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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 05-Jul-2021 15:47:59 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/2_msa/Q86X60_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/2_msa/Q86X60_trimmed_msa.fasta
[00:00:00] Loaded alignment with 294 taxa and 121 sites

WARNING: Sequences tr_E1C083_E1C083_CHICK_9031 and tr_G1MWK5_G1MWK5_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3YKU0_M3YKU0_MUSPF_9669 and tr_D2HZZ7_D2HZZ7_AILME_9646 are exactly identical!
WARNING: Sequences tr_M3YKU0_M3YKU0_MUSPF_9669 and tr_A0A2U3VEJ9_A0A2U3VEJ9_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YKU0_M3YKU0_MUSPF_9669 and tr_A0A2U3YDQ8_A0A2U3YDQ8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YKU0_M3YKU0_MUSPF_9669 and tr_A0A2Y9JTJ0_A0A2Y9JTJ0_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YKU0_M3YKU0_MUSPF_9669 and tr_A0A384CSI0_A0A384CSI0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and sp_Q5TYM5_FA72A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and tr_G7NVB7_G7NVB7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and tr_A0A2I3M934_A0A2I3M934_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and tr_A0A0D9RQW2_A0A0D9RQW2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and tr_A0A2K5N5R4_A0A2K5N5R4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2N3Y6_H2N3Y6_PONAB_9601 and tr_A0A2K6DU31_A0A2K6DU31_MACNE_9545 are exactly identical!
WARNING: Sequences tr_W5P4X7_W5P4X7_SHEEP_9940 and sp_A6QL50_FA72A_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5P4X7_W5P4X7_SHEEP_9940 and tr_A0A2U3V1W3_A0A2U3V1W3_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5P4X7_W5P4X7_SHEEP_9940 and tr_A0A2Y9EF40_A0A2Y9EF40_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A3B5PXS3_A0A3B5PXS3_XIPMA_8083 and tr_A0A087YG18_A0A087YG18_POEFO_48698 are exactly identical!
WARNING: Sequences tr_F4P0P9_F4P0P9_BATDJ_684364 and tr_A0A177WD72_A0A177WD72_BATDE_403673 are exactly identical!
WARNING: Sequences tr_E6ZTG6_E6ZTG6_SPORE_999809 and tr_A0A0F7RTE4_A0A0F7RTE4_9BASI_49012 are exactly identical!
WARNING: Sequences tr_R1C6H0_R1C6H0_EMIHU_2903 and tr_R1CIU8_R1CIU8_EMIHU_2903 are exactly identical!
WARNING: Sequences tr_U5GYN1_U5GYN1_USTV1_683840 and tr_A0A2X0MUY5_A0A2X0MUY5_9BASI_796604 are exactly identical!
WARNING: Sequences tr_A0A091JB25_A0A091JB25_EGRGA_188379 and tr_A0A091V3K2_A0A091V3K2_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JB25_A0A091JB25_EGRGA_188379 and tr_A0A093HB78_A0A093HB78_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091JB25_A0A091JB25_EGRGA_188379 and tr_A0A091WQH1_A0A091WQH1_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091JB25_A0A091JB25_EGRGA_188379 and tr_A0A0A0AS67_A0A0A0AS67_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091JB25_A0A091JB25_EGRGA_188379 and tr_A0A093G6W2_A0A093G6W2_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A0P1BDJ6_A0A0P1BDJ6_9BASI_401625 and tr_A0A316W195_A0A316W195_9BASI_1522189 are exactly identical!
WARNING: Sequences tr_A0A166BEC7_A0A166BEC7_EXIGL_1314781 and tr_A0A166MMD6_A0A166MMD6_EXIGL_1314781 are exactly identical!
WARNING: Sequences tr_A0A226NIA5_A0A226NIA5_CALSU_9009 and tr_A0A226PXR4_A0A226PXR4_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2H3BUG5_A0A2H3BUG5_9AGAR_1076256 and tr_A0A284QMA9_A0A284QMA9_9AGAR_47428 are exactly identical!
WARNING: Duplicate sequences found: 29

