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 26-Jul-2021 00:10:20 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/2_msa/A6NFY7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7 --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/250721_run/phylogeny-snakemake/results/A6NFY7/2_msa/A6NFY7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 568 taxa and 146 sites

WARNING: Sequences tr_J3K9Z7_J3K9Z7_COCIM_246410 and tr_A0A0J6Y172_A0A0J6Y172_COCIT_404692 are exactly identical!
WARNING: Sequences tr_G2X2J1_G2X2J1_VERDV_498257 and tr_A0A0G4LDH5_A0A0G4LDH5_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_G2X2J1_G2X2J1_VERDV_498257 and tr_A0A0G4M7L6_A0A0G4M7L6_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_A0A179UFM2_A0A179UFM2_BLAGS_559298 and tr_C5GG44_C5GG44_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2R660_H2R660_PANTR_9598 and tr_A0A2R8ZEV3_A0A2R8ZEV3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_M4AZN8_M4AZN8_XIPMA_8083 and tr_A0A087YPX9_A0A087YPX9_POEFO_48698 are exactly identical!
WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A0A0MVB5_A0A0A0MVB5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A2K5L3U3_A0A2K5L3U3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6X7B7_F6X7B7_MACMU_9544 and tr_A0A2K6AYR1_A0A2K6AYR1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_A0A0E0QGQ3_A0A0E0QGQ3_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_A0A0E0AT71_A0A0E0AT71_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2YTD3_A2YTD3_ORYSI_39946 and tr_Q6Z1L3_Q6Z1L3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F2SHD0_F2SHD0_TRIRC_559305 and tr_F2Q497_F2Q497_TRIEC_559882 are exactly identical!
WARNING: Sequences tr_G3YEM3_G3YEM3_ASPNA_380704 and tr_A0A319AB55_A0A319AB55_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_S0DNC0_S0DNC0_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_N4TN99_N4TN99_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_X0CDH2_X0CDH2_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2H3SV16_A0A2H3SV16_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2H3I448_A0A2H3I448_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_W7LRE5_W7LRE5_GIBM7_334819 and tr_A0A2K0WDI3_A0A2K0WDI3_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_M4DKM5_M4DKM5_BRARP_51351 and tr_A0A0D3C579_A0A0D3C579_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M8A8G7_M8A8G7_TRIUA_4572 and tr_A0A3B6HM86_A0A3B6HM86_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2XR52_V2XR52_MONRO_1381753 and tr_A0A0W0F3W1_A0A0W0F3W1_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QPU5_W2QPU5_PHYPN_761204 and tr_W2JPF4_W2JPF4_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_V4T3W6_V4T3W6_9ROSI_85681 and tr_A0A2H5QIH1_A0A2H5QIH1_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2VEU1_A0A0D2VEU1_GOSRA_29730 and tr_A0A1U8KMI7_A0A1U8KMI7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0E0RQ37_A0A0E0RQ37_GIBZE_229533 and tr_A0A2T4H658_A0A2T4H658_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A161VLD0_A0A161VLD0_9PEZI_708197 and tr_A0A167BGN0_A0A167BGN0_9PEZI_1573173 are exactly identical!
WARNING: Sequences tr_A0A164TE16_A0A164TE16_9HOMO_1314777 and tr_A0A166DUI5_A0A166DUI5_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4DDE5_A0A1S4DDE5_TOBAC_4097 and tr_A0A1U7XE57_A0A1U7XE57_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1L9NMH1_A0A1L9NMH1_ASPTU_767770 and tr_A0A317UPM5_A0A317UPM5_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A2H3C9Q0_A0A2H3C9Q0_9AGAR_1076256 and tr_A0A284RG11_A0A284RG11_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A1U8E5C9_A0A1U8E5C9_CAPAN_4072 and tr_A0A2G3BJN4_A0A2G3BJN4_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2I2F6P8_A0A2I2F6P8_9EURO_41067 and tr_A0A2J5I304_A0A2J5I304_9EURO_482145 are exactly identical!
WARNING: Sequences tr_A0A2S7PE33_A0A2S7PE33_9HELO_2070414 and tr_A0A2S7QNZ6_A0A2S7QNZ6_9HELO_2070412 are exactly identical!
WARNING: Duplicate sequences found: 35

