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-Jul-2021 12:35:12 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/2_msa/Q96RK1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/2_msa/Q96RK1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 226 taxa and 138 sites

WARNING: Sequences tr_M3Y1U7_M3Y1U7_MUSPF_9669 and tr_A0A2Y9L9E2_A0A2Y9L9E2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_G1RYG3_G1RYG3_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_G3RJ28_G3RJ28_GORGO_9595 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2J8X9X6_A0A2J8X9X6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2I3SY88_A0A2I3SY88_PANTR_9598 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_Q99MA1_Q99MA1_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_H0XPI8_H0XPI8_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and sp_Q99967_CITE2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A1D5QPF9_A0A1D5QPF9_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2R8P6R0_A0A2R8P6R0_CALJA_9483 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_L5KDA0_L5KDA0_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_M3X852_M3X852_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A0D9SAC0_A0A0D9SAC0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A1U7Q8B9_A0A1U7Q8B9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K5LUA5_A0A2K5LUA5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K6D2U1_A0A2K6D2U1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K5Y5Z7_A0A2K5Y5Z7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2U3WMT0_A0A2U3WMT0_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2U3YZF2_A0A2U3YZF2_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2Y9JGV1_A0A2Y9JGV1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1NRH9_G1NRH9_MELGA_9103 and tr_A0A226P5C4_A0A226P5C4_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2J8IVZ1_A0A2J8IVZ1_PANTR_9598 and tr_A0A2R9BGL8_A0A2R9BGL8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F6VSF3_F6VSF3_MONDO_13616 and tr_G3VUR7_G3VUR7_SARHA_9305 are exactly identical!
WARNING: Sequences tr_U3KKR2_U3KKR2_FICAL_59894 and tr_A0A218UZT2_A0A218UZT2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A2I3MLN7_A0A2I3MLN7_PAPAN_9555 and tr_A0A2K5MLU3_A0A2K5MLU3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A087RGD5_A0A087RGD5_APTFO_9233 and tr_A0A093IA60_A0A093IA60_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A2I0LRQ7_A0A2I0LRQ7_COLLI_8932 and tr_A0A1V4JI28_A0A1V4JI28_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3M9S8_A0A1S3M9S8_SALSA_8030 and tr_A0A060W8P5_A0A060W8P5_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A2Y9M8F4_A0A2Y9M8F4_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A2Y9SQ03_A0A2Y9SQ03_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A384AUV4_A0A384AUV4_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2U3V8D0_A0A2U3V8D0_TURTR_9739 and tr_A0A2Y9MVR4_A0A2Y9MVR4_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 32

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.reduced.phy

Alignment comprises 1 partitions and 134 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 138 / 134
Gaps: 7.95 %
Invariant sites: 9.42 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.rba

Parallelization scheme autoconfig: 3 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 226 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 134 / 10720
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -44461.297931] Initial branch length optimization
[00:00:00 -34782.736644] Model parameter optimization (eps = 10.000000)
[00:00:06 -34718.140651] AUTODETECT spr round 1 (radius: 5)
[00:00:13 -18826.379642] AUTODETECT spr round 2 (radius: 10)
[00:00:22 -14063.792047] AUTODETECT spr round 3 (radius: 15)
[00:00:32 -12083.234181] AUTODETECT spr round 4 (radius: 20)
[00:00:44 -11211.744154] AUTODETECT spr round 5 (radius: 25)
[00:00:58 -11045.160210] SPR radius for FAST iterations: 25 (autodetect)
[00:00:58 -11045.160210] Model parameter optimization (eps = 3.000000)
[00:01:03 -11009.035382] FAST spr round 1 (radius: 25)
[00:01:12 -9769.046262] FAST spr round 2 (radius: 25)
[00:01:20 -9707.721876] FAST spr round 3 (radius: 25)
[00:01:27 -9691.360601] FAST spr round 4 (radius: 25)
[00:01:33 -9689.273816] FAST spr round 5 (radius: 25)
[00:01:38 -9689.088283] FAST spr round 6 (radius: 25)
[00:01:44 -9689.087604] Model parameter optimization (eps = 1.000000)
[00:01:51 -9671.650849] SLOW spr round 1 (radius: 5)
[00:02:01 -9664.722623] SLOW spr round 2 (radius: 5)
[00:02:11 -9664.340628] SLOW spr round 3 (radius: 5)
[00:02:21 -9664.340462] SLOW spr round 4 (radius: 10)
[00:02:30 -9664.340453] SLOW spr round 5 (radius: 15)
[00:02:42 -9664.340277] SLOW spr round 6 (radius: 20)
[00:02:57 -9664.340277] SLOW spr round 7 (radius: 25)
[00:03:13 -9664.340277] Model parameter optimization (eps = 0.100000)

