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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 03-Jun-2021 14:54:48 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/2_msa/Q8NBS3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/2_msa/Q8NBS3_trimmed_msa.fasta
[00:00:00] Loaded alignment with 438 taxa and 234 sites

WARNING: Sequences tr_A0A1D5PYH6_A0A1D5PYH6_CHICK_9031 and tr_G1NKL9_G1NKL9_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A0R3P886_A0A0R3P886_DROPS_46245 and tr_B4HAE8_B4HAE8_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2QJV7_H2QJV7_PANTR_9598 and sp_Q8NBS3_S4A11_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_W5QGA0_W5QGA0_SHEEP_9940 and tr_E1BKK3_E1BKK3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5QG87_A0A3B5QG87_XIPMA_8083 and tr_A0A087X7C0_A0A087X7C0_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A0J9XWR0_A0A0J9XWR0_BRUMA_6279 and tr_A0A0N4TRD0_A0A0N4TRD0_BRUPA_6280 are exactly identical!
WARNING: Sequences tr_A0A0J9XWR0_A0A0J9XWR0_BRUMA_6279 and tr_A0A0R3QJS4_A0A0R3QJS4_9BILA_42155 are exactly identical!
WARNING: Sequences tr_M1UX91_M1UX91_CYAM1_280699 and tr_M1VGR9_M1VGR9_CYAM1_280699 are exactly identical!
WARNING: Sequences tr_H0ZL69_H0ZL69_TAEGU_59729 and tr_A0A218USP0_A0A218USP0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_E3LRC0_E3LRC0_CAERE_31234 and tr_A0A1I7UA90_A0A1I7UA90_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A8WU00_A8WU00_CAEBR_6238 and tr_A0A2G5V439_A0A2G5V439_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_B3S500_B3S500_TRIAD_10228 and tr_A0A369S6V9_A0A369S6V9_9METZ_287889 are exactly identical!
WARNING: Sequences tr_R1E9B7_R1E9B7_EMIHU_2903 and tr_R1EC79_R1EC79_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_A0A044QXL5_A0A044QXL5_ONCVO_6282 and tr_A0A182EJP8_A0A182EJP8_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A078FKH3_A0A078FKH3_BRANA_3708 and tr_A0A0D3DHC9_A0A0D3DHC9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0K0EX16_A0A0K0EX16_STRVS_75913 and tr_A0A0N5C1G3_A0A0N5C1G3_STREA_174720 are exactly identical!
WARNING: Sequences tr_A0A151MYD2_A0A151MYD2_ALLMI_8496 and tr_A0A3Q0GDG5_A0A3Q0GDG5_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091JA23_A0A091JA23_EGRGA_188379 and tr_A0A091VPB0_A0A091VPB0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JA23_A0A091JA23_EGRGA_188379 and tr_A0A087QN33_A0A087QN33_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2I0MN14_A0A2I0MN14_COLLI_8932 and tr_A0A1V4JGF9_A0A1V4JGF9_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V1DCI0_A0A0V1DCI0_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V0WPL9_A0A0V0WPL9_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V0V1H5_A0A0V0V1H5_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V1KQY0_A0A0V1KQY0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V0Y912_A0A0V0Y912_TRIPS_6337 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V1PMZ0_A0A0V1PMZ0_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0S215_A0A0V0S215_9BILA_6336 and tr_A0A0V0TLJ4_A0A0V0TLJ4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A195DA49_A0A195DA49_9HYME_471704 and tr_A0A195BPA4_A0A195BPA4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A1S4C3K6_A0A1S4C3K6_TOBAC_4097 and tr_A0A1U7YK05_A0A1U7YK05_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3RQH3_A0A1S3RQH3_SALSA_8030 and tr_A0A060XPK9_A0A060XPK9_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1I7T050_A0A1I7T050_9PELO_1561998 and tr_A0A1I7T051_A0A1I7T051_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A226MX71_A0A226MX71_CALSU_9009 and tr_A0A226P706_A0A226P706_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2A2LNJ0_A0A2A2LNJ0_9BILA_2018661 and tr_A0A2A2LUR4_A0A2A2LUR4_9BILA_2018661 are exactly identical!
WARNING: Sequences tr_A0A2D0QMZ2_A0A2D0QMZ2_ICTPU_7998 and tr_W5UIJ0_W5UIJ0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5LIQ0_A0A2K5LIQ0_CERAT_9531 and tr_A0A2K6AMD8_A0A2K6AMD8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2P5EYY4_A0A2P5EYY4_TREOI_63057 and tr_A0A2P5CAA4_A0A2P5CAA4_PARAD_3476 are exactly identical!
WARNING: Duplicate sequences found: 36

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.reduced.phy

Alignment comprises 1 partitions and 234 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 234 / 234
Gaps: 15.14 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.rba

