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 23-Jun-2021 13:02:39 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/2_msa/Q14315_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/2_msa/Q14315_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 2853 sites

WARNING: Sequences sp_Q9JI91_ACTN2_MOUSE_10090 and tr_D3ZCV0_D3ZCV0_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Y7F4_M3Y7F4_MUSPF_9669 and tr_A0A2Y9JK69_A0A2Y9JK69_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_E9DI27_E9DI27_COCPS_443226 are exactly identical!
WARNING: Sequences tr_A0A0D8JUP7_A0A0D8JUP7_COCIM_246410 and tr_A0A0J6Y5M8_A0A0J6Y5M8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_E2QUQ0_E2QUQ0_CANLF_9615 and tr_G1L2Z4_G1L2Z4_AILME_9646 are exactly identical!
WARNING: Sequences tr_E2QY08_E2QY08_CANLF_9615 and tr_A0A2U3ZCZ8_A0A2U3ZCZ8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A0A0MU58_A0A0A0MU58_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2K5LF87_A0A2K5LF87_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3STF2_A0A2I3STF2_PANTR_9598 and tr_A0A2R9C199_A0A2R9C199_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7CD41_K7CD41_PANTR_9598 and tr_A0A2R9AD40_A0A2R9AD40_PANPA_9597 are exactly identical!
WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_F7HU82_F7HU82_MACMU_9544 are exactly identical!
WARNING: Sequences sp_O43707_ACTN4_HUMAN_9606 and tr_A0A0D9QVJ0_A0A0D9QVJ0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A0D9RKZ5_A0A0D9RKZ5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5N6P5_A0A2K5N6P5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K6CYT7_A0A2K6CYT7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QZP3_A0A1D5QZP3_MACMU_9544 and tr_A0A2K5ZZ84_A0A2K5ZZ84_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6VRJ5_F6VRJ5_MACMU_9544 and tr_A0A2K5N9D6_A0A2K5N9D6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0D9RBH8_A0A0D9RBH8_CHLSB_60711 and tr_A0A2K6E8I1_A0A2K6E8I1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0D9RC89_A0A0D9RC89_CHLSB_60711 and tr_A0A2K6A9D6_A0A2K6A9D6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A091UMG4_A0A091UMG4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A087R6Z3_A0A087R6Z3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JKQ5_A0A091JKQ5_EGRGA_188379 and tr_A0A0A0AHU9_A0A0A0AHU9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MTN9_A0A2I0MTN9_COLLI_8932 and tr_A0A1V4JKI3_A0A1V4JKI3_PATFA_372326 are exactly identical!
WARNING: Duplicate sequences found: 23

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/Q14315/3_mltree/Q14315.raxml.reduced.phy

Alignment comprises 1 partitions and 2851 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 2853 / 2851
Gaps: 54.15 %
Invariant sites: 0.25 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 8 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 / 357 / 28560
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -2073853.201406] Initial branch length optimization
[00:00:17 -1676460.643878] Model parameter optimization (eps = 10.000000)
[00:01:54 -1670217.040370] AUTODETECT spr round 1 (radius: 5)
[00:05:57 -1089388.953853] AUTODETECT spr round 2 (radius: 10)
[00:10:20 -802019.007717] AUTODETECT spr round 3 (radius: 15)
[00:15:10 -681295.594600] AUTODETECT spr round 4 (radius: 20)
[00:21:27 -622588.845130] AUTODETECT spr round 5 (radius: 25)
[00:28:36 -603052.268522] SPR radius for FAST iterations: 25 (autodetect)
[00:28:37 -603052.268522] Model parameter optimization (eps = 3.000000)
[00:29:35 -602199.371037] FAST spr round 1 (radius: 25)
[00:36:36 -527308.099583] FAST spr round 2 (radius: 25)
[00:41:20 -524637.816675] FAST spr round 3 (radius: 25)
[00:45:05 -524545.495742] FAST spr round 4 (radius: 25)
[00:48:02 -524542.984660] FAST spr round 5 (radius: 25)
[00:50:44 -524542.984034] Model parameter optimization (eps = 1.000000)
[00:51:14 -524499.822309] SLOW spr round 1 (radius: 5)
[00:55:12 -524426.326486] SLOW spr round 2 (radius: 5)
[00:59:10 -524418.367621] SLOW spr round 3 (radius: 5)
[01:02:52 -524418.364151] SLOW spr round 4 (radius: 10)
[01:06:54 -524411.260952] SLOW spr round 5 (radius: 5)
[01:11:58 -524407.627549] SLOW spr round 6 (radius: 5)
[01:16:31 -524407.624718] SLOW spr round 7 (radius: 10)
[01:20:58 -524407.465840] SLOW spr round 8 (radius: 5)
[01:26:14 -524400.789444] SLOW spr round 9 (radius: 5)
[01:30:44 -524400.789141] SLOW spr round 10 (radius: 10)
[01:35:08 -524400.665027] SLOW spr round 11 (radius: 5)
[01:40:11 -524400.664242] SLOW spr round 12 (radius: 10)
[01:44:56 -524400.664214] SLOW spr round 13 (radius: 15)
[01:52:32 -524399.611625] SLOW spr round 14 (radius: 5)
[01:57:59 -524399.558065] SLOW spr round 15 (radius: 10)
[02:03:15 -524399.558038] SLOW spr round 16 (radius: 15)
[02:10:49 -524399.558013] SLOW spr round 17 (radius: 20)
[02:23:06 -524399.557989] SLOW spr round 18 (radius: 25)
[02:39:51 -524399.557965] Model parameter optimization (eps = 0.100000)

