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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM

RAxML-NG was called at 26-Jul-2021 05:25:32 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/2_msa/A6NKN8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8 --seed 2 --threads 1 --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), NONE/sequential

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/2_msa/A6NKN8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 156 taxa and 53 sites

WARNING: Sequences tr_F1N9D3_F1N9D3_CHICK_9031 and tr_A0A287CTQ0_A0A287CTQ0_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_F1N9D3_F1N9D3_CHICK_9031 and tr_A0A286XUW8_A0A286XUW8_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_F1N9D3_F1N9D3_CHICK_9031 and tr_A0A2I2V204_A0A2I2V204_FELCA_9685 are exactly identical!
WARNING: Sequences tr_F1N9D3_F1N9D3_CHICK_9031 and tr_A0A226PJ48_A0A226PJ48_COLVI_9014 are exactly identical!
WARNING: Sequences sp_P63054_PCP4_MOUSE_10090 and sp_P63055_PCP4_RAT_10116 are exactly identical!
WARNING: Sequences sp_P63054_PCP4_MOUSE_10090 and tr_A0A1U7QSJ8_A0A1U7QSJ8_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q6W8Q3_PC4L1_MOUSE_10090 and tr_G3HTZ0_G3HTZ0_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q6W8Q3_PC4L1_MOUSE_10090 and tr_A0A0G2KBA5_A0A0G2KBA5_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q6W8Q3_PC4L1_MOUSE_10090 and tr_A0A1U8CR67_A0A1U8CR67_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G1RRW7_G1RRW7_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G1PPL2_G1PPL2_MYOLU_59463 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G3R093_G3R093_GORGO_9595 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H2P365_H2P365_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_J9PBP8_J9PBP8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H2QL15_H2QL15_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_F6SRG1_F6SRG1_HORSE_9796 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and sp_P48539_PCP4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H9EPH8_H9EPH8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A286ZI58_A0A286ZI58_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G1LIJ2_G1LIJ2_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G7P0Z1_G7P0Z1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A096NJ12_A0A096NJ12_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A0D9R7H4_A0A0D9R7H4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A1S3WS82_A0A1S3WS82_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A1U7U993_A0A1U7U993_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K5NWH4_A0A2K5NWH4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K6DYS2_A0A2K6DYS2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K5YGP8_A0A2K5YGP8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2R9C7L1_A0A2R9C7L1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3V1E5_A0A2U3V1E5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3WQC6_A0A2U3WQC6_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3YMS5_A0A2U3YMS5_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2Y9LG75_A0A2Y9LG75_DELLE_9749 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2Y9SBI3_A0A2Y9SBI3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A384CZD1_A0A384CZD1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_H2N508_H2N508_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_H9FYP4_H9FYP4_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_A0A2I3MX63_A0A2I3MX63_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_A0A0D9S3C8_A0A0D9S3C8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_A0A2K5Z886_A0A2K5Z886_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2YRD4_A0A2I2YRD4_GORGO_9595 and tr_H2Q0G7_H2Q0G7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YRD4_A0A2I2YRD4_GORGO_9595 and sp_A6NKN8_PC4L1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YRD4_A0A2I2YRD4_GORGO_9595 and tr_A0A2R9AUB3_A0A2R9AUB3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J9NXK9_J9NXK9_CANLF_9615 and tr_G1MA39_G1MA39_AILME_9646 are exactly identical!
WARNING: Sequences tr_F6Q1W3_F6Q1W3_HORSE_9796 and tr_A0A2Y9EAE1_A0A2Y9EAE1_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_F6Q1W3_F6Q1W3_HORSE_9796 and tr_A0A2Y9IGZ6_A0A2Y9IGZ6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_W5PJK6_W5PJK6_SHEEP_9940 and tr_H0WYL0_H0WYL0_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_W5PJK6_W5PJK6_SHEEP_9940 and sp_Q148C4_PCP4_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5PJS8_W5PJS8_SHEEP_9940 and sp_A8R4Q8_PC4L1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_R0KEN3_R0KEN3_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091ETK0_A0A091ETK0_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091K1X0_A0A091K1X0_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093PRY3_A0A093PRY3_9PASS_328815 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091VW12_A0A091VW12_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A087R974_A0A087R974_APTFO_9233 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093HLY8_A0A093HLY8_STRCA_441894 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091VYN2_A0A091VYN2_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A099ZEX3_A0A099ZEX3_TINGU_94827 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A0A0AXU0_A0A0A0AXU0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093IXJ4_A0A093IXJ4_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091I7Z8_A0A091I7Z8_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091V0R8_A0A091V0R8_NIPNI_128390 and tr_A0A0A0A8L1_A0A0A0A8L1_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MSP5_A0A2I0MSP5_COLLI_8932 and tr_A0A1S3G455_A0A1S3G455_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_A0A2I0MSP5_A0A2I0MSP5_COLLI_8932 and tr_A0A2Y9S0Q3_A0A2Y9S0Q3_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A1S3N9I3_A0A1S3N9I3_SALSA_8030 and tr_A0A060ZJS4_A0A060ZJS4_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_B9EM62_B9EM62_SALSA_8030 and tr_A0A060W927_A0A060W927_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2U3YL82_A0A2U3YL82_LEPWE_9713 and tr_A0A384CVZ2_A0A384CVZ2_URSMA_29073 are exactly identical!
WARNING: Duplicate sequences found: 67

