:46:41 -135865.160589] SLOW spr round 12 (radius: 25)
[02:51:01 -135865.160589] Model parameter optimization (eps = 0.100000)

[02:51:04] ML tree search #4, logLikelihood: -135865.153221

[02:51:04 -422018.821070] Initial branch length optimization
[02:51:07 -374666.848379] Model parameter optimization (eps = 10.000000)
[02:51:24 -374582.864478] AUTODETECT spr round 1 (radius: 5)
[02:53:05 -261070.935958] AUTODETECT spr round 2 (radius: 10)
[02:55:14 -194954.253899] AUTODETECT spr round 3 (radius: 15)
[02:57:04 -164279.506658] AUTODETECT spr round 4 (radius: 20)
[02:59:17 -154593.938624] AUTODETECT spr round 5 (radius: 25)
[03:01:55 -153749.477317] SPR radius for FAST iterations: 25 (autodetect)
[03:01:55 -153749.477317] Model parameter optimization (eps = 3.000000)
[03:02:09 -153599.204707] FAST spr round 1 (radius: 25)
[03:04:16 -136492.498768] FAST spr round 2 (radius: 25)
[03:06:04 -135944.623186] FAST spr round 3 (radius: 25)
[03:07:50 -135899.910682] FAST spr round 4 (radius: 25)
[03:09:20 -135884.937610] FAST spr round 5 (radius: 25)
[03:10:39 -135880.119034] FAST spr round 6 (radius: 25)
[03:11:56 -135878.156421] FAST spr round 7 (radius: 25)
[03:13:12 -135878.156368] Model parameter optimization (eps = 1.000000)
[03:13:30 -135859.172451] SLOW spr round 1 (radius: 5)
[03:15:28 -135815.235563] SLOW spr round 2 (radius: 5)
[03:17:41 -135797.019424] SLOW spr round 3 (radius: 5)
[03:19:17 -135792.839617] SLOW spr round 4 (radius: 5)
[03:20:55 -135788.296322] SLOW spr round 5 (radius: 5)
[03:22:32 -135788.296285] SLOW spr round 6 (radius: 10)
[03:24:11 -135785.126897] SLOW spr round 7 (radius: 5)
[03:26:09 -135784.191853] SLOW spr round 8 (radius: 5)
[03:27:55 -135784.191847] SLOW spr round 9 (radius: 10)
[03:29:37 -135784.191847] SLOW spr round 10 (radius: 15)
[03:32:02 -135784.191847] SLOW spr round 11 (radius: 20)
[03:35:10 -135784.191847] SLOW spr round 12 (radius: 25)
[03:39:10 -135784.191847] Model parameter optimization (eps = 0.100000)

[03:39:18] ML tree search #5, logLikelihood: -135783.444952

[03:39:18 -428087.776698] Initial branch length optimization
[03:39:21 -378957.392209] Model parameter optimization (eps = 10.000000)
[03:39:45 -378902.739345] AUTODETECT spr round 1 (radius: 5)
[03:41:29 -257396.394981] AUTODETECT spr round 2 (radius: 10)
[03:43:34 -184910.614292] AUTODETECT spr round 3 (radius: 15)
[03:45:27 -160943.628230] AUTODETECT spr round 4 (radius: 20)
[03:47:28 -152861.538946] AUTODETECT spr round 5 (radius: 25)
[03:49:57 -151790.066227] SPR radius for FAST iterations: 25 (autodetect)
[03:49:57 -151790.066227] Model parameter optimization (eps = 3.000000)
[03:50:12 -151611.730420] FAST spr round 1 (radius: 25)
[03:52:18 -136390.161999] FAST spr round 2 (radius: 25)
[03:53:56 -135978.581568] FAST spr round 3 (radius: 25)
[03:55:26 -135932.745977] FAST spr round 4 (radius: 25)
[03:56:44 -135923.695423] FAST spr round 5 (radius: 25)
[03:58:02 -135923.694825] Model parameter optimization (eps = 1.000000)
[03:58:18 -135910.412367] SLOW spr round 1 (radius: 5)
[04:00:07 -135854.707489] SLOW spr round 2 (radius: 5)
[04:01:50 -135844.461278] SLOW spr round 3 (radius: 5)
[04:03:30 -135844.239913] SLOW spr round 4 (radius: 5)
[04:05:06 -135844.239753] SLOW spr round 5 (radius: 10)
[04:06:45 -135840.541950] SLOW spr round 6 (radius: 5)
[04:08:35 -135840.157695] SLOW spr round 7 (radius: 5)
[04:10:22 -135840.157622] SLOW spr round 8 (radius: 10)
[04:12:05 -135832.106799] SLOW spr round 9 (radius: 5)
[04:14:05 -135831.519813] SLOW spr round 10 (radius: 5)
[04:15:52 -135831.519589] SLOW spr round 11 (radius: 10)
[04:17:36 -135830.439131] SLOW spr round 12 (radius: 5)
[04:19:35 -135819.404765] SLOW spr round 13 (radius: 5)
[04:21:22 -135819.404731] SLOW spr round 14 (radius: 10)
[04:23:04 -135818.251314] SLOW spr round 15 (radius: 5)
[04:25:04 -135818.251093] SLOW spr round 16 (radius: 10)
[04:26:56 -135818.251076] SLOW spr round 17 (radius: 15)
[04:29:12 -135818.251061] SLOW spr round 18 (radius: 20)
[04:32:24 -135818.251046] SLOW spr round 19 (radius: 25)
[04:36:14 -135818.251033] Model parameter optimization (eps = 0.100000)