Parallelization scheme autoconfig: 5 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 438 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 234 / 18720
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -157415.433980] Initial branch length optimization
[00:00:02 -126167.999292] Model parameter optimization (eps = 10.000000)
[00:00:29 -125357.854402] AUTODETECT spr round 1 (radius: 5)
[00:01:06 -87581.476417] AUTODETECT spr round 2 (radius: 10)
[00:01:51 -63706.435381] AUTODETECT spr round 3 (radius: 15)
[00:02:45 -55523.224477] AUTODETECT spr round 4 (radius: 20)
[00:03:45 -52216.321362] AUTODETECT spr round 5 (radius: 25)
[00:04:50 -51127.777779] SPR radius for FAST iterations: 25 (autodetect)
[00:04:50 -51127.777779] Model parameter optimization (eps = 3.000000)
[00:05:09 -50881.579496] FAST spr round 1 (radius: 25)
[00:06:02 -44290.965553] FAST spr round 2 (radius: 25)
[00:06:43 -43775.903078] FAST spr round 3 (radius: 25)
[00:07:19 -43747.200829] FAST spr round 4 (radius: 25)
[00:07:52 -43732.784023] FAST spr round 5 (radius: 25)
[00:08:20 -43730.706352] FAST spr round 6 (radius: 25)
[00:08:46 -43730.700213] Model parameter optimization (eps = 1.000000)
[00:08:55 -43715.889404] SLOW spr round 1 (radius: 5)
[00:09:41 -43705.207043] SLOW spr round 2 (radius: 5)
[00:10:22 -43704.885958] SLOW spr round 3 (radius: 5)
[00:11:02 -43704.885554] SLOW spr round 4 (radius: 10)
[00:11:48 -43703.027514] SLOW spr round 5 (radius: 5)
[00:12:52 -43697.708551] SLOW spr round 6 (radius: 5)
[00:13:43 -43697.603266] SLOW spr round 7 (radius: 5)
[00:14:30 -43696.883102] SLOW spr round 8 (radius: 5)
[00:15:14 -43696.273545] SLOW spr round 9 (radius: 5)
[00:15:55 -43696.273453] SLOW spr round 10 (radius: 10)
[00:16:41 -43695.548604] SLOW spr round 11 (radius: 5)
[00:17:44 -43694.598533] SLOW spr round 12 (radius: 5)
[00:18:37 -43694.595206] SLOW spr round 13 (radius: 10)
[00:19:25 -43694.595203] SLOW spr round 14 (radius: 15)
[00:20:06] [worker #3] ML tree search #4, logLikelihood: -43685.287543
[00:20:37] [worker #4] ML tree search #5, logLikelihood: -43693.077569
[00:20:49 -43694.595203] SLOW spr round 15 (radius: 20)

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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 03-Jun-2021 15:19:29 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/2_msa/Q8NBS3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3 --seed 2 --threads 5 --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 (5 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.rba
[00:00:00] Alignment comprises 438 taxa, 1 partitions and 234 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 234 / 234
Gaps: 15.14 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

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

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -43694.60, ML trees: 2, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 234 / 18720
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -43694.595203] SPR radius for FAST iterations: 25 (autodetect)
[00:00:00 -43694.595203] SLOW spr round 15 (radius: 20)
[00:04:26] [worker #2] ML tree search #3, logLikelihood: -43683.314294
[00:05:32 -43694.431105] SLOW spr round 16 (radius: 5)
[00:08:40 -43693.950288] SLOW spr round 17 (radius: 5)
[00:09:35] [worker #1] ML tree search #2, logLikelihood: -43683.523009
[00:11:15 -43693.950264] SLOW spr round 18 (radius: 10)
[00:13:34 -43693.950263] SLOW spr round 19 (radius: 15)
[00:17:25 -43693.950263] SLOW spr round 20 (radius: 20)
[00:22:52 -43693.950263] SLOW spr round 21 (radius: 25)
[00:24:17] [worker #3] ML tree search #9, logLikelihood: -43692.690914
[00:28:42] [worker #2] ML tree search #8, logLikelihood: -43687.307039
[00:28:58 -43693.950263] Model parameter optimization (eps = 0.100000)

