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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM

RAxML-NG was called at 04-Jun-2021 03:53:05 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/2_msa/Q8IVF2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/2_msa/Q8IVF2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 160 taxa and 95 sites

WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_H2QGC5_H2QGC5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_G1M1B1_G1M1B1_AILME_9646 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A1U7QV17_A0A1U7QV17_MESAU_10036 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2U3VMX0_A0A2U3VMX0_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2U3YP63_A0A2U3YP63_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2Y9EBI6_A0A2Y9EBI6_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2Y9LBK2_A0A2Y9LBK2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2Y9PDK5_A0A2Y9PDK5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A2Y9FPX8_A0A2Y9FPX8_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A384BWH0_A0A384BWH0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_F1PYD0_F1PYD0_CANLF_9615 and tr_A0A383YVI3_A0A383YVI3_BALAS_310752 are exactly identical!
WARNING: Sequences tr_F6UT32_F6UT32_HORSE_9796 and tr_A0A0U1RNE3_A0A0U1RNE3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F6UT32_F6UT32_HORSE_9796 and sp_E1BM58_PRAX_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A087ZXR8_A0A087ZXR8_APIME_7460 and tr_A0A2A3E423_A0A2A3E423_APICC_94128 are exactly identical!
WARNING: Sequences tr_H0ZRQ4_H0ZRQ4_TAEGU_59729 and tr_H0ZZD2_H0ZZD2_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_H0ZRQ4_H0ZRQ4_TAEGU_59729 and tr_A0A218U8A4_A0A218U8A4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_G0N8L6_G0N8L6_CAEBE_135651 and tr_G0PN37_G0PN37_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_E3NHL3_E3NHL3_CAERE_31234 and tr_A0A261BF69_A0A261BF69_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_A8Y4L7_A8Y4L7_CAEBR_6238 and tr_A0A2G5THQ9_A0A2G5THQ9_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_A0A2I0MQ36_A0A2I0MQ36_COLLI_8932 and tr_A0A1V4KAH4_A0A1V4KAH4_PATFA_372326 are exactly identical!
WARNING: Duplicate sequences found: 20

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/Q8IVF2/3_mltree/Q8IVF2.raxml.reduced.phy

Alignment comprises 1 partitions and 95 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 95 / 95
Gaps: 15.86 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.rba

Parallelization scheme autoconfig: 2 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 160 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 95 / 7600
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -22179.084780] Initial branch length optimization
[00:00:00 -16832.794415] Model parameter optimization (eps = 10.000000)
[00:00:06 -16800.676197] AUTODETECT spr round 1 (radius: 5)
[00:00:09 -11655.496870] AUTODETECT spr round 2 (radius: 10)
[00:00:15 -8784.505655] AUTODETECT spr round 3 (radius: 15)
[00:00:21 -8129.241089] AUTODETECT spr round 4 (radius: 20)
[00:00:27 -7770.433289] AUTODETECT spr round 5 (radius: 25)
[00:00:33 -7585.837986] SPR radius for FAST iterations: 25 (autodetect)
[00:00:33 -7585.837986] Model parameter optimization (eps = 3.000000)
[00:00:39 -7569.618610] FAST spr round 1 (radius: 25)
[00:00:45 -7093.693521] FAST spr round 2 (radius: 25)
[00:00:50 -7053.228357] FAST spr round 3 (radius: 25)
[00:00:54 -7049.810037] FAST spr round 4 (radius: 25)
[00:00:57 -7049.794814] Model parameter optimization (eps = 1.000000)
[00:01:02 -7044.892280] SLOW spr round 1 (radius: 5)
[00:01:08 -7044.646646] SLOW spr round 2 (radius: 5)
[00:01:15 -7044.611852] SLOW spr round 3 (radius: 10)
[00:01:21 -7043.753392] SLOW spr round 4 (radius: 5)
[00:01:31 -7043.362861] SLOW spr round 5 (radius: 5)
[00:01:38 -7043.351760] SLOW spr round 6 (radius: 10)
[00:01:45 -7043.351499] SLOW spr round 7 (radius: 15)
[00:01:54 -7043.351424] SLOW spr round 8 (radius: 20)
[00:01:59] [worker #1] ML tree search #2, logLikelihood: -7029.538840
[00:02:04 -7042.932180] SLOW spr round 9 (radius: 5)
[00:02:15 -7040.036879] SLOW spr round 10 (radius: 5)
[00:02:24 -7039.146968] SLOW spr round 11 (radius: 5)
[00:02:31 -7038.925566] SLOW spr round 12 (radius: 5)
[00:02:38 -7038.925312] SLOW spr round 13 (radius: 10)
[00:02:44 -7038.925282] SLOW spr round 14 (radius: 15)
[00:02:52 -7038.463234] SLOW spr round 15 (radius: 5)
[00:03:02 -7038.337335] SLOW spr round 16 (radius: 5)
[00:03:10 -7038.336853] SLOW spr round 17 (radius: 10)
[00:03:16 -7038.336818] SLOW spr round 18 (radius: 15)
[00:03:25 -7038.336802] SLOW spr round 19 (radius: 20)
[00:03:34 -7038.336791] SLOW spr round 20 (radius: 25)
[00:03:43 -7038.336783] Model parameter optimization (eps = 0.100000)