[04:36:23] ML tree search #6, logLikelihood: -135818.035748

[04:36:23 -423653.852409] Initial branch length optimization
[04:36:25 -375954.609337] Model parameter optimization (eps = 10.000000)
[04:36:47 -375850.004908] AUTODETECT spr round 1 (radius: 5)
[04:38:29 -260610.629946] AUTODETECT spr round 2 (radius: 10)
[04:40:37 -191459.782466] AUTODETECT spr round 3 (radius: 15)
[04:42:34 -161135.878871] AUTODETECT spr round 4 (radius: 20)
[04:44:47 -154083.857922] AUTODETECT spr round 5 (radius: 25)
[04:47:22 -153631.673283] SPR radius for FAST iterations: 25 (autodetect)
[04:47:22 -153631.673283] Model parameter optimization (eps = 3.000000)
[04:47:38 -153439.857846] FAST spr round 1 (radius: 25)
[04:49:47 -136570.409733] FAST spr round 2 (radius: 25)
[04:51:27 -135995.108066] FAST spr round 3 (radius: 25)
[04:53:01 -135928.000470] FAST spr round 4 (radius: 25)
[04:54:30 -135915.200419] FAST spr round 5 (radius: 25)
[04:55:48 -135913.584040] FAST spr round 6 (radius: 25)
[04:57:08 -135913.583897] Model parameter optimization (eps = 1.000000)
[04:57:11 -135913.542990] SLOW spr round 1 (radius: 5)
[04:59:04 -135878.688178] SLOW spr round 2 (radius: 5)
[05:00:50 -135853.985512] SLOW spr round 3 (radius: 5)
[05:02:57 -135853.985366] SLOW spr round 4 (radius: 10)
[05:04:40 -135851.502576] SLOW spr round 5 (radius: 5)
[05:06:42 -135849.900140] SLOW spr round 6 (radius: 5)
[05:08:33 -135844.489853] SLOW spr round 7 (radius: 5)
[05:10:16 -135844.489815] SLOW spr round 8 (radius: 10)
[05:11:58 -135844.093292] SLOW spr round 9 (radius: 5)
[05:14:00 -135842.222467] SLOW spr round 10 (radius: 5)
[05:15:46 -135842.222085] SLOW spr round 11 (radius: 10)
[05:17:32 -135842.222044] SLOW spr round 12 (radius: 15)
[05:20:05 -135838.870878] SLOW spr round 13 (radius: 5)
[05:22:14 -135830.111419] SLOW spr round 14 (radius: 5)
[05:24:06 -135829.838582] SLOW spr round 15 (radius: 5)
[05:25:49 -135829.838559] SLOW spr round 16 (radius: 10)
[05:27:32 -135829.838559] SLOW spr round 17 (radius: 15)
[05:30:04 -135829.838559] SLOW spr round 18 (radius: 20)
[05:33:28 -135829.838559] SLOW spr round 19 (radius: 25)
[05:37:57 -135829.838559] Model parameter optimization (eps = 0.100000)

[05:38:11] ML tree search #7, logLikelihood: -135807.066371

[05:38:11 -426522.322234] Initial branch length optimization
[05:38:14 -378483.384407] Model parameter optimization (eps = 10.000000)
[05:38:36 -378425.594248] AUTODETECT spr round 1 (radius: 5)
[05:40:16 -258729.513413] AUTODETECT spr round 2 (radius: 10)
[05:42:23 -193276.986048] AUTODETECT spr round 3 (radius: 15)
[05:44:13 -167481.365635] AUTODETECT spr round 4 (radius: 20)
[05:46:22 -156107.221151] AUTODETECT spr round 5 (radius: 25)
[05:48:38 -154303.321547] SPR radius for FAST iterations: 25 (autodetect)
[05:48:38 -154303.321547] Model parameter optimization (eps = 3.000000)
[05:48:54 -154130.293377] FAST spr round 1 (radius: 25)
[05:51:00 -136755.786766] FAST spr round 2 (radius: 25)
[05:52:40 -135969.930480] FAST spr round 3 (radius: 25)
[05:54:10 -135876.115557] FAST spr round 4 (radius: 25)
[05:55:32 -135855.292294] FAST spr round 5 (radius: 25)
[05:56:52 -135850.752129] FAST spr round 6 (radius: 25)
[05:58:10 -135850.751748] Model parameter optimization (eps = 1.000000)
[05:58:25 -135833.595774] SLOW spr round 1 (radius: 5)
[06:00:10 -135793.329833] SLOW spr round 2 (radius: 5)
[06:01:51 -135784.797940] SLOW spr round 3 (radius: 5)
[06:03:27 -135784.797720] SLOW spr round 4 (radius: 10)
[06:05:06 -135784.797717] SLOW spr round 5 (radius: 15)
[06:07:35 -135784.797717] SLOW spr round 6 (radius: 20)
[06:10:44 -135784.797717] SLOW spr round 7 (radius: 25)
[06:14:50 -135784.797717] Model parameter optimization (eps = 0.100000)