[02:40:05] ML tree search #1, logLikelihood: -524399.443722

[02:40:05 -2099452.951459] Initial branch length optimization
[02:40:21 -1708690.143074] Model parameter optimization (eps = 10.000000)
[02:42:08 -1701859.779553] AUTODETECT spr round 1 (radius: 5)
[02:46:16 -1108403.524577] AUTODETECT spr round 2 (radius: 10)
[02:50:47 -793587.168418] AUTODETECT spr round 3 (radius: 15)
[02:55:36 -669292.326197] AUTODETECT spr round 4 (radius: 20)
[03:01:16 -611970.786545] AUTODETECT spr round 5 (radius: 25)
[03:08:49 -599161.452063] SPR radius for FAST iterations: 25 (autodetect)
[03:08:49 -599161.452063] Model parameter optimization (eps = 3.000000)
[03:09:34 -598133.227716] FAST spr round 1 (radius: 25)
[03:15:46 -526847.433899] FAST spr round 2 (radius: 25)
[03:20:13 -524728.261628] FAST spr round 3 (radius: 25)
[03:24:03 -524521.681170] FAST spr round 4 (radius: 25)
[03:27:12 -524506.829906] FAST spr round 5 (radius: 25)
[03:29:55 -524506.829841] Model parameter optimization (eps = 1.000000)
[03:30:27 -524479.425976] SLOW spr round 1 (radius: 5)
[03:34:29 -524426.009144] SLOW spr round 2 (radius: 5)
[03:38:39 -524423.155716] SLOW spr round 3 (radius: 5)
[03:42:35 -524423.155056] SLOW spr round 4 (radius: 10)
[03:46:51 -524417.284966] SLOW spr round 5 (radius: 5)
[03:52:07 -524416.973756] SLOW spr round 6 (radius: 5)
[03:56:39 -524416.971910] SLOW spr round 7 (radius: 10)
[04:01:06 -524411.540154] SLOW spr round 8 (radius: 5)
[04:06:08 -524411.486095] SLOW spr round 9 (radius: 10)
[04:10:55 -524411.486074] SLOW spr round 10 (radius: 15)
[04:18:50 -524411.486055] SLOW spr round 11 (radius: 20)
[04:31:53 -524411.154587] SLOW spr round 12 (radius: 5)
[04:37:29 -524411.063159] SLOW spr round 13 (radius: 10)
[04:42:53 -524411.052331] SLOW spr round 14 (radius: 15)
[04:50:35 -524411.052296] SLOW spr round 15 (radius: 20)
[05:03:43 -524411.052274] SLOW spr round 16 (radius: 25)
[05:21:37 -524411.052256] Model parameter optimization (eps = 0.100000)

[05:21:56] ML tree search #2, logLikelihood: -524410.831743

[05:21:56 -2093268.589625] Initial branch length optimization
[05:22:08 -1685941.455808] Model parameter optimization (eps = 10.000000)
[05:24:14 -1679653.526899] AUTODETECT spr round 1 (radius: 5)
[05:28:17 -1109591.750248] AUTODETECT spr round 2 (radius: 10)
[05:32:31 -797823.247769] AUTODETECT spr round 3 (radius: 15)
[05:37:23 -690158.718549] AUTODETECT spr round 4 (radius: 20)
[05:43:10 -622884.508868] AUTODETECT spr round 5 (radius: 25)
[05:49:56 -602997.841017] SPR radius for FAST iterations: 25 (autodetect)
[05:49:56 -602997.841017] Model parameter optimization (eps = 3.000000)
[05:50:17 -602716.601501] FAST spr round 1 (radius: 25)
[05:57:33 -528376.967953] FAST spr round 2 (radius: 25)
[06:02:35 -525409.606774] FAST spr round 3 (radius: 25)
[06:06:31 -525211.888659] FAST spr round 4 (radius: 25)
[06:09:28 -525211.884862] Model parameter optimization (eps = 1.000000)
[06:10:16 -524550.659509] SLOW spr round 1 (radius: 5)
[06:14:53 -524426.735566] SLOW spr round 2 (radius: 5)
[06:19:16 -524419.993144] SLOW spr round 3 (radius: 5)
[06:23:17 -524419.983265] SLOW spr round 4 (radius: 10)
[06:27:38 -524412.793259] SLOW spr round 5 (radius: 5)
[06:32:55 -524412.574230] SLOW spr round 6 (radius: 5)
[06:37:29 -524411.509239] SLOW spr round 7 (radius: 5)
[06:41:40 -524411.507124] SLOW spr round 8 (radius: 10)
[06:46:01 -524406.917513] SLOW spr round 9 (radius: 5)
[06:51:08 -524406.097595] SLOW spr round 10 (radius: 5)
[06:55:31 -524406.096995] SLOW spr round 11 (radius: 10)
[07:00:01 -524406.096658] SLOW spr round 12 (radius: 15)
[07:08:18 -524404.292856] SLOW spr round 13 (radius: 5)
[07:13:49 -524404.283846] SLOW spr round 14 (radius: 10)
[07:19:10 -524404.281549] SLOW spr round 15 (radius: 15)
[07:26:49 -524402.938461] SLOW spr round 16 (radius: 5)
[07:32:16 -524402.891214] SLOW spr round 17 (radius: 10)
[07:37:39 -524402.891103] SLOW spr round 18 (radius: 15)
[07:45:25 -524402.891029] SLOW spr round 19 (radius: 20)
[07:58:12 -524402.890968] SLOW spr round 20 (radius: 25)
[08:15:46 -524402.269686] SLOW spr round 21 (radius: 5)
[08:21:34 -524402.209175] SLOW spr round 22 (radius: 10)
[08:27:14 -524402.207677] SLOW spr round 23 (radius: 15)
[08:34:51 -524402.206397] SLOW spr round 24 (radius: 20)
[08:47:36 -524402.205292] SLOW spr round 25 (radius: 25)
[09:05:12 -524402.204336] Model parameter optimization (eps = 0.100000)

[09:05:25] ML tree search #3, logLikelihood: -524402.113441

[09:05:25 -2092409.566007] Initial branch length optimization
[09:05:38 -1699945.961058] Model parameter optimization (eps = 10.000000)
[09:07:18 -1693052.091703] AUTODETECT spr round 1 (radius: 5)
[09:11:27 -1104105.115979] AUTODETECT spr round 2 (radius: 10)
[09:15:53 -805865.087326] AUTODETECT spr round 3 (radius: 15)
[09:20:36 -659359.300708] AUTODETECT spr round 4 (radius: 20)
[09:26:09 -611221.815286] AUTODETECT spr round 5 (radius: 25)
[09:32:48 -597663.126328] SPR radius for FAST iterations: 25 (autodetect)
[09:32:48 -597663.126328] Model parameter optimization (eps = 3.000000)
[09:34:01 -596840.541719] FAST spr round 1 (radius: 25)
[09:40:55 -537052.384067] FAST spr round 2 (radius: 25)
[09:46:05 -530140.681977] FAST spr round 3 (radius: 25)
[09:50:15 -524964.972906] FAST spr round 4 (radius: 25)
[09:54:00 -524571.005189] FAST spr round 5 (radius: 25)
[09:57:13 -524536.310882] FAST spr round 6 (radius: 25)
[10:00:00 -524534.826618] FAST spr round 7 (radius: 25)
[10:02:44 -524534.753683] Model parameter optimization (eps = 1.000000)
[10:03:18 -524511.169641] SLOW spr round 1 (radius: 5)
[10:07:41 -524434.807639] SLOW spr round 2 (radius: 5)
[10:11:52 -524416.990562] SLOW spr round 3 (radius: 5)
[10:15:46 -524416.190939] SLOW spr round 4 (radius: 5)
[10:19:39 -524416.190832] SLOW spr round 5 (radius: 10)
[10:23:51 -524408.178483] SLOW spr round 6 (radius: 5)
[10:28:58 -524408.123800] SLOW spr round 7 (radius: 10)
[10:34:03 -524406.055293] SLOW spr round 8 (radius: 5)
[10:39:14 -524403.008349] SLOW spr round 9 (radius: 5)
[10:43:43 -524403.008094] SLOW spr round 10 (radius: 10)
[10:48:07 -524403.008058] SLOW spr round 11 (radius: 15)
[10:56:16 -524403.008023] SLOW spr round 12 (radius: 20)
[11:09:01 -524403.007987] SLOW spr round 13 (radius: 25)
[11:27:20 -524403.007952] Model parameter optimization (eps = 0.100000)