[00:03:46] [worker #0] ML tree search #1, logLikelihood: -7036.930791

[00:03:46 -21673.545097] Initial branch length optimization
[00:03:46 -16297.838889] Model parameter optimization (eps = 10.000000)
[00:03:47] [worker #1] ML tree search #4, logLikelihood: -7031.162203
[00:03:51 -16281.088963] AUTODETECT spr round 1 (radius: 5)
[00:03:55 -11004.590129] AUTODETECT spr round 2 (radius: 10)
[00:04:00 -8956.805852] AUTODETECT spr round 3 (radius: 15)
[00:04:06 -7825.952794] AUTODETECT spr round 4 (radius: 20)
[00:04:11 -7727.597728] AUTODETECT spr round 5 (radius: 25)
[00:04:17 -7682.449565] SPR radius for FAST iterations: 25 (autodetect)
[00:04:17 -7682.449565] Model parameter optimization (eps = 3.000000)
[00:04:22 -7663.747977] FAST spr round 1 (radius: 25)
[00:04:27 -7089.711485] FAST spr round 2 (radius: 25)
[00:04:31 -7058.408639] FAST spr round 3 (radius: 25)
[00:04:35 -7055.575075] FAST spr round 4 (radius: 25)
[00:04:39 -7053.803445] FAST spr round 5 (radius: 25)
[00:04:42 -7053.802284] Model parameter optimization (eps = 1.000000)
[00:04:46 -7045.076720] SLOW spr round 1 (radius: 5)
[00:04:52 -7041.702046] SLOW spr round 2 (radius: 5)
[00:04:59 -7041.169310] SLOW spr round 3 (radius: 5)
[00:05:05 -7041.163174] SLOW spr round 4 (radius: 10)
[00:05:12 -7037.674418] SLOW spr round 5 (radius: 5)
[00:05:21 -7036.874448] SLOW spr round 6 (radius: 5)
[00:05:28 -7036.870464] SLOW spr round 7 (radius: 10)
[00:05:34 -7036.870458] SLOW spr round 8 (radius: 15)
[00:05:43 -7036.870457] SLOW spr round 9 (radius: 20)
[00:05:52 -7036.870456] SLOW spr round 10 (radius: 25)
[00:06:02 -7036.870456] Model parameter optimization (eps = 0.100000)