[06:14:55] ML tree search #8, logLikelihood: -135784.709629

[06:14:55 -424357.839894] Initial branch length optimization
[06:14:58 -375043.415654] Model parameter optimization (eps = 10.000000)
[06:15:20 -374966.597489] AUTODETECT spr round 1 (radius: 5)
[06:16:59 -258881.735173] AUTODETECT spr round 2 (radius: 10)
[06:19:07 -193632.810281] AUTODETECT spr round 3 (radius: 15)
[06:21:01 -161494.193603] AUTODETECT spr round 4 (radius: 20)
[06:23:08 -154770.628480] AUTODETECT spr round 5 (radius: 25)
[06:25:38 -153378.988515] SPR radius for FAST iterations: 25 (autodetect)
[06:25:38 -153378.988515] Model parameter optimization (eps = 3.000000)
[06:26:01 -153189.641492] FAST spr round 1 (radius: 25)
[06:28:06 -136622.429866] FAST spr round 2 (radius: 25)
[06:29:42 -135931.882400] FAST spr round 3 (radius: 25)
[06:31:12 -135873.312996] FAST spr round 4 (radius: 25)
[06:32:32 -135863.460816] FAST spr round 5 (radius: 25)
[06:33:50 -135858.516018] FAST spr round 6 (radius: 25)
[06:35:04 -135858.516006] Model parameter optimization (eps = 1.000000)
[06:35:18 -135844.415971] SLOW spr round 1 (radius: 5)
[06:37:05 -135808.340361] SLOW spr round 2 (radius: 5)
[06:38:46 -135800.933924] SLOW spr round 3 (radius: 5)
[06:40:25 -135800.695162] SLOW spr round 4 (radius: 5)
[06:42:00 -135800.695153] SLOW spr round 5 (radius: 10)
[06:43:37 -135799.336845] SLOW spr round 6 (radius: 5)
[06:45:37 -135798.713743] SLOW spr round 7 (radius: 5)
[06:47:23 -135798.713735] SLOW spr round 8 (radius: 10)
[06:49:06 -135798.713735] SLOW spr round 9 (radius: 15)
[06:51:28 -135798.713735] SLOW spr round 10 (radius: 20)
[06:54:37 -135798.713735] SLOW spr round 11 (radius: 25)
[06:58:28 -135798.713735] Model parameter optimization (eps = 0.100000)

[06:58:35] ML tree search #9, logLikelihood: -135798.471615

[06:58:35 -427283.532959] Initial branch length optimization
[06:58:38 -378215.397286] Model parameter optimization (eps = 10.000000)
[06:58:59 -378100.264864] AUTODETECT spr round 1 (radius: 5)
[07:00:38 -259079.644389] AUTODETECT spr round 2 (radius: 10)
[07:02:39 -191058.222630] AUTODETECT spr round 3 (radius: 15)
[07:04:30 -160687.951671] AUTODETECT spr round 4 (radius: 20)
[07:06:36 -153441.062037] AUTODETECT spr round 5 (radius: 25)
[07:09:11 -152540.080454] SPR radius for FAST iterations: 25 (autodetect)
[07:09:11 -152540.080454] Model parameter optimization (eps = 3.000000)
[07:09:32 -152327.241417] FAST spr round 1 (radius: 25)
[07:11:36 -136682.591486] FAST spr round 2 (radius: 25)
[07:13:15 -135954.070650] FAST spr round 3 (radius: 25)
[07:14:44 -135871.597047] FAST spr round 4 (radius: 25)
[07:16:07 -135852.152131] FAST spr round 5 (radius: 25)
[07:17:22 -135852.152127] Model parameter optimization (eps = 1.000000)
[07:17:32 -135849.156082] SLOW spr round 1 (radius: 5)
[07:19:19 -135825.199529] SLOW spr round 2 (radius: 5)
[07:20:59 -135822.233506] SLOW spr round 3 (radius: 5)
[07:22:35 -135822.233374] SLOW spr round 4 (radius: 10)
[07:24:13 -135821.614713] SLOW spr round 5 (radius: 5)
[07:26:08 -135821.614707] SLOW spr round 6 (radius: 10)
[07:27:57 -135821.054909] SLOW spr round 7 (radius: 5)
[07:29:51 -135819.648712] SLOW spr round 8 (radius: 5)
[07:31:35 -135819.648551] SLOW spr round 9 (radius: 10)
[07:33:14 -135819.648550] SLOW spr round 10 (radius: 15)
[07:35:38 -135819.648550] SLOW spr round 11 (radius: 20)
[07:38:55 -135819.648550] SLOW spr round 12 (radius: 25)
[07:43:07 -135819.648550] Model parameter optimization (eps = 0.100000)

