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 14-Jul-2021 11:21:10 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/2_msa/P78381_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381 --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_300621/phylogeny-snakemake/results/P78381/2_msa/P78381_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 379 sites

WARNING: Sequences tr_M3YLG7_M3YLG7_MUSPF_9669 and tr_A0A2Y9J5C7_A0A2Y9J5C7_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1RR48_G1RR48_NOMLE_61853 and tr_Q5RAS4_Q5RAS4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QT26_G3QT26_GORGO_9595 and tr_H2R738_H2R738_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QT26_G3QT26_GORGO_9595 and sp_P78382_S35A1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QT26_G3QT26_GORGO_9595 and tr_A0A2R9C1A2_A0A2R9C1A2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S1I8_G3S1I8_GORGO_9595 and tr_A0A2R8ZWY1_A0A2R8ZWY1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q29HR6_Q29HR6_DROPS_46245 and tr_B4GYF7_B4GYF7_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3STL5_A0A2I3STL5_PANTR_9598 and tr_A0A2R9C118_A0A2R9C118_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FAD8_F9FAD8_FUSOF_660025 and tr_N4UES5_N4UES5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FAD8_F9FAD8_FUSOF_660025 and tr_X0DHX0_X0DHX0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FAD8_F9FAD8_FUSOF_660025 and tr_A0A2H3TKF1_A0A2H3TKF1_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9FAD8_F9FAD8_FUSOF_660025 and tr_A0A2H3HU98_A0A2H3HU98_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A1P6CBH3_A0A1P6CBH3_BRUMA_6279 and tr_A0A0N4TR32_A0A0N4TR32_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A1P6CBH3_A0A1P6CBH3_BRUMA_6279 and tr_A0A0R3QV02_A0A0R3QV02_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A0A1D5RI26_A0A1D5RI26_MACMU_9544 and tr_G7Q2P0_G7Q2P0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5RI26_A0A1D5RI26_MACMU_9544 and tr_A0A096NBK5_A0A096NBK5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5RI26_A0A1D5RI26_MACMU_9544 and tr_A0A2K5NE78_A0A2K5NE78_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5RI26_A0A1D5RI26_MACMU_9544 and tr_A0A2K6C546_A0A2K6C546_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5RI26_A0A1D5RI26_MACMU_9544 and tr_A0A2K5ZNB7_A0A2K5ZNB7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F4P4L0_F4P4L0_BATDJ_684364 and tr_A0A177WG25_A0A177WG25_BATDE_403673 are exactly identical!
WARNING: Sequences tr_H0Z4I6_H0Z4I6_TAEGU_59729 and tr_A0A218VF06_A0A218VF06_9PASE_299123 are exactly identical!
WARNING: Sequences tr_B3RNG5_B3RNG5_TRIAD_10228 and tr_A0A369SC69_A0A369SC69_9METZ_287889 are exactly identical!
WARNING: Sequences sp_Q6YC49_S35A3_BOVIN_9913 and tr_A0A383Z3Z0_A0A383Z3Z0_BALAS_310752 are exactly identical!
WARNING: Sequences tr_S0DNP5_S0DNP5_GIBF5_1279085 and tr_A0A365N7R1_A0A365N7R1_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_V2XPR8_V2XPR8_MONRO_1381753 and tr_A0A0W0FLK3_A0A0W0FLK3_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_V2YMK7_V2YMK7_MONRO_1381753 and tr_A0A0W0GDU6_A0A0W0GDU6_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QFZ8_W2QFZ8_PHYPN_761204 and tr_A0A0W8D214_A0A0W8D214_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QFZ8_W2QFZ8_PHYPN_761204 and tr_W2NQN1_W2NQN1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A044R6H3_A0A044R6H3_ONCVO_6282 and tr_A0A182EE85_A0A182EE85_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A2I3MTZ6_A0A2I3MTZ6_PAPAN_9555 and tr_A0A2K6CVM3_A0A2K6CVM3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MTZ6_A0A2I3MTZ6_PAPAN_9555 and tr_A0A2K5Y9T3_A0A2K5Y9T3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A094E3C1_A0A094E3C1_9PEZI_1420912 and tr_A0A1B8GTT7_A0A1B8GTT7_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0V1CMD2_A0A0V1CMD2_TRIBR_45882 and tr_A0A0V1P1X7_A0A0V1P1X7_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A164S2Q0_A0A164S2Q0_9HOMO_1314777 and tr_A0A166FQ97_A0A166FQ97_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A2K6D555_A0A2K6D555_MACNE_9545 and tr_A0A2K5ZN38_A0A2K5ZN38_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2N5SSU4_A0A2N5SSU4_9BASI_200324 and tr_A0A2N5TFL6_A0A2N5TFL6_9BASI_200324 are exactly identical!
WARNING: Duplicate sequences found: 36

