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

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

RAxML-NG was called at 24-Jun-2021 13:41:13 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/2_msa/P17661_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/2_msa/P17661_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 429 sites

WARNING: Sequences tr_M3YJK3_M3YJK3_MUSPF_9669 and tr_A0A2Y9KC89_A0A2Y9KC89_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1S823_G1S823_NOMLE_61853 and tr_H2NH69_H2NH69_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Y3K0_A0A2I2Y3K0_GORGO_9595 and tr_A0A2I3RCP5_A0A2I3RCP5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Y3K0_A0A2I2Y3K0_GORGO_9595 and tr_A0A2R9CBG0_A0A2R9CBG0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and sp_P17661_DESM_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and tr_H2Q2I4_H2Q2I4_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and sp_Q16352_AINX_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QK94_G3QK94_GORGO_9595 and tr_A0A2R9BN98_A0A2R9BN98_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and tr_G2HJ38_G2HJ38_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and sp_P08670_VIME_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R2A8_G3R2A8_GORGO_9595 and tr_A0A2R9BXN0_A0A2R9BXN0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2J8KDC3_A0A2J8KDC3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and sp_P05787_K2C8_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2R9A6T6_A0A2R9A6T6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and sp_Q5R408_NFL_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and tr_A0A2I3SJH8_A0A2I3SJH8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and sp_P07196_NFL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and tr_A0A2R9BTF6_A0A2R9BTF6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_H2Q5V1_H2Q5V1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and sp_P41219_PERI_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_A0A2R9AZE7_A0A2R9AZE7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1N6W4_G1N6W4_MELGA_9103 and tr_A0A091JIL7_A0A091JIL7_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_F1PLS4_F1PLS4_CANLF_9615 and tr_G1LVM5_G1LVM5_AILME_9646 are exactly identical!
WARNING: Sequences tr_F6UNV5_F6UNV5_CANLF_9615 and tr_G1L164_G1L164_AILME_9646 are exactly identical!
WARNING: Sequences tr_F6UNV5_F6UNV5_CANLF_9615 and tr_A0A2U3WX90_A0A2U3WX90_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F6UNV5_F6UNV5_CANLF_9615 and tr_A0A2U3XE40_A0A2U3XE40_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_F6UNV5_F6UNV5_CANLF_9615 and tr_A0A384CZN2_A0A384CZN2_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3SA52_A0A2I3SA52_PANTR_9598 and tr_A0A2R9A8H7_A0A2R9A8H7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SZW5_A0A2I3SZW5_PANTR_9598 and tr_A0A2R9AE10_A0A2R9AE10_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QLG1_H2QLG1_PANTR_9598 and sp_P12036_NFH_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and sp_O62654_DESM_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_G7PCX0_G7PCX0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2I3LJD5_A0A2I3LJD5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A0D9RUC0_A0A0D9RUC0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2K6BBU8_A0A2K6BBU8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QRV5_A0A1D5QRV5_MACMU_9544 and tr_A0A2K6ACN1_A0A2K6ACN1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7DY27_F7DY27_MACMU_9544 and tr_A0A096P6G7_A0A096P6G7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7DY27_F7DY27_MACMU_9544 and tr_A0A2K5N141_A0A2K5N141_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7DY27_F7DY27_MACMU_9544 and tr_A0A2K6DWL8_A0A2K6DWL8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7ED68_F7ED68_MACMU_9544 and tr_A0A2K6DB76_A0A2K6DB76_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7ED68_F7ED68_MACMU_9544 and tr_A0A2K5XH32_A0A2K5XH32_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_B0CM49_B0CM49_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A0D9R6T4_A0A0D9R6T4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K5LDT7_A0A2K5LDT7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K6D3R9_A0A2K6D3R9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K5YQE7_A0A2K5YQE7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A096NJD8_A0A096NJD8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A096NAQ5_A0A096NAQ5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A0D9R1E9_A0A0D9R1E9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K5N8A5_A0A2K5N8A5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K6C7C4_A0A2K6C7C4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K5Y3J4_A0A2K5Y3J4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K5N2V1_A0A2K5N2V1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_G7PEG3_G7PEG3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A096NQ21_A0A096NQ21_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A0D9RJU1_A0A0D9RJU1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K5KZZ4_A0A2K5KZZ4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K6CXT7_A0A2K6CXT7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7N1N6_G7N1N6_MACMU_9544 and tr_A0A2K5ZIJ1_A0A2K5ZIJ1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A087X4R7_A0A087X4R7_POEFO_48698 and tr_A0A087XIV6_A0A087XIV6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A2I3NFW1_A0A2I3NFW1_PAPAN_9555 and tr_A0A2K6BAT9_A0A2K6BAT9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3NFW1_A0A2I3NFW1_PAPAN_9555 and tr_A0A2K5ZFI5_A0A2K5ZFI5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A1S3NPJ3_A0A1S3NPJ3_SALSA_8030 and tr_A0A060X6X7_A0A060X6X7_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1U7QL88_A0A1U7QL88_MESAU_10036 and sp_P02544_VIME_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A226MLA7_A0A226MLA7_CALSU_9009 and tr_A0A226P5G2_A0A226P5G2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NIZ1_A0A226NIZ1_CALSU_9009 and tr_A0A226PYW6_A0A226PYW6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NN62_A0A226NN62_CALSU_9009 and tr_A0A226PAN0_A0A226PAN0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0T9N3_A0A2D0T9N3_ICTPU_7998 and tr_A0A2D0T9P6_A0A2D0T9P6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3V3D7_A0A2U3V3D7_TURTR_9739 and tr_A0A2U4BA02_A0A2U4BA02_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U4BAE0_A0A2U4BAE0_TURTR_9739 and tr_A0A2Y9N997_A0A2Y9N997_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3XCY0_A0A2U3XCY0_LEPWE_9713 and tr_A0A2U3Z699_A0A2U3Z699_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9PZZ2_A0A2Y9PZZ2_DELLE_9749 and tr_A0A2Y9FDY3_A0A2Y9FDY3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9PZZ2_A0A2Y9PZZ2_DELLE_9749 and tr_A0A384B0L5_A0A384B0L5_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 73