[07:43:11] ML tree search #10, logLikelihood: -135819.607759

[07:43:11 -425942.042630] Initial branch length optimization
[07:43:14 -376005.164388] Model parameter optimization (eps = 10.000000)
[07:43:35 -375913.280465] AUTODETECT spr round 1 (radius: 5)
[07:45:12 -257224.457780] AUTODETECT spr round 2 (radius: 10)
[07:47:16 -196295.344880] AUTODETECT spr round 3 (radius: 15)
[07:49:06 -180535.161323] AUTODETECT spr round 4 (radius: 20)
[07:51:13 -170020.720563] AUTODETECT spr round 5 (radius: 25)
[07:54:04 -161448.772716] SPR radius for FAST iterations: 25 (autodetect)
[07:54:04 -161448.772716] Model parameter optimization (eps = 3.000000)
[07:54:18 -161240.702081] FAST spr round 1 (radius: 25)
[07:56:27 -137165.146252] FAST spr round 2 (radius: 25)
[07:58:08 -135999.534767] FAST spr round 3 (radius: 25)
[07:59:33 -135927.333626] FAST spr round 4 (radius: 25)
[08:00:53 -135919.147904] FAST spr round 5 (radius: 25)
[08:02:09 -135916.436491] FAST spr round 6 (radius: 25)
[08:03:23 -135916.436480] Model parameter optimization (eps = 1.000000)
[08:03:40 -135870.222244] SLOW spr round 1 (radius: 5)
[08:05:28 -135826.003464] SLOW spr round 2 (radius: 5)
[08:07:08 -135815.326224] SLOW spr round 3 (radius: 5)
[08:08:45 -135806.778822] SLOW spr round 4 (radius: 5)
[08:10:18 -135806.778764] SLOW spr round 5 (radius: 10)
[08:11:34 -135805.740233] SLOW spr round 6 (radius: 5)
[08:13:06 -135800.751251] SLOW spr round 7 (radius: 5)
[08:14:28 -135800.751232] SLOW spr round 8 (radius: 10)
[08:15:46 -135800.751232] SLOW spr round 9 (radius: 15)
[08:17:37 -135800.751232] SLOW spr round 10 (radius: 20)
[08:20:04 -135800.751232] SLOW spr round 11 (radius: 25)
[08:23:07 -135800.751232] Model parameter optimization (eps = 0.100000)

[08:23:15] ML tree search #11, logLikelihood: -135800.119025

[08:23:15 -426768.208423] Initial branch length optimization
[08:23:17 -378592.011081] Model parameter optimization (eps = 10.000000)
[08:23:34 -378449.271080] AUTODETECT spr round 1 (radius: 5)
[08:24:50 -257046.113139] AUTODETECT spr round 2 (radius: 10)
[08:26:25 -194433.632272] AUTODETECT spr round 3 (radius: 15)
[08:27:53 -162447.827882] AUTODETECT spr round 4 (radius: 20)
[08:29:33 -156685.167978] AUTODETECT spr round 5 (radius: 25)
[08:31:30 -152234.918529] SPR radius for FAST iterations: 25 (autodetect)
[08:31:30 -152234.918529] Model parameter optimization (eps = 3.000000)
[08:31:41 -152026.603284] FAST spr round 1 (radius: 25)
[08:33:16 -136591.883395] FAST spr round 2 (radius: 25)
[08:34:33 -135956.255518] FAST spr round 3 (radius: 25)
[08:35:40 -135913.208585] FAST spr round 4 (radius: 25)
[08:36:41 -135908.432990] FAST spr round 5 (radius: 25)
[08:37:41 -135908.432976] Model parameter optimization (eps = 1.000000)
[08:37:50 -135903.989441] SLOW spr round 1 (radius: 5)
[08:39:13 -135856.950664] SLOW spr round 2 (radius: 5)
[08:40:33 -135838.746417] SLOW spr round 3 (radius: 5)
[08:41:50 -135836.557145] SLOW spr round 4 (radius: 5)
[08:43:07 -135833.998539] SLOW spr round 5 (radius: 5)
[08:44:21 -135833.998535] SLOW spr round 6 (radius: 10)
[08:45:37 -135827.557173] SLOW spr round 7 (radius: 5)
[08:47:11 -135823.039800] SLOW spr round 8 (radius: 5)
[08:48:33 -135823.039714] SLOW spr round 9 (radius: 10)
[08:49:51 -135821.575936] SLOW spr round 10 (radius: 5)
[08:51:21 -135821.575792] SLOW spr round 11 (radius: 10)
[08:52:43 -135821.301883] SLOW spr round 12 (radius: 5)
[08:54:13 -135817.439257] SLOW spr round 13 (radius: 5)
[08:55:35 -135815.321889] SLOW spr round 14 (radius: 5)
[08:56:52 -135815.276773] SLOW spr round 15 (radius: 10)
[08:58:08 -135815.276763] SLOW spr round 16 (radius: 15)
[09:00:01 -135815.276763] SLOW spr round 17 (radius: 20)
[09:02:30 -135815.276763] SLOW spr round 18 (radius: 25)
[09:05:36 -135815.276763] Model parameter optimization (eps = 0.100000)