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.raxml.reduced.phy

Alignment comprises 1 partitions and 379 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 379 / 379
Gaps: 13.54 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.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 / 190 / 15200
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -600099.128370] Initial branch length optimization
[00:00:06 -513475.679762] Model parameter optimization (eps = 10.000000)
[00:01:02 -512116.792589] AUTODETECT spr round 1 (radius: 5)
[00:04:09 -368276.932365] AUTODETECT spr round 2 (radius: 10)
[00:07:35 -270108.444736] AUTODETECT spr round 3 (radius: 15)
[00:11:38 -232494.957205] AUTODETECT spr round 4 (radius: 20)
[00:16:11 -218271.377824] AUTODETECT spr round 5 (radius: 25)
[00:21:39 -214791.658127] SPR radius for FAST iterations: 25 (autodetect)
[00:21:39 -214791.658127] Model parameter optimization (eps = 3.000000)
[00:22:06 -214665.885992] FAST spr round 1 (radius: 25)
[00:26:29 -189029.971966] FAST spr round 2 (radius: 25)
[00:29:34 -188307.382955] FAST spr round 3 (radius: 25)
[00:32:16 -188190.863074] FAST spr round 4 (radius: 25)
[00:34:38 -188150.594907] FAST spr round 5 (radius: 25)
[00:36:49 -188146.059602] FAST spr round 6 (radius: 25)
[00:38:55 -188142.668545] FAST spr round 7 (radius: 25)
[00:40:56 -188140.487269] FAST spr round 8 (radius: 25)
[00:42:56 -188140.486738] Model parameter optimization (eps = 1.000000)
[00:43:18 -188126.195683] SLOW spr round 1 (radius: 5)
[00:46:19 -188088.984201] SLOW spr round 2 (radius: 5)
[00:49:17 -188075.299454] SLOW spr round 3 (radius: 5)
[00:52:07 -188069.682088] SLOW spr round 4 (radius: 5)
[00:54:50 -188069.682023] SLOW spr round 5 (radius: 10)
[00:57:48 -188068.061743] SLOW spr round 6 (radius: 5)
[01:01:18 -188065.688401] SLOW spr round 7 (radius: 5)
[01:04:22 -188063.300485] SLOW spr round 8 (radius: 5)
[01:07:13 -188063.300367] SLOW spr round 9 (radius: 10)
[01:10:13 -188063.300365] SLOW spr round 10 (radius: 15)
[01:15:25 -188063.300365] SLOW spr round 11 (radius: 20)
[01:18:00] [worker #1] ML tree search #2, logLikelihood: -188080.293812
[01:23:06 -188063.300365] SLOW spr round 12 (radius: 25)
[01:30:10] [worker #2] ML tree search #3, logLikelihood: -188062.730600
[01:32:48 -188063.300365] Model parameter optimization (eps = 0.100000)

