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 01-Jul-2021 11:07:35 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/2_msa/O60936_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/3_mltree/O60936 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/2_msa/O60936_trimmed_msa.fasta
[00:00:00] Loaded alignment with 209 taxa and 106 sites

WARNING: Sequences tr_G1QJH9_G1QJH9_NOMLE_61853 and tr_H2QB32_H2QB32_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QJH9_G1QJH9_NOMLE_61853 and sp_Q53B87_NOD2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1QJH9_G1QJH9_NOMLE_61853 and tr_A0A2R9CI28_A0A2R9CI28_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3S971_A0A2I3S971_PANTR_9598 and tr_A0A2R9C0M4_A0A2R9C0M4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R2R8_H2R2R8_PANTR_9598 and tr_A0A2R9BTP1_A0A2R9BTP1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6UJ43_F6UJ43_MACMU_9544 and tr_A0A2I3N4T6_A0A2I3N4T6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6UJ43_F6UJ43_MACMU_9544 and tr_A0A0D9QUV9_A0A0D9QUV9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6UJ43_F6UJ43_MACMU_9544 and tr_A0A2K5MB37_A0A2K5MB37_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F4NUV0_F4NUV0_BATDJ_684364 and tr_A0A177WCR9_A0A177WCR9_BATDE_403673 are exactly identical!
WARNING: Sequences tr_B3RV56_B3RV56_TRIAD_10228 and tr_A0A369SB63_A0A369SB63_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7Q140_G7Q140_MACFA_9541 and tr_A0A096NI85_A0A096NI85_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7Q140_G7Q140_MACFA_9541 and tr_A0A2K6C058_A0A2K6C058_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2K5MWG6_A0A2K5MWG6_CERAT_9531 and tr_A0A2K5YI65_A0A2K5YI65_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2H5R6V8_A0A2H5R6V8_RHIID_747089 and tr_A0A2H5RBG0_A0A2H5RBG0_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2H5TYV6_A0A2H5TYV6_RHIID_747089 and tr_A0A2H5TYY9_A0A2H5TYY9_RHIID_747089 are exactly identical!
WARNING: Duplicate sequences found: 15

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/O60936/3_mltree/O60936.raxml.reduced.phy

Alignment comprises 1 partitions and 106 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 106 / 106
Gaps: 13.57 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/3_mltree/O60936.raxml.rba

Parallelization scheme autoconfig: 2 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 209 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 106 / 8480
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -44645.201477] Initial branch length optimization
[00:00:00 -35499.954696] Model parameter optimization (eps = 10.000000)
[00:00:06 -35229.170728] AUTODETECT spr round 1 (radius: 5)
[00:00:13 -27419.336635] AUTODETECT spr round 2 (radius: 10)
[00:00:23 -23094.964011] AUTODETECT spr round 3 (radius: 15)
[00:00:35 -20858.148349] AUTODETECT spr round 4 (radius: 20)
[00:00:47 -20682.849298] AUTODETECT spr round 5 (radius: 25)
[00:00:58 -20674.588123] SPR radius for FAST iterations: 25 (autodetect)
[00:00:58 -20674.588123] Model parameter optimization (eps = 3.000000)
[00:01:08 -20643.533581] FAST spr round 1 (radius: 25)
[00:01:20 -19025.301061] FAST spr round 2 (radius: 25)
[00:01:30 -18948.158418] FAST spr round 3 (radius: 25)
[00:01:38 -18940.456611] FAST spr round 4 (radius: 25)
[00:01:44 -18939.570389] FAST spr round 5 (radius: 25)
[00:01:51 -18936.897479] FAST spr round 6 (radius: 25)
[00:01:58 -18936.896990] Model parameter optimization (eps = 1.000000)
[00:02:02 -18933.603936] SLOW spr round 1 (radius: 5)
[00:02:16 -18928.893265] SLOW spr round 2 (radius: 5)
[00:02:28 -18928.816609] SLOW spr round 3 (radius: 10)
[00:02:42 -18928.592329] SLOW spr round 4 (radius: 5)
[00:02:58 -18928.590020] SLOW spr round 5 (radius: 10)
[00:03:15 -18928.589935] SLOW spr round 6 (radius: 15)
[00:03:38 -18928.589930] SLOW spr round 7 (radius: 20)
[00:04:02 -18928.589928] SLOW spr round 8 (radius: 25)
[00:04:20 -18928.589928] Model parameter optimization (eps = 0.100000)