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.reduced.phy

Alignment comprises 1 partitions and 146 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 146 / 146
Gaps: 40.34 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.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 568 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 146 / 11680
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -89155.893056] Initial branch length optimization
[00:00:03 -77733.203834] Model parameter optimization (eps = 10.000000)
[00:00:34 -77029.558301] AUTODETECT spr round 1 (radius: 5)
[00:01:59 -60695.837511] AUTODETECT spr round 2 (radius: 10)
[00:03:40 -48147.661813] AUTODETECT spr round 3 (radius: 15)
[00:05:51 -43605.828978] AUTODETECT spr round 4 (radius: 20)
[00:08:46 -42722.155864] AUTODETECT spr round 5 (radius: 25)
[00:12:06 -42647.251641] SPR radius for FAST iterations: 25 (autodetect)
[00:12:06 -42647.251641] Model parameter optimization (eps = 3.000000)
[00:12:30 -42555.875147] FAST spr round 1 (radius: 25)
[00:14:45 -39291.558101] FAST spr round 2 (radius: 25)
[00:16:23 -39054.924113] FAST spr round 3 (radius: 25)
[00:17:51 -39029.927694] FAST spr round 4 (radius: 25)
[00:19:09 -39020.568725] FAST spr round 5 (radius: 25)
[00:20:27 -39004.841767] FAST spr round 6 (radius: 25)
[00:21:35 -39004.300343] FAST spr round 7 (radius: 25)
[00:22:41 -39004.297912] Model parameter optimization (eps = 1.000000)
[00:22:58 -38997.357783] SLOW spr round 1 (radius: 5)
[00:24:50 -38986.726787] SLOW spr round 2 (radius: 5)
[00:26:36 -38982.626966] SLOW spr round 3 (radius: 5)
[00:28:15 -38982.435779] SLOW spr round 4 (radius: 5)
[00:29:51 -38982.435512] SLOW spr round 5 (radius: 10)
[00:31:29 -38977.220082] SLOW spr round 6 (radius: 5)
[00:33:36 -38976.336945] SLOW spr round 7 (radius: 5)
[00:35:27 -38974.775024] SLOW spr round 8 (radius: 5)
[00:37:08 -38974.774323] SLOW spr round 9 (radius: 10)
[00:38:46 -38974.774311] SLOW spr round 10 (radius: 15)
[00:41:35 -38973.813061] SLOW spr round 11 (radius: 5)
[00:43:44 -38973.812643] SLOW spr round 12 (radius: 10)
[00:45:39 -38973.812638] SLOW spr round 13 (radius: 15)
[00:48:16 -38973.812638] SLOW spr round 14 (radius: 20)
[00:52:20 -38973.812638] SLOW spr round 15 (radius: 25)
[00:57:27 -38973.812638] Model parameter optimization (eps = 0.100000)