[09:05:44] ML tree search #12, logLikelihood: -135814.635220

[09:05:44 -425178.447610] Initial branch length optimization
[09:05:47 -376049.614336] Model parameter optimization (eps = 10.000000)
[09:06:03 -375985.226304] AUTODETECT spr round 1 (radius: 5)
[09:07:21 -255647.693855] AUTODETECT spr round 2 (radius: 10)
[09:09:03 -183758.976150] AUTODETECT spr round 3 (radius: 15)
[09:10:30 -156047.344040] AUTODETECT spr round 4 (radius: 20)
[09:12:10 -151634.376263] AUTODETECT spr round 5 (radius: 25)
[09:14:06 -151559.649537] SPR radius for FAST iterations: 25 (autodetect)
[09:14:06 -151559.649537] Model parameter optimization (eps = 3.000000)
[09:14:18 -151391.297200] FAST spr round 1 (radius: 25)
[09:15:51 -136565.023689] FAST spr round 2 (radius: 25)
[09:17:06 -135954.574532] FAST spr round 3 (radius: 25)
[09:18:17 -135911.992866] FAST spr round 4 (radius: 25)
[09:19:20 -135908.029497] FAST spr round 5 (radius: 25)
[09:20:33 -135901.732214] FAST spr round 6 (radius: 25)
[09:21:44 -135901.731827] Model parameter optimization (eps = 1.000000)
[09:21:57 -135885.761333] SLOW spr round 1 (radius: 5)
[09:23:38 -135846.892333] SLOW spr round 2 (radius: 5)
[09:25:14 -135830.170858] SLOW spr round 3 (radius: 5)
[09:26:46 -135823.373550] SLOW spr round 4 (radius: 5)
[09:28:15 -135823.373549] SLOW spr round 5 (radius: 10)
[09:29:48 -135818.843155] SLOW spr round 6 (radius: 5)
[09:31:38 -135818.842171] SLOW spr round 7 (radius: 10)
[09:33:19 -135818.751216] SLOW spr round 8 (radius: 15)
[09:35:06 -135810.099567] SLOW spr round 9 (radius: 5)
[09:36:44 -135795.128360] SLOW spr round 10 (radius: 5)
[09:38:09 -135792.047720] SLOW spr round 11 (radius: 5)
[09:39:27 -135792.047634] SLOW spr round 12 (radius: 10)
[09:40:45 -135791.981356] SLOW spr round 13 (radius: 15)
[09:42:40 -135791.698268] SLOW spr round 14 (radius: 5)
[09:44:16 -135787.813132] SLOW spr round 15 (radius: 5)
[09:45:39 -135787.813129] SLOW spr round 16 (radius: 10)
[09:46:59 -135785.772985] SLOW spr round 17 (radius: 5)
[09:48:29 -135785.772981] SLOW spr round 18 (radius: 10)
[09:49:53 -135785.772981] SLOW spr round 19 (radius: 15)
[09:51:42 -135785.772981] SLOW spr round 20 (radius: 20)
[09:54:19 -135785.772981] SLOW spr round 21 (radius: 25)
[09:57:30 -135785.772981] Model parameter optimization (eps = 0.100000)

[09:57:36] ML tree search #13, logLikelihood: -135785.058430

[09:57:36 -425172.568185] Initial branch length optimization
[09:57:39 -376601.891753] Model parameter optimization (eps = 10.000000)
[09:57:57 -376501.394487] AUTODETECT spr round 1 (radius: 5)
[09:59:15 -257739.397690] AUTODETECT spr round 2 (radius: 10)
[10:00:54 -187894.051367] AUTODETECT spr round 3 (radius: 15)
[10:02:21 -167770.264361] AUTODETECT spr round 4 (radius: 20)
[10:04:10 -154496.590460] AUTODETECT spr round 5 (radius: 25)
[10:06:17 -153861.081662] SPR radius for FAST iterations: 25 (autodetect)
[10:06:17 -153861.081662] Model parameter optimization (eps = 3.000000)
[10:06:31 -153660.685836] FAST spr round 1 (radius: 25)
[10:08:10 -136454.049341] FAST spr round 2 (radius: 25)
[10:09:28 -135964.023508] FAST spr round 3 (radius: 25)
[10:10:38 -135939.307201] FAST spr round 4 (radius: 25)
[10:11:44 -135918.901337] FAST spr round 5 (radius: 25)
[10:12:43 -135914.274643] FAST spr round 6 (radius: 25)
[10:13:42 -135914.274640] Model parameter optimization (eps = 1.000000)
[10:13:53 -135911.992449] SLOW spr round 1 (radius: 5)
[10:15:17 -135850.870091] SLOW spr round 2 (radius: 5)
[10:16:36 -135823.889755] SLOW spr round 3 (radius: 5)
[10:17:52 -135820.894206] SLOW spr round 4 (radius: 5)
[10:19:06 -135820.893544] SLOW spr round 5 (radius: 10)
[10:20:22 -135817.291160] SLOW spr round 6 (radius: 5)
[10:21:54 -135813.780021] SLOW spr round 7 (radius: 5)
[10:23:16 -135813.779956] SLOW spr round 8 (radius: 10)
[10:24:34 -135813.779955] SLOW spr round 9 (radius: 15)
[10:26:58 -135813.779955] SLOW spr round 10 (radius: 20)
[10:30:18 -135813.779955] SLOW spr round 11 (radius: 25)
[10:34:33 -135813.779955] Model parameter optimization (eps = 0.100000)

