RAxML-NG v. 1.2.0 released on 09.05.2023 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: AMD EPYC 7742 64-Core Processor, 128 cores, 251 GB RAM

RAxML-NG was called at 20-Dec-2023 10:34:06 as follows:

raxml-ng --threads 120 --force perf_threads -msa infile.txt --workers 10 --search --model part.txt

Analysis options:
  run mode: ML tree search
  start tree(s): random (10) + parsimony (10)
  random seed: 1703097246
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  fast CLV updates: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (10 workers), PTHREADS (120 threads), thread pinning: OFF

WARNING: Running in FORCE mode: some safety checks are disabled!

[00:00:00] Reading alignment from file: infile.txt
[00:00:00] Loaded alignment with 236 taxa and 23001 sites

WARNING: Fully undetermined columns found: 14

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.reduced.phy

NOTE: The corresponding reduced partition file was saved to:
/expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.reduced.partition

Alignment comprises 20 partitions and 12138 patterns

Partition 0: DNA,10_ND2
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1047 / 768
Gaps: 16.65 %
Invariant sites: 32.00 %

Partition 1: DNA,16_COI
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1551 / 772
Gaps: 34.53 %
Invariant sites: 56.87 %

Partition 2: DNA,19_COII
Model: GTR+FO+G4m+B
Alignment sites / patterns: 684 / 338
Gaps: 44.65 %
Invariant sites: 52.05 %

Partition 3: DNA,21_ATP_subunit8
Model: GTR+FO+G4m+B
Alignment sites / patterns: 180 / 143
Gaps: 41.57 %
Invariant sites: 30.00 %

Partition 4: DNA,22_ATP_subunit6
Model: GTR+FO+G4m+B
Alignment sites / patterns: 684 / 423
Gaps: 36.96 %
Invariant sites: 40.64 %

Partition 5: DNA,23_COIII
Model: GTR+FO+G4m+B
Alignment sites / patterns: 784 / 392
Gaps: 44.71 %
Invariant sites: 52.04 %

Partition 6: DNA,25_ND3
Model: GTR+FO+G4m+B
Alignment sites / patterns: 352 / 212
Gaps: 44.18 %
Invariant sites: 42.90 %

Partition 7: DNA,27_ND4L
Model: GTR+FO+G4m+B
Alignment sites / patterns: 297 / 186
Gaps: 44.63 %
Invariant sites: 40.07 %

Partition 8: DNA,28_ND4
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1378 / 824
Gaps: 44.65 %
Invariant sites: 40.93 %

Partition 9: DNA,2_12s
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1061 / 571
Gaps: 41.30 %
Invariant sites: 50.99 %

Partition 10: DNA,32_ND5
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1839 / 1128
Gaps: 45.29 %
Invariant sites: 40.02 %

Partition 11: DNA,33_cytb
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1147 / 678
Gaps: 15.50 %
Invariant sites: 47.08 %

Partition 12: DNA,37_ND6
Model: GTR+FO+G4m+B
Alignment sites / patterns: 531 / 374
Gaps: 37.95 %
Invariant sites: 34.46 %

Partition 13: DNA,4_16s
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1770 / 1052
Gaps: 43.06 %
Invariant sites: 46.89 %

Partition 14: DNA,6_ND1
Model: GTR+FO+G4m+B
Alignment sites / patterns: 996 / 540
Gaps: 40.34 %
Invariant sites: 47.59 %

Partition 15: DNA,FIB_reduced_final_fasta
Model: GTR+FO+G4m+B
Alignment sites / patterns: 3038 / 1649
Gaps: 46.18 %
Invariant sites: 59.05 %

Partition 16: DNA,MB_reduced_final_fasta
Model: GTR+FO+G4m+B
Alignment sites / patterns: 737 / 306
Gaps: 44.56 %
Invariant sites: 68.93 %

Partition 17: DNA,RAG1_reduced_final_fasta
Model: GTR+FO+G4m+B
Alignment sites / patterns: 2872 / 882
Gaps: 35.90 %
Invariant sites: 75.24 %

Partition 18: DNA,TGFB2_reduced_final_fasta
Model: GTR+FO+G4m+B
Alignment sites / patterns: 693 / 399
Gaps: 47.23 %
Invariant sites: 57.29 %

Partition 19: DNA,myc_reduced_final_fasta
Model: GTR+FO+G4m+B
Alignment sites / patterns: 1346 / 501
Gaps: 39.63 %
Invariant sites: 74.29 %


NOTE: Binary MSA file created: infile.txt.raxml.rba

[00:00:00] Generating 10 random starting tree(s) with 236 taxa
[00:00:00] Generating 10 parsimony starting tree(s) with 236 taxa
Parallel parsimony with 120 threads
Parallel reduction/worker buffer size: 37 KB  / 0 KB

[00:00:00] Data distribution: max. partitions/sites/weight per thread: 3 / 1012 / 16192
[00:00:00] Data distribution: max. searches per worker: 2