[00:06:04] [worker #0] ML tree search #3, logLikelihood: -7036.277573

[00:06:04 -21958.695255] Initial branch length optimization
[00:06:04 -16752.146217] Model parameter optimization (eps = 10.000000)
[00:06:08 -16731.951244] AUTODETECT spr round 1 (radius: 5)
[00:06:11 -11237.780474] AUTODETECT spr round 2 (radius: 10)
[00:06:17 -8795.907446] AUTODETECT spr round 3 (radius: 15)
[00:06:21] [worker #1] ML tree search #6, logLikelihood: -7029.804990
[00:06:23 -7507.915661] AUTODETECT spr round 4 (radius: 20)
[00:06:30 -7482.804403] AUTODETECT spr round 5 (radius: 25)
[00:06:35 -7482.212917] SPR radius for FAST iterations: 25 (autodetect)
[00:06:35 -7482.212917] Model parameter optimization (eps = 3.000000)
[00:06:38 -7459.458678] FAST spr round 1 (radius: 25)
[00:06:44 -7050.106237] FAST spr round 2 (radius: 25)
[00:06:49 -7034.026344] FAST spr round 3 (radius: 25)
[00:06:53 -7030.542420] FAST spr round 4 (radius: 25)
[00:06:56 -7030.510940] Model parameter optimization (eps = 1.000000)
[00:06:57 -7029.928617] SLOW spr round 1 (radius: 5)
[00:07:04 -7026.066471] SLOW spr round 2 (radius: 5)
[00:07:10 -7025.859491] SLOW spr round 3 (radius: 5)
[00:07:17 -7025.858587] SLOW spr round 4 (radius: 10)
[00:07:23 -7025.645853] SLOW spr round 5 (radius: 5)
[00:07:31 -7025.642718] SLOW spr round 6 (radius: 10)
[00:07:38 -7024.422064] SLOW spr round 7 (radius: 5)
[00:07:47 -7024.421598] SLOW spr round 8 (radius: 10)
[00:07:53 -7024.421541] SLOW spr round 9 (radius: 15)
[00:08:01 -7024.421535] SLOW spr round 10 (radius: 20)
[00:08:10 -7024.421535] SLOW spr round 11 (radius: 25)
[00:08:19 -7024.421534] Model parameter optimization (eps = 0.100000)

[00:08:21] [worker #0] ML tree search #5, logLikelihood: -7024.261690

[00:08:21 -21729.918774] Initial branch length optimization
[00:08:21 -16858.410924] Model parameter optimization (eps = 10.000000)
[00:08:27 -16796.004143] AUTODETECT spr round 1 (radius: 5)
[00:08:31 -11231.553453] AUTODETECT spr round 2 (radius: 10)
[00:08:36 -9181.396787] AUTODETECT spr round 3 (radius: 15)
[00:08:42 -7823.341889] AUTODETECT spr round 4 (radius: 20)
[00:08:48 -7749.181380] AUTODETECT spr round 5 (radius: 25)
[00:08:54 -7741.078786] SPR radius for FAST iterations: 25 (autodetect)
[00:08:54 -7741.078786] Model parameter optimization (eps = 3.000000)
[00:08:58 -7726.342377] FAST spr round 1 (radius: 25)
[00:09:04 -7091.350216] FAST spr round 2 (radius: 25)
[00:09:08 -7061.843792] FAST spr round 3 (radius: 25)
[00:09:12 -7057.847678] FAST spr round 4 (radius: 25)
[00:09:16 -7051.125440] FAST spr round 5 (radius: 25)
[00:09:19] [worker #1] ML tree search #8, logLikelihood: -7032.312578
[00:09:19 -7050.568225] FAST spr round 6 (radius: 25)
[00:09:23 -7050.568222] Model parameter optimization (eps = 1.000000)
[00:09:29 -7044.732975] SLOW spr round 1 (radius: 5)
[00:09:35 -7040.492671] SLOW spr round 2 (radius: 5)
[00:09:42 -7039.665131] SLOW spr round 3 (radius: 5)
[00:09:48 -7039.055352] SLOW spr round 4 (radius: 5)
[00:09:54 -7037.849208] SLOW spr round 5 (radius: 5)
[00:10:00 -7037.848793] SLOW spr round 6 (radius: 10)
[00:10:06 -7035.875105] SLOW spr round 7 (radius: 5)
[00:10:14 -7034.883042] SLOW spr round 8 (radius: 5)
[00:10:21 -7034.881814] SLOW spr round 9 (radius: 10)
[00:10:27 -7034.881790] SLOW spr round 10 (radius: 15)
[00:10:35 -7034.881777] SLOW spr round 11 (radius: 20)
[00:10:44 -7034.881769] SLOW spr round 12 (radius: 25)
[00:10:54 -7034.881764] Model parameter optimization (eps = 0.100000)