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.reduced.phy

Alignment comprises 1 partitions and 121 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 121 / 121
Gaps: 8.80 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.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 294 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -57918.724098] Initial branch length optimization
[00:00:00 -46088.159270] Model parameter optimization (eps = 10.000000)
[00:00:15 -45913.157483] AUTODETECT spr round 1 (radius: 5)
[00:00:29 -34637.012518] AUTODETECT spr round 2 (radius: 10)
[00:00:46 -27375.956442] AUTODETECT spr round 3 (radius: 15)
[00:01:07 -24635.797874] AUTODETECT spr round 4 (radius: 20)
[00:01:31 -24200.247967] AUTODETECT spr round 5 (radius: 25)
[00:01:55 -23780.874041] SPR radius for FAST iterations: 25 (autodetect)
[00:01:55 -23780.874041] Model parameter optimization (eps = 3.000000)
[00:02:03 -23675.817261] FAST spr round 1 (radius: 25)
[00:02:22 -21210.522612] FAST spr round 2 (radius: 25)
[00:02:37 -21098.283513] FAST spr round 3 (radius: 25)
[00:02:52 -21083.587445] FAST spr round 4 (radius: 25)
[00:03:05 -21073.195567] FAST spr round 5 (radius: 25)
[00:03:17 -21073.195409] Model parameter optimization (eps = 1.000000)
[00:03:22 -21067.508669] SLOW spr round 1 (radius: 5)
[00:03:45 -21057.686102] SLOW spr round 2 (radius: 5)
[00:04:06 -21054.481777] SLOW spr round 3 (radius: 5)
[00:04:26 -21054.334699] SLOW spr round 4 (radius: 5)
[00:04:45 -21054.334685] SLOW spr round 5 (radius: 10)
[00:05:04 -21054.334684] SLOW spr round 6 (radius: 15)
[00:05:36 -21053.554923] SLOW spr round 7 (radius: 5)
[00:06:03 -21052.830369] SLOW spr round 8 (radius: 5)
[00:06:26 -21052.826244] SLOW spr round 9 (radius: 10)
[00:06:47 -21052.498881] SLOW spr round 10 (radius: 5)
[00:07:11 -21052.498698] SLOW spr round 11 (radius: 10)
[00:07:33 -21052.498697] SLOW spr round 12 (radius: 15)
[00:08:02] [worker #1] ML tree search #2, logLikelihood: -21042.763888
[00:08:03 -21052.498697] SLOW spr round 13 (radius: 20)
[00:08:36 -21052.498697] SLOW spr round 14 (radius: 25)
[00:09:10 -21052.498697] Model parameter optimization (eps = 0.100000)

[00:09:15] [worker #0] ML tree search #1, logLikelihood: -21051.857301

[00:09:15 -58207.320738] Initial branch length optimization
[00:09:15 -46090.955101] Model parameter optimization (eps = 10.000000)
[00:09:24 -45914.900419] AUTODETECT spr round 1 (radius: 5)
[00:09:37 -34813.770051] AUTODETECT spr round 2 (radius: 10)
[00:09:55 -27481.525282] AUTODETECT spr round 3 (radius: 15)
[00:10:16 -25044.443200] AUTODETECT spr round 4 (radius: 20)
[00:10:38 -23670.703344] AUTODETECT spr round 5 (radius: 25)
[00:11:01 -23628.471672] SPR radius for FAST iterations: 25 (autodetect)
[00:11:01 -23628.471672] Model parameter optimization (eps = 3.000000)
[00:11:09 -23496.213925] FAST spr round 1 (radius: 25)
[00:11:26 -21169.543869] FAST spr round 2 (radius: 25)
[00:11:40 -21055.665135] FAST spr round 3 (radius: 25)
[00:11:52 -21049.931764] FAST spr round 4 (radius: 25)
[00:12:04 -21047.950148] FAST spr round 5 (radius: 25)
[00:12:15 -21047.948755] Model parameter optimization (eps = 1.000000)
[00:12:20 -21042.644676] SLOW spr round 1 (radius: 5)
[00:12:40 -21032.753443] SLOW spr round 2 (radius: 5)
[00:13:00 -21032.545753] SLOW spr round 3 (radius: 5)
[00:13:20 -21032.544255] SLOW spr round 4 (radius: 10)
[00:13:39 -21031.678872] SLOW spr round 5 (radius: 5)
[00:14:04 -21031.678779] SLOW spr round 6 (radius: 10)
[00:14:28 -21031.678779] SLOW spr round 7 (radius: 15)
[00:14:58 -21030.517443] SLOW spr round 8 (radius: 5)
[00:15:26 -21030.517375] SLOW spr round 9 (radius: 10)
[00:15:51 -21030.517372] SLOW spr round 10 (radius: 15)
[00:16:21 -21030.517372] SLOW spr round 11 (radius: 20)
[00:16:55 -21030.517372] SLOW spr round 12 (radius: 25)
[00:17:05] [worker #1] ML tree search #4, logLikelihood: -21032.670660
[00:17:33 -21030.517372] Model parameter optimization (eps = 0.100000)