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.reduced.phy

Alignment comprises 1 partitions and 51 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 53 / 51
Gaps: 4.14 %
Invariant sites: 16.98 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 156 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 51 / 4080
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -8434.550479] Initial branch length optimization
[00:00:00 -5989.893126] Model parameter optimization (eps = 10.000000)
[00:00:03 -5984.237114] AUTODETECT spr round 1 (radius: 5)
[00:00:07 -3716.784532] AUTODETECT spr round 2 (radius: 10)
[00:00:13 -2843.666396] AUTODETECT spr round 3 (radius: 15)
[00:00:19 -2302.632250] AUTODETECT spr round 4 (radius: 20)
[00:00:25 -2302.299996] AUTODETECT spr round 5 (radius: 25)
[00:00:30 -2297.674132] SPR radius for FAST iterations: 25 (autodetect)
[00:00:30 -2297.674132] Model parameter optimization (eps = 3.000000)
[00:00:40 -2277.734352] FAST spr round 1 (radius: 25)
[00:00:46 -2135.736882] FAST spr round 2 (radius: 25)
[00:00:52 -2067.366611] FAST spr round 3 (radius: 25)
[00:00:56 -2063.593341] FAST spr round 4 (radius: 25)
[00:01:01 -2063.592628] Model parameter optimization (eps = 1.000000)
[00:01:06 -2063.195718] SLOW spr round 1 (radius: 5)
[00:01:13 -2063.187484] SLOW spr round 2 (radius: 10)
[00:01:19 -2063.187258] SLOW spr round 3 (radius: 15)
[00:01:28 -2063.187199] SLOW spr round 4 (radius: 20)
[00:01:36 -2063.187180] SLOW spr round 5 (radius: 25)
[00:01:43 -2063.187173] Model parameter optimization (eps = 0.100000)

[00:01:45] ML tree search #1, logLikelihood: -2063.171360

[00:01:45 -8720.409286] Initial branch length optimization
[00:01:45 -6076.994336] Model parameter optimization (eps = 10.000000)
[00:01:49 -6067.181631] AUTODETECT spr round 1 (radius: 5)
[00:01:53 -3682.469420] AUTODETECT spr round 2 (radius: 10)
[00:01:59 -2814.894016] AUTODETECT spr round 3 (radius: 15)
[00:02:05 -2438.322057] AUTODETECT spr round 4 (radius: 20)
[00:02:11 -2329.903748] AUTODETECT spr round 5 (radius: 25)
[00:02:16 -2329.898808] SPR radius for FAST iterations: 20 (autodetect)
[00:02:16 -2329.898808] Model parameter optimization (eps = 3.000000)
[00:02:22 -2312.480448] FAST spr round 1 (radius: 20)
[00:02:27 -2119.000843] FAST spr round 2 (radius: 20)
[00:02:32 -2110.840154] FAST spr round 3 (radius: 20)
[00:02:37 -2078.788221] FAST spr round 4 (radius: 20)
[00:02:42 -2076.461559] FAST spr round 5 (radius: 20)
[00:02:46 -2076.461552] Model parameter optimization (eps = 1.000000)
[00:02:50 -2076.050287] SLOW spr round 1 (radius: 5)
[00:02:57 -2075.817906] SLOW spr round 2 (radius: 5)
[00:03:03 -2075.061417] SLOW spr round 3 (radius: 5)
[00:03:10 -2075.061329] SLOW spr round 4 (radius: 10)
[00:03:16 -2068.879412] SLOW spr round 5 (radius: 5)
[00:03:25 -2068.879219] SLOW spr round 6 (radius: 10)
[00:03:32 -2063.096648] SLOW spr round 7 (radius: 5)
[00:03:40 -2063.096638] SLOW spr round 8 (radius: 10)
[00:03:46 -2063.096636] SLOW spr round 9 (radius: 15)
[00:03:54 -2063.096634] SLOW spr round 10 (radius: 20)
[00:04:02 -2063.096634] SLOW spr round 11 (radius: 25)
[00:04:10 -2063.096634] Model parameter optimization (eps = 0.100000)

[00:04:17] ML tree search #2, logLikelihood: -2060.505592

[00:04:17 -8335.652336] Initial branch length optimization
[00:04:17 -5931.040893] Model parameter optimization (eps = 10.000000)
[00:04:22 -5919.166794] AUTODETECT spr round 1 (radius: 5)
[00:04:26 -3642.884511] AUTODETECT spr round 2 (radius: 10)
[00:04:31 -3018.152125] AUTODETECT spr round 3 (radius: 15)
[00:04:38 -2669.054987] AUTODETECT spr round 4 (radius: 20)
[00:04:45 -2305.677163] AUTODETECT spr round 5 (radius: 25)
[00:04:51 -2299.185728] SPR radius for FAST iterations: 25 (autodetect)
[00:04:51 -2299.185728] Model parameter optimization (eps = 3.000000)
[00:04:58 -2289.806086] FAST spr round 1 (radius: 25)
[00:05:03 -2078.746144] FAST spr round 2 (radius: 25)
[00:05:08 -2077.053678] FAST spr round 3 (radius: 25)
[00:05:13 -2076.538158] FAST spr round 4 (radius: 25)
[00:05:17 -2076.538030] Model parameter optimization (eps = 1.000000)
[00:05:19 -2075.924126] SLOW spr round 1 (radius: 5)
[00:05:26 -2074.839361] SLOW spr round 2 (radius: 5)
[00:05:32 -2074.838554] SLOW spr round 3 (radius: 10)
[00:05:39 -2073.044105] SLOW spr round 4 (radius: 5)
[00:05:48 -2071.812395] SLOW spr round 5 (radius: 5)
[00:05:55 -2070.905105] SLOW spr round 6 (radius: 5)
[00:06:01 -2070.904773] SLOW spr round 7 (radius: 10)
[00:06:08 -2070.904727] SLOW spr round 8 (radius: 15)
[00:06:17 -2065.337141] SLOW spr round 9 (radius: 5)
[00:06:26 -2064.864544] SLOW spr round 10 (radius: 5)
[00:06:33 -2064.864517] SLOW spr round 11 (radius: 10)
[00:06:40 -2064.864513] SLOW spr round 12 (radius: 15)
[00:06:48 -2064.864513] SLOW spr round 13 (radius: 20)
[00:06:56 -2064.864513] SLOW spr round 14 (radius: 25)
[00:07:04 -2064.864513] Model parameter optimization (eps = 0.100000)