[11:27:42] ML tree search #4, logLikelihood: -524402.802853

[11:27:42 -2071881.911195] Initial branch length optimization
[11:27:57 -1681647.107940] Model parameter optimization (eps = 10.000000)
[11:29:35 -1675234.396753] AUTODETECT spr round 1 (radius: 5)
[11:33:49 -1103353.809399] AUTODETECT spr round 2 (radius: 10)
[11:38:16 -816813.233106] AUTODETECT spr round 3 (radius: 15)
[11:43:06 -654780.742942] AUTODETECT spr round 4 (radius: 20)
[11:49:16 -605947.067278] AUTODETECT spr round 5 (radius: 25)
[11:56:47 -588440.644623] SPR radius for FAST iterations: 25 (autodetect)
[11:56:48 -588440.644623] Model parameter optimization (eps = 3.000000)
[11:57:56 -587564.381884] FAST spr round 1 (radius: 25)
[12:04:16 -526758.562860] FAST spr round 2 (radius: 25)
[12:08:43 -524658.254750] FAST spr round 3 (radius: 25)
[12:12:30 -524523.011421] FAST spr round 4 (radius: 25)
[12:15:49 -524514.002913] FAST spr round 5 (radius: 25)
[12:18:46 -524513.933742] Model parameter optimization (eps = 1.000000)
[12:19:16 -524491.182812] SLOW spr round 1 (radius: 5)
[12:23:19 -524427.247044] SLOW spr round 2 (radius: 5)
[12:27:17 -524425.229020] SLOW spr round 3 (radius: 5)
[12:31:11 -524425.227600] SLOW spr round 4 (radius: 10)
[12:35:28 -524421.258452] SLOW spr round 5 (radius: 5)
[12:40:42 -524421.258030] SLOW spr round 6 (radius: 10)
[12:45:38 -524421.132264] SLOW spr round 7 (radius: 5)
[12:50:36 -524421.131258] SLOW spr round 8 (radius: 10)
[12:55:32 -524421.131045] SLOW spr round 9 (radius: 15)
[13:03:29 -524421.130868] SLOW spr round 10 (radius: 20)
[13:16:11 -524421.130718] SLOW spr round 11 (radius: 25)
[13:34:01 -524421.130591] Model parameter optimization (eps = 0.100000)

[13:34:08] ML tree search #5, logLikelihood: -524421.091710

[13:34:09 -2081505.890285] Initial branch length optimization
[13:34:22 -1685010.238315] Model parameter optimization (eps = 10.000000)
[13:36:09 -1678591.323500] AUTODETECT spr round 1 (radius: 5)
[13:40:22 -1113334.405743] AUTODETECT spr round 2 (radius: 10)
[13:44:50 -828658.803781] AUTODETECT spr round 3 (radius: 15)
[13:49:41 -661903.232673] AUTODETECT spr round 4 (radius: 20)
[13:55:13 -617348.333903] AUTODETECT spr round 5 (radius: 25)
[14:01:51 -605384.413153] SPR radius for FAST iterations: 25 (autodetect)
[14:01:51 -605384.413153] Model parameter optimization (eps = 3.000000)
[14:02:59 -604372.764793] FAST spr round 1 (radius: 25)
[14:09:53 -527615.271069] FAST spr round 2 (radius: 25)
[14:14:44 -524597.349241] FAST spr round 3 (radius: 25)
[14:18:39 -524515.124657] FAST spr round 4 (radius: 25)
[14:21:51 -524504.767818] FAST spr round 5 (radius: 25)
[14:24:46 -524504.755048] Model parameter optimization (eps = 1.000000)
[14:25:16 -524490.036921] SLOW spr round 1 (radius: 5)
[14:29:32 -524425.839217] SLOW spr round 2 (radius: 5)
[14:33:34 -524418.433204] SLOW spr round 3 (radius: 5)
[14:37:27 -524417.621663] SLOW spr round 4 (radius: 5)
[14:41:28 -524417.621100] SLOW spr round 5 (radius: 10)
[14:45:47 -524411.564674] SLOW spr round 6 (radius: 5)
[14:51:06 -524411.507314] SLOW spr round 7 (radius: 10)
[14:56:11 -524410.529883] SLOW spr round 8 (radius: 5)
[15:01:16 -524410.528592] SLOW spr round 9 (radius: 10)
[15:06:04 -524410.528354] SLOW spr round 10 (radius: 15)
[15:13:49 -524410.528214] SLOW spr round 11 (radius: 20)
[15:26:21 -524410.528123] SLOW spr round 12 (radius: 25)
[15:43:50 -524410.387784] SLOW spr round 13 (radius: 5)
[15:49:40 -524410.347631] SLOW spr round 14 (radius: 10)
[15:55:29 -524410.344908] SLOW spr round 15 (radius: 15)
[16:03:11 -524410.344154] SLOW spr round 16 (radius: 20)
[16:15:44 -524410.343938] SLOW spr round 17 (radius: 25)
[16:32:59 -524410.343856] Model parameter optimization (eps = 0.100000)

[16:33:08] ML tree search #6, logLikelihood: -524410.266533

[16:33:08 -2071438.338393] Initial branch length optimization
[16:33:22 -1689730.157530] Model parameter optimization (eps = 10.000000)
[16:35:34 -1683153.735555] AUTODETECT spr round 1 (radius: 5)
[16:39:51 -1100269.045892] AUTODETECT spr round 2 (radius: 10)
[16:44:30 -825338.184934] AUTODETECT spr round 3 (radius: 15)
[16:49:55 -685167.002473] AUTODETECT spr round 4 (radius: 20)
[16:56:13 -594728.832655] AUTODETECT spr round 5 (radius: 25)
[17:03:16 -588432.430028] SPR radius for FAST iterations: 25 (autodetect)
[17:03:16 -588432.430028] Model parameter optimization (eps = 3.000000)
[17:04:14 -587473.767593] FAST spr round 1 (radius: 25)
[17:10:43 -527393.552543] FAST spr round 2 (radius: 25)
[17:15:10 -524697.922628] FAST spr round 3 (radius: 25)
[17:18:55 -524498.906760] FAST spr round 4 (radius: 25)
[17:21:55 -524498.811461] Model parameter optimization (eps = 1.000000)
[17:22:28 -524465.496004] SLOW spr round 1 (radius: 5)
[17:26:35 -524417.229466] SLOW spr round 2 (radius: 5)
[17:30:44 -524412.691639] SLOW spr round 3 (radius: 5)
[17:34:53 -524412.691384] SLOW spr round 4 (radius: 10)
[17:39:17 -524404.588333] SLOW spr round 5 (radius: 5)
[17:44:37 -524404.465430] SLOW spr round 6 (radius: 5)
[17:49:13 -524404.449772] SLOW spr round 7 (radius: 10)
[17:53:47 -524404.334579] SLOW spr round 8 (radius: 5)
[17:59:02 -524404.333217] SLOW spr round 9 (radius: 10)
[18:04:04 -524404.332905] SLOW spr round 10 (radius: 15)
[18:11:53 -524404.332714] SLOW spr round 11 (radius: 20)
[18:24:15 -524404.332593] SLOW spr round 12 (radius: 25)
[18:41:31 -524404.332512] Model parameter optimization (eps = 0.100000)