[00:04:22] [worker #0] ML tree search #1, logLikelihood: -18928.551962

[00:04:22 -44993.856454] Initial branch length optimization
[00:04:22 -36559.946595] Model parameter optimization (eps = 10.000000)
[00:04:27 -36520.723179] AUTODETECT spr round 1 (radius: 5)
[00:04:34 -28357.649113] AUTODETECT spr round 2 (radius: 10)
[00:04:44 -22515.235050] AUTODETECT spr round 3 (radius: 15)
[00:04:56 -20540.367621] AUTODETECT spr round 4 (radius: 20)
[00:05:10 -20489.813488] AUTODETECT spr round 5 (radius: 25)
[00:05:23 -20479.898172] SPR radius for FAST iterations: 25 (autodetect)
[00:05:23 -20479.898172] Model parameter optimization (eps = 3.000000)
[00:05:27 -20427.454277] FAST spr round 1 (radius: 25)
[00:05:39 -19066.930793] FAST spr round 2 (radius: 25)
[00:05:47] [worker #1] ML tree search #2, logLikelihood: -18924.107032
[00:05:48 -18973.975779] FAST spr round 3 (radius: 25)
[00:05:57 -18959.369526] FAST spr round 4 (radius: 25)
[00:06:04 -18957.237156] FAST spr round 5 (radius: 25)
[00:06:11 -18957.235170] Model parameter optimization (eps = 1.000000)
[00:06:14 -18953.278209] SLOW spr round 1 (radius: 5)
[00:06:27 -18952.709304] SLOW spr round 2 (radius: 5)
[00:06:39 -18951.699197] SLOW spr round 3 (radius: 5)
[00:06:51 -18951.696827] SLOW spr round 4 (radius: 10)
[00:07:04 -18950.493132] SLOW spr round 5 (radius: 5)
[00:07:20 -18950.490920] SLOW spr round 6 (radius: 10)
[00:07:36 -18950.321641] SLOW spr round 7 (radius: 5)
[00:07:51 -18950.321401] SLOW spr round 8 (radius: 10)
[00:08:06 -18950.321388] SLOW spr round 9 (radius: 15)
[00:08:30 -18950.321387] SLOW spr round 10 (radius: 20)
[00:08:54 -18950.321386] SLOW spr round 11 (radius: 25)
[00:09:13 -18950.321386] Model parameter optimization (eps = 0.100000)

[00:09:14] [worker #0] ML tree search #3, logLikelihood: -18950.310243

[00:09:14 -44644.430371] Initial branch length optimization
[00:09:14 -35514.221451] Model parameter optimization (eps = 10.000000)
[00:09:23 -35273.044686] AUTODETECT spr round 1 (radius: 5)
[00:09:29 -28066.569361] AUTODETECT spr round 2 (radius: 10)
[00:09:39 -23095.978712] AUTODETECT spr round 3 (radius: 15)
[00:09:50 -21128.844404] AUTODETECT spr round 4 (radius: 20)
[00:10:03 -20481.242557] AUTODETECT spr round 5 (radius: 25)
[00:10:15 -20469.972526] SPR radius for FAST iterations: 25 (autodetect)
[00:10:15 -20469.972526] Model parameter optimization (eps = 3.000000)
[00:10:22 -20433.753594] FAST spr round 1 (radius: 25)
[00:10:33 -19010.608550] FAST spr round 2 (radius: 25)
[00:10:42 -18954.803471] FAST spr round 3 (radius: 25)
[00:10:50 -18935.672918] FAST spr round 4 (radius: 25)
[00:10:57 -18931.830644] FAST spr round 5 (radius: 25)
[00:11:04 -18931.830189] Model parameter optimization (eps = 1.000000)
[00:11:07 -18930.719138] SLOW spr round 1 (radius: 5)
[00:11:20 -18928.447402] SLOW spr round 2 (radius: 5)
[00:11:32 -18928.446213] SLOW spr round 3 (radius: 10)
[00:11:44 -18928.009235] SLOW spr round 4 (radius: 5)
[00:12:00 -18926.833733] SLOW spr round 5 (radius: 5)
[00:12:14 -18926.830691] SLOW spr round 6 (radius: 10)
[00:12:27 -18926.830207] SLOW spr round 7 (radius: 15)
[00:12:49 -18926.830132] SLOW spr round 8 (radius: 20)
[00:13:12 -18924.832938] SLOW spr round 9 (radius: 5)
[00:13:29 -18924.825847] SLOW spr round 10 (radius: 10)
[00:13:34] [worker #1] ML tree search #4, logLikelihood: -18923.938632
[00:13:46 -18924.720933] SLOW spr round 11 (radius: 5)
[00:14:01 -18924.717927] SLOW spr round 12 (radius: 10)
[00:14:16 -18924.717829] SLOW spr round 13 (radius: 15)
[00:14:38 -18924.655445] SLOW spr round 14 (radius: 20)
[00:15:01 -18924.636194] SLOW spr round 15 (radius: 25)
[00:15:19 -18924.632054] Model parameter optimization (eps = 0.100000)