[00:03:15] [worker #0] ML tree search #1, logLikelihood: -9664.246250

[00:03:15 -43478.885786] Initial branch length optimization
[00:03:15 -34535.977606] Model parameter optimization (eps = 10.000000)
[00:03:21 -34451.062765] AUTODETECT spr round 1 (radius: 5)
[00:03:23] [worker #1] ML tree search #2, logLikelihood: -9657.635602
[00:03:27 -19369.861976] AUTODETECT spr round 2 (radius: 10)
[00:03:37 -13946.410180] AUTODETECT spr round 3 (radius: 15)
[00:03:49 -12277.771526] AUTODETECT spr round 4 (radius: 20)
[00:04:03 -11792.833966] AUTODETECT spr round 5 (radius: 25)
[00:04:04] [worker #2] ML tree search #3, logLikelihood: -9661.114746
[00:04:17 -11792.833026] SPR radius for FAST iterations: 20 (autodetect)
[00:04:17 -11792.833026] Model parameter optimization (eps = 3.000000)
[00:04:23 -11767.086599] FAST spr round 1 (radius: 20)
[00:04:31 -9889.972652] FAST spr round 2 (radius: 20)
[00:04:38 -9699.365677] FAST spr round 3 (radius: 20)
[00:04:45 -9690.872488] FAST spr round 4 (radius: 20)
[00:04:51 -9690.872347] Model parameter optimization (eps = 1.000000)
[00:04:58 -9681.693043] SLOW spr round 1 (radius: 5)
[00:05:08 -9670.110555] SLOW spr round 2 (radius: 5)
[00:05:19 -9662.784752] SLOW spr round 3 (radius: 5)
[00:05:29 -9660.194077] SLOW spr round 4 (radius: 5)
[00:05:39 -9659.868352] SLOW spr round 5 (radius: 5)
[00:05:49 -9659.523486] SLOW spr round 6 (radius: 5)
[00:05:59 -9659.523179] SLOW spr round 7 (radius: 10)
[00:06:08 -9659.523174] SLOW spr round 8 (radius: 15)
[00:06:21 -9659.523174] SLOW spr round 9 (radius: 20)
[00:06:37 -9659.523174] SLOW spr round 10 (radius: 25)
[00:06:44] [worker #1] ML tree search #5, logLikelihood: -9654.301541
[00:06:53 -9659.523174] Model parameter optimization (eps = 0.100000)

[00:06:58] [worker #0] ML tree search #4, logLikelihood: -9657.523667

[00:06:58 -44922.311694] Initial branch length optimization
[00:06:58 -35798.065238] Model parameter optimization (eps = 10.000000)
[00:07:04 -35699.955968] AUTODETECT spr round 1 (radius: 5)
[00:07:11 -19159.453047] AUTODETECT spr round 2 (radius: 10)
[00:07:19 -14493.668614] AUTODETECT spr round 3 (radius: 15)
[00:07:30 -12553.065573] AUTODETECT spr round 4 (radius: 20)
[00:07:38] [worker #2] ML tree search #6, logLikelihood: -9662.033647
[00:07:42 -11077.463308] AUTODETECT spr round 5 (radius: 25)
[00:07:53 -11076.148207] SPR radius for FAST iterations: 25 (autodetect)
[00:07:53 -11076.148207] Model parameter optimization (eps = 3.000000)
[00:07:56 -11060.392126] FAST spr round 1 (radius: 25)
[00:08:05 -9862.938048] FAST spr round 2 (radius: 25)
[00:08:13 -9713.956785] FAST spr round 3 (radius: 25)
[00:08:19 -9702.011747] FAST spr round 4 (radius: 25)
[00:08:25 -9701.852842] FAST spr round 5 (radius: 25)
[00:08:30 -9701.850835] Model parameter optimization (eps = 1.000000)
[00:08:34 -9687.863810] SLOW spr round 1 (radius: 5)
[00:08:44 -9680.053916] SLOW spr round 2 (radius: 5)
[00:08:54 -9677.528977] SLOW spr round 3 (radius: 5)
[00:09:04 -9677.528122] SLOW spr round 4 (radius: 10)
[00:09:14 -9677.527945] SLOW spr round 5 (radius: 15)
[00:09:30 -9677.527936] SLOW spr round 6 (radius: 20)
[00:09:49 -9677.527930] SLOW spr round 7 (radius: 25)
[00:10:05 -9677.527925] Model parameter optimization (eps = 0.100000)