[18:41:42] ML tree search #7, logLikelihood: -524404.293292

[18:41:42 -2070384.840906] Initial branch length optimization
[18:41:56 -1683657.841880] Model parameter optimization (eps = 10.000000)
[18:43:51 -1677143.682955] AUTODETECT spr round 1 (radius: 5)
[18:48:07 -1109307.185287] AUTODETECT spr round 2 (radius: 10)
[18:52:43 -806105.902723] AUTODETECT spr round 3 (radius: 15)
[18:57:40 -656909.959616] AUTODETECT spr round 4 (radius: 20)
[19:03:52 -593780.801435] AUTODETECT spr round 5 (radius: 25)
[19:11:18 -587431.436754] SPR radius for FAST iterations: 25 (autodetect)
[19:11:18 -587431.436754] Model parameter optimization (eps = 3.000000)
[19:12:28 -586469.378992] FAST spr round 1 (radius: 25)
[19:19:39 -526646.265905] FAST spr round 2 (radius: 25)
[19:24:30 -524711.467314] FAST spr round 3 (radius: 25)
[19:28:22 -524527.843422] FAST spr round 4 (radius: 25)
[19:31:25 -524513.515738] FAST spr round 5 (radius: 25)
[19:34:12 -524513.514684] Model parameter optimization (eps = 1.000000)
[19:34:42 -524488.840731] SLOW spr round 1 (radius: 5)
[19:38:45 -524424.890233] SLOW spr round 2 (radius: 5)
[19:43:00 -524401.388232] SLOW spr round 3 (radius: 5)
[19:47:00 -524401.385853] SLOW spr round 4 (radius: 10)
[19:51:21 -524396.165306] SLOW spr round 5 (radius: 5)
[19:56:41 -524395.117524] SLOW spr round 6 (radius: 5)
[20:01:18 -524395.115216] SLOW spr round 7 (radius: 10)
[20:05:52 -524395.088386] SLOW spr round 8 (radius: 15)
[20:14:09 -524395.087198] SLOW spr round 9 (radius: 20)
[20:26:41 -524395.086339] SLOW spr round 10 (radius: 25)
[20:44:05 -524395.085713] Model parameter optimization (eps = 0.100000)

[20:44:28] ML tree search #8, logLikelihood: -524394.851822

[20:44:28 -2081263.310211] Initial branch length optimization
[20:44:42 -1693445.795620] Model parameter optimization (eps = 10.000000)
[20:46:43 -1686871.420751] AUTODETECT spr round 1 (radius: 5)
[20:51:01 -1099392.185726] AUTODETECT spr round 2 (radius: 10)
[20:55:42 -803452.193427] AUTODETECT spr round 3 (radius: 15)
[21:00:37 -654537.252867] AUTODETECT spr round 4 (radius: 20)
[21:06:46 -587349.301069] AUTODETECT spr round 5 (radius: 25)
[21:14:01 -579439.126062] SPR radius for FAST iterations: 25 (autodetect)
[21:14:01 -579439.126062] Model parameter optimization (eps = 3.000000)
[21:15:07 -578429.772521] FAST spr round 1 (radius: 25)
[21:22:34 -526884.284646] FAST spr round 2 (radius: 25)
[21:27:50 -524664.371147] FAST spr round 3 (radius: 25)
[21:32:01 -524534.265503] FAST spr round 4 (radius: 25)
[21:35:09 -524530.339971] FAST spr round 5 (radius: 25)
[21:38:05 -524530.339276] Model parameter optimization (eps = 1.000000)
[21:38:36 -524507.949674] SLOW spr round 1 (radius: 5)
[21:43:02 -524410.475276] SLOW spr round 2 (radius: 5)
[21:47:05 -524408.810855] SLOW spr round 3 (radius: 5)
[21:50:56 -524408.806984] SLOW spr round 4 (radius: 10)
[21:54:59 -524407.562289] SLOW spr round 5 (radius: 5)
[22:00:05 -524407.560524] SLOW spr round 6 (radius: 10)
[22:05:10 -524407.559327] SLOW spr round 7 (radius: 15)
[22:13:02 -524407.558498] SLOW spr round 8 (radius: 20)
[22:26:09 -524407.557912] SLOW spr round 9 (radius: 25)
[22:44:18 -524407.557489] Model parameter optimization (eps = 0.100000)

[22:44:41] ML tree search #9, logLikelihood: -524407.192861

[22:44:41 -2086705.767280] Initial branch length optimization
[22:44:56 -1700540.837954] Model parameter optimization (eps = 10.000000)
[22:46:55 -1694036.464506] AUTODETECT spr round 1 (radius: 5)
[22:51:00 -1088871.342704] AUTODETECT spr round 2 (radius: 10)
[22:55:22 -804318.343944] AUTODETECT spr round 3 (radius: 15)

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 16:27:55 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/2_msa/Q14315_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

WARNING: The model you specified on the command line (LG4X) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.rba
[00:00:00] Alignment comprises 1001 taxa, 1 partitions and 2851 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 2853 / 2851
Gaps: 54.15 %
Invariant sites: 0.25 %


Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -804318.34, ML trees: 9, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 357 / 28560
[00:00:00] Data distribution: max. searches per worker: 11

Starting ML tree search with 20 distinct starting trees

[00:00:00 -804318.343944] AUTODETECT spr round 3 (radius: 15)
[00:04:47 -684925.802154] AUTODETECT spr round 4 (radius: 20)
[00:10:31 -602100.451318] AUTODETECT spr round 5 (radius: 25)
[00:16:24 -587372.548501] SPR radius for FAST iterations: 25 (autodetect)
[00:16:24 -587372.548501] Model parameter optimization (eps = 3.000000)
[00:17:16 -586327.739418] FAST spr round 1 (radius: 25)
[00:23:08 -527030.795872] FAST spr round 2 (radius: 25)
[00:27:36 -524626.569030] FAST spr round 3 (radius: 25)
[00:31:04 -524548.164009] FAST spr round 4 (radius: 25)
[00:33:55 -524540.500561] FAST spr round 5 (radius: 25)
[00:36:35 -524537.016441] FAST spr round 6 (radius: 25)
[00:39:10 -524537.015393] Model parameter optimization (eps = 1.000000)
[00:39:34 -524528.325505] SLOW spr round 1 (radius: 5)
[00:43:28 -524454.722618] SLOW spr round 2 (radius: 5)
[00:47:19 -524427.259170] SLOW spr round 3 (radius: 5)
[00:50:59 -524427.257661] SLOW spr round 4 (radius: 10)
[00:54:57 -524425.566725] SLOW spr round 5 (radius: 5)
[00:59:55 -524425.552362] SLOW spr round 6 (radius: 10)
[01:04:42 -524425.448323] SLOW spr round 7 (radius: 5)
[01:09:31 -524425.446603] SLOW spr round 8 (radius: 10)
[01:14:06 -524425.445888] SLOW spr round 9 (radius: 15)
[01:21:37 -524425.445355] SLOW spr round 10 (radius: 20)
[01:33:54 -524425.444954] SLOW spr round 11 (radius: 25)
[01:51:04 -524425.444649] Model parameter optimization (eps = 0.100000)