[00:10:56] [worker #0] ML tree search #7, logLikelihood: -7033.925896

[00:10:56 -22046.781668] Initial branch length optimization
[00:10:56 -16716.557188] Model parameter optimization (eps = 10.000000)
[00:11:00 -16698.149101] AUTODETECT spr round 1 (radius: 5)
[00:11:04 -11861.698987] AUTODETECT spr round 2 (radius: 10)
[00:11:09 -8665.407952] AUTODETECT spr round 3 (radius: 15)
[00:11:14 -8152.739709] AUTODETECT spr round 4 (radius: 20)
[00:11:21 -7678.332636] AUTODETECT spr round 5 (radius: 25)
[00:11:28 -7677.942049] SPR radius for FAST iterations: 25 (autodetect)
[00:11:28 -7677.942049] Model parameter optimization (eps = 3.000000)
[00:11:32 -7638.351190] FAST spr round 1 (radius: 25)
[00:11:38 -7083.176051] FAST spr round 2 (radius: 25)
[00:11:42 -7032.307824] FAST spr round 3 (radius: 25)
[00:11:46 -7031.714656] FAST spr round 4 (radius: 25)
[00:11:49 -7031.713846] Model parameter optimization (eps = 1.000000)
[00:11:52 -7028.346265] SLOW spr round 1 (radius: 5)
[00:11:56] [worker #1] ML tree search #10, logLikelihood: -7026.115206
[00:11:58 -7027.793529] SLOW spr round 2 (radius: 5)
[00:12:05 -7026.024462] SLOW spr round 3 (radius: 5)
[00:12:11 -7026.024455] SLOW spr round 4 (radius: 10)
[00:12:17 -7026.024451] SLOW spr round 5 (radius: 15)
[00:12:26 -7025.767502] SLOW spr round 6 (radius: 5)
[00:12:35 -7025.476139] SLOW spr round 7 (radius: 5)
[00:12:43 -7025.474066] SLOW spr round 8 (radius: 10)
[00:12:49 -7025.473591] SLOW spr round 9 (radius: 15)
[00:12:57 -7025.473310] SLOW spr round 10 (radius: 20)
[00:13:06 -7025.473132] SLOW spr round 11 (radius: 25)
[00:13:15 -7025.472989] Model parameter optimization (eps = 0.100000)

[00:13:17] [worker #0] ML tree search #9, logLikelihood: -7025.416860

[00:13:17 -21535.272698] Initial branch length optimization
[00:13:17 -16434.347156] Model parameter optimization (eps = 10.000000)
[00:13:21 -16408.632548] AUTODETECT spr round 1 (radius: 5)
[00:13:25 -11592.820869] AUTODETECT spr round 2 (radius: 10)
[00:13:30 -9134.926896] AUTODETECT spr round 3 (radius: 15)
[00:13:36 -8301.949969] AUTODETECT spr round 4 (radius: 20)
[00:13:43 -7949.937866] AUTODETECT spr round 5 (radius: 25)
[00:13:48 -7949.881315] SPR radius for FAST iterations: 20 (autodetect)
[00:13:48 -7949.881315] Model parameter optimization (eps = 3.000000)
[00:13:53 -7928.747354] FAST spr round 1 (radius: 20)
[00:13:58 -7154.204338] FAST spr round 2 (radius: 20)
[00:14:04 -7062.380706] FAST spr round 3 (radius: 20)
[00:14:08 -7054.527770] FAST spr round 4 (radius: 20)
[00:14:11 -7054.339449] FAST spr round 5 (radius: 20)
[00:14:15 -7053.469410] FAST spr round 6 (radius: 20)
[00:14:18 -7053.219342] FAST spr round 7 (radius: 20)
[00:14:21 -7053.197517] Model parameter optimization (eps = 1.000000)
[00:14:26 -7048.363773] SLOW spr round 1 (radius: 5)
[00:14:33 -7046.616346] SLOW spr round 2 (radius: 5)
[00:14:40 -7045.675400] SLOW spr round 3 (radius: 5)
[00:14:43] [worker #1] ML tree search #12, logLikelihood: -7034.588955
[00:14:47 -7044.548286] SLOW spr round 4 (radius: 5)
[00:14:54 -7044.547354] SLOW spr round 5 (radius: 10)
[00:15:00 -7044.014247] SLOW spr round 6 (radius: 5)
[00:15:09 -7044.010276] SLOW spr round 7 (radius: 10)
[00:15:16 -7044.009599] SLOW spr round 8 (radius: 15)
[00:15:25 -7043.088079] SLOW spr round 9 (radius: 5)
[00:15:35 -7042.981674] SLOW spr round 10 (radius: 5)
[00:15:43 -7042.981183] SLOW spr round 11 (radius: 10)
[00:15:50 -7042.822790] SLOW spr round 12 (radius: 5)
[00:15:59 -7042.448893] SLOW spr round 13 (radius: 5)
[00:16:06 -7042.332083] SLOW spr round 14 (radius: 5)
[00:16:13 -7042.331632] SLOW spr round 15 (radius: 10)
[00:16:19 -7042.331583] SLOW spr round 16 (radius: 15)
[00:16:27 -7042.331569] SLOW spr round 17 (radius: 20)
[00:16:36] [worker #1] ML tree search #14, logLikelihood: -7024.996309
[00:16:37 -7042.331562] SLOW spr round 18 (radius: 25)
[00:16:46 -7042.331556] Model parameter optimization (eps = 0.100000)