[00:15:21] [worker #0] ML tree search #5, logLikelihood: -18924.549623

[00:15:21 -44744.585469] Initial branch length optimization
[00:15:21 -35291.719540] Model parameter optimization (eps = 10.000000)
[00:15:29 -35241.005384] AUTODETECT spr round 1 (radius: 5)
[00:15:35 -28522.902788] AUTODETECT spr round 2 (radius: 10)
[00:15:45 -23008.376577] AUTODETECT spr round 3 (radius: 15)
[00:15:57 -20774.148529] AUTODETECT spr round 4 (radius: 20)
[00:16:11 -20736.060775] AUTODETECT spr round 5 (radius: 25)
[00:16:21 -20718.373494] SPR radius for FAST iterations: 25 (autodetect)
[00:16:21 -20718.373494] Model parameter optimization (eps = 3.000000)
[00:16:29 -20613.028539] FAST spr round 1 (radius: 25)
[00:16:42 -19023.665881] FAST spr round 2 (radius: 25)
[00:16:52 -18954.666957] FAST spr round 3 (radius: 25)
[00:17:00 -18947.028362] FAST spr round 4 (radius: 25)
[00:17:07 -18941.495499] FAST spr round 5 (radius: 25)
[00:17:14 -18939.165161] FAST spr round 6 (radius: 25)
[00:17:20 -18939.164218] Model parameter optimization (eps = 1.000000)
[00:17:23 -18937.662265] SLOW spr round 1 (radius: 5)
[00:17:36 -18935.485728] SLOW spr round 2 (radius: 5)
[00:17:37] [worker #1] ML tree search #6, logLikelihood: -18924.087305
[00:17:48 -18935.485199] SLOW spr round 3 (radius: 10)
[00:18:02 -18931.807172] SLOW spr round 4 (radius: 5)
[00:18:18 -18931.686479] SLOW spr round 5 (radius: 5)
[00:18:32 -18931.684556] SLOW spr round 6 (radius: 10)
[00:18:47 -18927.854977] SLOW spr round 7 (radius: 5)
[00:19:03 -18926.307844] SLOW spr round 8 (radius: 5)
[00:19:16 -18926.306609] SLOW spr round 9 (radius: 10)
[00:19:30 -18926.210993] SLOW spr round 10 (radius: 15)
[00:19:54 -18926.209686] SLOW spr round 11 (radius: 20)
[00:20:17 -18926.209579] SLOW spr round 12 (radius: 25)
[00:20:34 -18926.209570] Model parameter optimization (eps = 0.100000)