[01:51:21] ML tree search #10, logLikelihood: -524424.961931

[01:51:21 -2074545.442202] Initial branch length optimization
[01:51:39 -1681005.934873] Model parameter optimization (eps = 10.000000)
[01:53:29 -1674786.820770] AUTODETECT spr round 1 (radius: 5)
[01:57:21 -1124115.113424] AUTODETECT spr round 2 (radius: 10)
[02:01:27 -826251.863041] AUTODETECT spr round 3 (radius: 15)
[02:05:53 -669533.547036] AUTODETECT spr round 4 (radius: 20)
[02:11:13 -609695.626621] AUTODETECT spr round 5 (radius: 25)
[02:17:40 -592978.749081] SPR radius for FAST iterations: 25 (autodetect)
[02:17:40 -592978.749081] Model parameter optimization (eps = 3.000000)
[02:18:39 -591954.053235] FAST spr round 1 (radius: 25)
[02:25:34 -527097.723870] FAST spr round 2 (radius: 25)
[02:30:27 -524622.125875] FAST spr round 3 (radius: 25)
[02:34:19 -524518.919012] FAST spr round 4 (radius: 25)
[02:37:16 -524503.382676] FAST spr round 5 (radius: 25)
[02:39:56 -524503.316139] Model parameter optimization (eps = 1.000000)
[02:40:27 -524465.377479] SLOW spr round 1 (radius: 5)
[02:44:36 -524407.216090] SLOW spr round 2 (radius: 5)
[02:48:26 -524406.276640] SLOW spr round 3 (radius: 5)
[02:52:10 -524406.276094] SLOW spr round 4 (radius: 10)
[02:56:10 -524403.634602] SLOW spr round 5 (radius: 5)
[03:01:10 -524403.633594] SLOW spr round 6 (radius: 10)
[03:05:54 -524403.633388] SLOW spr round 7 (radius: 15)
[03:13:33 -524402.603722] SLOW spr round 8 (radius: 5)
[03:18:53 -524402.547502] SLOW spr round 9 (radius: 10)
[03:24:00 -524402.547379] SLOW spr round 10 (radius: 15)
[03:31:32 -524402.547276] SLOW spr round 11 (radius: 20)
[03:44:03 -524402.547185] SLOW spr round 12 (radius: 25)
[04:01:44 -524402.547104] Model parameter optimization (eps = 0.100000)

[04:01:58] ML tree search #11, logLikelihood: -524402.385112

[04:01:58 -2096104.903272] Initial branch length optimization
[04:02:14 -1705459.099854] Model parameter optimization (eps = 10.000000)
[04:03:52 -1699177.106910] AUTODETECT spr round 1 (radius: 5)
[04:07:45 -1049832.026410] AUTODETECT spr round 2 (radius: 10)
[04:11:57 -793474.335310] AUTODETECT spr round 3 (radius: 15)
[04:16:39 -638762.401641] AUTODETECT spr round 4 (radius: 20)
[04:21:57 -596569.303068] AUTODETECT spr round 5 (radius: 25)
[04:28:10 -581453.072283] SPR radius for FAST iterations: 25 (autodetect)
[04:28:10 -581453.072283] Model parameter optimization (eps = 3.000000)
[04:28:55 -580359.040456] FAST spr round 1 (radius: 25)
[04:35:19 -526969.500626] FAST spr round 2 (radius: 25)
[04:40:14 -524697.866512] FAST spr round 3 (radius: 25)
[04:44:05 -524547.792338] FAST spr round 4 (radius: 25)
[04:47:04 -524534.835964] FAST spr round 5 (radius: 25)
[04:49:46 -524533.454686] FAST spr round 6 (radius: 25)
[04:52:22 -524533.447975] Model parameter optimization (eps = 1.000000)
[04:52:52 -524509.372441] SLOW spr round 1 (radius: 5)
[04:57:07 -524426.591001] SLOW spr round 2 (radius: 5)
[05:01:14 -524405.877909] SLOW spr round 3 (radius: 5)
[05:05:04 -524403.703714] SLOW spr round 4 (radius: 5)
[05:08:47 -524403.703537] SLOW spr round 5 (radius: 10)
[05:12:47 -524401.412568] SLOW spr round 6 (radius: 5)
[05:17:49 -524398.363488] SLOW spr round 7 (radius: 5)
[05:22:09 -524398.363234] SLOW spr round 8 (radius: 10)
[05:26:31 -524398.239123] SLOW spr round 9 (radius: 5)
[05:31:45 -524398.238335] SLOW spr round 10 (radius: 10)
[05:36:34 -524398.238299] SLOW spr round 11 (radius: 15)
[05:44:18 -524398.238263] SLOW spr round 12 (radius: 20)
[05:57:10 -524398.238228] SLOW spr round 13 (radius: 25)
[06:15:16 -524398.238192] Model parameter optimization (eps = 0.100000)