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.reduced.phy

Alignment comprises 1 partitions and 429 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 429 / 429
Gaps: 8.71 %
Invariant sites: 0.00 %


NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 215 / 17200
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -646845.516707] Initial branch length optimization
[00:00:07 -553080.351849] Model parameter optimization (eps = 10.000000)
[00:01:16 -549589.903990] AUTODETECT spr round 1 (radius: 5)
[00:04:38 -335312.332335] AUTODETECT spr round 2 (radius: 10)
[00:08:05 -226166.733167] AUTODETECT spr round 3 (radius: 15)
[00:11:53 -175122.768545] AUTODETECT spr round 4 (radius: 20)
[00:16:30 -158341.811219] AUTODETECT spr round 5 (radius: 25)
[00:22:19 -156158.592263] SPR radius for FAST iterations: 25 (autodetect)
[00:22:19 -156158.592263] Model parameter optimization (eps = 3.000000)
[00:22:54 -156056.473227] FAST spr round 1 (radius: 25)
[00:26:29 -134250.263322] FAST spr round 2 (radius: 25)
[00:29:09 -133198.048193] FAST spr round 3 (radius: 25)
[00:31:47 -133121.174113] FAST spr round 4 (radius: 25)
[00:34:12 -133113.430372] FAST spr round 5 (radius: 25)
[00:36:37 -133107.821845] FAST spr round 6 (radius: 25)
[00:38:50 -133107.821733] Model parameter optimization (eps = 1.000000)
[00:39:05 -133106.328059] SLOW spr round 1 (radius: 5)
[00:42:11 -133086.569567] SLOW spr round 2 (radius: 5)
[00:45:12 -133082.119913] SLOW spr round 3 (radius: 5)
[00:48:12 -133082.076661] SLOW spr round 4 (radius: 10)
[00:51:09 -133078.793586] SLOW spr round 5 (radius: 5)
[00:54:37 -133075.755543] SLOW spr round 6 (radius: 5)
[00:57:45 -133075.755510] SLOW spr round 7 (radius: 10)
[01:00:48 -133075.755505] SLOW spr round 8 (radius: 15)
[01:05:07 -133075.755500] SLOW spr round 9 (radius: 20)
[01:12:29 -133075.755495] SLOW spr round 10 (radius: 25)
[01:17:54] [worker #1] ML tree search #2, logLikelihood: -132999.009403
[01:23:01 -133075.755490] Model parameter optimization (eps = 0.100000)