Starting ML tree search with 20 distinct starting trees

[00:00:01 -874137.799647] Initial branch length optimization
[00:00:02 -750577.612004] Model parameter optimization (eps = 10.000000)
[00:01:50 -624781.502627] AUTODETECT spr round 1 (radius: 5)
[00:01:54 -534754.549497] AUTODETECT spr round 2 (radius: 10)
[00:02:01 -454742.955657] AUTODETECT spr round 3 (radius: 15)
[00:02:14 -442773.028205] AUTODETECT spr round 4 (radius: 20)
[00:02:28 -442268.456781] AUTODETECT spr round 5 (radius: 25)
[00:02:38 -442267.533106] SPR radius for FAST iterations: 25 (autodetect)
[00:02:38 -442267.533106] Model parameter optimization (eps = 3.000000)
[00:03:12 -437815.893205] FAST spr round 1 (radius: 25)
[00:03:23 -414664.723817] FAST spr round 2 (radius: 25)
[00:03:29 -413986.592408] FAST spr round 3 (radius: 25)
[00:03:33 -413981.596107] Model parameter optimization (eps = 1.000000)
[00:03:47 -413600.429303] SLOW spr round 1 (radius: 5)
[00:03:54 -413593.079829] SLOW spr round 2 (radius: 10)
[00:04:02 -413593.041921] SLOW spr round 3 (radius: 15)
[00:04:21 -413593.005763] SLOW spr round 4 (radius: 20)
[00:04:43 -413592.970855] SLOW spr round 5 (radius: 25)
[00:04:59] [worker #4] ML tree search #5, logLikelihood: -413276.409631
[00:05:01 -413592.956989] Model parameter optimization (eps = 0.100000)
[00:05:18] [worker #9] ML tree search #10, logLikelihood: -413618.480960

[00:05:19] [worker #0] ML tree search #1, logLikelihood: -413588.385997

[00:05:19 -576789.061437] Initial branch length optimization
[00:05:20 -477658.096633] Model parameter optimization (eps = 10.000000)
[00:05:20] [worker #6] ML tree search #7, logLikelihood: -413345.075526
[00:05:42] [worker #8] ML tree search #9, logLikelihood: -412435.289416
[00:05:48] [worker #7] ML tree search #8, logLikelihood: -413140.718499
[00:05:51] [worker #5] ML tree search #6, logLikelihood: -412657.362170
[00:05:54] [worker #3] ML tree search #4, logLikelihood: -412843.252187
[00:06:02] [worker #1] ML tree search #2, logLikelihood: -412447.595720
[00:06:03] [worker #2] ML tree search #3, logLikelihood: -412650.615791
[00:06:11 -413779.268385] AUTODETECT spr round 1 (radius: 5)
[00:06:13 -412153.674543] AUTODETECT spr round 2 (radius: 10)
[00:06:20 -412081.163009] AUTODETECT spr round 3 (radius: 15)
[00:06:32 -412078.493542] AUTODETECT spr round 4 (radius: 20)
[00:06:45 -412076.798324] AUTODETECT spr round 5 (radius: 25)
[00:06:53 -412075.611277] SPR radius for FAST iterations: 25 (autodetect)
[00:06:54 -412075.611277] Model parameter optimization (eps = 3.000000)
[00:06:59 -412065.589919] FAST spr round 1 (radius: 25)
[00:07:05 -411856.463049] FAST spr round 2 (radius: 25)
[00:07:09 -411837.879159] FAST spr round 3 (radius: 25)
[00:07:12 -411832.982034] Model parameter optimization (eps = 1.000000)
[00:07:21 -411825.968800] SLOW spr round 1 (radius: 5)
[00:07:27 -411822.310912] SLOW spr round 2 (radius: 10)
[00:07:34 -411822.250280] SLOW spr round 3 (radius: 15)
[00:07:52 -411822.207919] SLOW spr round 4 (radius: 20)
[00:08:12] [worker #4] ML tree search #15, logLikelihood: -411812.665725
[00:08:15 -411822.167224] SLOW spr round 5 (radius: 25)
[00:08:19] [worker #6] ML tree search #17, logLikelihood: -411826.896183
[00:08:20] [worker #9] ML tree search #20, logLikelihood: -411813.399407
[00:08:31 -411822.127619] Model parameter optimization (eps = 0.100000)

[00:08:39] [worker #0] ML tree search #11, logLikelihood: -411821.160608

[00:08:46] [worker #5] ML tree search #16, logLikelihood: -411835.957892
[00:08:47] [worker #8] ML tree search #19, logLikelihood: -411821.100639
[00:08:55] [worker #7] ML tree search #18, logLikelihood: -411827.741190
[00:09:04] [worker #3] ML tree search #14, logLikelihood: -411827.267106
[00:09:11] [worker #1] ML tree search #12, logLikelihood: -411811.716012
[00:09:20] [worker #2] ML tree search #13, logLikelihood: -411811.963655


Final LogLikelihood: -411811.716012

AIC score: 824959.432023 / AICc score: 824999.479698 / BIC score: 830331.945014
Free parameters (model + branch lengths): 668

Best ML tree saved to: /expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.bestTree
All ML trees saved to: /expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.mlTrees
Optimized model saved to: /expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.bestModel

Execution log saved to: /expanse/projects/ngbt/backend/expanse_test_workspace/NGBW-JOB-RAXMLNG_XSEDE-13ACE97B28424D30928606324DCEF54E/infile.txt.raxml.log

Analysis started: 20-Dec-2023 10:34:06 / finished: 20-Dec-2023 10:43:26

Elapsed time: 560.874 seconds

Consumed energy: 74.666 Wh