[00:07:10] ML tree search #3, logLikelihood: -2059.310851

[00:07:10 -8461.376226] Initial branch length optimization
[00:07:10 -6014.601261] Model parameter optimization (eps = 10.000000)
[00:07:13 -6005.684691] AUTODETECT spr round 1 (radius: 5)
[00:07:17 -3484.422228] AUTODETECT spr round 2 (radius: 10)
[00:07:24 -2700.204588] AUTODETECT spr round 3 (radius: 15)
[00:07:29 -2393.513755] AUTODETECT spr round 4 (radius: 20)
[00:07:36 -2296.882185] AUTODETECT spr round 5 (radius: 25)
[00:07:41 -2296.881591] SPR radius for FAST iterations: 20 (autodetect)
[00:07:41 -2296.881591] Model parameter optimization (eps = 3.000000)
[00:07:50 -2277.348519] FAST spr round 1 (radius: 20)
[00:07:55 -2095.738667] FAST spr round 2 (radius: 20)
[00:08:00 -2072.722422] FAST spr round 3 (radius: 20)
[00:08:05 -2071.855360] FAST spr round 4 (radius: 20)
[00:08:09 -2071.855316] Model parameter optimization (eps = 1.000000)
[00:08:17 -2070.701408] SLOW spr round 1 (radius: 5)
[00:08:23 -2070.498980] SLOW spr round 2 (radius: 5)
[00:08:30 -2070.498815] SLOW spr round 3 (radius: 10)
[00:08:36 -2065.772951] SLOW spr round 4 (radius: 5)
[00:08:45 -2062.230697] SLOW spr round 5 (radius: 5)
[00:08:52 -2062.176203] SLOW spr round 6 (radius: 10)
[00:08:59 -2062.176198] SLOW spr round 7 (radius: 15)
[00:09:07 -2062.176198] SLOW spr round 8 (radius: 20)
[00:09:15 -2062.176198] SLOW spr round 9 (radius: 25)
[00:09:22 -2062.176198] Model parameter optimization (eps = 0.100000)

[00:09:25] ML tree search #4, logLikelihood: -2062.091622

[00:09:25 -8285.662095] Initial branch length optimization
[00:09:26 -5869.035517] Model parameter optimization (eps = 10.000000)
[00:09:28 -5862.868758] AUTODETECT spr round 1 (radius: 5)
[00:09:32 -3567.583548] AUTODETECT spr round 2 (radius: 10)
[00:09:38 -2950.087775] AUTODETECT spr round 3 (radius: 15)
[00:09:44 -2676.517967] AUTODETECT spr round 4 (radius: 20)
[00:09:50 -2449.510731] AUTODETECT spr round 5 (radius: 25)
[00:09:57 -2449.173053] SPR radius for FAST iterations: 25 (autodetect)
[00:09:57 -2449.173053] Model parameter optimization (eps = 3.000000)
[00:10:04 -2433.457346] FAST spr round 1 (radius: 25)
[00:10:09 -2075.964245] FAST spr round 2 (radius: 25)
[00:10:15 -2066.342324] FAST spr round 3 (radius: 25)
[00:10:19 -2064.309064] FAST spr round 4 (radius: 25)
[00:10:23 -2064.306290] Model parameter optimization (eps = 1.000000)
[00:10:26 -2064.087566] SLOW spr round 1 (radius: 5)
[00:10:33 -2063.511158] SLOW spr round 2 (radius: 5)
[00:10:39 -2063.510837] SLOW spr round 3 (radius: 10)
[00:10:45 -2063.510813] SLOW spr round 4 (radius: 15)
[00:10:53 -2062.627174] SLOW spr round 5 (radius: 5)
[00:11:01 -2061.972020] SLOW spr round 6 (radius: 5)
[00:11:08 -2061.972020] SLOW spr round 7 (radius: 10)
[00:11:15 -2061.972020] SLOW spr round 8 (radius: 15)
[00:11:23 -2061.972020] SLOW spr round 9 (radius: 20)
[00:11:30 -2061.972020] SLOW spr round 10 (radius: 25)
[00:11:38 -2061.972020] Model parameter optimization (eps = 0.100000)

[00:11:45] ML tree search #5, logLikelihood: -2061.647265

[00:11:45 -8046.243405] Initial branch length optimization
[00:11:45 -5759.351008] Model parameter optimization (eps = 10.000000)
[00:11:49 -5754.418503] AUTODETECT spr round 1 (radius: 5)
[00:11:53 -3862.733624] AUTODETECT spr round 2 (radius: 10)
[00:11:58 -3011.433526] AUTODETECT spr round 3 (radius: 15)
[00:12:04 -2440.140282] AUTODETECT spr round 4 (radius: 20)
[00:12:11 -2238.532575] AUTODETECT spr round 5 (radius: 25)
[00:12:15 -2237.403729] SPR radius for FAST iterations: 25 (autodetect)
[00:12:15 -2237.403729] Model parameter optimization (eps = 3.000000)
[00:12:22 -2226.404537] FAST spr round 1 (radius: 25)
[00:12:28 -2083.144539] FAST spr round 2 (radius: 25)
[00:12:33 -2074.586616] FAST spr round 3 (radius: 25)
[00:12:38 -2071.452449] FAST spr round 4 (radius: 25)
[00:12:42 -2070.140833] FAST spr round 5 (radius: 25)
[00:12:47 -2070.140670] Model parameter optimization (eps = 1.000000)
[00:12:50 -2069.719623] SLOW spr round 1 (radius: 5)
[00:12:57 -2068.352472] SLOW spr round 2 (radius: 5)
[00:13:03 -2062.237243] SLOW spr round 3 (radius: 5)
[00:13:10 -2062.237002] SLOW spr round 4 (radius: 10)
[00:13:16 -2062.002159] SLOW spr round 5 (radius: 5)
[00:13:24 -2062.001755] SLOW spr round 6 (radius: 10)
[00:13:30 -2062.001746] SLOW spr round 7 (radius: 15)
[00:13:38 -2062.001745] SLOW spr round 8 (radius: 20)
[00:13:46 -2062.001745] SLOW spr round 9 (radius: 25)
[00:13:54 -2062.001745] Model parameter optimization (eps = 0.100000)