[00:17:35] [worker #0] ML tree search #3, logLikelihood: -21030.448678

[00:17:35 -57954.000064] Initial branch length optimization
[00:17:36 -45939.373990] Model parameter optimization (eps = 10.000000)
[00:17:44 -45765.500716] AUTODETECT spr round 1 (radius: 5)
[00:17:58 -35489.691804] AUTODETECT spr round 2 (radius: 10)
[00:18:14 -29499.116313] AUTODETECT spr round 3 (radius: 15)
[00:18:35 -24854.580691] AUTODETECT spr round 4 (radius: 20)
[00:19:01 -23877.258558] AUTODETECT spr round 5 (radius: 25)
[00:19:26 -23828.249553] SPR radius for FAST iterations: 25 (autodetect)
[00:19:26 -23828.249553] Model parameter optimization (eps = 3.000000)
[00:19:34 -23724.153030] FAST spr round 1 (radius: 25)
[00:19:55 -21165.993077] FAST spr round 2 (radius: 25)
[00:20:11 -21074.941720] FAST spr round 3 (radius: 25)
[00:20:25 -21070.446697] FAST spr round 4 (radius: 25)
[00:20:37 -21068.668570] FAST spr round 5 (radius: 25)
[00:20:49 -21068.668498] Model parameter optimization (eps = 1.000000)
[00:20:54 -21060.860606] SLOW spr round 1 (radius: 5)
[00:21:15 -21056.426032] SLOW spr round 2 (radius: 5)
[00:21:35 -21056.424524] SLOW spr round 3 (radius: 10)
[00:21:54 -21056.424114] SLOW spr round 4 (radius: 15)
[00:22:26 -21054.562836] SLOW spr round 5 (radius: 5)
[00:22:53 -21054.014123] SLOW spr round 6 (radius: 5)
[00:23:16 -21054.013995] SLOW spr round 7 (radius: 10)
[00:23:38 -21054.013994] SLOW spr round 8 (radius: 15)
[00:24:09 -21053.235407] SLOW spr round 9 (radius: 5)
[00:24:37 -21050.373989] SLOW spr round 10 (radius: 5)
[00:24:59 -21050.369575] SLOW spr round 11 (radius: 10)
[00:25:20 -21046.783480] SLOW spr round 12 (radius: 5)
[00:25:45 -21045.385292] SLOW spr round 13 (radius: 5)
[00:26:07 -21045.121295] SLOW spr round 14 (radius: 5)
[00:26:27 -21045.120772] SLOW spr round 15 (radius: 10)
[00:26:46 -21045.120752] SLOW spr round 16 (radius: 15)
[00:27:17 -21045.120751] SLOW spr round 17 (radius: 20)
[00:27:49 -21045.120751] SLOW spr round 18 (radius: 25)
[00:28:25 -21045.120751] Model parameter optimization (eps = 0.100000)