[01:23:07] [worker #0] ML tree search #1, logLikelihood: -133075.724503

[01:23:07 -646779.385078] Initial branch length optimization
[01:23:17 -551153.395694] Model parameter optimization (eps = 10.000000)
[01:24:17 -548064.940998] AUTODETECT spr round 1 (radius: 5)
[01:25:19] [worker #2] ML tree search #3, logLikelihood: -133004.005367
[01:27:37 -334632.540471] AUTODETECT spr round 2 (radius: 10)
[01:31:05 -219415.528314] AUTODETECT spr round 3 (radius: 15)
[01:34:42 -179291.157591] AUTODETECT spr round 4 (radius: 20)
[01:39:44 -163543.539565] AUTODETECT spr round 5 (radius: 25)
[01:45:45 -158021.821407] SPR radius for FAST iterations: 25 (autodetect)
[01:45:45 -158021.821407] Model parameter optimization (eps = 3.000000)
[01:46:14 -157925.091967] FAST spr round 1 (radius: 25)
[01:49:30 -134659.920327] FAST spr round 2 (radius: 25)
[01:52:07 -133117.732278] FAST spr round 3 (radius: 25)
[01:54:33 -133073.130277] FAST spr round 4 (radius: 25)
[01:56:54 -133068.469711] FAST spr round 5 (radius: 25)
[01:59:04 -133065.059113] FAST spr round 6 (radius: 25)
[02:01:13 -133064.721529] FAST spr round 7 (radius: 25)
[02:03:20 -133064.720995] Model parameter optimization (eps = 1.000000)
[02:03:43 -133059.160994] SLOW spr round 1 (radius: 5)
[02:06:40 -133019.203833] SLOW spr round 2 (radius: 5)
[02:09:38 -133006.598261] SLOW spr round 3 (radius: 5)
[02:12:27 -133006.597600] SLOW spr round 4 (radius: 10)
[02:15:23 -133005.799499] SLOW spr round 5 (radius: 5)
[02:18:49 -133005.799491] SLOW spr round 6 (radius: 10)
[02:22:05 -133005.799488] SLOW spr round 7 (radius: 15)
[02:26:30 -133005.799487] SLOW spr round 8 (radius: 20)
[02:34:28 -133005.799487] SLOW spr round 9 (radius: 25)
[02:39:57] [worker #1] ML tree search #5, logLikelihood: -133023.815409
[02:45:44 -133005.799486] Model parameter optimization (eps = 0.100000)