[06:15:32] ML tree search #12, logLikelihood: -524398.124780

[06:15:32 -2074189.980580] Initial branch length optimization
[06:15:46 -1680556.983395] Model parameter optimization (eps = 10.000000)
[06:17:26 -1674340.235880] AUTODETECT spr round 1 (radius: 5)
[06:21:22 -1079177.435924] AUTODETECT spr round 2 (radius: 10)
[06:25:46 -784059.977659] AUTODETECT spr round 3 (radius: 15)
[06:30:36 -635458.643481] AUTODETECT spr round 4 (radius: 20)
[06:36:16 -601103.638169] AUTODETECT spr round 5 (radius: 25)
[06:42:57 -585240.750905] SPR radius for FAST iterations: 25 (autodetect)
[06:42:57 -585240.750905] Model parameter optimization (eps = 3.000000)
[06:44:08 -584242.721760] FAST spr round 1 (radius: 25)
[06:50:10 -526629.514035] FAST spr round 2 (radius: 25)
[06:54:39 -524541.929038] FAST spr round 3 (radius: 25)
[06:58:05 -524503.045210] FAST spr round 4 (radius: 25)
[07:00:58 -524496.915218] FAST spr round 5 (radius: 25)
[07:03:39 -524496.523625] FAST spr round 6 (radius: 25)
[07:06:15 -524484.193940] FAST spr round 7 (radius: 25)
[07:08:46 -524484.191816] Model parameter optimization (eps = 1.000000)
[07:09:13 -524468.760576] SLOW spr round 1 (radius: 5)
[07:13:02 -524403.301265] SLOW spr round 2 (radius: 5)
[07:16:49 -524402.264295] SLOW spr round 3 (radius: 5)
[07:20:33 -524402.262640] SLOW spr round 4 (radius: 10)
[07:24:37 -524395.068703] SLOW spr round 5 (radius: 5)
[07:29:40 -524395.017390] SLOW spr round 6 (radius: 10)
[07:34:28 -524394.998459] SLOW spr round 7 (radius: 15)
[07:41:55 -524394.998301] SLOW spr round 8 (radius: 20)
[07:54:14 -524394.492520] SLOW spr round 9 (radius: 5)
[07:59:41 -524394.397964] SLOW spr round 10 (radius: 10)
[08:05:01 -524394.396833] SLOW spr round 11 (radius: 15)
[08:12:22 -524394.396292] SLOW spr round 12 (radius: 20)
[08:24:44 -524394.396016] SLOW spr round 13 (radius: 25)
[08:41:48 -524394.395860] Model parameter optimization (eps = 0.100000)

[08:42:04] ML tree search #13, logLikelihood: -524394.152942

[08:42:05 -2089009.930497] Initial branch length optimization
[08:42:18 -1688812.067938] Model parameter optimization (eps = 10.000000)
[08:44:15 -1682416.746071] AUTODETECT spr round 1 (radius: 5)
[08:48:07 -1125101.687540] AUTODETECT spr round 2 (radius: 10)
[08:52:24 -816317.630362] AUTODETECT spr round 3 (radius: 15)
[08:56:56 -695948.733679] AUTODETECT spr round 4 (radius: 20)
[09:02:44 -617981.756064] AUTODETECT spr round 5 (radius: 25)
[09:09:47 -598266.178899] SPR radius for FAST iterations: 25 (autodetect)
[09:09:47 -598266.178899] Model parameter optimization (eps = 3.000000)
[09:10:42 -597143.278137] FAST spr round 1 (radius: 25)
[09:17:43 -526343.651935] FAST spr round 2 (radius: 25)
[09:22:36 -524705.195270] FAST spr round 3 (radius: 25)
[09:26:26 -524585.677579] FAST spr round 4 (radius: 25)
[09:29:26 -524578.750974] FAST spr round 5 (radius: 25)
[09:32:05 -524578.737130] Model parameter optimization (eps = 1.000000)
[09:32:35 -524552.210173] SLOW spr round 1 (radius: 5)
[09:36:47 -524470.512744] SLOW spr round 2 (radius: 5)
[09:40:48 -524462.353641] SLOW spr round 3 (radius: 5)
[09:44:37 -524461.466703] SLOW spr round 4 (radius: 5)
[09:48:19 -524461.465455] SLOW spr round 5 (radius: 10)
[09:52:21 -524460.325279] SLOW spr round 6 (radius: 5)
[09:57:22 -524460.257829] SLOW spr round 7 (radius: 10)
[10:02:08 -524460.134878] SLOW spr round 8 (radius: 5)
[10:06:59 -524460.133746] SLOW spr round 9 (radius: 10)
[10:11:34 -524460.133480] SLOW spr round 10 (radius: 15)
[10:19:19 -524460.133280] SLOW spr round 11 (radius: 20)
[10:32:30 -524458.954654] SLOW spr round 12 (radius: 5)
[10:37:53 -524458.915648] SLOW spr round 13 (radius: 10)
[10:43:09 -524458.914570] SLOW spr round 14 (radius: 15)
[10:50:41 -524458.913932] SLOW spr round 15 (radius: 20)
[11:03:58 -524458.913549] SLOW spr round 16 (radius: 25)
[11:21:43 -524446.204458] SLOW spr round 17 (radius: 5)
[11:27:17 -524412.621691] SLOW spr round 18 (radius: 5)
[11:31:54 -524412.620323] SLOW spr round 19 (radius: 10)
[11:36:22 -524408.755863] SLOW spr round 20 (radius: 5)
[11:41:16 -524408.268991] SLOW spr round 21 (radius: 5)
[11:45:29 -524408.268886] SLOW spr round 22 (radius: 10)
[11:49:41 -524408.268824] SLOW spr round 23 (radius: 15)
[11:57:43 -524408.268779] SLOW spr round 24 (radius: 20)
[12:10:28 -524408.268740] SLOW spr round 25 (radius: 25)
[12:28:03 -524408.268704] Model parameter optimization (eps = 0.100000)

[12:28:19] ML tree search #14, logLikelihood: -524407.880941

[12:28:19 -2083226.983117] Initial branch length optimization
[12:28:32 -1686955.379625] Model parameter optimization (eps = 10.000000)
[12:30:20 -1680764.323930] AUTODETECT spr round 1 (radius: 5)
[12:34:17 -1097687.519969] AUTODETECT spr round 2 (radius: 10)
[12:38:30 -777635.314985] AUTODETECT spr round 3 (radius: 15)
[12:43:15 -643559.862244] AUTODETECT spr round 4 (radius: 20)
[12:49:08 -595721.154976] AUTODETECT spr round 5 (radius: 25)
[12:56:06 -579837.912794] SPR radius for FAST iterations: 25 (autodetect)
[12:56:06 -579837.912794] Model parameter optimization (eps = 3.000000)
[12:57:00 -578982.260696] FAST spr round 1 (radius: 25)
[13:03:11 -527498.197332] FAST spr round 2 (radius: 25)
[13:07:50 -525170.083342] FAST spr round 3 (radius: 25)
[13:11:33 -524629.674871] FAST spr round 4 (radius: 25)
[13:14:38 -524486.542093] FAST spr round 5 (radius: 25)
[13:17:17 -524486.541628] Model parameter optimization (eps = 1.000000)
[13:17:48 -524463.432754] SLOW spr round 1 (radius: 5)
[13:21:50 -524417.685359] SLOW spr round 2 (radius: 5)
[13:25:45 -524414.820278] SLOW spr round 3 (radius: 5)
[13:29:34 -524414.134201] SLOW spr round 4 (radius: 5)
[13:33:17 -524414.133490] SLOW spr round 5 (radius: 10)
[13:37:19 -524409.361231] SLOW spr round 6 (radius: 5)
[13:42:23 -524406.375124] SLOW spr round 7 (radius: 5)
[13:46:43 -524406.374752] SLOW spr round 8 (radius: 10)
[13:50:56 -524406.246951] SLOW spr round 9 (radius: 5)
[13:55:57 -524406.245830] SLOW spr round 10 (radius: 10)
[14:00:56 -524406.245506] SLOW spr round 11 (radius: 15)
[14:08:55 -524406.245194] SLOW spr round 12 (radius: 20)
[14:21:39 -524405.523777] SLOW spr round 13 (radius: 5)
[14:27:07 -524405.434201] SLOW spr round 14 (radius: 10)
[14:32:23 -524405.430618] SLOW spr round 15 (radius: 15)
[14:39:51 -524405.428986] SLOW spr round 16 (radius: 20)
[14:52:49 -524405.428238] SLOW spr round 17 (radius: 25)
[15:10:36 -524405.427887] Model parameter optimization (eps = 0.100000)