[00:10:08] [worker #0] ML tree search #7, logLikelihood: -9676.871213

[00:10:08 -43490.596724] Initial branch length optimization
[00:10:09 -34899.220840] Model parameter optimization (eps = 10.000000)
[00:10:15 -34827.204938] AUTODETECT spr round 1 (radius: 5)
[00:10:22 -18656.272195] AUTODETECT spr round 2 (radius: 10)
[00:10:31 -13114.527253] AUTODETECT spr round 3 (radius: 15)
[00:10:41] [worker #1] ML tree search #8, logLikelihood: -9658.884692
[00:10:42 -11112.900441] AUTODETECT spr round 4 (radius: 20)
[00:10:53 -11055.051392] AUTODETECT spr round 5 (radius: 25)
[00:11:06 -11052.720041] SPR radius for FAST iterations: 25 (autodetect)
[00:11:06 -11052.720041] Model parameter optimization (eps = 3.000000)
[00:11:13 -11032.189011] FAST spr round 1 (radius: 25)
[00:11:22 -9811.314819] FAST spr round 2 (radius: 25)
[00:11:29 -9680.868280] FAST spr round 3 (radius: 25)
[00:11:34] [worker #2] ML tree search #9, logLikelihood: -9659.726083
[00:11:35 -9673.720213] FAST spr round 4 (radius: 25)
[00:11:41 -9673.716694] Model parameter optimization (eps = 1.000000)
[00:11:45 -9663.461985] SLOW spr round 1 (radius: 5)
[00:11:55 -9659.494426] SLOW spr round 2 (radius: 5)
[00:12:05 -9658.912125] SLOW spr round 3 (radius: 5)
[00:12:14 -9658.912041] SLOW spr round 4 (radius: 10)
[00:12:24 -9658.912010] SLOW spr round 5 (radius: 15)
[00:12:39 -9658.912010] SLOW spr round 6 (radius: 20)
[00:12:58 -9658.912010] SLOW spr round 7 (radius: 25)
[00:13:15 -9658.912010] Model parameter optimization (eps = 0.100000)

[00:13:18] [worker #0] ML tree search #10, logLikelihood: -9658.615529

[00:13:18 -44210.981427] Initial branch length optimization
[00:13:18 -35318.645228] Model parameter optimization (eps = 10.000000)
[00:13:24 -35263.965287] AUTODETECT spr round 1 (radius: 5)
[00:13:31 -17535.074277] AUTODETECT spr round 2 (radius: 10)
[00:13:40 -13088.670321] AUTODETECT spr round 3 (radius: 15)
[00:13:51 -11093.207506] AUTODETECT spr round 4 (radius: 20)
[00:14:02] [worker #1] ML tree search #11, logLikelihood: -9666.180498
[00:14:04 -10612.420611] AUTODETECT spr round 5 (radius: 25)
[00:14:18 -10612.402560] SPR radius for FAST iterations: 20 (autodetect)
[00:14:18 -10612.402560] Model parameter optimization (eps = 3.000000)
[00:14:23 -10583.908392] FAST spr round 1 (radius: 20)
[00:14:31 -9739.688275] FAST spr round 2 (radius: 20)
[00:14:31] [worker #2] ML tree search #12, logLikelihood: -9661.011327
[00:14:37 -9698.037154] FAST spr round 3 (radius: 20)
[00:14:45 -9683.077459] FAST spr round 4 (radius: 20)
[00:14:52 -9675.774433] FAST spr round 5 (radius: 20)
[00:14:57 -9675.773869] Model parameter optimization (eps = 1.000000)
[00:15:01 -9667.436975] SLOW spr round 1 (radius: 5)
[00:15:11 -9665.338910] SLOW spr round 2 (radius: 5)
[00:15:20 -9665.338296] SLOW spr round 3 (radius: 10)
[00:15:30 -9664.286950] SLOW spr round 4 (radius: 5)
[00:15:44 -9664.285399] SLOW spr round 5 (radius: 10)
[00:15:55 -9664.285100] SLOW spr round 6 (radius: 15)
[00:16:08 -9664.285043] SLOW spr round 7 (radius: 20)
[00:16:27 -9664.285032] SLOW spr round 8 (radius: 25)
[00:16:45 -9664.285030] Model parameter optimization (eps = 0.100000)