[02:45:53] [worker #0] ML tree search #4, logLikelihood: -133005.726125

[02:45:53 -641440.845346] Initial branch length optimization
[02:45:58 -549545.638279] Model parameter optimization (eps = 10.000000)
[02:46:55 -546268.688349] AUTODETECT spr round 1 (radius: 5)
[02:50:10 -344685.533877] AUTODETECT spr round 2 (radius: 10)
[02:53:34 -228979.997764] AUTODETECT spr round 3 (radius: 15)
[02:57:18 -181933.243016] AUTODETECT spr round 4 (radius: 20)
[03:01:48 -158795.716901] AUTODETECT spr round 5 (radius: 25)
[03:06:59 -156502.985863] SPR radius for FAST iterations: 25 (autodetect)
[03:06:59 -156502.985863] Model parameter optimization (eps = 3.000000)
[03:07:31 -156415.571271] FAST spr round 1 (radius: 25)
[03:07:36] [worker #2] ML tree search #6, logLikelihood: -133005.934898
[03:11:08 -134049.379857] FAST spr round 2 (radius: 25)
[03:13:54 -133192.143956] FAST spr round 3 (radius: 25)
[03:16:29 -133116.567199] FAST spr round 4 (radius: 25)
[03:18:53 -133110.437474] FAST spr round 5 (radius: 25)
[03:21:09 -133110.436855] Model parameter optimization (eps = 1.000000)
[03:21:29 -133099.704965] SLOW spr round 1 (radius: 5)
[03:24:29 -133080.050446] SLOW spr round 2 (radius: 5)
[03:27:27 -133073.101799] SLOW spr round 3 (radius: 5)
[03:30:16 -133073.101424] SLOW spr round 4 (radius: 10)
[03:33:09 -133064.906695] SLOW spr round 5 (radius: 5)
[03:36:36 -133063.199208] SLOW spr round 6 (radius: 5)
[03:39:39 -133063.199155] SLOW spr round 7 (radius: 10)
[03:42:42 -133060.066319] SLOW spr round 8 (radius: 5)
[03:46:06 -133060.066255] SLOW spr round 9 (radius: 10)
[03:49:20 -133060.066250] SLOW spr round 10 (radius: 15)
[03:50:53] [worker #1] ML tree search #8, logLikelihood: -133010.598913
[03:53:43 -133055.653972] SLOW spr round 11 (radius: 5)
[03:57:37 -133020.408250] SLOW spr round 12 (radius: 5)
[04:00:51 -133020.408222] SLOW spr round 13 (radius: 10)
[04:04:01 -133015.838936] SLOW spr round 14 (radius: 5)
[04:07:22 -133015.838814] SLOW spr round 15 (radius: 10)
[04:10:35 -133015.838808] SLOW spr round 16 (radius: 15)
[04:14:59 -133015.838802] SLOW spr round 17 (radius: 20)
[04:22:49 -133015.838796] SLOW spr round 18 (radius: 25)
[04:34:03 -133015.838790] Model parameter optimization (eps = 0.100000)

[04:34:12] [worker #0] ML tree search #7, logLikelihood: -133015.758539

[04:34:12 -640681.470671] Initial branch length optimization
[04:34:19 -548713.382786] Model parameter optimization (eps = 10.000000)
[04:35:43 -545674.286772] AUTODETECT spr round 1 (radius: 5)
[04:38:58 -337568.933173] AUTODETECT spr round 2 (radius: 10)
[04:42:20 -226784.741333] AUTODETECT spr round 3 (radius: 15)
[04:46:06 -189955.671455] AUTODETECT spr round 4 (radius: 20)
[04:48:06] [worker #2] ML tree search #9, logLikelihood: -133009.051921
[04:50:48 -170082.070529] AUTODETECT spr round 5 (radius: 25)
[04:56:47 -163989.618680] SPR radius for FAST iterations: 25 (autodetect)
[04:56:47 -163989.618680] Model parameter optimization (eps = 3.000000)
[04:57:23 -163849.660746] FAST spr round 1 (radius: 25)
[05:00:46 -135357.881884] FAST spr round 2 (radius: 25)
[05:03:24] [worker #1] ML tree search #11, logLikelihood: -133007.438098
[05:03:35 -133275.782672] FAST spr round 3 (radius: 25)
[05:06:06 -133100.022794] FAST spr round 4 (radius: 25)
[05:08:29 -133060.885575] FAST spr round 5 (radius: 25)
[05:10:43 -133060.003433] FAST spr round 6 (radius: 25)
[05:12:51 -133060.003393] Model parameter optimization (eps = 1.000000)
[05:13:12 -133047.205847] SLOW spr round 1 (radius: 5)
[05:16:06 -133022.289874] SLOW spr round 2 (radius: 5)
[05:19:05 -133020.268376] SLOW spr round 3 (radius: 5)
[05:21:59 -133020.268105] SLOW spr round 4 (radius: 10)
[05:24:57 -133014.186122] SLOW spr round 5 (radius: 5)
[05:28:31 -133010.720916] SLOW spr round 6 (radius: 5)
[05:31:38 -133010.720810] SLOW spr round 7 (radius: 10)
[05:34:43 -133010.720805] SLOW spr round 8 (radius: 15)
[05:39:19 -133009.925427] SLOW spr round 9 (radius: 5)
[05:43:11 -133008.181437] SLOW spr round 10 (radius: 5)
[05:46:26 -133008.181181] SLOW spr round 11 (radius: 10)
[05:49:32 -133008.181176] SLOW spr round 12 (radius: 15)
[05:53:58 -133005.706758] SLOW spr round 13 (radius: 5)
[05:57:40 -133005.704960] SLOW spr round 14 (radius: 10)
[06:01:05 -133005.702759] SLOW spr round 15 (radius: 15)
[06:05:29 -133005.702756] SLOW spr round 16 (radius: 20)
[06:11:39] [worker #2] ML tree search #12, logLikelihood: -133010.700297
[06:13:27 -133005.702753] SLOW spr round 17 (radius: 25)
[06:24:41 -133005.702750] Model parameter optimization (eps = 0.100000)