[10:34:42] ML tree search #14, logLikelihood: -135813.697184

[10:34:42 -428015.489733] Initial branch length optimization
[10:34:45 -379268.323165] Model parameter optimization (eps = 10.000000)
[10:35:06 -379190.636590] AUTODETECT spr round 1 (radius: 5)
[10:36:51 -259859.873701] AUTODETECT spr round 2 (radius: 10)
[10:39:00 -200275.664146] AUTODETECT spr round 3 (radius: 15)
[10:41:01 -165454.747057] AUTODETECT spr round 4 (radius: 20)
[10:43:18 -159063.731716] AUTODETECT spr round 5 (radius: 25)
[10:45:50 -158715.088824] SPR radius for FAST iterations: 25 (autodetect)
[10:45:50 -158715.088824] Model parameter optimization (eps = 3.000000)
[10:46:05 -158523.032466] FAST spr round 1 (radius: 25)
[10:48:19 -136998.839992] FAST spr round 2 (radius: 25)
[10:50:01 -135946.397143] FAST spr round 3 (radius: 25)
[10:51:33 -135910.143654] FAST spr round 4 (radius: 25)
[10:52:55 -135905.529295] FAST spr round 5 (radius: 25)
[10:54:15 -135903.552941] FAST spr round 6 (radius: 25)
[10:55:34 -135903.552250] Model parameter optimization (eps = 1.000000)
[10:55:48 -135877.486040] SLOW spr round 1 (radius: 5)
[10:57:42 -135820.458521] SLOW spr round 2 (radius: 5)
[10:59:30 -135810.605081] SLOW spr round 3 (radius: 5)
[11:01:13 -135810.385125] SLOW spr round 4 (radius: 5)
[11:02:55 -135810.385094] SLOW spr round 5 (radius: 10)
[11:04:41 -135809.238998] SLOW spr round 6 (radius: 5)
[11:06:49 -135807.237489] SLOW spr round 7 (radius: 5)
[11:08:36 -135807.237429] SLOW spr round 8 (radius: 10)
[11:10:17 -135807.223833] SLOW spr round 9 (radius: 15)
[11:12:35 -135806.752186] SLOW spr round 10 (radius: 5)
[11:14:46 -135805.230978] SLOW spr round 11 (radius: 5)
[11:16:26 -135805.230825] SLOW spr round 12 (radius: 10)
[11:18:08 -135805.090993] SLOW spr round 13 (radius: 5)
[11:20:01 -135805.090964] SLOW spr round 14 (radius: 10)
[11:21:36 -135805.090964] SLOW spr round 15 (radius: 15)
[11:23:51 -135805.090964] SLOW spr round 16 (radius: 20)
[11:27:09 -135805.090964] SLOW spr round 17 (radius: 25)
[11:31:03 -135805.090964] Model parameter optimization (eps = 0.100000)

[11:31:10] ML tree search #15, logLikelihood: -135804.682249

[11:31:11 -426807.640162] Initial branch length optimization
[11:31:13 -377887.941674] Model parameter optimization (eps = 10.000000)
[11:31:34 -377769.458399] AUTODETECT spr round 1 (radius: 5)
[11:33:10 -260495.608857] AUTODETECT spr round 2 (radius: 10)
[11:35:08 -192348.919229] AUTODETECT spr round 3 (radius: 15)
[11:37:00 -160505.552444] AUTODETECT spr round 4 (radius: 20)
[11:39:14 -152279.973271] AUTODETECT spr round 5 (radius: 25)
[11:41:34 -151436.181214] SPR radius for FAST iterations: 25 (autodetect)
[11:41:34 -151436.181214] Model parameter optimization (eps = 3.000000)
[11:41:50 -151281.825338] FAST spr round 1 (radius: 25)
[11:43:49 -136794.868011] FAST spr round 2 (radius: 25)
[11:45:26 -136004.114933] FAST spr round 3 (radius: 25)
[11:46:48 -135948.140119] FAST spr round 4 (radius: 25)
[11:47:58 -135928.124239] FAST spr round 5 (radius: 25)
[11:49:16 -135914.212541] FAST spr round 6 (radius: 25)
[11:50:32 -135911.110675] FAST spr round 7 (radius: 25)
[11:51:45 -135911.110600] Model parameter optimization (eps = 1.000000)
[11:51:58 -135898.364556] SLOW spr round 1 (radius: 5)
[11:53:48 -135873.011986] SLOW spr round 2 (radius: 5)
[11:55:27 -135872.043063] SLOW spr round 3 (radius: 5)
[11:57:03 -135872.043029] SLOW spr round 4 (radius: 10)
[11:58:43 -135866.528828] SLOW spr round 5 (radius: 5)
[12:00:45 -135862.281434] SLOW spr round 6 (radius: 5)
[12:02:31 -135859.526150] SLOW spr round 7 (radius: 5)
[12:04:13 -135856.645103] SLOW spr round 8 (radius: 5)
[12:05:50 -135856.645063] SLOW spr round 9 (radius: 10)
[12:07:31 -135855.250300] SLOW spr round 10 (radius: 5)
[12:09:30 -135850.217992] SLOW spr round 11 (radius: 5)
[12:11:16 -135850.010706] SLOW spr round 12 (radius: 5)
[12:12:56 -135850.010133] SLOW spr round 13 (radius: 10)
[12:14:37 -135850.010132] SLOW spr round 14 (radius: 15)
[12:17:07 -135850.010132] SLOW spr round 15 (radius: 20)
[12:20:14 -135850.010132] SLOW spr round 16 (radius: 25)
[12:24:06 -135850.010132] Model parameter optimization (eps = 0.100000)