[00:20:37] [worker #0] ML tree search #7, logLikelihood: -18926.061729

[00:20:37 -44371.704197] Initial branch length optimization
[00:20:37 -35476.461554] Model parameter optimization (eps = 10.000000)
[00:20:44 -35179.547526] AUTODETECT spr round 1 (radius: 5)
[00:20:51 -27324.816685] AUTODETECT spr round 2 (radius: 10)
[00:21:00 -22434.635468] AUTODETECT spr round 3 (radius: 15)
[00:21:13 -20893.086671] AUTODETECT spr round 4 (radius: 20)
[00:21:24 -20140.200519] AUTODETECT spr round 5 (radius: 25)
[00:21:37 -20139.567753] SPR radius for FAST iterations: 25 (autodetect)
[00:21:37 -20139.567753] Model parameter optimization (eps = 3.000000)
[00:21:41 -20113.796238] FAST spr round 1 (radius: 25)
[00:21:52 -19024.598479] FAST spr round 2 (radius: 25)
[00:22:01 -18953.938888] FAST spr round 3 (radius: 25)
[00:22:09 -18935.120975] FAST spr round 4 (radius: 25)
[00:22:16 -18934.570427] FAST spr round 5 (radius: 25)
[00:22:23 -18934.568685] Model parameter optimization (eps = 1.000000)
[00:22:25 -18933.975651] SLOW spr round 1 (radius: 5)
[00:22:39 -18933.075517] SLOW spr round 2 (radius: 5)
[00:22:51 -18933.070761] SLOW spr round 3 (radius: 10)
[00:23:05 -18932.562798] SLOW spr round 4 (radius: 5)
[00:23:22 -18926.090954] SLOW spr round 5 (radius: 5)
[00:23:36 -18925.076987] SLOW spr round 6 (radius: 5)
[00:23:49 -18925.076820] SLOW spr round 7 (radius: 10)
[00:24:03 -18924.167373] SLOW spr round 8 (radius: 5)
[00:24:19 -18924.145461] SLOW spr round 9 (radius: 10)
[00:24:34] [worker #1] ML tree search #8, logLikelihood: -18923.212381
[00:24:36 -18924.144018] SLOW spr round 10 (radius: 15)
[00:24:59 -18923.234077] SLOW spr round 11 (radius: 5)
[00:25:16 -18923.094515] SLOW spr round 12 (radius: 5)
[00:25:30 -18923.094383] SLOW spr round 13 (radius: 10)
[00:25:45 -18923.094257] SLOW spr round 14 (radius: 15)
[00:26:09 -18923.094131] SLOW spr round 15 (radius: 20)
[00:26:32 -18923.094006] SLOW spr round 16 (radius: 25)
[00:26:50 -18921.030258] SLOW spr round 17 (radius: 5)
[00:27:08 -18920.910546] SLOW spr round 18 (radius: 5)
[00:27:23 -18920.909715] SLOW spr round 19 (radius: 10)
[00:27:38 -18920.909625] SLOW spr round 20 (radius: 15)
[00:28:01 -18920.521269] SLOW spr round 21 (radius: 5)
[00:28:18 -18920.519336] SLOW spr round 22 (radius: 10)
[00:28:35 -18920.519270] SLOW spr round 23 (radius: 15)
[00:28:58 -18920.519267] SLOW spr round 24 (radius: 20)
[00:29:22 -18920.519267] SLOW spr round 25 (radius: 25)
[00:29:40 -18920.519267] Model parameter optimization (eps = 0.100000)

[00:29:43] [worker #0] ML tree search #9, logLikelihood: -18919.854267

[00:29:43 -44388.735776] Initial branch length optimization
[00:29:43 -35697.438258] Model parameter optimization (eps = 10.000000)
[00:29:50 -35403.014976] AUTODETECT spr round 1 (radius: 5)
[00:29:57 -28044.684758] AUTODETECT spr round 2 (radius: 10)
[00:30:08 -21720.227529] AUTODETECT spr round 3 (radius: 15)
[00:30:20 -20596.917620] AUTODETECT spr round 4 (radius: 20)
[00:30:33 -20266.873824] AUTODETECT spr round 5 (radius: 25)
[00:30:44 -20263.150943] SPR radius for FAST iterations: 25 (autodetect)
[00:30:44 -20263.150943] Model parameter optimization (eps = 3.000000)
[00:30:48 -20239.676006] FAST spr round 1 (radius: 25)
[00:31:00 -18990.861434] FAST spr round 2 (radius: 25)
[00:31:09 -18955.340987] FAST spr round 3 (radius: 25)
[00:31:17 -18945.204090] FAST spr round 4 (radius: 25)
[00:31:24 -18937.641988] FAST spr round 5 (radius: 25)
[00:31:25] [worker #1] ML tree search #10, logLikelihood: -18929.551473
[00:31:31 -18929.487687] FAST spr round 6 (radius: 25)
[00:31:38 -18927.280955] FAST spr round 7 (radius: 25)
[00:31:45 -18927.280156] Model parameter optimization (eps = 1.000000)
[00:31:47 -18926.444187] SLOW spr round 1 (radius: 5)
[00:32:00 -18925.704765] SLOW spr round 2 (radius: 5)
[00:32:13 -18924.646537] SLOW spr round 3 (radius: 5)
[00:32:25 -18923.554769] SLOW spr round 4 (radius: 5)
[00:32:37 -18923.553563] SLOW spr round 5 (radius: 10)
[00:32:50 -18923.553329] SLOW spr round 6 (radius: 15)
[00:33:16 -18923.328624] SLOW spr round 7 (radius: 5)
[00:33:33 -18923.322131] SLOW spr round 8 (radius: 10)
[00:33:50 -18923.321387] SLOW spr round 9 (radius: 15)
[00:34:15 -18923.321229] SLOW spr round 10 (radius: 20)
[00:34:38 -18923.321137] SLOW spr round 11 (radius: 25)
[00:34:56 -18921.262767] SLOW spr round 12 (radius: 5)
[00:35:13 -18921.239449] SLOW spr round 13 (radius: 10)
[00:35:33 -18921.239322] SLOW spr round 14 (radius: 15)
[00:35:57 -18921.156564] SLOW spr round 15 (radius: 20)
[00:36:20 -18921.156502] SLOW spr round 16 (radius: 25)
[00:36:37 -18921.156499] Model parameter optimization (eps = 0.100000)