[00:14:08] ML tree search #6, logLikelihood: -2057.761379

[00:14:08 -8465.670082] Initial branch length optimization
[00:14:08 -5972.217827] Model parameter optimization (eps = 10.000000)
[00:14:11 -5966.468987] AUTODETECT spr round 1 (radius: 5)
[00:14:15 -3534.622601] AUTODETECT spr round 2 (radius: 10)
[00:14:21 -2743.388158] AUTODETECT spr round 3 (radius: 15)
[00:14:26 -2537.172761] AUTODETECT spr round 4 (radius: 20)
[00:14:32 -2439.534323] AUTODETECT spr round 5 (radius: 25)
[00:14:38 -2438.134778] SPR radius for FAST iterations: 25 (autodetect)
[00:14:38 -2438.134778] Model parameter optimization (eps = 3.000000)
[00:14:44 -2424.135379] FAST spr round 1 (radius: 25)
[00:14:50 -2198.794080] FAST spr round 2 (radius: 25)
[00:14:56 -2066.263956] FAST spr round 3 (radius: 25)
[00:15:00 -2063.955292] FAST spr round 4 (radius: 25)
[00:15:04 -2061.798905] FAST spr round 5 (radius: 25)
[00:15:09 -2061.792805] Model parameter optimization (eps = 1.000000)
[00:15:16 -2057.637180] SLOW spr round 1 (radius: 5)
[00:15:23 -2057.362613] SLOW spr round 2 (radius: 5)
[00:15:30 -2057.104416] SLOW spr round 3 (radius: 5)
[00:15:36 -2057.101303] SLOW spr round 4 (radius: 10)
[00:15:42 -2057.101189] SLOW spr round 5 (radius: 15)
[00:15:50 -2057.101183] SLOW spr round 6 (radius: 20)
[00:15:58 -2057.101183] SLOW spr round 7 (radius: 25)
[00:16:05 -2057.101183] Model parameter optimization (eps = 0.100000)

[00:16:12] ML tree search #7, logLikelihood: -2056.796786

[00:16:12 -8879.109800] Initial branch length optimization
[00:16:12 -6355.578914] Model parameter optimization (eps = 10.000000)
[00:16:15 -6349.426311] AUTODETECT spr round 1 (radius: 5)
[00:16:19 -3738.721278] AUTODETECT spr round 2 (radius: 10)
[00:16:25 -2674.274558] AUTODETECT spr round 3 (radius: 15)
[00:16:30 -2391.808294] AUTODETECT spr round 4 (radius: 20)
[00:16:36 -2270.597402] AUTODETECT spr round 5 (radius: 25)
[00:16:40 -2270.559125] SPR radius for FAST iterations: 20 (autodetect)
[00:16:40 -2270.559125] Model parameter optimization (eps = 3.000000)
[00:16:48 -2253.308303] FAST spr round 1 (radius: 20)
[00:16:53 -2096.486559] FAST spr round 2 (radius: 20)
[00:16:58 -2072.054024] FAST spr round 3 (radius: 20)
[00:17:03 -2064.228062] FAST spr round 4 (radius: 20)
[00:17:07 -2064.227663] Model parameter optimization (eps = 1.000000)
[00:17:10 -2063.981126] SLOW spr round 1 (radius: 5)
[00:17:16 -2063.882680] SLOW spr round 2 (radius: 10)
[00:17:23 -2058.830249] SLOW spr round 3 (radius: 5)
[00:17:31 -2058.401153] SLOW spr round 4 (radius: 5)
[00:17:38 -2058.400967] SLOW spr round 5 (radius: 10)
[00:17:45 -2058.400931] SLOW spr round 6 (radius: 15)
[00:17:53 -2058.400925] SLOW spr round 7 (radius: 20)
[00:17:59 -2058.400924] SLOW spr round 8 (radius: 25)
[00:18:07 -2058.400924] Model parameter optimization (eps = 0.100000)

[00:18:15] ML tree search #8, logLikelihood: -2058.029089

[00:18:15 -8866.382055] Initial branch length optimization
[00:18:15 -6292.058730] Model parameter optimization (eps = 10.000000)
[00:18:21 -6281.651384] AUTODETECT spr round 1 (radius: 5)
[00:18:25 -3862.202205] AUTODETECT spr round 2 (radius: 10)
[00:18:31 -2963.833200] AUTODETECT spr round 3 (radius: 15)
[00:18:37 -2637.093522] AUTODETECT spr round 4 (radius: 20)
[00:18:44 -2399.378479] AUTODETECT spr round 5 (radius: 25)
[00:18:50 -2399.377596] SPR radius for FAST iterations: 20 (autodetect)
[00:18:50 -2399.377596] Model parameter optimization (eps = 3.000000)
[00:18:56 -2387.832955] FAST spr round 1 (radius: 20)
[00:19:02 -2178.245373] FAST spr round 2 (radius: 20)
[00:19:07 -2101.879155] FAST spr round 3 (radius: 20)
[00:19:12 -2063.247264] FAST spr round 4 (radius: 20)
[00:19:16 -2062.403020] FAST spr round 5 (radius: 20)
[00:19:21 -2062.288936] FAST spr round 6 (radius: 20)
[00:19:25 -2062.287142] Model parameter optimization (eps = 1.000000)
[00:19:33 -2058.265062] SLOW spr round 1 (radius: 5)
[00:19:39 -2058.132679] SLOW spr round 2 (radius: 5)
[00:19:46 -2057.918198] SLOW spr round 3 (radius: 5)
[00:19:52 -2057.918032] SLOW spr round 4 (radius: 10)
[00:19:58 -2057.917956] SLOW spr round 5 (radius: 15)
[00:20:06 -2057.917913] SLOW spr round 6 (radius: 20)
[00:20:14 -2057.917876] SLOW spr round 7 (radius: 25)
[00:20:22 -2057.917845] Model parameter optimization (eps = 0.100000)

