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 04-Jul-2021 20:09:08 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/2_msa/Q8IYT1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1 --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/Q8IYT1/2_msa/Q8IYT1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 324 taxa and 125 sites

WARNING: Sequences tr_M3YPY4_M3YPY4_MUSPF_9669 and tr_A0A2U3W989_A0A2U3W989_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YPY4_M3YPY4_MUSPF_9669 and tr_A0A2U3XGD9_A0A2U3XGD9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YPY4_M3YPY4_MUSPF_9669 and tr_A0A384C772_A0A384C772_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I3GPE7_A0A2I3GPE7_NOMLE_61853 and sp_Q8N5Q1_F71E2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3I4G4_G3I4G4_CRIGR_10029 and tr_A0A1U7QGT0_A0A1U7QGT0_MESAU_10036 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_F7GS60_F7GS60_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_G7P6Q9_G7P6Q9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_A0A096MQA5_A0A096MQA5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_A0A0D9RE83_A0A0D9RE83_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_A0A2K5M366_A0A2K5M366_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_A0A2K6DLG9_A0A2K6DLG9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2PH69_H2PH69_PONAB_9601 and tr_A0A2K5XN97_A0A2K5XN97_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3S9T8_A0A2I3S9T8_PANTR_9598 and tr_A0A2R9CIB6_A0A2R9CIB6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G2HEQ4_G2HEQ4_PANTR_9598 and tr_A0A2R8ZHJ8_A0A2R8ZHJ8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G2HI77_G2HI77_PANTR_9598 and tr_A0A2R9AEK9_A0A2R9AEK9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QGX9_H2QGX9_PANTR_9598 and sp_Q6IPT2_F71E1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QGX9_H2QGX9_PANTR_9598 and tr_A0A2R9B925_A0A2R9B925_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QH61_H2QH61_PANTR_9598 and tr_A0A2R8ZIL3_A0A2R8ZIL3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QRW2_H2QRW2_PANTR_9598 and tr_A0A2R9AMH9_A0A2R9AMH9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5PN67_W5PN67_SHEEP_9940 and tr_F1RQD7_F1RQD7_PIG_9823 are exactly identical!
WARNING: Sequences tr_W5PN67_W5PN67_SHEEP_9940 and tr_F1N7X7_F1N7X7_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F6WN69_F6WN69_MACMU_9544 and tr_A0A096MRI7_A0A096MRI7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6WN69_F6WN69_MACMU_9544 and tr_A0A2K6BR85_A0A2K6BR85_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6WN69_F6WN69_MACMU_9544 and tr_A0A2K6A676_A0A2K6A676_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_G7PAK2_G7PAK2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_A0A096NVN2_A0A096NVN2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_A0A0D9RLP8_A0A0D9RLP8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_A0A2K5P8G0_A0A2K5P8G0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_A0A2K6E095_A0A2K6E095_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7C137_F7C137_MACMU_9544 and tr_A0A2K5ZFM1_A0A2K5ZFM1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1LE12_G1LE12_AILME_9646 and tr_A0A384DAJ3_A0A384DAJ3_URSMA_29073 are exactly identical!
WARNING: Sequences tr_F1N2V1_F1N2V1_BOVIN_9913 and sp_Q2YDE8_FA71D_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A151P1C2_A0A151P1C2_ALLMI_8496 and tr_A0A3Q0H471_A0A3Q0H471_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A2I0MP40_A0A2I0MP40_COLLI_8932 and tr_A0A1V4KF34_A0A1V4KF34_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A2K5NES0_A0A2K5NES0_CERAT_9531 and tr_A0A2K5Z2H6_A0A2K5Z2H6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2U4AHT9_A0A2U4AHT9_TURTR_9739 and tr_A0A2Y9PL52_A0A2Y9PL52_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2Y9JKX8_A0A2Y9JKX8_ENHLU_391180 and tr_A0A2Y9JP01_A0A2Y9JP01_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A384ACF4_A0A384ACF4_BALAS_310752 and tr_A0A384ACK6_A0A384ACK6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A384ACF4_A0A384ACF4_BALAS_310752 and tr_A0A384ACP0_A0A384ACP0_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A384ACF4_A0A384ACF4_BALAS_310752 and tr_A0A384AD06_A0A384AD06_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 40

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/Q8IYT1/3_mltree/Q8IYT1.raxml.reduced.phy