[00:28:29] [worker #0] ML tree search #5, logLikelihood: -21044.337923

[00:28:29 -57960.725573] Initial branch length optimization
[00:28:29 -45796.557481] Model parameter optimization (eps = 10.000000)
[00:28:39 -45633.563428] AUTODETECT spr round 1 (radius: 5)
[00:28:53 -35107.435279] AUTODETECT spr round 2 (radius: 10)
[00:29:11 -27733.291350] AUTODETECT spr round 3 (radius: 15)
[00:29:33 -24483.916072] AUTODETECT spr round 4 (radius: 20)
[00:29:56 -23983.848295] AUTODETECT spr round 5 (radius: 25)
[00:30:22 -23532.155715] SPR radius for FAST iterations: 25 (autodetect)
[00:30:22 -23532.155715] Model parameter optimization (eps = 3.000000)
[00:30:30 -23426.021156] FAST spr round 1 (radius: 25)
[00:30:31] [worker #1] ML tree search #6, logLikelihood: -21060.897644
[00:30:49 -21710.475028] FAST spr round 2 (radius: 25)
[00:31:07 -21437.323789] FAST spr round 3 (radius: 25)
[00:31:24 -21126.082806] FAST spr round 4 (radius: 25)
[00:31:38 -21074.248028] FAST spr round 5 (radius: 25)
[00:31:50 -21071.323957] FAST spr round 6 (radius: 25)
[00:32:01 -21071.323944] Model parameter optimization (eps = 1.000000)
[00:32:06 -21060.850735] SLOW spr round 1 (radius: 5)
[00:32:26 -21058.564780] SLOW spr round 2 (radius: 5)
[00:32:46 -21058.564394] SLOW spr round 3 (radius: 10)
[00:33:05 -21057.718489] SLOW spr round 4 (radius: 5)
[00:33:32 -21057.462648] SLOW spr round 5 (radius: 5)
[00:33:55 -21057.462155] SLOW spr round 6 (radius: 10)
[00:34:16 -21057.462144] SLOW spr round 7 (radius: 15)
[00:34:46 -21057.170032] SLOW spr round 8 (radius: 5)
[00:35:14 -21057.167510] SLOW spr round 9 (radius: 10)
[00:35:39 -21057.167441] SLOW spr round 10 (radius: 15)
[00:36:08 -21057.167439] SLOW spr round 11 (radius: 20)
[00:36:43 -21055.808357] SLOW spr round 12 (radius: 5)
[00:37:12 -21055.795977] SLOW spr round 13 (radius: 10)
[00:37:39 -21055.795004] SLOW spr round 14 (radius: 15)
[00:38:08 -21055.794931] SLOW spr round 15 (radius: 20)
[00:38:43 -21055.794925] SLOW spr round 16 (radius: 25)
[00:39:18 -21055.794925] Model parameter optimization (eps = 0.100000)

[00:39:20] [worker #0] ML tree search #7, logLikelihood: -21055.710363

[00:39:20 -56535.697907] Initial branch length optimization
[00:39:21 -44830.179101] Model parameter optimization (eps = 10.000000)
[00:39:30 -44680.088400] AUTODETECT spr round 1 (radius: 5)
[00:39:43 -34768.714641] AUTODETECT spr round 2 (radius: 10)
[00:39:45] [worker #1] ML tree search #8, logLikelihood: -21121.399414
[00:40:01 -28053.539718] AUTODETECT spr round 3 (radius: 15)
[00:40:22 -24175.236408] AUTODETECT spr round 4 (radius: 20)
[00:40:43 -23423.547374] AUTODETECT spr round 5 (radius: 25)
[00:41:06 -23102.122879] SPR radius for FAST iterations: 25 (autodetect)
[00:41:06 -23102.122879] Model parameter optimization (eps = 3.000000)
[00:41:14 -22975.246190] FAST spr round 1 (radius: 25)
[00:41:33 -21215.595994] FAST spr round 2 (radius: 25)
[00:41:50 -21093.151069] FAST spr round 3 (radius: 25)
[00:42:04 -21076.511020] FAST spr round 4 (radius: 25)
[00:42:16 -21076.510761] Model parameter optimization (eps = 1.000000)
[00:42:22 -21066.175614] SLOW spr round 1 (radius: 5)
[00:42:44 -21060.110893] SLOW spr round 2 (radius: 5)
[00:43:04 -21059.435011] SLOW spr round 3 (radius: 5)
[00:43:24 -21059.434530] SLOW spr round 4 (radius: 10)
[00:43:44 -21059.368136] SLOW spr round 5 (radius: 15)
[00:44:16 -21056.133473] SLOW spr round 6 (radius: 5)
[00:44:43 -21056.113749] SLOW spr round 7 (radius: 10)
[00:45:07 -21056.111117] SLOW spr round 8 (radius: 15)
[00:45:38 -21056.110687] SLOW spr round 9 (radius: 20)
[00:46:12 -21056.110618] SLOW spr round 10 (radius: 25)
[00:46:47 -21056.110608] Model parameter optimization (eps = 0.100000)