[00:16:49] [worker #0] ML tree search #11, logLikelihood: -7039.973808

[00:16:49 -22329.615725] Initial branch length optimization
[00:16:50 -17191.792015] Model parameter optimization (eps = 10.000000)
[00:16:53 -17170.831985] AUTODETECT spr round 1 (radius: 5)
[00:16:57 -10832.846342] AUTODETECT spr round 2 (radius: 10)
[00:17:01 -9669.344406] AUTODETECT spr round 3 (radius: 15)
[00:17:08 -8111.666616] AUTODETECT spr round 4 (radius: 20)
[00:17:14 -8039.443380] AUTODETECT spr round 5 (radius: 25)
[00:17:19 -8034.773783] SPR radius for FAST iterations: 25 (autodetect)
[00:17:19 -8034.773783] Model parameter optimization (eps = 3.000000)
[00:17:24 -8009.422281] FAST spr round 1 (radius: 25)
[00:17:30 -7090.380433] FAST spr round 2 (radius: 25)
[00:17:34 -7062.687516] FAST spr round 3 (radius: 25)
[00:17:38 -7054.662085] FAST spr round 4 (radius: 25)
[00:17:41 -7052.875507] FAST spr round 5 (radius: 25)
[00:17:45 -7052.732717] FAST spr round 6 (radius: 25)
[00:17:48 -7052.732361] Model parameter optimization (eps = 1.000000)
[00:17:51 -7050.573506] SLOW spr round 1 (radius: 5)
[00:17:57 -7048.565000] SLOW spr round 2 (radius: 5)
[00:18:04 -7046.129199] SLOW spr round 3 (radius: 5)
[00:18:10 -7046.129026] SLOW spr round 4 (radius: 10)
[00:18:17 -7046.125912] SLOW spr round 5 (radius: 15)
[00:18:23] [worker #1] ML tree search #16, logLikelihood: -7026.871254
[00:18:25 -7046.125894] SLOW spr round 6 (radius: 20)
[00:18:36 -7046.125877] SLOW spr round 7 (radius: 25)
[00:18:44 -7046.125860] Model parameter optimization (eps = 0.100000)