[01:32:55] [worker #0] ML tree search #1, logLikelihood: -188063.288628

[01:32:55 -601929.260714] Initial branch length optimization
[01:33:02 -515370.671979] Model parameter optimization (eps = 10.000000)
[01:33:42 -514019.750999] AUTODETECT spr round 1 (radius: 5)
[01:36:52 -381486.212324] AUTODETECT spr round 2 (radius: 10)
[01:40:24 -272386.075309] AUTODETECT spr round 3 (radius: 15)
[01:44:29 -233048.718774] AUTODETECT spr round 4 (radius: 20)
[01:49:02 -221594.413732] AUTODETECT spr round 5 (radius: 25)
[01:54:19 -216307.047513] SPR radius for FAST iterations: 25 (autodetect)
[01:54:19 -216307.047513] Model parameter optimization (eps = 3.000000)
[01:54:47 -216048.764257] FAST spr round 1 (radius: 25)
[01:59:17 -189285.080288] FAST spr round 2 (radius: 25)
[02:02:10 -188202.404329] FAST spr round 3 (radius: 25)
[02:04:46 -188164.836683] FAST spr round 4 (radius: 25)
[02:07:01 -188160.369966] FAST spr round 5 (radius: 25)
[02:09:07 -188160.368599] Model parameter optimization (eps = 1.000000)
[02:09:29 -188157.451495] SLOW spr round 1 (radius: 5)
[02:12:33 -188107.430408] SLOW spr round 2 (radius: 5)
[02:15:28 -188104.906522] SLOW spr round 3 (radius: 5)
[02:18:17 -188104.906408] SLOW spr round 4 (radius: 10)
[02:21:14 -188104.906405] SLOW spr round 5 (radius: 15)
[02:26:34 -188103.380809] SLOW spr round 6 (radius: 5)
[02:30:14 -188103.380781] SLOW spr round 7 (radius: 10)
[02:33:45 -188103.380779] SLOW spr round 8 (radius: 15)
[02:38:39 -188103.380778] SLOW spr round 9 (radius: 20)
[02:45:59] [worker #1] ML tree search #5, logLikelihood: -188085.862924
[02:46:48 -188103.380777] SLOW spr round 10 (radius: 25)
[02:52:44] [worker #2] ML tree search #6, logLikelihood: -188105.500537
[02:56:53 -188103.380777] Model parameter optimization (eps = 0.100000)

[02:56:59] [worker #0] ML tree search #4, logLikelihood: -188103.343889

[02:57:00 -599214.960229] Initial branch length optimization
[02:57:06 -512753.070817] Model parameter optimization (eps = 10.000000)
[02:57:58 -511490.662487] AUTODETECT spr round 1 (radius: 5)
[03:01:05 -377225.603603] AUTODETECT spr round 2 (radius: 10)
[03:04:33 -277435.576755] AUTODETECT spr round 3 (radius: 15)
[03:08:38 -227473.621007] AUTODETECT spr round 4 (radius: 20)
[03:13:36 -212881.545959] AUTODETECT spr round 5 (radius: 25)
[03:18:51 -212336.982003] SPR radius for FAST iterations: 25 (autodetect)
[03:18:51 -212336.982003] Model parameter optimization (eps = 3.000000)
[03:19:24 -212096.601749] FAST spr round 1 (radius: 25)
[03:23:51 -189027.638268] FAST spr round 2 (radius: 25)
[03:26:58 -188242.348682] FAST spr round 3 (radius: 25)
[03:29:38 -188176.151289] FAST spr round 4 (radius: 25)
[03:32:03 -188155.984973] FAST spr round 5 (radius: 25)
[03:34:12 -188150.855760] FAST spr round 6 (radius: 25)
[03:36:19 -188149.729722] FAST spr round 7 (radius: 25)
[03:38:25 -188144.260574] FAST spr round 8 (radius: 25)
[03:40:28 -188144.259742] Model parameter optimization (eps = 1.000000)
[03:40:40 -188142.636397] SLOW spr round 1 (radius: 5)
[03:43:39 -188085.755854] SLOW spr round 2 (radius: 5)
[03:46:36 -188073.979625] SLOW spr round 3 (radius: 5)
[03:49:31 -188064.488207] SLOW spr round 4 (radius: 5)
[03:52:21 -188061.854336] SLOW spr round 5 (radius: 5)
[03:55:08 -188061.539681] SLOW spr round 6 (radius: 5)
[03:57:53 -188061.539620] SLOW spr round 7 (radius: 10)
[04:00:51 -188060.228701] SLOW spr round 8 (radius: 5)
[04:04:23 -188055.007142] SLOW spr round 9 (radius: 5)
[04:07:29 -188055.006787] SLOW spr round 10 (radius: 10)
[04:10:30 -188055.006760] SLOW spr round 11 (radius: 15)
[04:15:31 -188054.323938] SLOW spr round 12 (radius: 5)
[04:19:11 -188054.323487] SLOW spr round 13 (radius: 10)
[04:21:25] [worker #1] ML tree search #8, logLikelihood: -188078.528433
[04:22:38 -188054.323487] SLOW spr round 14 (radius: 15)
[04:27:26 -188054.323487] SLOW spr round 15 (radius: 20)
[04:34:51 -188054.323487] SLOW spr round 16 (radius: 25)
[04:36:22] [worker #2] ML tree search #9, logLikelihood: -188091.354295
[04:43:55 -188054.323487] Model parameter optimization (eps = 0.100000)

