raxml-ng re-generating parsimony starting tree

stdout

RAxML-NG v. 0.9.0git released on 26.11.2019 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

RAxML-NG was called at 02-Jun-2020 09:39:21 as follows:

./raxml-ng --tree pars{1} --msa b-nuc.translated.sort.hd1.curated.fasta --prefix FLU --model FLU+F+I --log VERBOSE --threads 8

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 1591108761
  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: AVX
  parallelization: PTHREADS (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: b-nuc.translated.sort.hd1.curated.fasta
[00:00:00] Loaded alignment with 8852 taxa and 570 sites
[00:00:00] Extracting partitions... 
[00:00:00] Checking the alignment...
[00:00:00] Compressing alignment patterns... 

Alignment comprises 1 partitions and 570 patterns

Partition 0: noname
Model: FLU+FC+I
Alignment sites / patterns: 570 / 570
Gaps: 8.76 %
Invariant sites: 2.46 %


NOTE: Binary MSA file created: FLU.raxml.rba


WARNING: You might be using too many threads (8) for your alignment with 570 unique patterns.
NOTE:    For the optimal throughput, please consider using fewer threads 
NOTE:    and parallelize across starting trees/bootstrap replicates.
NOTE:    As a general rule-of-thumb, please assign at least 200-1000 alignment patterns per thread.


NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.

[00:00:00] Generating 1 parsimony starting tree(s) with 8852 taxa

Initial model parameters:
   Partition: noname
   Rate heterogeneity: NONE
   P-inv (ML): 0.012281
   Base frequencies (empirical): 0.069303 0.035045 0.055778 0.045579 0.028473 0.028469 0.050421 0.092762 0.027270 0.061971 0.090903 0.068469 0.016673 0.025965 0.051080 0.070198 0.083585 0.010702 0.028278 0.059075 
   Substitution rates (model): 0.138659 0.053367 0.584852 0.026447 0.353754 1.484235 1.132313 0.214758 0.149927 0.023117 0.474334 0.058745 0.080491 0.659311 3.011345 5.418298 0.196000 0.018289 3.532005 0.161001 0.006772 0.167207 3.292717 0.124898 1.190624 1.879570 0.246117 0.296046 15.300097 0.890162 0.016100 0.154027 0.950138 0.183077 1.369429 0.099855 0.103964 7.737393 0.000013 0.530643 0.061652 0.322525 1.387096 0.218572 0.000836 2.646848 0.005252 0.000836 0.036400 3.881311 2.140332 0.000536 0.373102 0.010258 0.014100 0.145469 5.370511 1.934833 0.887571 0.014086 0.005731 0.290043 0.041763 0.000001 0.188539 0.338372 0.135481 0.000015 0.525399 0.297124 0.002547 0.000000 0.116941 0.021800 0.001112 0.005614 0.000004 0.111457 0.104054 0.000000 0.336263 0.011975 0.094107 0.601692 0.054905 1.195629 0.108051 5.330313 0.028840 1.020367 2.559587 0.190259 0.032681 0.712770 0.487822 0.602341 0.044000 0.072206 0.406698 1.593099 0.256492 0.014200 0.016500 3.881489 0.313974 0.001004 0.319559 0.307140 0.280125 0.155245 0.104093 0.285048 0.058775 0.000016 0.006516 0.264149 0.001500 0.001237 0.038632 1.585647 0.018808 0.196486 0.074815 0.337230 0.243190 0.321612 0.347303 0.001274 0.119029 0.924467 0.580704 0.368714 0.022400 6.448954 0.098631 3.512072 0.227708 9.017954 1.463357 0.080543 0.290381 2.904052 0.032132 0.273934 14.394052 0.129224 6.746936 2.986800 0.634309 0.570767 0.044926 0.431278 0.340058 0.890599 1.331292 0.320000 0.195751 0.283808 1.526964 0.000050 0.012416 0.073128 0.279911 0.056900 0.007027 2.031511 0.070460 0.874272 4.904842 0.007132 0.996686 0.000135 0.814753 5.393924 0.592588 2.087385 0.542251 0.000431 0.000182 0.058972 2.206860 0.099836 0.392552 0.088256 0.207066 0.124898 0.654109 0.427755 0.256900 0.167582 

[03:54:02] Data distribution: max. partitions/sites/weight per thread: 1 / 72 / 1440