[00:36:39] [worker #0] ML tree search #11, logLikelihood: -18921.127613

[00:36:39 -44714.240924] Initial branch length optimization
[00:36:40 -36050.848721] Model parameter optimization (eps = 10.000000)
[00:36:47 -35735.188988] AUTODETECT spr round 1 (radius: 5)
[00:36:54 -28586.181001] AUTODETECT spr round 2 (radius: 10)
[00:37:03 -21603.149960] AUTODETECT spr round 3 (radius: 15)
[00:37:16 -20351.226042] AUTODETECT spr round 4 (radius: 20)
[00:37:20] [worker #1] ML tree search #12, logLikelihood: -18922.425578
[00:37:30 -20228.133889] AUTODETECT spr round 5 (radius: 25)
[00:37:42 -20226.410573] SPR radius for FAST iterations: 25 (autodetect)
[00:37:42 -20226.410573] Model parameter optimization (eps = 3.000000)
[00:37:47 -20182.730920] FAST spr round 1 (radius: 25)
[00:37:58 -19014.368401] FAST spr round 2 (radius: 25)
[00:38:07 -18932.120779] FAST spr round 3 (radius: 25)
[00:38:15 -18927.952283] FAST spr round 4 (radius: 25)
[00:38:21 -18927.952102] Model parameter optimization (eps = 1.000000)
[00:38:24 -18925.980050] SLOW spr round 1 (radius: 5)
[00:38:38 -18925.362358] SLOW spr round 2 (radius: 5)
[00:38:51 -18924.879126] SLOW spr round 3 (radius: 5)
[00:39:03 -18924.736274] SLOW spr round 4 (radius: 5)
[00:39:15 -18924.735700] SLOW spr round 5 (radius: 10)
[00:39:28 -18923.007894] SLOW spr round 6 (radius: 5)
[00:39:44 -18922.735349] SLOW spr round 7 (radius: 5)
[00:39:58 -18922.734916] SLOW spr round 8 (radius: 10)
[00:40:12 -18922.734888] SLOW spr round 9 (radius: 15)
[00:40:36 -18922.734884] SLOW spr round 10 (radius: 20)
[00:41:00 -18922.734884] SLOW spr round 11 (radius: 25)
[00:41:19 -18922.734884] Model parameter optimization (eps = 0.100000)