[00:46:50] [worker #0] ML tree search #9, logLikelihood: -21055.940086

[00:46:50 -57073.202510] Initial branch length optimization
[00:46:50 -45523.818024] Model parameter optimization (eps = 10.000000)
[00:46:59 -45357.520986] AUTODETECT spr round 1 (radius: 5)
[00:47:13 -35431.741869] AUTODETECT spr round 2 (radius: 10)
[00:47:29 -29928.230821] AUTODETECT spr round 3 (radius: 15)
[00:47:42] [worker #1] ML tree search #10, logLikelihood: -21048.605147
[00:47:51 -24807.654063] AUTODETECT spr round 4 (radius: 20)
[00:48:13 -23566.940860] AUTODETECT spr round 5 (radius: 25)
[00:48:36 -23502.828539] SPR radius for FAST iterations: 25 (autodetect)
[00:48:36 -23502.828539] Model parameter optimization (eps = 3.000000)
[00:48:45 -23388.038420] FAST spr round 1 (radius: 25)
[00:49:06 -21397.083985] FAST spr round 2 (radius: 25)
[00:49:23 -21104.088785] FAST spr round 3 (radius: 25)
[00:49:36 -21088.180175] FAST spr round 4 (radius: 25)
[00:49:48 -21083.857308] FAST spr round 5 (radius: 25)
[00:50:00 -21083.856587] Model parameter optimization (eps = 1.000000)
[00:50:04 -21082.189353] SLOW spr round 1 (radius: 5)
[00:50:25 -21079.037814] SLOW spr round 2 (radius: 5)
[00:50:46 -21075.422437] SLOW spr round 3 (radius: 5)
[00:51:06 -21075.422148] SLOW spr round 4 (radius: 10)
[00:51:26 -21072.942355] SLOW spr round 5 (radius: 5)
[00:51:52 -21072.942353] SLOW spr round 6 (radius: 10)
[00:52:17 -21072.942353] SLOW spr round 7 (radius: 15)
[00:52:47 -21072.452329] SLOW spr round 8 (radius: 5)
[00:53:15 -21072.450826] SLOW spr round 9 (radius: 10)
[00:53:43 -21072.450810] SLOW spr round 10 (radius: 15)
[00:53:50] [worker #1] ML tree search #12, logLikelihood: -21062.606069
[00:54:13 -21072.450809] SLOW spr round 11 (radius: 20)
[00:54:49 -21072.093144] SLOW spr round 12 (radius: 5)
[00:55:17 -21072.090238] SLOW spr round 13 (radius: 10)
[00:55:47 -21072.089974] SLOW spr round 14 (radius: 15)
[00:56:16 -21072.089950] SLOW spr round 15 (radius: 20)
[00:56:53 -21072.089948] SLOW spr round 16 (radius: 25)
[00:57:31 -21072.089947] Model parameter optimization (eps = 0.100000)