[12:24:13] ML tree search #16, logLikelihood: -135848.955004

[12:24:14 -425427.803436] Initial branch length optimization
[12:24:16 -377620.919731] Model parameter optimization (eps = 10.000000)
[12:24:36 -377538.840660] AUTODETECT spr round 1 (radius: 5)
[12:26:18 -254585.494825] AUTODETECT spr round 2 (radius: 10)
[12:28:29 -187203.379082] AUTODETECT spr round 3 (radius: 15)
[12:30:18 -156879.591415] AUTODETECT spr round 4 (radius: 20)
[12:32:32 -153085.806181] AUTODETECT spr round 5 (radius: 25)
[12:34:56 -152681.327030] SPR radius for FAST iterations: 25 (autodetect)
[12:34:56 -152681.327030] Model parameter optimization (eps = 3.000000)
[12:35:11 -152484.096063] FAST spr round 1 (radius: 25)
[12:37:14 -136690.948913] FAST spr round 2 (radius: 25)
[12:38:53 -135981.358165] FAST spr round 3 (radius: 25)
[12:40:23 -135871.483824] FAST spr round 4 (radius: 25)
[12:41:46 -135849.974701] FAST spr round 5 (radius: 25)
[12:43:02 -135844.585309] FAST spr round 6 (radius: 25)
[12:44:17 -135844.585115] Model parameter optimization (eps = 1.000000)
[12:44:21 -135844.171419] SLOW spr round 1 (radius: 5)
[12:46:09 -135823.886165] SLOW spr round 2 (radius: 5)
[12:47:50 -135817.655686] SLOW spr round 3 (radius: 5)
[12:49:29 -135812.442151] SLOW spr round 4 (radius: 5)
[12:51:06 -135812.441539] SLOW spr round 5 (radius: 10)
[12:52:45 -135812.441522] SLOW spr round 6 (radius: 15)
[12:55:19 -135812.441522] SLOW spr round 7 (radius: 20)
[12:58:41 -135812.441522] SLOW spr round 8 (radius: 25)
[13:02:54 -135812.441522] Model parameter optimization (eps = 0.100000)

[13:03:07] ML tree search #17, logLikelihood: -135800.149024

[13:03:07 -427308.132695] Initial branch length optimization
[13:03:09 -378182.021104] Model parameter optimization (eps = 10.000000)
[13:03:31 -378122.257634] AUTODETECT spr round 1 (radius: 5)
[13:05:10 -258215.472431] AUTODETECT spr round 2 (radius: 10)
[13:07:17 -197079.219843] AUTODETECT spr round 3 (radius: 15)
[13:09:09 -163930.249295] AUTODETECT spr round 4 (radius: 20)
[13:11:26 -155901.200277] AUTODETECT spr round 5 (radius: 25)
[13:14:24 -154397.511884] SPR radius for FAST iterations: 25 (autodetect)
[13:14:24 -154397.511884] Model parameter optimization (eps = 3.000000)
[13:14:40 -154204.069383] FAST spr round 1 (radius: 25)
[13:16:40 -136702.791923] FAST spr round 2 (radius: 25)
[13:18:18 -136005.119008] FAST spr round 3 (radius: 25)
[13:19:50 -135929.287414] FAST spr round 4 (radius: 25)
[13:21:10 -135919.617081] FAST spr round 5 (radius: 25)
[13:22:27 -135918.191641] FAST spr round 6 (radius: 25)
[13:23:44 -135914.192302] FAST spr round 7 (radius: 25)
[13:24:58 -135914.192245] Model parameter optimization (eps = 1.000000)
[13:25:09 -135907.690328] SLOW spr round 1 (radius: 5)
[13:26:58 -135833.054804] SLOW spr round 2 (radius: 5)
[13:28:40 -135816.510295] SLOW spr round 3 (radius: 5)
[13:30:17 -135815.295473] SLOW spr round 4 (radius: 5)
[13:31:52 -135815.295395] SLOW spr round 5 (radius: 10)
[13:33:28 -135813.705952] SLOW spr round 6 (radius: 5)
[13:35:27 -135813.705935] SLOW spr round 7 (radius: 10)
[13:37:17 -135812.395513] SLOW spr round 8 (radius: 5)
[13:39:13 -135812.395511] SLOW spr round 9 (radius: 10)
[13:40:57 -135811.427186] SLOW spr round 10 (radius: 5)
[13:42:53 -135811.427183] SLOW spr round 11 (radius: 10)
[13:44:39 -135810.748237] SLOW spr round 12 (radius: 5)
[13:46:39 -135803.530815] SLOW spr round 13 (radius: 5)
[13:48:26 -135800.838280] SLOW spr round 14 (radius: 5)
[13:50:05 -135800.837633] SLOW spr round 15 (radius: 10)
[13:51:42 -135800.837601] SLOW spr round 16 (radius: 15)
[13:54:11 -135800.837599] SLOW spr round 17 (radius: 20)
[13:57:20 -135800.837599] SLOW spr round 18 (radius: 25)
[14:01:22 -135800.837599] Model parameter optimization (eps = 0.100000)