[00:41:20] [worker #0] ML tree search #13, logLikelihood: -18922.707278

[00:41:20 -44947.355002] Initial branch length optimization
[00:41:21 -35818.149847] Model parameter optimization (eps = 10.000000)
[00:41:28 -35546.685447] AUTODETECT spr round 1 (radius: 5)
[00:41:35 -28254.764542] AUTODETECT spr round 2 (radius: 10)
[00:41:45 -23364.053081] AUTODETECT spr round 3 (radius: 15)
[00:41:56 -21426.377330] AUTODETECT spr round 4 (radius: 20)
[00:42:07 -20216.660261] AUTODETECT spr round 5 (radius: 25)
[00:42:19 -20196.668318] SPR radius for FAST iterations: 25 (autodetect)
[00:42:19 -20196.668318] Model parameter optimization (eps = 3.000000)
[00:42:24 -20159.228618] FAST spr round 1 (radius: 25)
[00:42:36 -19077.860123] FAST spr round 2 (radius: 25)
[00:42:45 -18956.069611] FAST spr round 3 (radius: 25)
[00:42:54 -18935.743993] FAST spr round 4 (radius: 25)
[00:43:00 -18935.550717] FAST spr round 5 (radius: 25)
[00:43:07 -18935.549699] Model parameter optimization (eps = 1.000000)
[00:43:09 -18934.590049] SLOW spr round 1 (radius: 5)
[00:43:23 -18929.997857] SLOW spr round 2 (radius: 5)
[00:43:36 -18927.709660] SLOW spr round 3 (radius: 5)
[00:43:48 -18927.291652] SLOW spr round 4 (radius: 5)
[00:44:00 -18926.519076] SLOW spr round 5 (radius: 5)
[00:44:11 -18926.517262] SLOW spr round 6 (radius: 10)
[00:44:25 -18926.285705] SLOW spr round 7 (radius: 5)
[00:44:41 -18925.919634] SLOW spr round 8 (radius: 5)
[00:44:55 -18925.919485] SLOW spr round 9 (radius: 10)
[00:45:09 -18925.919390] SLOW spr round 10 (radius: 15)
[00:45:34 -18925.919303] SLOW spr round 11 (radius: 20)
[00:45:48] [worker #1] ML tree search #14, logLikelihood: -18918.977055
[00:45:57 -18925.919217] SLOW spr round 12 (radius: 25)
[00:46:16 -18924.005225] SLOW spr round 13 (radius: 5)
[00:46:34 -18924.003197] SLOW spr round 14 (radius: 10)
[00:46:54 -18924.002998] SLOW spr round 15 (radius: 15)
[00:47:18 -18923.635999] SLOW spr round 16 (radius: 5)
[00:47:35 -18923.635697] SLOW spr round 17 (radius: 10)
[00:47:53 -18923.635674] SLOW spr round 18 (radius: 15)
[00:48:17 -18923.635672] SLOW spr round 19 (radius: 20)
[00:48:40 -18923.635671] SLOW spr round 20 (radius: 25)
[00:48:58 -18923.635671] Model parameter optimization (eps = 0.100000)

[00:49:01] [worker #0] ML tree search #15, logLikelihood: -18923.495875

[00:49:01 -43823.001496] Initial branch length optimization
[00:49:01 -35149.239631] Model parameter optimization (eps = 10.000000)
[00:49:09 -34908.836007] AUTODETECT spr round 1 (radius: 5)
[00:49:15 -27602.603343] AUTODETECT spr round 2 (radius: 10)
[00:49:25 -21465.689839] AUTODETECT spr round 3 (radius: 15)
[00:49:38 -20315.372060] AUTODETECT spr round 4 (radius: 20)
[00:49:48 -20301.461127] AUTODETECT spr round 5 (radius: 25)
[00:50:01 -20275.462374] SPR radius for FAST iterations: 25 (autodetect)
[00:50:01 -20275.462374] Model parameter optimization (eps = 3.000000)
[00:50:06 -20236.512049] FAST spr round 1 (radius: 25)
[00:50:18 -18979.014875] FAST spr round 2 (radius: 25)
[00:50:27 -18942.615776] FAST spr round 3 (radius: 25)
[00:50:34 -18937.982174] FAST spr round 4 (radius: 25)
[00:50:41 -18937.611562] FAST spr round 5 (radius: 25)
[00:50:47 -18937.611349] Model parameter optimization (eps = 1.000000)
[00:50:50 -18935.922779] SLOW spr round 1 (radius: 5)
[00:51:03 -18933.049672] SLOW spr round 2 (radius: 5)
[00:51:15 -18933.049573] SLOW spr round 3 (radius: 10)
[00:51:28 -18932.817077] SLOW spr round 4 (radius: 5)
[00:51:44 -18932.610298] SLOW spr round 5 (radius: 5)
[00:51:59 -18932.523046] SLOW spr round 6 (radius: 10)
[00:52:13 -18932.522245] SLOW spr round 7 (radius: 15)
[00:52:30] [worker #1] ML tree search #16, logLikelihood: -18929.169132
[00:52:38 -18932.010118] SLOW spr round 8 (radius: 5)
[00:52:55 -18932.008788] SLOW spr round 9 (radius: 10)
[00:53:12 -18930.404422] SLOW spr round 10 (radius: 5)
[00:53:28 -18929.880471] SLOW spr round 11 (radius: 5)
[00:53:42 -18929.879451] SLOW spr round 12 (radius: 10)
[00:53:55 -18929.879270] SLOW spr round 13 (radius: 15)
[00:54:21 -18929.879237] SLOW spr round 14 (radius: 20)
[00:54:46 -18929.879231] SLOW spr round 15 (radius: 25)
[00:55:03 -18929.879230] Model parameter optimization (eps = 0.100000)