[00:29:07] [worker #0] ML tree search #1, logLikelihood: -43693.915491

[00:29:07 -156677.485181] Initial branch length optimization
[00:29:09 -125609.416685] Model parameter optimization (eps = 10.000000)
[00:29:39 -124913.333326] AUTODETECT spr round 1 (radius: 5)
[00:30:01] [worker #1] ML tree search #7, logLikelihood: -43689.426861
[00:30:25 -87737.516243] AUTODETECT spr round 2 (radius: 10)
[00:31:22 -66042.783483] AUTODETECT spr round 3 (radius: 15)
[00:32:29 -55244.166284] AUTODETECT spr round 4 (radius: 20)
[00:33:49 -52420.983037] AUTODETECT spr round 5 (radius: 25)
[00:35:12 -50497.944802] SPR radius for FAST iterations: 25 (autodetect)
[00:35:12 -50497.944802] Model parameter optimization (eps = 3.000000)
[00:35:36 -50333.538196] FAST spr round 1 (radius: 25)
[00:36:40 -44100.007847] FAST spr round 2 (radius: 25)
[00:37:31 -43721.418689] FAST spr round 3 (radius: 25)
[00:38:13 -43715.739748] FAST spr round 4 (radius: 25)
[00:38:51 -43714.293681] FAST spr round 5 (radius: 25)
[00:39:27 -43713.435954] FAST spr round 6 (radius: 25)
[00:40:02 -43713.434867] Model parameter optimization (eps = 1.000000)
[00:40:12 -43706.691482] SLOW spr round 1 (radius: 5)
[00:41:08 -43693.456058] SLOW spr round 2 (radius: 5)
[00:42:04 -43688.322692] SLOW spr round 3 (radius: 5)
[00:42:58 -43688.322074] SLOW spr round 4 (radius: 10)
[00:43:56 -43687.771400] SLOW spr round 5 (radius: 5)
[00:45:13 -43687.684041] SLOW spr round 6 (radius: 10)
[00:46:19 -43687.684036] SLOW spr round 7 (radius: 15)
[00:48:00 -43687.684035] SLOW spr round 8 (radius: 20)
[00:50:26 -43687.684031] SLOW spr round 9 (radius: 25)
[00:53:07 -43687.684031] Model parameter optimization (eps = 0.100000)

[00:53:11] [worker #0] ML tree search #6, logLikelihood: -43687.648559

[00:53:11 -155854.961138] Initial branch length optimization
[00:53:13 -125663.346424] Model parameter optimization (eps = 10.000000)
[00:53:30] [worker #1] ML tree search #14, logLikelihood: -43691.617555
[00:53:47 -124703.415384] AUTODETECT spr round 1 (radius: 5)
[00:54:33 -90369.155578] AUTODETECT spr round 2 (radius: 10)
[00:55:18] [worker #2] ML tree search #15, logLikelihood: -43692.256062
[00:55:30 -65979.849478] AUTODETECT spr round 3 (radius: 15)
[00:56:43 -51480.841131] AUTODETECT spr round 4 (radius: 20)
[00:57:58 -49168.399265] AUTODETECT spr round 5 (radius: 25)
[00:59:24 -48414.879873] SPR radius for FAST iterations: 25 (autodetect)
[00:59:24 -48414.879873] Model parameter optimization (eps = 3.000000)
[00:59:49 -48160.655175] FAST spr round 1 (radius: 25)
[01:00:43 -43907.456887] FAST spr round 2 (radius: 25)
[01:01:30 -43742.896021] FAST spr round 3 (radius: 25)
[01:02:14 -43723.229986] FAST spr round 4 (radius: 25)
[01:02:52 -43717.274264] FAST spr round 5 (radius: 25)
[01:03:28 -43714.199072] FAST spr round 6 (radius: 25)
[01:04:03 -43714.198487] Model parameter optimization (eps = 1.000000)
[01:04:14 -43709.245980] SLOW spr round 1 (radius: 5)
[01:05:10 -43697.824450] SLOW spr round 2 (radius: 5)
[01:06:03 -43697.681683] SLOW spr round 3 (radius: 5)
[01:06:56 -43697.681129] SLOW spr round 4 (radius: 10)
[01:07:53 -43696.622791] SLOW spr round 5 (radius: 5)
[01:09:12 -43696.472469] SLOW spr round 6 (radius: 5)
[01:10:18 -43696.472468] SLOW spr round 7 (radius: 10)
[01:11:18 -43696.369805] SLOW spr round 8 (radius: 5)
[01:12:35 -43695.238045] SLOW spr round 9 (radius: 5)
[01:13:40 -43695.238012] SLOW spr round 10 (radius: 10)
[01:14:40 -43695.134375] SLOW spr round 11 (radius: 5)
[01:15:59 -43691.068658] SLOW spr round 12 (radius: 5)
[01:17:05 -43689.952095] SLOW spr round 13 (radius: 5)
[01:18:03 -43689.951867] SLOW spr round 14 (radius: 10)
[01:19:02 -43689.431678] SLOW spr round 15 (radius: 5)
[01:20:20 -43689.268983] SLOW spr round 16 (radius: 5)
[01:20:38] [worker #2] ML tree search #20, logLikelihood: -43695.842650
[01:21:25 -43689.268584] SLOW spr round 17 (radius: 10)
[01:22:24 -43689.268583] SLOW spr round 18 (radius: 15)
[01:24:02 -43689.233957] SLOW spr round 19 (radius: 20)
[01:26:10 -43689.232785] SLOW spr round 20 (radius: 25)
[01:28:39 -43688.863244] SLOW spr round 21 (radius: 5)
[01:28:54] [worker #3] ML tree search #11, logLikelihood: -43699.224893
[01:29:27] [worker #1] ML tree search #19, logLikelihood: -43683.198206
[01:30:04 -43688.863199] SLOW spr round 22 (radius: 10)
[01:31:17 -43688.863199] SLOW spr round 23 (radius: 15)
[01:32:51 -43688.863199] SLOW spr round 24 (radius: 20)
[01:35:01 -43688.863199] SLOW spr round 25 (radius: 25)
[01:37:29 -43688.863199] Model parameter optimization (eps = 0.100000)