[00:20:29] ML tree search #9, logLikelihood: -2057.554066

[00:20:29 -8567.008365] Initial branch length optimization
[00:20:29 -6164.153089] Model parameter optimization (eps = 10.000000)
[00:20:32 -6157.941230] AUTODETECT spr round 1 (radius: 5)
[00:20:36 -3717.710004] AUTODETECT spr round 2 (radius: 10)
[00:20:41 -2928.903403] AUTODETECT spr round 3 (radius: 15)
[00:20:48 -2320.755913] AUTODETECT spr round 4 (radius: 20)
[00:20:53 -2291.281524] AUTODETECT spr round 5 (radius: 25)
[00:20:58 -2290.941470] SPR radius for FAST iterations: 25 (autodetect)
[00:20:58 -2290.941470] Model parameter optimization (eps = 3.000000)
[00:21:09 -2279.475136] FAST spr round 1 (radius: 25)
[00:21:14 -2108.417194] FAST spr round 2 (radius: 25)
[00:21:19 -2069.432137] FAST spr round 3 (radius: 25)
[00:21:24 -2067.211594] FAST spr round 4 (radius: 25)
[00:21:28 -2067.211384] Model parameter optimization (eps = 1.000000)
[00:21:35 -2063.594189] SLOW spr round 1 (radius: 5)
[00:21:41 -2063.177605] SLOW spr round 2 (radius: 5)
[00:21:48 -2063.177491] SLOW spr round 3 (radius: 10)
[00:21:54 -2058.794191] SLOW spr round 4 (radius: 5)
[00:22:04 -2058.316015] SLOW spr round 5 (radius: 5)
[00:22:10 -2058.315751] SLOW spr round 6 (radius: 10)
[00:22:17 -2058.315710] SLOW spr round 7 (radius: 15)
[00:22:25 -2058.315703] SLOW spr round 8 (radius: 20)
[00:22:32 -2058.315702] SLOW spr round 9 (radius: 25)
[00:22:39 -2058.315701] Model parameter optimization (eps = 0.100000)

[00:22:47] ML tree search #10, logLikelihood: -2058.027866

[00:22:47 -8715.238228] Initial branch length optimization
[00:22:47 -6317.159143] Model parameter optimization (eps = 10.000000)
[00:22:50 -6310.948441] AUTODETECT spr round 1 (radius: 5)
[00:22:54 -3773.288350] AUTODETECT spr round 2 (radius: 10)
[00:22:59 -2934.804705] AUTODETECT spr round 3 (radius: 15)
[00:23:06 -2348.976787] AUTODETECT spr round 4 (radius: 20)
[00:23:13 -2345.727790] AUTODETECT spr round 5 (radius: 25)
[00:23:18 -2301.244103] SPR radius for FAST iterations: 25 (autodetect)
[00:23:18 -2301.244103] Model parameter optimization (eps = 3.000000)
[00:23:25 -2285.973197] FAST spr round 1 (radius: 25)
[00:23:30 -2105.148874] FAST spr round 2 (radius: 25)
[00:23:35 -2065.561814] FAST spr round 3 (radius: 25)
[00:23:39 -2065.558994] Model parameter optimization (eps = 1.000000)
[00:23:44 -2061.382693] SLOW spr round 1 (radius: 5)
[00:23:50 -2061.012587] SLOW spr round 2 (radius: 5)
[00:23:57 -2061.012231] SLOW spr round 3 (radius: 10)
[00:24:03 -2061.012167] SLOW spr round 4 (radius: 15)
[00:24:12 -2061.012147] SLOW spr round 5 (radius: 20)
[00:24:20 -2061.012147] SLOW spr round 6 (radius: 25)
[00:24:27 -2061.012147] Model parameter optimization (eps = 0.100000)

[00:24:34] ML tree search #11, logLikelihood: -2060.795196

[00:24:34 -8784.383570] Initial branch length optimization
[00:24:34 -6302.433745] Model parameter optimization (eps = 10.000000)
[00:24:38 -6292.208964] AUTODETECT spr round 1 (radius: 5)
[00:24:42 -3593.120742] AUTODETECT spr round 2 (radius: 10)
[00:24:48 -2478.015819] AUTODETECT spr round 3 (radius: 15)
[00:24:56 -2215.881281] AUTODETECT spr round 4 (radius: 20)
[00:25:03 -2215.836586] SPR radius for FAST iterations: 15 (autodetect)
[00:25:03 -2215.836586] Model parameter optimization (eps = 3.000000)
[00:25:12 -2204.677053] FAST spr round 1 (radius: 15)
[00:25:18 -2093.344028] FAST spr round 2 (radius: 15)
[00:25:24 -2069.548307] FAST spr round 3 (radius: 15)
[00:25:29 -2066.442160] FAST spr round 4 (radius: 15)
[00:25:33 -2066.292881] FAST spr round 5 (radius: 15)
[00:25:37 -2066.292737] Model parameter optimization (eps = 1.000000)
[00:25:43 -2062.921682] SLOW spr round 1 (radius: 5)
[00:25:50 -2061.485013] SLOW spr round 2 (radius: 5)
[00:25:56 -2061.461109] SLOW spr round 3 (radius: 10)
[00:26:02 -2061.460830] SLOW spr round 4 (radius: 15)
[00:26:10 -2061.460821] SLOW spr round 5 (radius: 20)
[00:26:18 -2061.460821] SLOW spr round 6 (radius: 25)
[00:26:26 -2061.460821] Model parameter optimization (eps = 0.100000)