[15:10:52] ML tree search #15, logLikelihood: -524405.322700

[15:10:52 -2085231.528835] Initial branch length optimization
[15:11:07 -1676662.300655] Model parameter optimization (eps = 10.000000)
[15:13:08 -1670687.080420] AUTODETECT spr round 1 (radius: 5)
[15:17:06 -1094337.500100] AUTODETECT spr round 2 (radius: 10)
[15:21:22 -789623.783985] AUTODETECT spr round 3 (radius: 15)
[15:26:00 -656142.942399] AUTODETECT spr round 4 (radius: 20)
[15:31:36 -619983.414487] AUTODETECT spr round 5 (radius: 25)
[15:39:18 -595485.020372] SPR radius for FAST iterations: 25 (autodetect)
[15:39:18 -595485.020372] Model parameter optimization (eps = 3.000000)
[15:40:15 -594493.051734] FAST spr round 1 (radius: 25)
[15:47:44 -527558.118803] FAST spr round 2 (radius: 25)
[15:52:55 -524788.107951] FAST spr round 3 (radius: 25)
[15:56:59 -524561.632615] FAST spr round 4 (radius: 25)
[16:00:16 -524545.658870] FAST spr round 5 (radius: 25)
[16:03:14 -524537.782816] FAST spr round 6 (radius: 25)
[16:05:55 -524537.782521] Model parameter optimization (eps = 1.000000)
[16:06:37 -524483.238134] SLOW spr round 1 (radius: 5)
[16:10:45 -524404.215563] SLOW spr round 2 (radius: 5)
[16:14:51 -524393.290735] SLOW spr round 3 (radius: 5)
[16:18:44 -524392.582454] SLOW spr round 4 (radius: 5)
[16:22:31 -524392.581402] SLOW spr round 5 (radius: 10)
[16:26:38 -524392.360727] SLOW spr round 6 (radius: 5)
[16:31:44 -524392.359956] SLOW spr round 7 (radius: 10)
[16:36:41 -524392.178770] SLOW spr round 8 (radius: 5)
[16:41:38 -524392.175381] SLOW spr round 9 (radius: 10)
[16:46:13 -524392.052621] SLOW spr round 10 (radius: 5)
[16:51:07 -524392.051450] SLOW spr round 11 (radius: 10)
[16:55:46 -524392.051212] SLOW spr round 12 (radius: 15)
[17:03:35 -524391.808232] SLOW spr round 13 (radius: 5)
[17:08:59 -524391.804094] SLOW spr round 14 (radius: 10)
[17:14:10 -524391.803989] SLOW spr round 15 (radius: 15)
[17:21:46 -524391.803899] SLOW spr round 16 (radius: 20)
[17:34:36 -524391.343060] SLOW spr round 17 (radius: 5)
[17:40:04 -524391.312803] SLOW spr round 18 (radius: 10)
[17:45:21 -524391.312713] SLOW spr round 19 (radius: 15)
[17:52:46 -524391.312644] SLOW spr round 20 (radius: 20)
[18:05:30 -524391.312587] SLOW spr round 21 (radius: 25)
[18:23:06 -524391.312537] Model parameter optimization (eps = 0.100000)

[18:23:13] ML tree search #16, logLikelihood: -524391.277184

[18:23:14 -2072984.456102] Initial branch length optimization
[18:23:31 -1683489.938339] Model parameter optimization (eps = 10.000000)
[18:25:00 -1677102.163561] AUTODETECT spr round 1 (radius: 5)
[18:29:00 -1086975.609251] AUTODETECT spr round 2 (radius: 10)
[18:33:16 -787559.549028] AUTODETECT spr round 3 (radius: 15)
[18:38:01 -645564.477276] AUTODETECT spr round 4 (radius: 20)
[18:43:40 -600072.138104] AUTODETECT spr round 5 (radius: 25)
[18:50:49 -588279.372911] SPR radius for FAST iterations: 25 (autodetect)
[18:50:49 -588279.372911] Model parameter optimization (eps = 3.000000)
[18:51:47 -587288.108381] FAST spr round 1 (radius: 25)
[18:58:06 -526740.919557] FAST spr round 2 (radius: 25)
[19:02:54 -524589.640871] FAST spr round 3 (radius: 25)
[19:06:45 -524500.318409] FAST spr round 4 (radius: 25)
[19:09:52 -524493.247493] FAST spr round 5 (radius: 25)
[19:12:42 -524493.095183] FAST spr round 6 (radius: 25)
[19:15:26 -524493.093062] Model parameter optimization (eps = 1.000000)
[19:15:55 -524480.274467] SLOW spr round 1 (radius: 5)
[19:20:03 -524420.540593] SLOW spr round 2 (radius: 5)
[19:24:07 -524413.865830] SLOW spr round 3 (radius: 5)
[19:28:03 -524413.860078] SLOW spr round 4 (radius: 10)
[19:32:15 -524413.732755] SLOW spr round 5 (radius: 5)
[19:37:24 -524413.719039] SLOW spr round 6 (radius: 10)
[19:42:20 -524413.717723] SLOW spr round 7 (radius: 15)
[19:49:59 -524413.716550] SLOW spr round 8 (radius: 20)
[20:02:29 -524413.715501] SLOW spr round 9 (radius: 25)
[20:19:47 -524413.608544] SLOW spr round 10 (radius: 5)
[20:25:30 -524413.542370] SLOW spr round 11 (radius: 10)
[20:31:06 -524413.540043] SLOW spr round 12 (radius: 15)
[20:38:40 -524413.538853] SLOW spr round 13 (radius: 20)
[20:51:19 -524413.538299] SLOW spr round 14 (radius: 25)
[21:08:36 -524413.538049] Model parameter optimization (eps = 0.100000)