[00:57:36] [worker #0] ML tree search #11, logLikelihood: -21071.544964

[00:57:36 -57536.654826] Initial branch length optimization
[00:57:36 -46263.849392] Model parameter optimization (eps = 10.000000)
[00:57:45 -46073.829824] AUTODETECT spr round 1 (radius: 5)
[00:57:59 -34980.459514] AUTODETECT spr round 2 (radius: 10)
[00:58:16 -27675.644359] AUTODETECT spr round 3 (radius: 15)
[00:58:37 -24956.223192] AUTODETECT spr round 4 (radius: 20)
[00:59:02 -23182.245227] AUTODETECT spr round 5 (radius: 25)
[00:59:26 -23143.767230] SPR radius for FAST iterations: 25 (autodetect)
[00:59:26 -23143.767230] Model parameter optimization (eps = 3.000000)
[00:59:32 -23031.539123] FAST spr round 1 (radius: 25)
[00:59:53 -21181.175038] FAST spr round 2 (radius: 25)
[01:00:09 -21089.231051] FAST spr round 3 (radius: 25)
[01:00:23 -21062.902735] FAST spr round 4 (radius: 25)
[01:00:36 -21060.632152] FAST spr round 5 (radius: 25)
[01:00:47 -21060.630674] Model parameter optimization (eps = 1.000000)
[01:00:53 -21050.813048] SLOW spr round 1 (radius: 5)
[01:01:14 -21046.449362] SLOW spr round 2 (radius: 5)
[01:01:35 -21045.126073] SLOW spr round 3 (radius: 5)
[01:01:54 -21045.013426] SLOW spr round 4 (radius: 5)
[01:02:13 -21045.010680] SLOW spr round 5 (radius: 10)
[01:02:33 -21044.471782] SLOW spr round 6 (radius: 5)
[01:02:59 -21044.471750] SLOW spr round 7 (radius: 10)
[01:03:01] [worker #1] ML tree search #14, logLikelihood: -21052.877180
[01:03:22 -21044.471748] SLOW spr round 8 (radius: 15)
[01:03:52 -21043.424393] SLOW spr round 9 (radius: 5)
[01:04:19 -21043.422435] SLOW spr round 10 (radius: 10)
[01:04:45 -21043.422311] SLOW spr round 11 (radius: 15)
[01:05:15 -21042.565846] SLOW spr round 12 (radius: 5)
[01:05:42 -21042.565642] SLOW spr round 13 (radius: 10)
[01:06:08 -21042.565636] SLOW spr round 14 (radius: 15)
[01:06:38 -21042.565636] SLOW spr round 15 (radius: 20)
[01:07:13 -21042.565636] SLOW spr round 16 (radius: 25)
[01:07:52 -21042.565636] Model parameter optimization (eps = 0.100000)