[00:26:30] ML tree search #12, logLikelihood: -2061.092540

[00:26:30 -8345.274407] Initial branch length optimization
[00:26:30 -6123.022461] Model parameter optimization (eps = 10.000000)
[00:26:33 -6113.595080] AUTODETECT spr round 1 (radius: 5)
[00:26:38 -3074.268644] AUTODETECT spr round 2 (radius: 10)
[00:26:43 -2453.280283] AUTODETECT spr round 3 (radius: 15)
[00:26:49 -2316.171800] AUTODETECT spr round 4 (radius: 20)
[00:26:54 -2312.377790] AUTODETECT spr round 5 (radius: 25)
[00:26:58 -2312.331212] SPR radius for FAST iterations: 20 (autodetect)
[00:26:58 -2312.331212] Model parameter optimization (eps = 3.000000)
[00:27:06 -2293.196482] FAST spr round 1 (radius: 20)
[00:27:11 -2084.124756] FAST spr round 2 (radius: 20)
[00:27:16 -2069.255834] FAST spr round 3 (radius: 20)
[00:27:21 -2066.736698] FAST spr round 4 (radius: 20)
[00:27:25 -2066.735971] Model parameter optimization (eps = 1.000000)
[00:27:30 -2063.623156] SLOW spr round 1 (radius: 5)
[00:27:37 -2062.715199] SLOW spr round 2 (radius: 5)
[00:27:43 -2062.519856] SLOW spr round 3 (radius: 5)
[00:27:50 -2062.519780] SLOW spr round 4 (radius: 10)
[00:27:56 -2062.519778] SLOW spr round 5 (radius: 15)
[00:28:05 -2058.398219] SLOW spr round 6 (radius: 5)
[00:28:13 -2057.745610] SLOW spr round 7 (radius: 5)
[00:28:20 -2057.745610] SLOW spr round 8 (radius: 10)
[00:28:27 -2057.745610] SLOW spr round 9 (radius: 15)
[00:28:35 -2057.745610] SLOW spr round 10 (radius: 20)
[00:28:42 -2057.745610] SLOW spr round 11 (radius: 25)
[00:28:50 -2057.745610] Model parameter optimization (eps = 0.100000)

[00:28:56] ML tree search #13, logLikelihood: -2057.556906

[00:28:56 -8637.811934] Initial branch length optimization
[00:28:56 -6283.354375] Model parameter optimization (eps = 10.000000)
[00:28:59 -6276.333386] AUTODETECT spr round 1 (radius: 5)
[00:29:04 -3620.706387] AUTODETECT spr round 2 (radius: 10)
[00:29:09 -2740.624157] AUTODETECT spr round 3 (radius: 15)
[00:29:15 -2450.680929] AUTODETECT spr round 4 (radius: 20)
[00:29:22 -2347.204990] AUTODETECT spr round 5 (radius: 25)
[00:29:28 -2314.822733] SPR radius for FAST iterations: 25 (autodetect)
[00:29:28 -2314.822733] Model parameter optimization (eps = 3.000000)
[00:29:36 -2302.047202] FAST spr round 1 (radius: 25)
[00:29:42 -2080.700566] FAST spr round 2 (radius: 25)
[00:29:47 -2066.411143] FAST spr round 3 (radius: 25)
[00:29:52 -2066.039166] FAST spr round 4 (radius: 25)
[00:29:56 -2066.037282] Model parameter optimization (eps = 1.000000)
[00:30:00 -2064.543503] SLOW spr round 1 (radius: 5)
[00:30:06 -2063.953329] SLOW spr round 2 (radius: 5)
[00:30:13 -2063.953009] SLOW spr round 3 (radius: 10)
[00:30:19 -2063.952970] SLOW spr round 4 (radius: 15)
[00:30:28 -2058.874290] SLOW spr round 5 (radius: 5)
[00:30:37 -2058.219042] SLOW spr round 6 (radius: 5)
[00:30:44 -2058.219038] SLOW spr round 7 (radius: 10)
[00:30:51 -2057.631964] SLOW spr round 8 (radius: 5)
[00:30:59 -2057.631401] SLOW spr round 9 (radius: 10)
[00:31:06 -2057.631379] SLOW spr round 10 (radius: 15)
[00:31:14 -2057.631378] SLOW spr round 11 (radius: 20)
[00:31:21 -2057.631378] SLOW spr round 12 (radius: 25)
[00:31:28 -2057.631378] Model parameter optimization (eps = 0.100000)

[00:31:35] ML tree search #14, logLikelihood: -2057.361380

[00:31:35 -8925.964972] Initial branch length optimization
[00:31:35 -6326.730687] Model parameter optimization (eps = 10.000000)
[00:31:40 -6316.989893] AUTODETECT spr round 1 (radius: 5)
[00:31:45 -3640.460528] AUTODETECT spr round 2 (radius: 10)
[00:31:50 -2866.420548] AUTODETECT spr round 3 (radius: 15)
[00:31:56 -2473.511478] AUTODETECT spr round 4 (radius: 20)
[00:32:02 -2339.256936] AUTODETECT spr round 5 (radius: 25)
[00:32:08 -2339.256756] SPR radius for FAST iterations: 20 (autodetect)
[00:32:08 -2339.256756] Model parameter optimization (eps = 3.000000)
[00:32:18 -2315.399402] FAST spr round 1 (radius: 20)
[00:32:23 -2124.303225] FAST spr round 2 (radius: 20)
[00:32:28 -2075.218283] FAST spr round 3 (radius: 20)
[00:32:33 -2075.217391] Model parameter optimization (eps = 1.000000)
[00:32:36 -2075.002537] SLOW spr round 1 (radius: 5)
[00:32:42 -2074.558935] SLOW spr round 2 (radius: 5)
[00:32:49 -2074.558802] SLOW spr round 3 (radius: 10)
[00:32:56 -2064.404829] SLOW spr round 4 (radius: 5)
[00:33:05 -2063.332618] SLOW spr round 5 (radius: 5)
[00:33:12 -2063.332154] SLOW spr round 6 (radius: 10)
[00:33:18 -2063.332073] SLOW spr round 7 (radius: 15)
[00:33:26 -2063.332050] SLOW spr round 8 (radius: 20)
[00:33:34 -2063.332048] SLOW spr round 9 (radius: 25)
[00:33:41 -2063.332048] Model parameter optimization (eps = 0.100000)