Alignment comprises 1 partitions and 125 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 125 / 125
Gaps: 3.76 %
Invariant sites: 0.80 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.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 324 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 125 / 10000
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -62710.979583] Initial branch length optimization
[00:00:00 -50253.813828] Model parameter optimization (eps = 10.000000)
[00:00:10 -50198.505413] AUTODETECT spr round 1 (radius: 5)
[00:00:23 -30493.479680] AUTODETECT spr round 2 (radius: 10)
[00:00:41 -21159.868865] AUTODETECT spr round 3 (radius: 15)
[00:01:04 -18476.322641] AUTODETECT spr round 4 (radius: 20)
[00:01:37 -17002.865460] AUTODETECT spr round 5 (radius: 25)
[00:02:11 -17001.189838] SPR radius for FAST iterations: 25 (autodetect)
[00:02:11 -17001.189838] Model parameter optimization (eps = 3.000000)
[00:02:16 -16987.380246] FAST spr round 1 (radius: 25)
[00:02:33 -15062.994866] FAST spr round 2 (radius: 25)
[00:02:47 -14952.769036] FAST spr round 3 (radius: 25)
[00:02:59 -14943.350226] FAST spr round 4 (radius: 25)
[00:03:10 -14943.089987] FAST spr round 5 (radius: 25)
[00:03:21 -14943.087676] Model parameter optimization (eps = 1.000000)
[00:03:32 -14936.726565] SLOW spr round 1 (radius: 5)
[00:03:51 -14931.081066] SLOW spr round 2 (radius: 5)
[00:04:09 -14930.808614] SLOW spr round 3 (radius: 5)
[00:04:26 -14930.808555] SLOW spr round 4 (radius: 10)
[00:04:42 -14926.050225] SLOW spr round 5 (radius: 5)
[00:05:07 -14926.050079] SLOW spr round 6 (radius: 10)
[00:05:26 -14926.050079] SLOW spr round 7 (radius: 15)
[00:05:51 -14925.488801] SLOW spr round 8 (radius: 5)
[00:06:07] [worker #1] ML tree search #2, logLikelihood: -14925.375458
[00:06:17 -14925.485656] SLOW spr round 9 (radius: 10)
[00:06:37 -14925.485551] SLOW spr round 10 (radius: 15)
[00:06:52] [worker #2] ML tree search #3, logLikelihood: -14930.280130
[00:07:02 -14925.485547] SLOW spr round 11 (radius: 20)
[00:07:40 -14925.485547] SLOW spr round 12 (radius: 25)
[00:08:21 -14925.485547] Model parameter optimization (eps = 0.100000)

[00:08:25] [worker #0] ML tree search #1, logLikelihood: -14925.245520

[00:08:25 -62810.022711] Initial branch length optimization
[00:08:25 -50987.418758] Model parameter optimization (eps = 10.000000)
[00:08:32 -50951.784496] AUTODETECT spr round 1 (radius: 5)
[00:08:45 -31654.926071] AUTODETECT spr round 2 (radius: 10)
[00:09:03 -20835.964900] AUTODETECT spr round 3 (radius: 15)
[00:09:24 -17598.040944] AUTODETECT spr round 4 (radius: 20)
[00:09:49 -16788.846500] AUTODETECT spr round 5 (radius: 25)
[00:10:17 -16773.337628] SPR radius for FAST iterations: 25 (autodetect)
[00:10:17 -16773.337628] Model parameter optimization (eps = 3.000000)
[00:10:23 -16755.577308] FAST spr round 1 (radius: 25)
[00:10:38 -15043.794115] FAST spr round 2 (radius: 25)
[00:10:51 -14972.719514] FAST spr round 3 (radius: 25)
[00:11:04 -14950.481304] FAST spr round 4 (radius: 25)
[00:11:15 -14948.655145] FAST spr round 5 (radius: 25)
[00:11:26 -14948.655128] Model parameter optimization (eps = 1.000000)
[00:11:36 -14938.467166] SLOW spr round 1 (radius: 5)
[00:11:56 -14936.227060] SLOW spr round 2 (radius: 5)
[00:12:15 -14933.584755] SLOW spr round 3 (radius: 5)
[00:12:34 -14931.616811] SLOW spr round 4 (radius: 5)
[00:12:52 -14931.616713] SLOW spr round 5 (radius: 10)
[00:13:08 -14927.445183] SLOW spr round 6 (radius: 5)
[00:13:34 -14925.458157] SLOW spr round 7 (radius: 5)
[00:13:55 -14925.457592] SLOW spr round 8 (radius: 10)
[00:13:55] [worker #1] ML tree search #5, logLikelihood: -14937.541809
[00:14:12 -14925.457583] SLOW spr round 9 (radius: 15)
[00:14:37 -14925.457583] SLOW spr round 10 (radius: 20)
[00:14:41] [worker #2] ML tree search #6, logLikelihood: -14920.118237
[00:15:15 -14923.943726] SLOW spr round 11 (radius: 5)
[00:15:41 -14923.943427] SLOW spr round 12 (radius: 10)
[00:16:02 -14923.943418] SLOW spr round 13 (radius: 15)
[00:16:26 -14923.943418] SLOW spr round 14 (radius: 20)
[00:17:05 -14923.943418] SLOW spr round 15 (radius: 25)
[00:17:51 -14923.943418] Model parameter optimization (eps = 0.100000)