[06:24:49] [worker #0] ML tree search #10, logLikelihood: -133005.667003

[06:24:49 -647679.448109] Initial branch length optimization
[06:24:59 -554035.632849] Model parameter optimization (eps = 10.000000)
[06:26:01 -551093.507622] AUTODETECT spr round 1 (radius: 5)
[06:27:04] [worker #1] ML tree search #14, logLikelihood: -133011.828432
[06:29:22 -335523.164180] AUTODETECT spr round 2 (radius: 10)
[06:32:53 -231907.594793] AUTODETECT spr round 3 (radius: 15)
[06:36:48 -184062.255315] AUTODETECT spr round 4 (radius: 20)
[06:41:21 -161013.209090] AUTODETECT spr round 5 (radius: 25)
[06:47:21 -159328.086353] SPR radius for FAST iterations: 25 (autodetect)
[06:47:21 -159328.086353] Model parameter optimization (eps = 3.000000)
[06:47:51 -159256.403855] FAST spr round 1 (radius: 25)
[06:51:32 -134226.712788] FAST spr round 2 (radius: 25)
[06:54:22 -133152.274088] FAST spr round 3 (radius: 25)
[06:56:51 -133092.572045] FAST spr round 4 (radius: 25)
[06:59:09 -133089.661301] FAST spr round 5 (radius: 25)
[07:01:22 -133089.661044] Model parameter optimization (eps = 1.000000)
[07:01:40 -133070.276922] SLOW spr round 1 (radius: 5)
[07:04:47 -133036.366035] SLOW spr round 2 (radius: 5)
[07:07:44 -133033.649872] SLOW spr round 3 (radius: 5)
[07:10:41 -133031.267300] SLOW spr round 4 (radius: 5)
[07:13:35 -133031.266912] SLOW spr round 5 (radius: 10)
[07:16:33 -133027.843737] SLOW spr round 6 (radius: 5)
[07:20:03 -133025.712347] SLOW spr round 7 (radius: 5)
[07:23:08 -133025.712321] SLOW spr round 8 (radius: 10)
[07:26:09 -133025.712317] SLOW spr round 9 (radius: 15)
[07:30:35 -133025.712314] SLOW spr round 10 (radius: 20)
[07:38:29 -133025.712310] SLOW spr round 11 (radius: 25)
[07:43:18] [worker #2] ML tree search #15, logLikelihood: -133007.519223
[07:45:12] [worker #1] ML tree search #17, logLikelihood: -133021.696674
[07:50:04 -133025.712307] Model parameter optimization (eps = 0.100000)