[00:33:49] ML tree search #15, logLikelihood: -2063.065072

[00:33:49 -8657.484789] Initial branch length optimization
[00:33:49 -6236.221461] Model parameter optimization (eps = 10.000000)
[00:33:53 -6230.012614] AUTODETECT spr round 1 (radius: 5)
[00:33:57 -3494.253254] AUTODETECT spr round 2 (radius: 10)
[00:34:02 -2721.367399] AUTODETECT spr round 3 (radius: 15)
[00:34:08 -2272.098504] AUTODETECT spr round 4 (radius: 20)
[00:34:15 -2215.253970] AUTODETECT spr round 5 (radius: 25)
[00:34:21 -2215.210826] SPR radius for FAST iterations: 20 (autodetect)
[00:34:21 -2215.210826] Model parameter optimization (eps = 3.000000)
[00:34:27 -2204.069201] FAST spr round 1 (radius: 20)
[00:34:32 -2071.247059] FAST spr round 2 (radius: 20)
[00:34:37 -2065.892844] FAST spr round 3 (radius: 20)
[00:34:41 -2065.892824] Model parameter optimization (eps = 1.000000)
[00:34:51 -2063.223432] SLOW spr round 1 (radius: 5)
[00:34:58 -2062.055436] SLOW spr round 2 (radius: 5)
[00:35:05 -2061.734750] SLOW spr round 3 (radius: 5)
[00:35:11 -2061.605263] SLOW spr round 4 (radius: 5)
[00:35:17 -2061.601996] SLOW spr round 5 (radius: 10)
[00:35:24 -2057.464952] SLOW spr round 6 (radius: 5)
[00:35:32 -2057.447873] SLOW spr round 7 (radius: 10)
[00:35:39 -2057.447845] SLOW spr round 8 (radius: 15)
[00:35:47 -2057.447833] SLOW spr round 9 (radius: 20)
[00:35:55 -2057.447827] SLOW spr round 10 (radius: 25)
[00:36:03 -2057.447825] Model parameter optimization (eps = 0.100000)

[00:36:09] ML tree search #16, logLikelihood: -2057.195609

[00:36:09 -8668.747709] Initial branch length optimization
[00:36:09 -6153.928322] Model parameter optimization (eps = 10.000000)
[00:36:12 -6147.790264] AUTODETECT spr round 1 (radius: 5)
[00:36:16 -3597.899574] AUTODETECT spr round 2 (radius: 10)
[00:36:21 -2894.253939] AUTODETECT spr round 3 (radius: 15)
[00:36:28 -2331.921568] AUTODETECT spr round 4 (radius: 20)
[00:36:34 -2262.254299] AUTODETECT spr round 5 (radius: 25)
[00:36:40 -2261.410999] SPR radius for FAST iterations: 25 (autodetect)
[00:36:40 -2261.410999] Model parameter optimization (eps = 3.000000)
[00:36:50 -2249.608450] FAST spr round 1 (radius: 25)
[00:36:55 -2127.780784] FAST spr round 2 (radius: 25)
[00:37:00 -2072.219235] FAST spr round 3 (radius: 25)
[00:37:05 -2071.859024] FAST spr round 4 (radius: 25)
[00:37:09 -2071.858775] Model parameter optimization (eps = 1.000000)
[00:37:11 -2071.668872] SLOW spr round 1 (radius: 5)
[00:37:18 -2071.667931] SLOW spr round 2 (radius: 10)
[00:37:24 -2071.667682] SLOW spr round 3 (radius: 15)
[00:37:32 -2071.667682] SLOW spr round 4 (radius: 20)
[00:37:40 -2071.667682] SLOW spr round 5 (radius: 25)
[00:37:47 -2071.667682] Model parameter optimization (eps = 0.100000)

[00:37:48] ML tree search #17, logLikelihood: -2071.665988

[00:37:48 -8330.787010] Initial branch length optimization
[00:37:48 -5996.925448] Model parameter optimization (eps = 10.000000)
[00:37:51 -5988.922636] AUTODETECT spr round 1 (radius: 5)
[00:37:55 -3811.741788] AUTODETECT spr round 2 (radius: 10)
[00:38:01 -2613.023586] AUTODETECT spr round 3 (radius: 15)
[00:38:07 -2350.531189] AUTODETECT spr round 4 (radius: 20)
[00:38:13 -2327.165063] AUTODETECT spr round 5 (radius: 25)
[00:38:18 -2327.158748] SPR radius for FAST iterations: 20 (autodetect)
[00:38:18 -2327.158748] Model parameter optimization (eps = 3.000000)
[00:38:26 -2315.343128] FAST spr round 1 (radius: 20)
[00:38:31 -2111.076159] FAST spr round 2 (radius: 20)
[00:38:37 -2078.645295] FAST spr round 3 (radius: 20)
[00:38:41 -2078.491382] FAST spr round 4 (radius: 20)
[00:38:45 -2078.491365] Model parameter optimization (eps = 1.000000)
[00:38:49 -2076.843351] SLOW spr round 1 (radius: 5)
[00:38:56 -2076.670656] SLOW spr round 2 (radius: 5)
[00:39:02 -2076.670041] SLOW spr round 3 (radius: 10)
[00:39:09 -2065.032191] SLOW spr round 4 (radius: 5)
[00:39:18 -2059.976385] SLOW spr round 5 (radius: 5)
[00:39:25 -2059.120313] SLOW spr round 6 (radius: 5)
[00:39:32 -2059.118592] SLOW spr round 7 (radius: 10)
[00:39:38 -2059.118444] SLOW spr round 8 (radius: 15)
[00:39:46 -2058.261926] SLOW spr round 9 (radius: 5)
[00:39:55 -2058.261289] SLOW spr round 10 (radius: 10)
[00:40:03 -2058.261229] SLOW spr round 11 (radius: 15)
[00:40:11 -2058.261223] SLOW spr round 12 (radius: 20)
[00:40:19 -2058.261222] SLOW spr round 13 (radius: 25)
[00:40:27 -2058.261222] Model parameter optimization (eps = 0.100000)