[01:37:33] [worker #0] ML tree search #13, logLikelihood: -43688.817930

[01:37:33 -155568.741457] Initial branch length optimization
[01:37:35 -124955.043914] Model parameter optimization (eps = 10.000000)
[01:38:03 -124256.791225] AUTODETECT spr round 1 (radius: 5)
[01:38:49 -82944.608532] AUTODETECT spr round 2 (radius: 10)
[01:39:43 -62443.630477] AUTODETECT spr round 3 (radius: 15)
[01:40:52 -52745.360262] AUTODETECT spr round 4 (radius: 20)
[01:42:06 -49463.032303] AUTODETECT spr round 5 (radius: 25)
[01:43:40 -48986.654754] SPR radius for FAST iterations: 25 (autodetect)
[01:43:40 -48986.654754] Model parameter optimization (eps = 3.000000)
[01:44:12 -48726.441701] FAST spr round 1 (radius: 25)
[01:45:14 -43826.896564] FAST spr round 2 (radius: 25)
[01:46:01 -43726.018037] FAST spr round 3 (radius: 25)
[01:46:43 -43715.149755] FAST spr round 4 (radius: 25)
[01:47:00] [worker #4] ML tree search #10, logLikelihood: -43688.391886
[01:47:21 -43713.438658] FAST spr round 5 (radius: 25)
[01:47:56 -43713.438175] Model parameter optimization (eps = 1.000000)
[01:48:04 -43711.182568] SLOW spr round 1 (radius: 5)
[01:48:58 -43699.815895] SLOW spr round 2 (radius: 5)
[01:49:52 -43699.144524] SLOW spr round 3 (radius: 5)
[01:50:43 -43699.144393] SLOW spr round 4 (radius: 10)
[01:51:39 -43697.232249] SLOW spr round 5 (radius: 5)
[01:52:58 -43693.847255] SLOW spr round 6 (radius: 5)
[01:54:03 -43693.693935] SLOW spr round 7 (radius: 5)
[01:55:01 -43692.583194] SLOW spr round 8 (radius: 5)
[01:55:56 -43692.583058] SLOW spr round 9 (radius: 10)
[01:56:52 -43692.005387] SLOW spr round 10 (radius: 5)
[01:58:09 -43691.842709] SLOW spr round 11 (radius: 5)
[01:59:13 -43691.842650] SLOW spr round 12 (radius: 10)
[02:00:10 -43691.842646] SLOW spr round 13 (radius: 15)
[02:01:47 -43691.842644] SLOW spr round 14 (radius: 20)
[02:04:06 -43691.842644] SLOW spr round 15 (radius: 25)
[02:06:41 -43691.842643] Model parameter optimization (eps = 0.100000)

[02:06:44] [worker #0] ML tree search #18, logLikelihood: -43691.831892

[02:16:24] [worker #3] ML tree search #16, logLikelihood: -43694.656539
[02:36:37] [worker #4] ML tree search #12, logLikelihood: -43688.338552
[03:52:36] [worker #4] ML tree search #17, logLikelihood: -43834.882172

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.303608,0.719918) (0.246097,1.436557) (0.307707,0.643466) (0.142589,1.612303) 
   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: -43683.198206

AIC score: 89124.396412 / AICc score: 1636164.396412 / BIC score: 92161.623672
Free parameters (model + branch lengths): 879

WARNING: Number of free parameters (K=879) is larger than alignment size (n=234).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 65 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8NBS3/3_mltree/Q8NBS3.raxml.log

Analysis started: 03-Jun-2021 15:19:29 / finished: 03-Jun-2021 19:12:05

Elapsed time: 13956.459 seconds (this run) / 15205.681 seconds (total with restarts)

Consumed energy: 479.779 Wh (= 2 km in an electric car, or 12 km with an e-scooter!)