[00:18:48] [worker #0] ML tree search #13, logLikelihood: -7045.719895

[00:18:48 -22322.389228] Initial branch length optimization
[00:18:48 -16950.777559] Model parameter optimization (eps = 10.000000)
[00:18:52 -16929.854376] AUTODETECT spr round 1 (radius: 5)
[00:18:56 -10938.785532] AUTODETECT spr round 2 (radius: 10)
[00:19:01 -8420.059032] AUTODETECT spr round 3 (radius: 15)
[00:19:07 -7916.103032] AUTODETECT spr round 4 (radius: 20)
[00:19:13 -7848.166724] AUTODETECT spr round 5 (radius: 25)
[00:19:20 -7791.155496] SPR radius for FAST iterations: 25 (autodetect)
[00:19:20 -7791.155496] Model parameter optimization (eps = 3.000000)
[00:19:26 -7762.597450] FAST spr round 1 (radius: 25)
[00:19:30 -7067.755108] FAST spr round 2 (radius: 25)
[00:19:35 -7047.433617] FAST spr round 3 (radius: 25)
[00:19:39 -7038.907583] FAST spr round 4 (radius: 25)
[00:19:42 -7038.180733] FAST spr round 5 (radius: 25)
[00:19:46 -7038.179701] Model parameter optimization (eps = 1.000000)
[00:19:49 -7035.536889] SLOW spr round 1 (radius: 5)
[00:19:55 -7033.532157] SLOW spr round 2 (radius: 5)
[00:20:02 -7033.531977] SLOW spr round 3 (radius: 10)
[00:20:08 -7033.531964] SLOW spr round 4 (radius: 15)
[00:20:16 -7033.504569] SLOW spr round 5 (radius: 20)
[00:20:24] [worker #1] ML tree search #18, logLikelihood: -7026.891956
[00:20:25 -7031.701449] SLOW spr round 6 (radius: 5)
[00:20:36 -7030.282386] SLOW spr round 7 (radius: 5)
[00:20:44 -7030.262505] SLOW spr round 8 (radius: 10)
[00:20:50 -7030.261242] SLOW spr round 9 (radius: 15)
[00:20:58 -7030.146667] SLOW spr round 10 (radius: 5)
[00:21:07 -7029.678798] SLOW spr round 11 (radius: 5)
[00:21:15 -7029.678552] SLOW spr round 12 (radius: 10)
[00:21:22 -7029.678474] SLOW spr round 13 (radius: 15)
[00:21:29 -7029.678428] SLOW spr round 14 (radius: 20)
[00:21:38 -7029.678399] SLOW spr round 15 (radius: 25)
[00:21:47 -7029.678376] Model parameter optimization (eps = 0.100000)

[00:21:49] [worker #0] ML tree search #15, logLikelihood: -7029.514685

[00:21:49 -22128.504375] Initial branch length optimization
[00:21:49 -17224.193088] Model parameter optimization (eps = 10.000000)
[00:21:53 -17199.136009] AUTODETECT spr round 1 (radius: 5)
[00:21:57 -11375.558073] AUTODETECT spr round 2 (radius: 10)
[00:22:02 -8820.549750] AUTODETECT spr round 3 (radius: 15)
[00:22:08 -8015.436927] AUTODETECT spr round 4 (radius: 20)
[00:22:14 -7837.676037] AUTODETECT spr round 5 (radius: 25)
[00:22:20 -7834.407994] SPR radius for FAST iterations: 25 (autodetect)
[00:22:20 -7834.407994] Model parameter optimization (eps = 3.000000)
[00:22:27 -7805.070438] FAST spr round 1 (radius: 25)
[00:22:31] [worker #1] ML tree search #20, logLikelihood: -7027.500415
[00:22:33 -7061.295792] FAST spr round 2 (radius: 25)
[00:22:37 -7048.660993] FAST spr round 3 (radius: 25)
[00:22:40 -7048.476908] FAST spr round 4 (radius: 25)
[00:22:44 -7048.475312] Model parameter optimization (eps = 1.000000)
[00:22:46 -7046.345880] SLOW spr round 1 (radius: 5)
[00:22:52 -7042.885470] SLOW spr round 2 (radius: 5)
[00:22:59 -7042.884945] SLOW spr round 3 (radius: 10)
[00:23:05 -7042.839084] SLOW spr round 4 (radius: 15)
[00:23:13 -7042.657715] SLOW spr round 5 (radius: 5)
[00:23:23 -7042.272832] SLOW spr round 6 (radius: 5)
[00:23:30 -7042.271143] SLOW spr round 7 (radius: 10)
[00:23:37 -7042.270642] SLOW spr round 8 (radius: 15)
[00:23:45 -7042.270582] SLOW spr round 9 (radius: 20)
[00:23:53 -7042.270534] SLOW spr round 10 (radius: 25)
[00:24:02 -7042.270487] Model parameter optimization (eps = 0.100000)