thread#	part#	start	length	weight
0	0	504	66	1320

1	0	432	72	1440

2	0	360	72	1440

3	0	288	72	1440

4	0	216	72	1440

5	0	144	72	1440

6	0	72	72	1440

7	0	0	72	1440


Starting ML tree search with 1 distinct starting trees

[03:54:28 -981189.107312] Initial branch length optimization
[03:54:51 -101274.226438] Model parameter optimization (eps = 10.000000)
[03:54:59 -101272.645195] AUTODETECT spr round 1 (radius: 5)
[05:54:08 -100899.486568] AUTODETECT spr round 2 (radius: 10)
[08:38:38 -100605.336872] AUTODETECT spr round 3 (radius: 15)
[11:05:13 -100331.601394] AUTODETECT spr round 4 (radius: 20)
[12:38:34 -100098.520116] AUTODETECT spr round 5 (radius: 25)
[14:32:43 -99936.304952] SPR radius for FAST iterations: 25 (autodetect)
[14:32:43 -99936.304952] Model parameter optimization (eps = 3.000000)
[14:32:53 -99936.196942] FAST spr round 1 (radius: 25)
[17:23:23 -99672.444490] FAST spr round 2 (radius: 25)
[19:19:46 -99651.403503] FAST spr round 3 (radius: 25)
[20:28:10 -99649.922191] FAST spr round 4 (radius: 25)
[21:56:43 -99649.921237] Model parameter optimization (eps = 1.000000)
[21:56:52 -99649.912780] SLOW spr round 1 (radius: 5)
[23:00:47 -99648.284503] SLOW spr round 2 (radius: 5)
[24:03:57 -99647.591709] SLOW spr round 3 (radius: 5)
[25:06:58 -99647.590300] SLOW spr round 4 (radius: 10)
[26:10:42 -99645.044803] SLOW spr round 5 (radius: 5)
[27:13:38 -99645.042278] SLOW spr round 6 (radius: 10)
[28:16:26 -99645.040330] SLOW spr round 7 (radius: 15)
[29:20:52 -99643.432675] SLOW spr round 8 (radius: 5)
[30:23:53 -99636.998831] SLOW spr round 9 (radius: 5)
[31:27:31 -99636.996641] SLOW spr round 10 (radius: 10)
[32:33:32 -99634.985115] SLOW spr round 11 (radius: 5)
[33:38:44 -99634.983854] SLOW spr round 12 (radius: 10)
[34:43:04 -99634.982710] SLOW spr round 13 (radius: 15)
[35:50:25 -99632.504059] SLOW spr round 14 (radius: 5)
[36:56:14 -99632.503880] SLOW spr round 15 (radius: 10)
[38:25:30 -99632.503708] SLOW spr round 16 (radius: 15)
[39:48:14 -99632.503542] SLOW spr round 17 (radius: 20)
[41:18:28 -99620.361239] SLOW spr round 18 (radius: 5)
[42:33:52 -99619.740204] SLOW spr round 19 (radius: 5)
[43:38:34 -99619.739833] SLOW spr round 20 (radius: 10)
[44:43:48 -99619.739689] SLOW spr round 21 (radius: 15)
[45:50:51 -99612.718435] SLOW spr round 22 (radius: 5)
[46:56:27 -99612.718171] SLOW spr round 23 (radius: 10)
[48:07:42 -99612.718041] SLOW spr round 24 (radius: 15)
[49:13:17 -99612.717896] SLOW spr round 25 (radius: 20)
[50:22:41 -99607.086059] SLOW spr round 26 (radius: 5)
[51:26:53 -99607.085907] SLOW spr round 27 (radius: 10)
[52:31:20 -99607.019278] SLOW spr round 28 (radius: 15)
[53:39:41 -99606.810658] SLOW spr round 29 (radius: 5)
[54:44:23 -99606.810456] SLOW spr round 30 (radius: 10)
[55:49:54 -99606.810352] SLOW spr round 31 (radius: 15)
[56:55:41 -99606.810251] SLOW spr round 32 (radius: 20)
[58:07:31 -99597.272358] SLOW spr round 33 (radius: 5)
[59:15:24 -99597.271890] SLOW spr round 34 (radius: 10)
[60:19:10 -99597.271696] SLOW spr round 35 (radius: 15)
[61:25:35 -99597.271431] SLOW spr round 36 (radius: 20)
[62:37:57 -99594.100950] SLOW spr round 37 (radius: 5)
[63:51:00 -99591.490183] SLOW spr round 38 (radius: 5)
[65:09:35 -99591.490093] SLOW spr round 39 (radius: 10)
[68:04:37 -99591.490007] SLOW spr round 40 (radius: 15)
[70:41:36 -99590.416457] SLOW spr round 41 (radius: 5)

RAxML-NG v. 0.9.0git released on 26.11.2019 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

RAxML-NG was called at 05-Jun-2020 15:57:12 as follows:

raxml-ng --tree pars{1} --msa b-nuc.translated.sort.hd1.curated.fasta --prefix FLU --model FLU+F+I --log VERBOSE

Analysis options:
  run mode: ML tree search
  start tree(s): parsimony (1)
  random seed: 1591387032
  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: PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: b-nuc.translated.sort.hd1.curated.fasta
[00:00:00] Loaded alignment with 8852 taxa and 570 sites
[00:00:00] Extracting partitions... 
[00:00:00] Checking the alignment...
[00:00:00] Compressing alignment patterns... 

Alignment comprises 1 partitions and 570 patterns

Partition 0: noname
Model: FLU+FC+I
Alignment sites / patterns: 570 / 570
Gaps: 8.76 %
Invariant sites: 2.46 %


NOTE: Binary MSA file created: FLU.raxml.rba


NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.

[00:00:01] NOTE: Resuming execution from checkpoint (logLH: -99590.42, ML trees: 0, bootstraps: 0)
[00:00:01] Generating 1 parsimony starting tree(s) with 8852 taxa