[00:16:47] [worker #0] ML tree search #13, logLikelihood: -9664.223898

[00:16:47 -44028.524365] Initial branch length optimization
[00:16:47 -35019.280337] Model parameter optimization (eps = 10.000000)
[00:16:55 -34931.478247] AUTODETECT spr round 1 (radius: 5)
[00:17:02 -18324.593461] AUTODETECT spr round 2 (radius: 10)
[00:17:11 -14839.216030] AUTODETECT spr round 3 (radius: 15)
[00:17:22 -12328.061515] AUTODETECT spr round 4 (radius: 20)
[00:17:36 -11492.242033] AUTODETECT spr round 5 (radius: 25)
[00:17:39] [worker #1] ML tree search #14, logLikelihood: -9659.835315
[00:17:48] [worker #2] ML tree search #15, logLikelihood: -9663.187899
[00:17:51 -11450.684607] SPR radius for FAST iterations: 25 (autodetect)
[00:17:51 -11450.684607] Model parameter optimization (eps = 3.000000)
[00:17:56 -11419.168598] FAST spr round 1 (radius: 25)
[00:18:05 -9765.170146] FAST spr round 2 (radius: 25)
[00:18:14 -9688.548830] FAST spr round 3 (radius: 25)
[00:18:20 -9682.782317] FAST spr round 4 (radius: 25)
[00:18:26 -9681.647271] FAST spr round 5 (radius: 25)
[00:18:32 -9681.646536] Model parameter optimization (eps = 1.000000)
[00:18:37 -9663.105062] SLOW spr round 1 (radius: 5)
[00:18:47 -9660.369011] SLOW spr round 2 (radius: 5)
[00:18:56 -9659.985334] SLOW spr round 3 (radius: 5)
[00:19:06 -9659.985008] SLOW spr round 4 (radius: 10)
[00:19:15 -9659.985004] SLOW spr round 5 (radius: 15)
[00:19:29 -9659.985003] SLOW spr round 6 (radius: 20)
[00:19:45 -9659.985003] SLOW spr round 7 (radius: 25)
[00:20:01 -9659.985003] Model parameter optimization (eps = 0.100000)

[00:20:03] [worker #0] ML tree search #16, logLikelihood: -9659.917422

[00:20:03 -44004.591909] Initial branch length optimization
[00:20:03 -35469.122993] Model parameter optimization (eps = 10.000000)
[00:20:09 -35366.164753] AUTODETECT spr round 1 (radius: 5)
[00:20:16 -18701.023256] AUTODETECT spr round 2 (radius: 10)
[00:20:25 -13312.325461] AUTODETECT spr round 3 (radius: 15)
[00:20:36 -11213.983294] AUTODETECT spr round 4 (radius: 20)
[00:20:36] [worker #1] ML tree search #17, logLikelihood: -9657.153842
[00:20:48 -10684.332288] AUTODETECT spr round 5 (radius: 25)
[00:21:02 -10684.323763] SPR radius for FAST iterations: 20 (autodetect)
[00:21:02 -10684.323763] Model parameter optimization (eps = 3.000000)
[00:21:08 -10646.229659] FAST spr round 1 (radius: 20)
[00:21:16 -9776.420677] FAST spr round 2 (radius: 20)
[00:21:20] [worker #2] ML tree search #18, logLikelihood: -9665.745836
[00:21:23 -9685.662595] FAST spr round 3 (radius: 20)
[00:21:29 -9685.411912] FAST spr round 4 (radius: 20)
[00:21:35 -9685.317207] Model parameter optimization (eps = 1.000000)
[00:21:40 -9676.223189] SLOW spr round 1 (radius: 5)
[00:21:50 -9670.074804] SLOW spr round 2 (radius: 5)
[00:22:00 -9666.946097] SLOW spr round 3 (radius: 5)
[00:22:09 -9666.946087] SLOW spr round 4 (radius: 10)
[00:22:19 -9666.946086] SLOW spr round 5 (radius: 15)
[00:22:32 -9664.536911] SLOW spr round 6 (radius: 5)
[00:22:48 -9663.929318] SLOW spr round 7 (radius: 5)
[00:23:00 -9663.809878] SLOW spr round 8 (radius: 5)
[00:23:11 -9663.809745] SLOW spr round 9 (radius: 10)
[00:23:20 -9663.809736] SLOW spr round 10 (radius: 15)
[00:23:33 -9663.809736] SLOW spr round 11 (radius: 20)
[00:23:49 -9663.809735] SLOW spr round 12 (radius: 25)
[00:24:05 -9663.809735] Model parameter optimization (eps = 0.100000)

[00:24:08] [worker #0] ML tree search #19, logLikelihood: -9653.246836

[00:24:22] [worker #1] ML tree search #20, logLikelihood: -9669.067504

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.316885,0.484878) (0.254894,1.345852) (0.140287,0.440534) (0.287934,1.533333) 
   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: -9653.246836

AIC score: 20216.493672 / AICc score: 435176.493672 / BIC score: 21548.394099
Free parameters (model + branch lengths): 455

WARNING: Number of free parameters (K=455) is larger than alignment size (n=138).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.log

Analysis started: 03-Jul-2021 12:35:12 / finished: 03-Jul-2021 12:59:35

Elapsed time: 1462.304 seconds

Consumed energy: 119.683 Wh