[14:01:31] ML tree search #18, logLikelihood: -135800.301083

[14:01:31 -427222.134892] Initial branch length optimization
[14:01:35 -378813.567132] Model parameter optimization (eps = 10.000000)
[14:01:57 -378747.204070] AUTODETECT spr round 1 (radius: 5)
[14:03:37 -257200.985069] AUTODETECT spr round 2 (radius: 10)
[14:05:45 -194951.001912] AUTODETECT spr round 3 (radius: 15)
[14:07:36 -162701.870440] AUTODETECT spr round 4 (radius: 20)
[14:09:44 -153373.641084] AUTODETECT spr round 5 (radius: 25)
[14:12:23 -153216.274342] SPR radius for FAST iterations: 25 (autodetect)
[14:12:23 -153216.274342] Model parameter optimization (eps = 3.000000)
[14:12:40 -153047.032886] FAST spr round 1 (radius: 25)
[14:14:42 -136516.089571] FAST spr round 2 (radius: 25)
[14:16:19 -135913.440484] FAST spr round 3 (radius: 25)
[14:17:44 -135874.767313] FAST spr round 4 (radius: 25)
[14:19:03 -135868.089231] FAST spr round 5 (radius: 25)
[14:20:21 -135863.670332] FAST spr round 6 (radius: 25)
[14:21:36 -135861.808348] FAST spr round 7 (radius: 25)
[14:22:49 -135861.808267] Model parameter optimization (eps = 1.000000)
[14:23:03 -135855.478216] SLOW spr round 1 (radius: 5)
[14:24:46 -135807.574634] SLOW spr round 2 (radius: 5)
[14:26:26 -135801.216158] SLOW spr round 3 (radius: 5)
[14:28:03 -135797.931432] SLOW spr round 4 (radius: 5)
[14:29:37 -135797.931429] SLOW spr round 5 (radius: 10)
[14:31:12 -135797.931429] SLOW spr round 6 (radius: 15)
[14:33:37 -135797.931429] SLOW spr round 7 (radius: 20)
[14:36:49 -135797.931429] SLOW spr round 8 (radius: 25)
[14:40:56 -135797.931429] Model parameter optimization (eps = 0.100000)

[14:41:01] ML tree search #19, logLikelihood: -135797.850899

[14:41:01 -425374.795036] Initial branch length optimization
[14:41:03 -376690.746740] Model parameter optimization (eps = 10.000000)
[14:41:23 -376633.262301] AUTODETECT spr round 1 (radius: 5)
[14:43:03 -257228.316016] AUTODETECT spr round 2 (radius: 10)
[14:45:11 -182812.222504] AUTODETECT spr round 3 (radius: 15)
[14:46:59 -159678.266145] AUTODETECT spr round 4 (radius: 20)
[14:49:08 -152463.407336] AUTODETECT spr round 5 (radius: 25)
[14:51:47 -150670.879387] SPR radius for FAST iterations: 25 (autodetect)
[14:51:47 -150670.879387] Model parameter optimization (eps = 3.000000)
[14:52:05 -150491.901318] FAST spr round 1 (radius: 25)
[14:54:08 -136471.931051] FAST spr round 2 (radius: 25)
[14:55:46 -135941.772362] FAST spr round 3 (radius: 25)
[14:57:14 -135889.490475] FAST spr round 4 (radius: 25)
[14:58:32 -135874.426247] FAST spr round 5 (radius: 25)
[14:59:50 -135869.945038] FAST spr round 6 (radius: 25)
[15:01:05 -135869.945005] Model parameter optimization (eps = 1.000000)
[15:01:19 -135857.199987] SLOW spr round 1 (radius: 5)
[15:03:03 -135835.365759] SLOW spr round 2 (radius: 5)
[15:04:43 -135815.838199] SLOW spr round 3 (radius: 5)
[15:06:18 -135814.965671] SLOW spr round 4 (radius: 5)
[15:07:52 -135814.965667] SLOW spr round 5 (radius: 10)
[15:09:27 -135810.393202] SLOW spr round 6 (radius: 5)
[15:11:25 -135809.624294] SLOW spr round 7 (radius: 5)
[15:13:09 -135809.624292] SLOW spr round 8 (radius: 10)
[15:14:48 -135809.624292] SLOW spr round 9 (radius: 15)
[15:17:11 -135809.624292] SLOW spr round 10 (radius: 20)
[15:20:20 -135809.624292] SLOW spr round 11 (radius: 25)
[15:24:14 -135809.624292] Model parameter optimization (eps = 0.100000)

[15:24:20] ML tree search #20, logLikelihood: -135809.503864


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.369419,0.313651) (0.289877,0.674364) (0.201243,1.175375) (0.139462,3.241849) 
   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: -135783.444952

AIC score: 275576.889903 / AICc score: 8319636.889903 / BIC score: 283833.674785
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=454).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 75 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P07954/3_mltree/P07954.raxml.log

Analysis started: 05-Jul-2021 23:19:51 / finished: 06-Jul-2021 14:44:12

Elapsed time: 55461.053 seconds

Consumed energy: 5133.618 Wh (= 26 km in an electric car, or 128 km with an e-scooter!)