[00:17:54] [worker #0] ML tree search #4, logLikelihood: -14923.752313

[00:17:54 -62296.969550] Initial branch length optimization
[00:17:55 -50453.089589] Model parameter optimization (eps = 10.000000)
[00:18:03 -50402.212377] AUTODETECT spr round 1 (radius: 5)
[00:18:16 -31232.789616] AUTODETECT spr round 2 (radius: 10)
[00:18:34 -22441.238479] AUTODETECT spr round 3 (radius: 15)
[00:18:57 -19249.292073] AUTODETECT spr round 4 (radius: 20)
[00:19:22 -17217.172420] AUTODETECT spr round 5 (radius: 25)
[00:19:54 -16866.752392] SPR radius for FAST iterations: 25 (autodetect)
[00:19:54 -16866.752392] Model parameter optimization (eps = 3.000000)
[00:19:59 -16852.395479] FAST spr round 1 (radius: 25)
[00:20:17 -15118.155217] FAST spr round 2 (radius: 25)
[00:20:32 -14956.051626] FAST spr round 3 (radius: 25)
[00:20:35] [worker #2] ML tree search #9, logLikelihood: -14921.035689
[00:20:45 -14939.676329] FAST spr round 4 (radius: 25)
[00:20:56 -14939.676170] Model parameter optimization (eps = 1.000000)
[00:21:01 -14935.304245] SLOW spr round 1 (radius: 5)
[00:21:20 -14934.866854] SLOW spr round 2 (radius: 5)
[00:21:31] [worker #1] ML tree search #8, logLikelihood: -14926.187856
[00:21:38 -14934.866077] SLOW spr round 3 (radius: 10)
[00:21:56 -14934.423154] SLOW spr round 4 (radius: 5)
[00:22:21 -14934.420422] SLOW spr round 5 (radius: 10)
[00:22:40 -14934.420277] SLOW spr round 6 (radius: 15)
[00:23:06 -14934.420268] SLOW spr round 7 (radius: 20)
[00:23:45 -14934.420267] SLOW spr round 8 (radius: 25)
[00:24:27 -14934.420267] Model parameter optimization (eps = 0.100000)

[00:24:29] [worker #0] ML tree search #7, logLikelihood: -14934.417916

[00:24:29 -62359.131347] Initial branch length optimization
[00:24:29 -49964.011517] Model parameter optimization (eps = 10.000000)
[00:24:37 -49942.663607] AUTODETECT spr round 1 (radius: 5)
[00:24:51 -29510.382907] AUTODETECT spr round 2 (radius: 10)
[00:25:09 -21814.452232] AUTODETECT spr round 3 (radius: 15)
[00:25:29 -17725.125017] AUTODETECT spr round 4 (radius: 20)
[00:26:00 -16951.141069] AUTODETECT spr round 5 (radius: 25)
[00:26:33 -16894.393599] SPR radius for FAST iterations: 25 (autodetect)
[00:26:33 -16894.393599] Model parameter optimization (eps = 3.000000)
[00:26:42 -16860.202306] FAST spr round 1 (radius: 25)
[00:26:57 -15085.770708] FAST spr round 2 (radius: 25)
[00:27:10 -14940.237856] FAST spr round 3 (radius: 25)
[00:27:23 -14934.590296] FAST spr round 4 (radius: 25)
[00:27:34 -14932.245422] FAST spr round 5 (radius: 25)
[00:27:46 -14932.245412] Model parameter optimization (eps = 1.000000)
[00:27:49 -14929.462761] SLOW spr round 1 (radius: 5)
[00:27:56] [worker #2] ML tree search #12, logLikelihood: -14918.364466
[00:28:09 -14925.414791] SLOW spr round 2 (radius: 5)
[00:28:27 -14924.971784] SLOW spr round 3 (radius: 5)
[00:28:44 -14924.971588] SLOW spr round 4 (radius: 10)
[00:29:00 -14924.160809] SLOW spr round 5 (radius: 5)
[00:29:24 -14924.157227] SLOW spr round 6 (radius: 10)
[00:29:36] [worker #1] ML tree search #11, logLikelihood: -14921.783827
[00:29:43 -14924.157061] SLOW spr round 7 (radius: 15)
[00:30:07 -14924.157053] SLOW spr round 8 (radius: 20)
[00:30:44 -14924.157053] SLOW spr round 9 (radius: 25)
[00:31:30 -14924.157053] Model parameter optimization (eps = 0.100000)