[21:08:53] ML tree search #17, logLikelihood: -524413.426231

[21:08:53 -2076219.988409] Initial branch length optimization
[21:09:07 -1687631.093994] Model parameter optimization (eps = 10.000000)
[21:10:47 -1681232.748833] AUTODETECT spr round 1 (radius: 5)
[21:14:51 -1076790.072099] AUTODETECT spr round 2 (radius: 10)
[21:19:16 -790708.962102] AUTODETECT spr round 3 (radius: 15)
[21:24:08 -642796.863517] AUTODETECT spr round 4 (radius: 20)
[21:29:51 -605276.375688] AUTODETECT spr round 5 (radius: 25)
[21:36:31 -591067.865358] SPR radius for FAST iterations: 25 (autodetect)
[21:36:31 -591067.865358] Model parameter optimization (eps = 3.000000)
[21:37:29 -590178.194900] FAST spr round 1 (radius: 25)
[21:44:44 -527571.634313] FAST spr round 2 (radius: 25)
[21:49:48 -524758.607926] FAST spr round 3 (radius: 25)
[21:53:47 -524494.788395] FAST spr round 4 (radius: 25)
[21:56:50 -524484.543393] FAST spr round 5 (radius: 25)
[21:59:38 -524482.236633] FAST spr round 6 (radius: 25)
[22:02:18 -524482.235855] Model parameter optimization (eps = 1.000000)
[22:02:48 -524450.570979] SLOW spr round 1 (radius: 5)
[22:06:53 -524402.858059] SLOW spr round 2 (radius: 5)
[22:10:41 -524402.805582] SLOW spr round 3 (radius: 10)
[22:14:53 -524402.585315] SLOW spr round 4 (radius: 5)
[22:20:06 -524402.584494] SLOW spr round 5 (radius: 10)
[22:25:03 -524402.462017] SLOW spr round 6 (radius: 5)
[22:30:01 -524402.460830] SLOW spr round 7 (radius: 10)
[22:34:38 -524402.460501] SLOW spr round 8 (radius: 15)
[22:42:18 -524402.460248] SLOW spr round 9 (radius: 20)
[22:55:07 -524402.460049] SLOW spr round 10 (radius: 25)
[23:13:15 -524402.459891] Model parameter optimization (eps = 0.100000)

[23:13:22] ML tree search #18, logLikelihood: -524402.395491

[23:13:23 -2068191.878940] Initial branch length optimization
[23:13:36 -1685831.913768] Model parameter optimization (eps = 10.000000)
[23:15:08 -1679335.771738] AUTODETECT spr round 1 (radius: 5)
[23:19:05 -1091969.881035] AUTODETECT spr round 2 (radius: 10)
[23:23:17 -818319.053685] AUTODETECT spr round 3 (radius: 15)
[23:27:58 -675958.063519] AUTODETECT spr round 4 (radius: 20)
[23:33:29 -601979.439682] AUTODETECT spr round 5 (radius: 25)
[23:40:23 -596299.634825] SPR radius for FAST iterations: 25 (autodetect)
[23:40:23 -596299.634825] Model parameter optimization (eps = 3.000000)
[23:41:31 -595341.006301] FAST spr round 1 (radius: 25)
[23:47:46 -528144.709258] FAST spr round 2 (radius: 25)
[23:52:23 -525486.473846] FAST spr round 3 (radius: 25)
[23:55:59 -524966.326718] FAST spr round 4 (radius: 25)
[23:59:29 -524568.145947] FAST spr round 5 (radius: 25)
[24:02:28 -524522.958671] FAST spr round 6 (radius: 25)
[24:05:11 -524522.958079] Model parameter optimization (eps = 1.000000)
[24:05:37 -524510.852090] SLOW spr round 1 (radius: 5)
[24:09:34 -524417.908170] SLOW spr round 2 (radius: 5)
[24:13:28 -524417.008668] SLOW spr round 3 (radius: 5)
[24:17:15 -524417.007367] SLOW spr round 4 (radius: 10)
[24:21:21 -524407.779701] SLOW spr round 5 (radius: 5)
[24:26:34 -524406.880360] SLOW spr round 6 (radius: 5)
[24:31:02 -524406.880093] SLOW spr round 7 (radius: 10)
[24:35:22 -524406.879972] SLOW spr round 8 (radius: 15)
[24:43:14 -524406.879903] SLOW spr round 9 (radius: 20)
[24:55:37 -524406.879855] SLOW spr round 10 (radius: 25)
[25:13:03 -524406.879817] Model parameter optimization (eps = 0.100000)

[25:13:15] ML tree search #19, logLikelihood: -524406.766301

[25:13:15 -2084654.636444] Initial branch length optimization
[25:13:28 -1687678.116970] Model parameter optimization (eps = 10.000000)
[25:15:09 -1681184.051305] AUTODETECT spr round 1 (radius: 5)
[25:19:18 -1090524.371319] AUTODETECT spr round 2 (radius: 10)
[25:23:46 -795719.549811] AUTODETECT spr round 3 (radius: 15)
[25:28:39 -631871.089812] AUTODETECT spr round 4 (radius: 20)
[25:34:10 -592047.896251] AUTODETECT spr round 5 (radius: 25)
[25:40:39 -582174.124901] SPR radius for FAST iterations: 25 (autodetect)
[25:40:39 -582174.124901] Model parameter optimization (eps = 3.000000)
[25:41:35 -581266.828963] FAST spr round 1 (radius: 25)
[25:47:45 -527232.196326] FAST spr round 2 (radius: 25)
[25:52:22 -524711.739478] FAST spr round 3 (radius: 25)
[25:56:08 -524540.638329] FAST spr round 4 (radius: 25)
[25:59:11 -524538.892517] FAST spr round 5 (radius: 25)
[26:01:55 -524538.880429] Model parameter optimization (eps = 1.000000)
[26:02:23 -524512.919606] SLOW spr round 1 (radius: 5)
[26:06:33 -524417.406648] SLOW spr round 2 (radius: 5)
[26:10:36 -524403.233754] SLOW spr round 3 (radius: 5)
[26:14:31 -524402.409847] SLOW spr round 4 (radius: 5)
[26:18:23 -524402.408716] SLOW spr round 5 (radius: 10)
[26:22:34 -524402.021042] SLOW spr round 6 (radius: 5)
[26:27:53 -524395.897137] SLOW spr round 7 (radius: 5)
[26:32:23 -524395.894587] SLOW spr round 8 (radius: 10)
[26:36:48 -524395.871404] SLOW spr round 9 (radius: 15)
[26:44:45 -524394.211375] SLOW spr round 10 (radius: 5)
[26:50:09 -524394.202414] SLOW spr round 11 (radius: 10)
[26:55:17 -524394.200270] SLOW spr round 12 (radius: 15)
[27:02:37 -524394.199683] SLOW spr round 13 (radius: 20)
[27:15:01 -524394.199498] SLOW spr round 14 (radius: 25)
[27:32:20 -524394.199422] Model parameter optimization (eps = 0.100000)

[27:32:31] ML tree search #20, logLikelihood: -524394.099746


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.179703,0.541774) (0.135718,0.657498) (0.415773,0.813783) (0.268806,1.767290) 
   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: -524391.277184

AIC score: 1052792.554368 / AICc score: 1062289.673612 / BIC score: 1064734.587702
Free parameters (model + branch lengths): 2005

Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q14315/3_mltree/Q14315.raxml.log

Analysis started: 24-Jun-2021 16:27:55 / finished: 25-Jun-2021 20:00:27

Elapsed time: 99151.971 seconds (this run) / 181674.444 seconds (total with restarts)