[00:24:04] [worker #0] ML tree search #17, logLikelihood: -7041.789507

[00:24:04 -22799.190707] Initial branch length optimization
[00:24:05 -17402.944754] Model parameter optimization (eps = 10.000000)
[00:24:09 -17373.179525] AUTODETECT spr round 1 (radius: 5)
[00:24:13 -11296.502829] AUTODETECT spr round 2 (radius: 10)
[00:24:18 -9013.348316] AUTODETECT spr round 3 (radius: 15)
[00:24:24 -8396.134854] AUTODETECT spr round 4 (radius: 20)
[00:24:31 -7997.265676] AUTODETECT spr round 5 (radius: 25)
[00:24:37 -7986.293810] SPR radius for FAST iterations: 25 (autodetect)
[00:24:37 -7986.293810] Model parameter optimization (eps = 3.000000)
[00:24:41 -7945.584787] FAST spr round 1 (radius: 25)
[00:24:47 -7071.168380] FAST spr round 2 (radius: 25)
[00:24:52 -7049.497999] FAST spr round 3 (radius: 25)
[00:24:56 -7045.702800] FAST spr round 4 (radius: 25)
[00:24:59 -7045.591536] FAST spr round 5 (radius: 25)
[00:25:03 -7045.576503] Model parameter optimization (eps = 1.000000)
[00:25:05 -7044.154903] SLOW spr round 1 (radius: 5)
[00:25:12 -7041.441558] SLOW spr round 2 (radius: 5)
[00:25:18 -7040.788217] SLOW spr round 3 (radius: 5)
[00:25:24 -7040.788026] SLOW spr round 4 (radius: 10)
[00:25:30 -7039.725643] SLOW spr round 5 (radius: 5)
[00:25:39 -7039.725189] SLOW spr round 6 (radius: 10)
[00:25:46 -7039.725147] SLOW spr round 7 (radius: 15)
[00:25:54 -7037.514798] SLOW spr round 8 (radius: 5)
[00:26:04 -7037.252462] SLOW spr round 9 (radius: 5)
[00:26:12 -7037.250803] SLOW spr round 10 (radius: 10)
[00:26:19 -7037.250711] SLOW spr round 11 (radius: 15)
[00:26:27 -7037.250630] SLOW spr round 12 (radius: 20)
[00:26:36 -7036.764438] SLOW spr round 13 (radius: 5)
[00:26:47 -7036.132474] SLOW spr round 14 (radius: 5)
[00:26:55 -7036.130257] SLOW spr round 15 (radius: 10)
[00:27:01 -7036.129974] SLOW spr round 16 (radius: 15)
[00:27:09 -7036.129935] SLOW spr round 17 (radius: 20)
[00:27:19 -7035.659693] SLOW spr round 18 (radius: 5)
[00:27:29 -7035.484722] SLOW spr round 19 (radius: 5)
[00:27:37 -7035.484411] SLOW spr round 20 (radius: 10)
[00:27:44 -7035.484393] SLOW spr round 21 (radius: 15)
[00:27:52 -7035.484385] SLOW spr round 22 (radius: 20)
[00:28:02 -7035.484378] SLOW spr round 23 (radius: 25)
[00:28:11 -7035.484370] Model parameter optimization (eps = 0.100000)

[00:28:13] [worker #0] ML tree search #19, logLikelihood: -7034.876248


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.094631,1.990244) (0.141268,0.332657) (0.501498,0.610559) (0.262604,1.745878) 
   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: -7024.261690

AIC score: 14694.523380 / AICc score: 223998.523380 / BIC score: 15519.425616
Free parameters (model + branch lengths): 323

WARNING: Number of free parameters (K=323) is larger than alignment size (n=95).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 43 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IVF2/3_mltree/Q8IVF2.raxml.log

Analysis started: 04-Jun-2021 03:53:05 / finished: 04-Jun-2021 04:21:19

Elapsed time: 1693.553 seconds

Consumed energy: 165.213 Wh