[04:44:06] [worker #0] ML tree search #7, logLikelihood: -188054.216933

[04:44:06 -600604.285490] Initial branch length optimization
[04:44:13 -512434.897262] Model parameter optimization (eps = 10.000000)
[04:45:10 -511140.345540] AUTODETECT spr round 1 (radius: 5)
[04:48:21 -380305.495875] AUTODETECT spr round 2 (radius: 10)
[04:51:54 -299282.686542] AUTODETECT spr round 3 (radius: 15)
[04:55:58 -234172.137683] AUTODETECT spr round 4 (radius: 20)
[05:00:24 -216214.029475] AUTODETECT spr round 5 (radius: 25)
[05:05:23 -213959.837682] SPR radius for FAST iterations: 25 (autodetect)
[05:05:23 -213959.837682] Model parameter optimization (eps = 3.000000)
[05:05:52 -213733.938066] FAST spr round 1 (radius: 25)
[05:10:15 -189469.638033] FAST spr round 2 (radius: 25)
[05:13:18 -188256.985160] FAST spr round 3 (radius: 25)
[05:15:56 -188176.614173] FAST spr round 4 (radius: 25)
[05:18:16 -188149.023920] FAST spr round 5 (radius: 25)
[05:20:27 -188140.610469] FAST spr round 6 (radius: 25)
[05:22:35 -188135.507815] FAST spr round 7 (radius: 25)
[05:24:39 -188135.507048] Model parameter optimization (eps = 1.000000)
[05:25:01 -188128.735410] SLOW spr round 1 (radius: 5)
[05:28:09 -188076.651440] SLOW spr round 2 (radius: 5)
[05:31:05 -188069.503889] SLOW spr round 3 (radius: 5)
[05:33:52 -188069.502452] SLOW spr round 4 (radius: 10)
[05:36:50 -188069.501479] SLOW spr round 5 (radius: 15)
[05:42:07 -188069.501064] SLOW spr round 6 (radius: 20)
[05:45:33] [worker #1] ML tree search #11, logLikelihood: -188074.123691
[05:49:27 -188069.501037] SLOW spr round 7 (radius: 25)
[05:53:06] [worker #2] ML tree search #12, logLikelihood: -188079.384940
[05:58:54 -188069.501024] Model parameter optimization (eps = 0.100000)