[00:57:36] [worker #0] ML tree search #1, logLikelihood: -38973.507824

[00:57:36 -89553.395753] Initial branch length optimization
[00:57:38 -78102.652539] Model parameter optimization (eps = 10.000000)
[00:58:17 -77418.715856] AUTODETECT spr round 1 (radius: 5)
[00:59:40 -60885.751238] AUTODETECT spr round 2 (radius: 10)
[01:01:20 -47811.381692] AUTODETECT spr round 3 (radius: 15)
[01:03:16 -43758.424285] AUTODETECT spr round 4 (radius: 20)
[01:05:34] [worker #2] ML tree search #3, logLikelihood: -38928.420801
[01:05:42 -42835.648303] AUTODETECT spr round 5 (radius: 25)
[01:08:22 -42587.928823] SPR radius for FAST iterations: 25 (autodetect)
[01:08:22 -42587.928823] Model parameter optimization (eps = 3.000000)
[01:08:46 -42480.193469] FAST spr round 1 (radius: 25)
[01:10:57 -39225.890629] FAST spr round 2 (radius: 25)
[01:12:09] [worker #1] ML tree search #2, logLikelihood: -38941.552435
[01:12:33 -39079.065106] FAST spr round 3 (radius: 25)
[01:14:00 -39029.647449] FAST spr round 4 (radius: 25)
[01:15:14 -39018.496544] FAST spr round 5 (radius: 25)
[01:16:22 -39017.620756] FAST spr round 6 (radius: 25)
[01:17:29 -39017.200430] FAST spr round 7 (radius: 25)
[01:18:34 -39017.200218] Model parameter optimization (eps = 1.000000)
[01:18:49 -39007.412023] SLOW spr round 1 (radius: 5)
[01:20:39 -38994.522348] SLOW spr round 2 (radius: 5)
[01:22:22 -38989.232461] SLOW spr round 3 (radius: 5)
[01:24:02 -38988.747809] SLOW spr round 4 (radius: 5)
[01:25:38 -38988.455391] SLOW spr round 5 (radius: 5)
[01:27:13 -38986.633479] SLOW spr round 6 (radius: 5)
[01:28:48 -38986.632669] SLOW spr round 7 (radius: 10)
[01:30:27 -38981.368706] SLOW spr round 8 (radius: 5)
[01:32:38 -38977.052870] SLOW spr round 9 (radius: 5)
[01:34:29 -38976.419197] SLOW spr round 10 (radius: 5)
[01:36:10 -38976.419173] SLOW spr round 11 (radius: 10)
[01:37:50 -38976.068318] SLOW spr round 12 (radius: 5)
[01:39:57 -38974.603038] SLOW spr round 13 (radius: 5)
[01:41:46 -38974.602650] SLOW spr round 14 (radius: 10)
[01:43:29 -38972.892667] SLOW spr round 15 (radius: 5)
[01:45:34 -38972.884333] SLOW spr round 16 (radius: 10)
[01:47:25 -38972.565471] SLOW spr round 17 (radius: 5)
[01:49:29 -38972.032314] SLOW spr round 18 (radius: 5)
[01:51:16 -38972.031855] SLOW spr round 19 (radius: 10)
[01:52:57 -38971.546062] SLOW spr round 20 (radius: 5)
[01:55:02 -38970.934282] SLOW spr round 21 (radius: 5)
[01:56:50 -38970.934041] SLOW spr round 22 (radius: 10)
[01:58:31 -38970.934038] SLOW spr round 23 (radius: 15)
[02:01:33 -38968.451010] SLOW spr round 24 (radius: 5)
[02:02:53] [worker #1] ML tree search #5, logLikelihood: -39079.949040
[02:03:45 -38964.900772] SLOW spr round 25 (radius: 5)
[02:05:37 -38964.890540] SLOW spr round 26 (radius: 10)
[02:07:19 -38964.862741] SLOW spr round 27 (radius: 15)
[02:10:18 -38964.092268] SLOW spr round 28 (radius: 5)
[02:11:38] [worker #2] ML tree search #6, logLikelihood: -38992.122707
[02:12:28 -38964.088164] SLOW spr round 29 (radius: 10)
[02:14:24 -38963.828707] SLOW spr round 30 (radius: 5)
[02:16:27 -38963.824553] SLOW spr round 31 (radius: 10)
[02:18:15 -38963.824392] SLOW spr round 32 (radius: 15)
[02:21:09 -38963.824385] SLOW spr round 33 (radius: 20)
[02:25:41 -38963.824384] SLOW spr round 34 (radius: 25)
[02:30:53 -38963.021542] SLOW spr round 35 (radius: 5)
[02:33:09 -38963.018560] SLOW spr round 36 (radius: 10)
[02:35:14 -38962.942223] SLOW spr round 37 (radius: 15)
[02:38:05 -38962.936353] SLOW spr round 38 (radius: 20)
[02:42:41 -38962.933617] SLOW spr round 39 (radius: 25)
[02:47:52 -38962.931731] Model parameter optimization (eps = 0.100000)