[01:07:54] [worker #0] ML tree search #13, logLikelihood: -21042.499390

[01:07:54 -57850.567903] Initial branch length optimization
[01:07:54 -45661.914442] Model parameter optimization (eps = 10.000000)
[01:08:05 -45476.839914] AUTODETECT spr round 1 (radius: 5)
[01:08:18 -35132.657907] AUTODETECT spr round 2 (radius: 10)
[01:08:36 -29016.921794] AUTODETECT spr round 3 (radius: 15)
[01:08:57 -25146.544623] AUTODETECT spr round 4 (radius: 20)
[01:09:19 -24716.456622] AUTODETECT spr round 5 (radius: 25)
[01:09:42 -24449.403927] SPR radius for FAST iterations: 25 (autodetect)
[01:09:42 -24449.403927] Model parameter optimization (eps = 3.000000)
[01:09:49 -24328.433653] FAST spr round 1 (radius: 25)
[01:10:10 -21530.668049] FAST spr round 2 (radius: 25)
[01:10:27 -21100.707589] FAST spr round 3 (radius: 25)
[01:10:42 -21071.630748] FAST spr round 4 (radius: 25)
[01:10:54 -21070.903407] FAST spr round 5 (radius: 25)
[01:11:06 -21070.902856] Model parameter optimization (eps = 1.000000)
[01:11:12 -21065.542910] SLOW spr round 1 (radius: 5)
[01:11:34 -21055.518658] SLOW spr round 2 (radius: 5)
[01:11:54 -21053.622614] SLOW spr round 3 (radius: 5)
[01:12:11] [worker #1] ML tree search #16, logLikelihood: -21043.178831
[01:12:13 -21053.620702] SLOW spr round 4 (radius: 10)
[01:12:33 -21053.620545] SLOW spr round 5 (radius: 15)
[01:13:05 -21052.286162] SLOW spr round 6 (radius: 5)
[01:13:33 -21052.248413] SLOW spr round 7 (radius: 10)
[01:13:59 -21050.084326] SLOW spr round 8 (radius: 5)
[01:14:25 -21049.896955] SLOW spr round 9 (radius: 5)
[01:14:46 -21049.895345] SLOW spr round 10 (radius: 10)
[01:15:07 -21049.894992] SLOW spr round 11 (radius: 15)
[01:15:40 -21049.894843] SLOW spr round 12 (radius: 20)
[01:16:15 -21049.894766] SLOW spr round 13 (radius: 25)
[01:16:51 -21049.894725] Model parameter optimization (eps = 0.100000)

[01:16:55] [worker #0] ML tree search #15, logLikelihood: -21049.182994

[01:16:55 -56843.218995] Initial branch length optimization
[01:16:56 -45931.954004] Model parameter optimization (eps = 10.000000)
[01:17:05 -45788.179399] AUTODETECT spr round 1 (radius: 5)
[01:17:18 -35146.393877] AUTODETECT spr round 2 (radius: 10)
[01:17:35 -28427.300817] AUTODETECT spr round 3 (radius: 15)
[01:17:55 -24097.202024] AUTODETECT spr round 4 (radius: 20)
[01:18:17 -23867.431428] AUTODETECT spr round 5 (radius: 25)
[01:18:43 -23619.040706] SPR radius for FAST iterations: 25 (autodetect)
[01:18:43 -23619.040706] Model parameter optimization (eps = 3.000000)
[01:18:51 -23536.235212] FAST spr round 1 (radius: 25)
[01:19:11 -21158.165744] FAST spr round 2 (radius: 25)
[01:19:28 -21077.711994] FAST spr round 3 (radius: 25)
[01:19:41 -21064.858924] FAST spr round 4 (radius: 25)
[01:19:53 -21062.921975] FAST spr round 5 (radius: 25)
[01:20:05 -21062.699221] FAST spr round 6 (radius: 25)
[01:20:16 -21062.699202] Model parameter optimization (eps = 1.000000)
[01:20:22 -21055.316183] SLOW spr round 1 (radius: 5)
[01:20:43 -21050.187021] SLOW spr round 2 (radius: 5)
[01:21:03 -21049.943891] SLOW spr round 3 (radius: 5)
[01:21:22 -21049.942962] SLOW spr round 4 (radius: 10)
[01:21:41 -21048.528623] SLOW spr round 5 (radius: 5)
[01:22:08 -21047.764558] SLOW spr round 6 (radius: 5)
[01:22:30 -21047.181364] SLOW spr round 7 (radius: 5)
[01:22:51 -21047.181293] SLOW spr round 8 (radius: 10)
[01:23:11 -21047.181293] SLOW spr round 9 (radius: 15)
[01:23:44 -21046.881288] SLOW spr round 10 (radius: 5)
[01:24:10 -21046.827359] SLOW spr round 11 (radius: 10)
[01:24:15] [worker #1] ML tree search #18, logLikelihood: -21073.688383
[01:24:36 -21046.825564] SLOW spr round 12 (radius: 15)
[01:25:07 -21046.824545] SLOW spr round 13 (radius: 20)
[01:25:43 -21045.697653] SLOW spr round 14 (radius: 5)
[01:26:11 -21044.636428] SLOW spr round 15 (radius: 5)
[01:26:35 -21043.367021] SLOW spr round 16 (radius: 5)
[01:26:56 -21043.366703] SLOW spr round 17 (radius: 10)
[01:27:16 -21043.366563] SLOW spr round 18 (radius: 15)
[01:27:49 -21043.366486] SLOW spr round 19 (radius: 20)
[01:28:25 -21043.366442] SLOW spr round 20 (radius: 25)
[01:29:03 -21043.366418] Model parameter optimization (eps = 0.100000)