[00:31:31] [worker #0] ML tree search #10, logLikelihood: -14924.151121

[00:31:31 -62593.920624] Initial branch length optimization
[00:31:32 -50553.820428] Model parameter optimization (eps = 10.000000)
[00:31:39 -50506.760112] AUTODETECT spr round 1 (radius: 5)
[00:31:53 -30631.938038] AUTODETECT spr round 2 (radius: 10)
[00:32:12 -19634.410755] AUTODETECT spr round 3 (radius: 15)
[00:32:32 -17021.558990] AUTODETECT spr round 4 (radius: 20)
[00:32:55 -16597.026900] AUTODETECT spr round 5 (radius: 25)
[00:33:20 -16506.743550] SPR radius for FAST iterations: 25 (autodetect)
[00:33:20 -16506.743550] Model parameter optimization (eps = 3.000000)
[00:33:28 -16490.173786] FAST spr round 1 (radius: 25)
[00:33:45 -15035.148863] FAST spr round 2 (radius: 25)
[00:34:00 -14952.423841] FAST spr round 3 (radius: 25)
[00:34:13 -14940.037244] FAST spr round 4 (radius: 25)
[00:34:24 -14940.036720] Model parameter optimization (eps = 1.000000)
[00:34:29 -14936.952251] SLOW spr round 1 (radius: 5)
[00:34:49 -14935.771073] SLOW spr round 2 (radius: 5)
[00:35:07 -14935.768724] SLOW spr round 3 (radius: 10)
[00:35:23 -14935.682863] SLOW spr round 4 (radius: 15)
[00:35:38] [worker #2] ML tree search #15, logLikelihood: -14928.822644
[00:35:51 -14929.728228] SLOW spr round 5 (radius: 5)
[00:36:19 -14923.479553] SLOW spr round 6 (radius: 5)
[00:36:42 -14920.580404] SLOW spr round 7 (radius: 5)
[00:37:02 -14918.659555] SLOW spr round 8 (radius: 5)
[00:37:20 -14918.659485] SLOW spr round 9 (radius: 10)
[00:37:36 -14918.659485] SLOW spr round 10 (radius: 15)
[00:38:03 -14918.659485] SLOW spr round 11 (radius: 20)
[00:38:40 -14918.659485] SLOW spr round 12 (radius: 25)
[00:39:23 -14918.659485] Model parameter optimization (eps = 0.100000)