[02:48:01] [worker #0] ML tree search #4, logLikelihood: -38962.690680

[02:48:01 -89098.071957] Initial branch length optimization
[02:48:03 -77656.460528] Model parameter optimization (eps = 10.000000)
[02:48:33 -77020.470870] AUTODETECT spr round 1 (radius: 5)
[02:49:55 -61082.321951] AUTODETECT spr round 2 (radius: 10)
[02:51:35 -47849.158552] AUTODETECT spr round 3 (radius: 15)
[02:53:38 -44194.766670] AUTODETECT spr round 4 (radius: 20)
[02:55:58 -42834.403524] AUTODETECT spr round 5 (radius: 25)
[02:56:43] [worker #1] ML tree search #8, logLikelihood: -38976.759379
[02:59:05 -42670.115492] SPR radius for FAST iterations: 25 (autodetect)
[02:59:05 -42670.115492] Model parameter optimization (eps = 3.000000)
[02:59:46 -42573.192689] FAST spr round 1 (radius: 25)
[03:01:48 -39283.980101] FAST spr round 2 (radius: 25)
[03:03:21 -39004.009450] FAST spr round 3 (radius: 25)
[03:04:42 -38977.803642] FAST spr round 4 (radius: 25)
[03:05:52 -38972.807142] FAST spr round 5 (radius: 25)
[03:06:59 -38971.143843] FAST spr round 6 (radius: 25)
[03:08:05 -38971.143659] Model parameter optimization (eps = 1.000000)
[03:08:27 -38955.964534] SLOW spr round 1 (radius: 5)
[03:09:29] [worker #2] ML tree search #9, logLikelihood: -38952.425137
[03:10:13 -38942.209042] SLOW spr round 2 (radius: 5)
[03:11:56 -38938.098492] SLOW spr round 3 (radius: 5)
[03:13:31 -38938.098482] SLOW spr round 4 (radius: 10)
[03:15:09 -38932.843662] SLOW spr round 5 (radius: 5)
[03:17:16 -38931.774873] SLOW spr round 6 (radius: 5)
[03:19:05 -38931.774569] SLOW spr round 7 (radius: 10)
[03:20:46 -38930.316357] SLOW spr round 8 (radius: 5)
[03:22:51 -38929.323402] SLOW spr round 9 (radius: 5)
[03:24:40 -38929.323243] SLOW spr round 10 (radius: 10)
[03:26:18 -38928.629242] SLOW spr round 11 (radius: 5)
[03:28:27 -38926.393877] SLOW spr round 12 (radius: 5)
[03:30:16 -38926.393755] SLOW spr round 13 (radius: 10)
[03:31:55 -38926.124930] SLOW spr round 14 (radius: 5)
[03:33:59 -38925.973478] SLOW spr round 15 (radius: 5)
[03:35:48 -38925.970837] SLOW spr round 16 (radius: 10)
[03:37:27 -38925.970589] SLOW spr round 17 (radius: 15)
[03:40:23 -38924.463925] SLOW spr round 18 (radius: 5)
[03:42:35 -38923.375335] SLOW spr round 19 (radius: 5)
[03:44:27 -38923.374076] SLOW spr round 20 (radius: 10)
[03:46:09 -38923.373728] SLOW spr round 21 (radius: 15)
[03:47:15] [worker #1] ML tree search #11, logLikelihood: -38992.579666
[03:49:12 -38923.373606] SLOW spr round 22 (radius: 20)
[03:54:00 -38923.373560] SLOW spr round 23 (radius: 25)
[03:59:30 -38923.373542] Model parameter optimization (eps = 0.100000)