[05:59:01] [worker #0] ML tree search #10, logLikelihood: -188069.472757

[05:59:01 -601519.015829] Initial branch length optimization
[05:59:09 -514169.702164] Model parameter optimization (eps = 10.000000)
[05:59:50 -512901.743050] AUTODETECT spr round 1 (radius: 5)
[06:03:00 -372815.205506] AUTODETECT spr round 2 (radius: 10)
[06:06:32 -284901.491666] AUTODETECT spr round 3 (radius: 15)
[06:10:34 -249948.020181] AUTODETECT spr round 4 (radius: 20)
[06:16:10 -223553.989459] AUTODETECT spr round 5 (radius: 25)
[06:21:21 -217017.191264] SPR radius for FAST iterations: 25 (autodetect)
[06:21:21 -217017.191264] Model parameter optimization (eps = 3.000000)
[06:21:53 -216790.299199] FAST spr round 1 (radius: 25)
[06:26:29 -189425.520357] FAST spr round 2 (radius: 25)
[06:29:31 -188253.904877] FAST spr round 3 (radius: 25)
[06:32:07 -188186.209012] FAST spr round 4 (radius: 25)
[06:34:25 -188180.446364] FAST spr round 5 (radius: 25)
[06:36:36 -188174.760659] FAST spr round 6 (radius: 25)
[06:38:40 -188174.760641] Model parameter optimization (eps = 1.000000)
[06:39:00 -188167.065555] SLOW spr round 1 (radius: 5)
[06:42:03 -188094.915684] SLOW spr round 2 (radius: 5)
[06:45:00 -188091.216224] SLOW spr round 3 (radius: 5)
[06:47:50 -188091.215602] SLOW spr round 4 (radius: 10)
[06:50:48 -188090.937832] SLOW spr round 5 (radius: 5)
[06:54:22 -188090.937754] SLOW spr round 6 (radius: 10)
[06:57:43 -188090.570060] SLOW spr round 7 (radius: 5)
[07:01:10 -188090.569935] SLOW spr round 8 (radius: 10)
[07:04:25 -188090.569935] SLOW spr round 9 (radius: 15)
[07:09:14 -188090.569935] SLOW spr round 10 (radius: 20)
[07:16:26 -188090.569935] SLOW spr round 11 (radius: 25)
[07:16:48] [worker #2] ML tree search #15, logLikelihood: -188109.261153
[07:25:22 -188090.569935] Model parameter optimization (eps = 0.100000)

[07:25:28] [worker #0] ML tree search #13, logLikelihood: -188090.560900

[07:25:28 -595920.980798] Initial branch length optimization
[07:25:33 -508940.261213] Model parameter optimization (eps = 10.000000)
[07:26:23 -507670.889204] AUTODETECT spr round 1 (radius: 5)
[07:29:31 -371163.628478] AUTODETECT spr round 2 (radius: 10)
[07:33:02 -281892.481510] AUTODETECT spr round 3 (radius: 15)
[07:37:09 -238202.381484] AUTODETECT spr round 4 (radius: 20)
[07:42:49 -217441.739416] AUTODETECT spr round 5 (radius: 25)
[07:49:20 -216219.874134] SPR radius for FAST iterations: 25 (autodetect)
[07:49:20 -216219.874134] Model parameter optimization (eps = 3.000000)
[07:49:48 -216058.673435] FAST spr round 1 (radius: 25)
[07:54:26 -188827.722051] FAST spr round 2 (radius: 25)
[07:57:34 -188230.722685] FAST spr round 3 (radius: 25)
[08:00:09 -188175.814908] FAST spr round 4 (radius: 25)
[08:02:29 -188152.578159] FAST spr round 5 (radius: 25)
[08:04:37 -188152.577439] Model parameter optimization (eps = 1.000000)
[08:04:49 -188151.378407] SLOW spr round 1 (radius: 5)
[08:07:58 -188091.743366] SLOW spr round 2 (radius: 5)
[08:10:56 -188089.840451] SLOW spr round 3 (radius: 5)
[08:13:51 -188086.855003] SLOW spr round 4 (radius: 5)
[08:16:38 -188086.853924] SLOW spr round 5 (radius: 10)
[08:19:36 -188085.026204] SLOW spr round 6 (radius: 5)
[08:23:11 -188079.215943] SLOW spr round 7 (radius: 5)
[08:26:17 -188079.215757] SLOW spr round 8 (radius: 10)
[08:26:39] [worker #1] ML tree search #14, logLikelihood: -188059.651243
[08:29:20 -188079.086848] SLOW spr round 9 (radius: 5)
[08:32:49 -188079.086586] SLOW spr round 10 (radius: 10)
[08:36:07 -188079.086583] SLOW spr round 11 (radius: 15)
[08:40:53 -188079.086583] SLOW spr round 12 (radius: 20)
[08:47:47 -188079.086583] SLOW spr round 13 (radius: 25)
[08:56:25 -188079.086583] Model parameter optimization (eps = 0.100000)