[01:29:06] [worker #0] ML tree search #17, logLikelihood: -21042.732252

[01:29:06 -57078.842824] Initial branch length optimization
[01:29:07 -45936.378875] Model parameter optimization (eps = 10.000000)
[01:29:16 -45791.348021] AUTODETECT spr round 1 (radius: 5)
[01:29:29 -35558.254883] AUTODETECT spr round 2 (radius: 10)
[01:29:46 -30080.944909] AUTODETECT spr round 3 (radius: 15)
[01:30:06 -25929.955767] AUTODETECT spr round 4 (radius: 20)
[01:30:30 -23914.144147] AUTODETECT spr round 5 (radius: 25)
[01:30:53 -23771.886403] SPR radius for FAST iterations: 25 (autodetect)
[01:30:53 -23771.886403] Model parameter optimization (eps = 3.000000)
[01:31:03 -23674.425165] FAST spr round 1 (radius: 25)
[01:31:24 -21285.356160] FAST spr round 2 (radius: 25)
[01:31:41 -21075.986428] FAST spr round 3 (radius: 25)
[01:31:55 -21070.221903] FAST spr round 4 (radius: 25)
[01:32:07 -21069.083292] FAST spr round 5 (radius: 25)
[01:32:19 -21065.499213] FAST spr round 6 (radius: 25)
[01:32:31 -21064.986917] FAST spr round 7 (radius: 25)
[01:32:42 -21064.986888] Model parameter optimization (eps = 1.000000)
[01:32:47 -21063.444491] SLOW spr round 1 (radius: 5)
[01:33:09 -21060.512366] SLOW spr round 2 (radius: 5)
[01:33:28 -21060.511352] SLOW spr round 3 (radius: 10)
[01:33:48 -21059.796979] SLOW spr round 4 (radius: 5)
[01:34:14 -21059.729744] SLOW spr round 5 (radius: 10)
[01:34:20] [worker #1] ML tree search #20, logLikelihood: -21052.526409
[01:34:38 -21059.729583] SLOW spr round 6 (radius: 15)
[01:35:07 -21059.467582] SLOW spr round 7 (radius: 5)
[01:35:34 -21059.466873] SLOW spr round 8 (radius: 10)
[01:36:00 -21059.466850] SLOW spr round 9 (radius: 15)
[01:36:29 -21059.466849] SLOW spr round 10 (radius: 20)
[01:37:00 -21058.696009] SLOW spr round 11 (radius: 5)
[01:37:28 -21057.932234] SLOW spr round 12 (radius: 5)
[01:37:52 -21057.929867] SLOW spr round 13 (radius: 10)
[01:38:14 -21057.929664] SLOW spr round 14 (radius: 15)
[01:38:44 -21057.929647] SLOW spr round 15 (radius: 20)
[01:39:16 -21057.929646] SLOW spr round 16 (radius: 25)
[01:39:50 -21057.929646] Model parameter optimization (eps = 0.100000)

[01:39:52] [worker #0] ML tree search #19, logLikelihood: -21057.850883


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.255354,0.301109) (0.149401,0.704262) (0.270827,0.712219) (0.324418,1.926540) 
   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: -21030.448678

AIC score: 43242.897356 / AICc score: 742986.897356 / BIC score: 44895.209568
Free parameters (model + branch lengths): 591

WARNING: Number of free parameters (K=591) is larger than alignment size (n=121).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 23 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q86X60/3_mltree/Q86X60.raxml.log

Analysis started: 05-Jul-2021 15:47:59 / finished: 05-Jul-2021 17:27:52

Elapsed time: 5992.661 seconds