[03:59:46] [worker #0] ML tree search #7, logLikelihood: -38923.153634

[03:59:46 -89167.553176] Initial branch length optimization
[03:59:49 -77593.131399] Model parameter optimization (eps = 10.000000)
[04:00:22 -76949.612938] AUTODETECT spr round 1 (radius: 5)
[04:01:45 -61061.639990] AUTODETECT spr round 2 (radius: 10)
[04:03:22 -48235.286556] AUTODETECT spr round 3 (radius: 15)
[04:05:19 -43931.771968] AUTODETECT spr round 4 (radius: 20)
[04:07:56 -42753.970479] AUTODETECT spr round 5 (radius: 25)
[04:10:59 -42462.854162] SPR radius for FAST iterations: 25 (autodetect)
[04:10:59 -42462.854162] Model parameter optimization (eps = 3.000000)
[04:11:22 -42366.630445] FAST spr round 1 (radius: 25)
[04:12:03] [worker #2] ML tree search #12, logLikelihood: -38957.606973
[04:13:31 -39307.292988] FAST spr round 2 (radius: 25)
[04:15:11 -39062.529814] FAST spr round 3 (radius: 25)
[04:16:40 -39024.782896] FAST spr round 4 (radius: 25)
[04:17:52 -39019.610869] FAST spr round 5 (radius: 25)
[04:19:01 -39018.863557] FAST spr round 6 (radius: 25)
[04:20:09 -39018.863511] Model parameter optimization (eps = 1.000000)
[04:20:33 -38988.993329] SLOW spr round 1 (radius: 5)
[04:22:26 -38970.570963] SLOW spr round 2 (radius: 5)
[04:24:12 -38968.124051] SLOW spr round 3 (radius: 5)
[04:25:55 -38965.864587] SLOW spr round 4 (radius: 5)
[04:27:33 -38965.864388] SLOW spr round 5 (radius: 10)
[04:29:12 -38962.679365] SLOW spr round 6 (radius: 5)
[04:31:18 -38962.678951] SLOW spr round 7 (radius: 10)
[04:33:09 -38962.678934] SLOW spr round 8 (radius: 15)
[04:36:03 -38960.045932] SLOW spr round 9 (radius: 5)
[04:38:20 -38955.025436] SLOW spr round 10 (radius: 5)
[04:40:13 -38955.025029] SLOW spr round 11 (radius: 10)
[04:41:55 -38954.801561] SLOW spr round 12 (radius: 5)
[04:43:59 -38954.801454] SLOW spr round 13 (radius: 10)
[04:45:48 -38954.801453] SLOW spr round 14 (radius: 15)
[04:48:42 -38954.801453] SLOW spr round 15 (radius: 20)
[04:53:02 -38953.445159] SLOW spr round 16 (radius: 5)
[04:55:18 -38952.065341] SLOW spr round 17 (radius: 5)
[04:57:19 -38949.506735] SLOW spr round 18 (radius: 5)
[04:59:09 -38947.595609] SLOW spr round 19 (radius: 5)
[05:00:54 -38947.364578] SLOW spr round 20 (radius: 5)
[05:02:31 -38947.364507] SLOW spr round 21 (radius: 10)
[05:04:06 -38947.364506] SLOW spr round 22 (radius: 15)
[05:07:05 -38947.364506] SLOW spr round 23 (radius: 20)
[05:11:13 -38945.196049] SLOW spr round 24 (radius: 5)
[05:13:35 -38943.941833] SLOW spr round 25 (radius: 5)
[05:15:33 -38942.831677] SLOW spr round 26 (radius: 5)
[05:17:17 -38942.831606] SLOW spr round 27 (radius: 10)
[05:18:54 -38941.042971] SLOW spr round 28 (radius: 5)
[05:20:59 -38941.040785] SLOW spr round 29 (radius: 10)
[05:21:35] [worker #1] ML tree search #14, logLikelihood: -38961.613452
[05:22:25] [worker #2] ML tree search #15, logLikelihood: -38985.395036
[05:22:45 -38941.040647] SLOW spr round 30 (radius: 15)
[05:25:32 -38941.040636] SLOW spr round 31 (radius: 20)
[05:29:40 -38941.040635] SLOW spr round 32 (radius: 25)
[05:34:37 -38941.040635] Model parameter optimization (eps = 0.100000)