[08:56:30] [worker #0] ML tree search #16, logLikelihood: -188079.073336

[08:56:31 -599548.310688] Initial branch length optimization
[08:56:38 -512922.735649] Model parameter optimization (eps = 10.000000)
[08:57:31 -511609.588531] AUTODETECT spr round 1 (radius: 5)
[09:00:48 -385815.394663] AUTODETECT spr round 2 (radius: 10)
[09:04:22 -278180.634794] AUTODETECT spr round 3 (radius: 15)
[09:08:33 -226676.307140] AUTODETECT spr round 4 (radius: 20)
[09:12:44 -215454.565613] AUTODETECT spr round 5 (radius: 25)
[09:18:05 -213330.041826] SPR radius for FAST iterations: 25 (autodetect)
[09:18:05 -213330.041826] Model parameter optimization (eps = 3.000000)
[09:18:41 -213123.269457] FAST spr round 1 (radius: 25)
[09:23:18 -188994.749013] FAST spr round 2 (radius: 25)
[09:26:27 -188288.308544] FAST spr round 3 (radius: 25)
[09:29:10 -188180.804138] FAST spr round 4 (radius: 25)
[09:31:29 -188173.059261] FAST spr round 5 (radius: 25)
[09:33:39 -188167.548329] FAST spr round 6 (radius: 25)
[09:35:45 -188167.548276] Model parameter optimization (eps = 1.000000)
[09:36:00 -188164.786468] SLOW spr round 1 (radius: 5)
[09:39:04 -188117.331722] SLOW spr round 2 (radius: 5)
[09:42:04 -188110.548603] SLOW spr round 3 (radius: 5)
[09:44:57 -188108.393231] SLOW spr round 4 (radius: 5)
[09:47:48 -188107.646152] SLOW spr round 5 (radius: 5)
[09:50:34 -188107.645725] SLOW spr round 6 (radius: 10)
[09:53:34 -188102.073536] SLOW spr round 7 (radius: 5)
[09:57:06 -188102.073428] SLOW spr round 8 (radius: 10)
[10:00:26 -188101.904777] SLOW spr round 9 (radius: 5)
[10:03:05] [worker #1] ML tree search #17, logLikelihood: -188084.690105
[10:03:59 -188093.992154] SLOW spr round 10 (radius: 5)
[10:07:11 -188093.166887] SLOW spr round 11 (radius: 5)
[10:10:06 -188093.165210] SLOW spr round 12 (radius: 10)
[10:12:15] [worker #2] ML tree search #18, logLikelihood: -188077.143289
[10:13:08 -188091.330771] SLOW spr round 13 (radius: 5)
[10:16:39 -188090.812394] SLOW spr round 14 (radius: 5)
[10:19:45 -188090.004076] SLOW spr round 15 (radius: 5)
[10:22:40 -188089.911099] SLOW spr round 16 (radius: 10)
[10:25:40 -188089.910891] SLOW spr round 17 (radius: 15)
[10:30:51 -188089.910890] SLOW spr round 18 (radius: 20)
[10:38:10 -188089.910890] SLOW spr round 19 (radius: 25)
[10:47:21 -188089.910890] Model parameter optimization (eps = 0.100000)

[10:47:27] [worker #0] ML tree search #19, logLikelihood: -188089.904183

[11:52:53] [worker #1] ML tree search #20, logLikelihood: -188082.789186

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.292844,0.313112) (0.293566,0.540364) (0.209828,1.434185) (0.203762,2.202290) 
   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: -188054.216933

AIC score: 380118.433865 / AICc score: 8424178.433865 / BIC score: 388013.193956
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=379).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P78381/3_mltree/P78381.raxml.log

Analysis started: 14-Jul-2021 11:21:10 / finished: 14-Jul-2021 23:14:04

Elapsed time: 42773.897 seconds