[00:40:33] ML tree search #18, logLikelihood: -2057.503831

[00:40:33 -8440.434119] Initial branch length optimization
[00:40:33 -5942.378771] Model parameter optimization (eps = 10.000000)
[00:40:36 -5935.051011] AUTODETECT spr round 1 (radius: 5)
[00:40:40 -3358.817695] AUTODETECT spr round 2 (radius: 10)
[00:40:45 -2718.944737] AUTODETECT spr round 3 (radius: 15)
[00:40:52 -2473.585391] AUTODETECT spr round 4 (radius: 20)
[00:40:59 -2369.995783] AUTODETECT spr round 5 (radius: 25)
[00:41:04 -2365.082520] SPR radius for FAST iterations: 25 (autodetect)
[00:41:04 -2365.082520] Model parameter optimization (eps = 3.000000)
[00:41:11 -2351.659034] FAST spr round 1 (radius: 25)
[00:41:16 -2116.600733] FAST spr round 2 (radius: 25)
[00:41:21 -2077.439976] FAST spr round 3 (radius: 25)
[00:41:26 -2073.416006] FAST spr round 4 (radius: 25)
[00:41:30 -2073.148720] FAST spr round 5 (radius: 25)
[00:41:34 -2073.148469] Model parameter optimization (eps = 1.000000)
[00:41:36 -2073.099237] SLOW spr round 1 (radius: 5)
[00:41:42 -2072.988328] SLOW spr round 2 (radius: 5)
[00:41:49 -2072.293018] SLOW spr round 3 (radius: 5)
[00:41:55 -2072.292938] SLOW spr round 4 (radius: 10)
[00:42:01 -2070.236813] SLOW spr round 5 (radius: 5)
[00:42:10 -2068.968058] SLOW spr round 6 (radius: 5)
[00:42:17 -2068.015758] SLOW spr round 7 (radius: 5)
[00:42:23 -2068.015221] SLOW spr round 8 (radius: 10)
[00:42:29 -2068.015212] SLOW spr round 9 (radius: 15)
[00:42:38 -2066.018463] SLOW spr round 10 (radius: 5)
[00:42:47 -2065.218077] SLOW spr round 11 (radius: 5)
[00:42:54 -2065.218077] SLOW spr round 12 (radius: 10)
[00:43:00 -2065.218077] SLOW spr round 13 (radius: 15)
[00:43:09 -2065.218077] SLOW spr round 14 (radius: 20)
[00:43:18 -2065.218077] SLOW spr round 15 (radius: 25)
[00:43:25 -2065.218077] Model parameter optimization (eps = 0.100000)

[00:43:31] ML tree search #19, logLikelihood: -2064.028179

[00:43:31 -8574.359581] Initial branch length optimization
[00:43:31 -6111.516190] Model parameter optimization (eps = 10.000000)
[00:43:34 -6105.873955] AUTODETECT spr round 1 (radius: 5)
[00:43:38 -3459.797394] AUTODETECT spr round 2 (radius: 10)
[00:43:43 -2634.144171] AUTODETECT spr round 3 (radius: 15)
[00:43:49 -2381.572850] AUTODETECT spr round 4 (radius: 20)
[00:43:55 -2300.847944] AUTODETECT spr round 5 (radius: 25)
[00:44:01 -2300.846479] SPR radius for FAST iterations: 20 (autodetect)
[00:44:01 -2300.846479] Model parameter optimization (eps = 3.000000)
[00:44:08 -2282.861002] FAST spr round 1 (radius: 20)
[00:44:13 -2087.012879] FAST spr round 2 (radius: 20)
[00:44:18 -2063.650613] FAST spr round 3 (radius: 20)
[00:44:22 -2061.767634] FAST spr round 4 (radius: 20)
[00:44:27 -2059.486755] FAST spr round 5 (radius: 20)
[00:44:31 -2059.486378] Model parameter optimization (eps = 1.000000)
[00:44:34 -2058.875334] SLOW spr round 1 (radius: 5)
[00:44:41 -2058.412043] SLOW spr round 2 (radius: 5)
[00:44:47 -2058.405802] SLOW spr round 3 (radius: 10)
[00:44:53 -2058.405187] SLOW spr round 4 (radius: 15)
[00:45:02 -2058.405031] SLOW spr round 5 (radius: 20)
[00:45:10 -2058.404984] SLOW spr round 6 (radius: 25)
[00:45:18 -2058.404970] Model parameter optimization (eps = 0.100000)

[00:45:24] ML tree search #20, logLikelihood: -2057.508897


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.199186,0.033535) (0.076500,1.438599) (0.399442,0.335114) (0.324872,2.306782) 
   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: -2056.796786

AIC score: 4743.593572 / AICc score: 203823.593572 / BIC score: 5364.235525
Free parameters (model + branch lengths): 315

WARNING: Number of free parameters (K=315) is larger than alignment size (n=53).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 88 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.log

Analysis started: 26-Jul-2021 05:25:32 / finished: 26-Jul-2021 06:10:57

Elapsed time: 2724.589 seconds

Consumed energy: 116.064 Wh