[05:34:47] [worker #0] ML tree search #10, logLikelihood: -38940.909147

[05:34:47 -88946.178188] Initial branch length optimization
[05:34:49 -77268.368865] Model parameter optimization (eps = 10.000000)
[05:35:19 -76582.919606] AUTODETECT spr round 1 (radius: 5)
[05:36:43 -61045.451638] AUTODETECT spr round 2 (radius: 10)
[05:38:24 -48420.977162] AUTODETECT spr round 3 (radius: 15)
[05:40:15 -44425.076720] AUTODETECT spr round 4 (radius: 20)
[05:43:10 -42977.820492] AUTODETECT spr round 5 (radius: 25)
[05:46:42 -42747.733782] SPR radius for FAST iterations: 25 (autodetect)
[05:46:42 -42747.733782] Model parameter optimization (eps = 3.000000)
[05:47:03 -42640.530721] FAST spr round 1 (radius: 25)
[05:49:17 -39423.737993] FAST spr round 2 (radius: 25)
[05:50:51 -39189.018862] FAST spr round 3 (radius: 25)
[05:52:12 -39144.323790] FAST spr round 4 (radius: 25)
[05:53:24 -39141.559704] FAST spr round 5 (radius: 25)
[05:54:31 -39141.555990] Model parameter optimization (eps = 1.000000)
[05:54:40 -39141.208619] SLOW spr round 1 (radius: 5)
[05:56:29 -39123.819135] SLOW spr round 2 (radius: 5)
[05:58:13 -39122.114751] SLOW spr round 3 (radius: 5)
[05:59:50 -39122.114613] SLOW spr round 4 (radius: 10)
[06:01:30 -39119.885715] SLOW spr round 5 (radius: 5)
[06:03:40 -39110.676786] SLOW spr round 6 (radius: 5)
[06:05:29 -39110.676414] SLOW spr round 7 (radius: 10)
[06:07:10 -39110.137650] SLOW spr round 8 (radius: 5)
[06:09:19 -39109.764501] SLOW spr round 9 (radius: 5)
[06:11:06 -39109.764434] SLOW spr round 10 (radius: 10)
[06:12:49 -39109.764433] SLOW spr round 11 (radius: 15)
[06:15:42 -39109.009567] SLOW spr round 12 (radius: 5)
[06:17:55 -39108.516308] SLOW spr round 13 (radius: 5)
[06:19:51 -39106.952786] SLOW spr round 14 (radius: 5)
[06:21:33 -39106.952685] SLOW spr round 15 (radius: 10)
[06:23:13 -39106.952684] SLOW spr round 16 (radius: 15)
[06:26:11 -39106.952683] SLOW spr round 17 (radius: 20)
[06:30:28 -39106.952683] SLOW spr round 18 (radius: 25)
[06:35:22 -39106.952683] Model parameter optimization (eps = 0.100000)

[06:35:31] [worker #0] ML tree search #13, logLikelihood: -39106.923071

[06:35:31 -89311.489762] Initial branch length optimization
[06:35:33 -77999.277728] Model parameter optimization (eps = 10.000000)
[06:36:06 -77271.564467] AUTODETECT spr round 1 (radius: 5)
[06:36:38] [worker #1] ML tree search #17, logLikelihood: -38971.410675
[06:37:29 -61775.356841] AUTODETECT spr round 2 (radius: 10)
[06:39:07 -49096.373436] AUTODETECT spr round 3 (radius: 15)
[06:41:11 -44720.580220] AUTODETECT spr round 4 (radius: 20)
[06:43:44 -43131.386470] AUTODETECT spr round 5 (radius: 25)
[06:45:21] [worker #2] ML tree search #18, logLikelihood: -38952.427160
[06:46:37 -42861.530744] SPR radius for FAST iterations: 25 (autodetect)
[06:46:37 -42861.530744] Model parameter optimization (eps = 3.000000)
[06:47:03 -42763.526670] FAST spr round 1 (radius: 25)
[06:49:07 -39280.812455] FAST spr round 2 (radius: 25)
[06:50:40 -39054.172472] FAST spr round 3 (radius: 25)
[06:52:02 -39021.885552] FAST spr round 4 (radius: 25)
[06:53:14 -39005.469131] FAST spr round 5 (radius: 25)
[06:54:23 -39001.994891] FAST spr round 6 (radius: 25)
[06:55:29 -39001.994736] Model parameter optimization (eps = 1.000000)
[06:55:47 -38975.465920] SLOW spr round 1 (radius: 5)
[06:57:38 -38966.127205] SLOW spr round 2 (radius: 5)
[06:59:16 -38966.126726] SLOW spr round 3 (radius: 10)
[07:00:56 -38961.014604] SLOW spr round 4 (radius: 5)
[07:03:07 -38956.976274] SLOW spr round 5 (radius: 5)
[07:04:57 -38955.147770] SLOW spr round 6 (radius: 5)
[07:06:38 -38955.147665] SLOW spr round 7 (radius: 10)
[07:08:18 -38954.263431] SLOW spr round 8 (radius: 5)
[07:10:27 -38953.255421] SLOW spr round 9 (radius: 5)
[07:12:17 -38953.255011] SLOW spr round 10 (radius: 10)
[07:13:59 -38952.963893] SLOW spr round 11 (radius: 5)
[07:16:07 -38951.663445] SLOW spr round 12 (radius: 5)
[07:17:55 -38951.663096] SLOW spr round 13 (radius: 10)
[07:19:35 -38951.662848] SLOW spr round 14 (radius: 15)
[07:22:52 -38951.662588] SLOW spr round 15 (radius: 20)
[07:27:47 -38951.662311] SLOW spr round 16 (radius: 25)
[07:32:53 -38951.662014] Model parameter optimization (eps = 0.100000)