[00:39:26] [worker #0] ML tree search #13, logLikelihood: -14918.551601

[00:39:26 -62034.985969] Initial branch length optimization
[00:39:27 -50164.203043] Model parameter optimization (eps = 10.000000)
[00:39:36 -50116.253225] AUTODETECT spr round 1 (radius: 5)
[00:39:50 -29464.741615] AUTODETECT spr round 2 (radius: 10)
[00:40:06 -21120.545461] AUTODETECT spr round 3 (radius: 15)
[00:40:27 -17547.320575] AUTODETECT spr round 4 (radius: 20)
[00:40:42] [worker #1] ML tree search #14, logLikelihood: -14919.755155
[00:40:49 -17330.589151] AUTODETECT spr round 5 (radius: 25)
[00:41:16 -16999.167477] SPR radius for FAST iterations: 25 (autodetect)
[00:41:16 -16999.167477] Model parameter optimization (eps = 3.000000)
[00:41:20 -16987.652300] FAST spr round 1 (radius: 25)
[00:41:37 -15120.138897] FAST spr round 2 (radius: 25)
[00:41:50 -14965.206591] FAST spr round 3 (radius: 25)
[00:42:02 -14944.968491] FAST spr round 4 (radius: 25)
[00:42:13 -14944.030542] FAST spr round 5 (radius: 25)
[00:42:24 -14943.593625] FAST spr round 6 (radius: 25)
[00:42:35 -14942.221174] FAST spr round 7 (radius: 25)
[00:42:45 -14942.221137] Model parameter optimization (eps = 1.000000)
[00:42:53 -14928.472322] SLOW spr round 1 (radius: 5)
[00:43:04] [worker #2] ML tree search #18, logLikelihood: -14922.612669
[00:43:12 -14925.076350] SLOW spr round 2 (radius: 5)
[00:43:31 -14920.704524] SLOW spr round 3 (radius: 5)
[00:43:48 -14920.704338] SLOW spr round 4 (radius: 10)
[00:44:04 -14920.704336] SLOW spr round 5 (radius: 15)
[00:44:30 -14920.704336] SLOW spr round 6 (radius: 20)
[00:45:06 -14920.704336] SLOW spr round 7 (radius: 25)
[00:45:49 -14920.704336] Model parameter optimization (eps = 0.100000)

[00:45:52] [worker #0] ML tree search #16, logLikelihood: -14920.506797

[00:45:52 -62579.487112] Initial branch length optimization
[00:45:53 -50693.495550] Model parameter optimization (eps = 10.000000)
[00:45:59 -50657.052169] AUTODETECT spr round 1 (radius: 5)
[00:46:13 -29205.437183] AUTODETECT spr round 2 (radius: 10)
[00:46:31 -21286.639513] AUTODETECT spr round 3 (radius: 15)
[00:46:53 -17095.554198] AUTODETECT spr round 4 (radius: 20)
[00:47:15 -16611.361154] AUTODETECT spr round 5 (radius: 25)
[00:47:44 -16595.341142] SPR radius for FAST iterations: 25 (autodetect)
[00:47:44 -16595.341142] Model parameter optimization (eps = 3.000000)
[00:47:53 -16557.643438] FAST spr round 1 (radius: 25)
[00:48:09 -15029.912751] FAST spr round 2 (radius: 25)
[00:48:23 -14939.050424] FAST spr round 3 (radius: 25)
[00:48:35 -14936.664885] FAST spr round 4 (radius: 25)
[00:48:46 -14936.276554] FAST spr round 5 (radius: 25)
[00:48:58 -14936.276522] Model parameter optimization (eps = 1.000000)
[00:49:01 -14935.412294] SLOW spr round 1 (radius: 5)
[00:49:21 -14928.981620] SLOW spr round 2 (radius: 5)
[00:49:40 -14928.271929] SLOW spr round 3 (radius: 5)
[00:49:50] [worker #1] ML tree search #17, logLikelihood: -14925.743600
[00:49:59 -14928.271926] SLOW spr round 4 (radius: 10)
[00:50:18 -14925.670718] SLOW spr round 5 (radius: 5)
[00:50:44 -14925.669696] SLOW spr round 6 (radius: 10)
[00:51:05 -14925.669660] SLOW spr round 7 (radius: 15)
[00:51:33 -14925.669658] SLOW spr round 8 (radius: 20)
[00:52:14 -14925.669658] SLOW spr round 9 (radius: 25)
[00:53:01 -14925.669658] Model parameter optimization (eps = 0.100000)

[00:53:05] [worker #0] ML tree search #19, logLikelihood: -14925.552181

[00:57:41] [worker #1] ML tree search #20, logLikelihood: -14921.514690

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.216066,0.623279) (0.118509,0.485846) (0.369765,0.739397) (0.295660,1.807313) 
   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: -14918.364466

AIC score: 31138.728933 / AICc score: 880042.728933 / BIC score: 32979.961176
Free parameters (model + branch lengths): 651

WARNING: Number of free parameters (K=651) is larger than alignment size (n=125).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 71 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYT1/3_mltree/Q8IYT1.raxml.log

Analysis started: 04-Jul-2021 20:09:08 / finished: 04-Jul-2021 21:06:50

Elapsed time: 3461.708 seconds

Consumed energy: 302.026 Wh (= 2 km in an electric car, or 8 km with an e-scooter!)