[07:50:12] [worker #0] ML tree search #13, logLikelihood: -133025.684176

[07:50:12 -641882.296630] Initial branch length optimization
[07:50:18 -547481.612967] Model parameter optimization (eps = 10.000000)
[07:51:05 -544285.488720] AUTODETECT spr round 1 (radius: 5)
[07:54:28 -348375.298174] AUTODETECT spr round 2 (radius: 10)
[07:57:56 -239361.911252] AUTODETECT spr round 3 (radius: 15)
[08:01:36 -183304.395781] AUTODETECT spr round 4 (radius: 20)
[08:06:34 -152864.562830] AUTODETECT spr round 5 (radius: 25)
[08:12:25 -151651.645685] SPR radius for FAST iterations: 25 (autodetect)
[08:12:25 -151651.645685] Model parameter optimization (eps = 3.000000)
[08:12:54 -151581.573041] FAST spr round 1 (radius: 25)
[08:16:26 -133793.222917] FAST spr round 2 (radius: 25)
[08:19:18 -133138.864245] FAST spr round 3 (radius: 25)
[08:21:51 -133078.442866] FAST spr round 4 (radius: 25)
[08:24:12 -133068.311445] FAST spr round 5 (radius: 25)
[08:26:23 -133067.949698] FAST spr round 6 (radius: 25)
[08:28:31 -133067.949447] Model parameter optimization (eps = 1.000000)
[08:28:50 -133054.374782] SLOW spr round 1 (radius: 5)
[08:31:52 -133026.861035] SLOW spr round 2 (radius: 5)
[08:34:50 -133020.121430] SLOW spr round 3 (radius: 5)
[08:37:44 -133019.685771] SLOW spr round 4 (radius: 5)
[08:40:33 -133019.685726] SLOW spr round 5 (radius: 10)
[08:43:26 -133019.685725] SLOW spr round 6 (radius: 15)
[08:48:00 -133019.685724] SLOW spr round 7 (radius: 20)
[08:55:52 -133019.685724] SLOW spr round 8 (radius: 25)
[09:07:21 -133019.685723] Model parameter optimization (eps = 0.100000)

[09:07:28] [worker #0] ML tree search #16, logLikelihood: -133019.657823

[09:07:28 -643771.337188] Initial branch length optimization
[09:07:34 -552992.449006] Model parameter optimization (eps = 10.000000)
[09:08:31 -549806.433754] AUTODETECT spr round 1 (radius: 5)
[09:11:46 -336691.376599] AUTODETECT spr round 2 (radius: 10)
[09:15:03 -230809.452413] AUTODETECT spr round 3 (radius: 15)
[09:15:12] [worker #1] ML tree search #20, logLikelihood: -133015.926153
[09:18:39 -179782.458367] AUTODETECT spr round 4 (radius: 20)
[09:23:06 -171978.167017] AUTODETECT spr round 5 (radius: 25)
[09:27:45] [worker #2] ML tree search #18, logLikelihood: -133004.432232
[09:28:36 -158885.912889] SPR radius for FAST iterations: 25 (autodetect)
[09:28:36 -158885.912889] Model parameter optimization (eps = 3.000000)
[09:29:09 -158795.366742] FAST spr round 1 (radius: 25)
[09:32:30 -134428.136250] FAST spr round 2 (radius: 25)
[09:35:07 -133147.127683] FAST spr round 3 (radius: 25)
[09:37:31 -133077.817427] FAST spr round 4 (radius: 25)
[09:39:47 -133066.178114] FAST spr round 5 (radius: 25)
[09:42:02 -133051.381728] FAST spr round 6 (radius: 25)
[09:44:08 -133051.381102] Model parameter optimization (eps = 1.000000)
[09:44:28 -133044.976252] SLOW spr round 1 (radius: 5)
[09:47:20 -133015.761675] SLOW spr round 2 (radius: 5)
[09:50:08 -133011.168806] SLOW spr round 3 (radius: 5)
[09:52:57 -133004.950775] SLOW spr round 4 (radius: 5)
[09:55:40 -133004.708786] SLOW spr round 5 (radius: 5)
[09:58:21 -133004.708776] SLOW spr round 6 (radius: 10)
[10:01:11 -132999.468835] SLOW spr round 7 (radius: 5)
[10:04:33 -132996.479989] SLOW spr round 8 (radius: 5)
[10:07:32 -132996.479979] SLOW spr round 9 (radius: 10)
[10:10:28 -132996.479977] SLOW spr round 10 (radius: 15)
[10:14:44 -132996.439961] SLOW spr round 11 (radius: 20)
[10:22:17 -132996.439959] SLOW spr round 12 (radius: 25)
[10:33:14 -132996.439958] Model parameter optimization (eps = 0.100000)

[10:33:24] [worker #0] ML tree search #19, logLikelihood: -132996.272281


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.170967,0.313926) (0.167739,0.458962) (0.381754,0.953899) (0.279540,1.807213) 
   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: -132996.272281

AIC score: 270002.544562 / AICc score: 8314062.544562 / BIC score: 278145.765685
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=429).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P17661/3_mltree/P17661.raxml.log

Analysis started: 24-Jun-2021 13:41:13 / finished: 25-Jun-2021 00:14:38

Elapsed time: 38004.798 seconds