[07:32:59] [worker #0] ML tree search #16, logLikelihood: -38951.645464

[07:32:59 -89378.353040] Initial branch length optimization
[07:33:02 -77742.492939] Model parameter optimization (eps = 10.000000)
[07:33:32 -77081.795980] AUTODETECT spr round 1 (radius: 5)
[07:34:54 -60626.885547] AUTODETECT spr round 2 (radius: 10)
[07:36:34 -47124.431837] AUTODETECT spr round 3 (radius: 15)
[07:38:24 -43683.199979] AUTODETECT spr round 4 (radius: 20)
[07:40:39 -42297.672001] AUTODETECT spr round 5 (radius: 25)
[07:43:24 -42160.134850] SPR radius for FAST iterations: 25 (autodetect)
[07:43:24 -42160.134850] Model parameter optimization (eps = 3.000000)
[07:43:48 -42055.383371] FAST spr round 1 (radius: 25)
[07:46:04 -39322.218261] FAST spr round 2 (radius: 25)
[07:47:37 -39038.197073] FAST spr round 3 (radius: 25)
[07:49:03 -39010.162189] FAST spr round 4 (radius: 25)
[07:50:13 -39007.183745] FAST spr round 5 (radius: 25)
[07:51:20 -39007.182413] Model parameter optimization (eps = 1.000000)
[07:51:44 -38978.952801] SLOW spr round 1 (radius: 5)
[07:53:36 -38966.560399] SLOW spr round 2 (radius: 5)
[07:55:22 -38962.758080] SLOW spr round 3 (radius: 5)
[07:57:00 -38962.755257] SLOW spr round 4 (radius: 10)
[07:58:40 -38959.512153] SLOW spr round 5 (radius: 5)
[08:00:46 -38959.511043] SLOW spr round 6 (radius: 10)
[08:02:36 -38959.287670] SLOW spr round 7 (radius: 5)
[08:04:38 -38959.285304] SLOW spr round 8 (radius: 10)
[08:06:05] [worker #1] ML tree search #20, logLikelihood: -38952.730911
[08:06:26 -38959.285262] SLOW spr round 9 (radius: 15)
[08:09:11 -38959.285261] SLOW spr round 10 (radius: 20)
[08:13:22 -38959.285261] SLOW spr round 11 (radius: 25)
[08:18:14 -38959.285261] Model parameter optimization (eps = 0.100000)

[08:18:27] [worker #0] ML tree search #19, logLikelihood: -38958.118979


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.131968,0.298068) (0.159809,0.392079) (0.387637,0.743872) (0.320585,1.901692) 
   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: -38923.153634

AIC score: 80124.307268 / AICc score: 2677044.307268 / BIC score: 83522.635210
Free parameters (model + branch lengths): 1139

WARNING: Number of free parameters (K=1139) is larger than alignment size (n=146).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A6NFY7/3_mltree/A6NFY7.raxml.log

Analysis started: 26-Jul-2021 00:10:20 / finished: 26-Jul-2021 08:28:47

Elapsed time: 29907.190 seconds

Consumed energy: 1022.615 Wh (= 5 km in an electric car, or 26 km with an e-scooter!)