[00:55:05] [worker #0] ML tree search #17, logLikelihood: -18929.585445

[00:55:05 -44734.494401] Initial branch length optimization
[00:55:05 -35812.256560] Model parameter optimization (eps = 10.000000)
[00:55:11 -35768.429175] AUTODETECT spr round 1 (radius: 5)
[00:55:18 -26469.202175] AUTODETECT spr round 2 (radius: 10)
[00:55:27 -21690.859602] AUTODETECT spr round 3 (radius: 15)
[00:55:39 -20400.942287] AUTODETECT spr round 4 (radius: 20)
[00:55:52 -20055.947780] AUTODETECT spr round 5 (radius: 25)
[00:56:06 -20052.400765] SPR radius for FAST iterations: 25 (autodetect)
[00:56:06 -20052.400765] Model parameter optimization (eps = 3.000000)
[00:56:12 -19941.499719] FAST spr round 1 (radius: 25)
[00:56:24 -19014.401692] FAST spr round 2 (radius: 25)
[00:56:34 -18941.720116] FAST spr round 3 (radius: 25)
[00:56:42 -18935.403902] FAST spr round 4 (radius: 25)
[00:56:48 -18934.819775] FAST spr round 5 (radius: 25)
[00:56:55 -18934.818022] Model parameter optimization (eps = 1.000000)
[00:56:58 -18933.707237] SLOW spr round 1 (radius: 5)
[00:57:12 -18930.624977] SLOW spr round 2 (radius: 5)
[00:57:25 -18928.487411] SLOW spr round 3 (radius: 5)
[00:57:37 -18928.484533] SLOW spr round 4 (radius: 10)
[00:57:52 -18926.155372] SLOW spr round 5 (radius: 5)
[00:58:08 -18922.170311] SLOW spr round 6 (radius: 5)
[00:58:23 -18922.165564] SLOW spr round 7 (radius: 10)
[00:58:37 -18921.886795] SLOW spr round 8 (radius: 5)
[00:58:53 -18921.884463] SLOW spr round 9 (radius: 10)
[00:59:00] [worker #1] ML tree search #18, logLikelihood: -18919.300454
[00:59:10 -18921.884213] SLOW spr round 10 (radius: 15)
[00:59:35 -18921.884082] SLOW spr round 11 (radius: 20)
[00:59:57 -18921.883960] SLOW spr round 12 (radius: 25)
[01:00:13 -18921.490572] SLOW spr round 13 (radius: 5)
[01:00:32 -18921.089628] SLOW spr round 14 (radius: 5)
[01:00:47 -18921.088681] SLOW spr round 15 (radius: 10)
[01:01:03 -18920.751762] SLOW spr round 16 (radius: 5)
[01:01:18 -18920.725754] SLOW spr round 17 (radius: 10)
[01:01:35 -18920.594327] SLOW spr round 18 (radius: 5)
[01:01:51 -18920.593308] SLOW spr round 19 (radius: 10)
[01:02:07 -18920.593252] SLOW spr round 20 (radius: 15)
[01:02:32 -18920.593246] SLOW spr round 21 (radius: 20)
[01:02:55 -18920.593245] SLOW spr round 22 (radius: 25)
[01:03:11 -18920.593245] Model parameter optimization (eps = 0.100000)

[01:03:14] [worker #0] ML tree search #19, logLikelihood: -18918.002984

[01:06:40] [worker #1] ML tree search #20, logLikelihood: -18929.607267

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.054210,0.587486) (0.037403,0.493919) (0.366288,0.796536) (0.542099,1.213646) 
   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: -18918.002984

AIC score: 38678.005967 / AICc score: 394002.005967 / BIC score: 39799.313826
Free parameters (model + branch lengths): 421

WARNING: Number of free parameters (K=421) is larger than alignment size (n=106).
         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/O60936/3_mltree/O60936.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/3_mltree/O60936.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/3_mltree/O60936.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O60936/3_mltree/O60936.raxml.log

Analysis started: 01-Jul-2021 11:07:35 / finished: 01-Jul-2021 12:14:16

Elapsed time: 4000.561 seconds