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 30-Jun-2021 17:36:17 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/2_msa/Q92802_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802 --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/Q92802/2_msa/Q92802_trimmed_msa.fasta
[00:00:00] Loaded alignment with 399 taxa and 141 sites

WARNING: Sequences tr_F8VQG7_F8VQG7_MOUSE_10090 and tr_D3ZLS6_D3ZLS6_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q8JZS6_N42L2_MOUSE_10090 and sp_Q66H65_N42L2_RAT_10116 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A2I2ZDL6_A0A2I2ZDL6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A2J8MLL6_A0A2J8MLL6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_G7PVZ6_G7PVZ6_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A096MP45_A0A096MP45_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A0D9RZ93_A0A0D9RZ93_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A2K5ZFZ4_A0A2K5ZFZ4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3GGQ8_A0A2I3GGQ8_NOMLE_61853 and tr_A0A2R9C466_A0A2R9C466_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_G3SH81_G3SH81_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_A0A2J8UTI5_A0A2J8UTI5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_H2Q7E3_H2Q7E3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and sp_Q5TBK1_N42L1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_F6WNV1_F6WNV1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_A0A0D9RZ96_A0A0D9RZ96_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_A0A2K5MNM6_A0A2K5MNM6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_A0A2K6D6J9_A0A2K6D6J9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GY40_A0A2I3GY40_NOMLE_61853 and tr_A0A2R9CB59_A0A2R9CB59_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and tr_A0A2I2Y270_A0A2I2Y270_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and tr_K7DTK3_K7DTK3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and sp_Q86UW6_N4BP2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and tr_A0A096MSH0_A0A096MSH0_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and tr_A0A0D9RWV8_A0A0D9RWV8_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1NW31_G1NW31_MYOLU_59463 and tr_A0A2R9AW01_A0A2R9AW01_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NJK9_H2NJK9_PONAB_9601 and sp_Q92802_N42L2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NJK9_H2NJK9_PONAB_9601 and tr_F7EQT1_F7EQT1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_H2NJK9_H2NJK9_PONAB_9601 and tr_F7HT14_F7HT14_CALJA_9483 are exactly identical!
WARNING: Sequences tr_Q29DM7_Q29DM7_DROPS_46245 and tr_B4H8P3_B4H8P3_DROPE_7234 are exactly identical!
WARNING: Sequences tr_E2R0W6_E2R0W6_CANLF_9615 and tr_W5PMX0_W5PMX0_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_E2R0W6_E2R0W6_CANLF_9615 and tr_A0A287AHP0_A0A287AHP0_PIG_9823 are exactly identical!
WARNING: Sequences tr_E2R0W6_E2R0W6_CANLF_9615 and tr_F1MV44_F1MV44_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_E2R0W6_E2R0W6_CANLF_9615 and tr_A0A2U4BGX1_A0A2U4BGX1_TURTR_9739 are exactly identical!
WARNING: Sequences tr_E2R0W6_E2R0W6_CANLF_9615 and tr_A0A2Y9KRL6_A0A2Y9KRL6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F1Q0X6_F1Q0X6_CANLF_9615 and tr_A0A287AHA0_A0A287AHA0_PIG_9823 are exactly identical!
WARNING: Sequences tr_F1Q0X6_F1Q0X6_CANLF_9615 and tr_A0A3Q0EC86_A0A3Q0EC86_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_W5PN00_W5PN00_SHEEP_9940 and tr_A0A2U4BGI8_A0A2U4BGI8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_W5PN00_W5PN00_SHEEP_9940 and tr_A0A2Y9NLY5_A0A2Y9NLY5_DELLE_9749 are exactly identical!
WARNING: Sequences tr_W5PN00_W5PN00_SHEEP_9940 and tr_A0A2Y9EP12_A0A2Y9EP12_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_W5PSH1_W5PSH1_SHEEP_9940 and tr_E1BIJ5_E1BIJ5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_F7H4P9_F7H4P9_MACMU_9544 and tr_G7P5G3_G7P5G3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7H4P9_F7H4P9_MACMU_9544 and tr_A0A2K6B9X9_A0A2K6B9X9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1LS22_G1LS22_AILME_9646 and tr_A0A337S4U5_A0A337S4U5_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1LS22_G1LS22_AILME_9646 and tr_A0A2U3X1M0_A0A2U3X1M0_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1LS22_G1LS22_AILME_9646 and tr_A0A2U3XC16_A0A2U3XC16_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_G1LSY7_G1LSY7_AILME_9646 and tr_A0A384CXX0_A0A384CXX0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A0W8BVY1_A0A0W8BVY1_PHYNI_4790 and tr_W2LF69_W2LF69_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A091VUQ6_A0A091VUQ6_NIPNI_128390 and tr_A0A087QM74_A0A087QM74_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091VUQ6_A0A091VUQ6_NIPNI_128390 and tr_A0A0A0ANF9_A0A0A0ANF9_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1DHT3_A0A0V1DHT3_TRIBR_45882 and tr_A0A0V1P5U3_A0A0V1P5U3_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0WAM3_A0A0V0WAM3_9BILA_92179 and tr_A0A0V1LU61_A0A0V1LU61_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0WAM3_A0A0V0WAM3_9BILA_92179 and tr_A0A0V0UGX3_A0A0V0UGX3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A2I4AIU2_A0A2I4AIU2_9TELE_52670 and tr_A0A2I4BLT4_A0A2I4BLT4_9TELE_52670 are exactly identical!
WARNING: Sequences tr_A0A226MS31_A0A226MS31_CALSU_9009 and tr_A0A226PMW2_A0A226PMW2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QDC0_A0A2D0QDC0_ICTPU_7998 and tr_A0A2D0QED6_A0A2D0QED6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4ASA8_A0A2U4ASA8_TURTR_9739 and tr_A0A2Y9MQH6_A0A2Y9MQH6_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4ASA8_A0A2U4ASA8_TURTR_9739 and tr_A0A2Y9TGJ3_A0A2Y9TGJ3_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3ZWL8_A0A2U3ZWL8_ODORO_9708 and tr_A0A2U3XCF5_A0A2U3XCF5_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 57

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/Q92802/3_mltree/Q92802.raxml.reduced.phy

Alignment comprises 1 partitions and 141 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 141 / 141
Gaps: 7.86 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.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 399 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 141 / 11280
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -84389.031425] Initial branch length optimization
[00:00:01 -69465.319599] Model parameter optimization (eps = 10.000000)
[00:00:18 -69090.241547] AUTODETECT spr round 1 (radius: 5)
[00:00:44 -49887.992006] AUTODETECT spr round 2 (radius: 10)
[00:01:15 -40044.207012] AUTODETECT spr round 3 (radius: 15)
[00:01:53 -35601.620710] AUTODETECT spr round 4 (radius: 20)
[00:02:44 -34568.966291] AUTODETECT spr round 5 (radius: 25)
[00:03:43 -34399.732182] SPR radius for FAST iterations: 25 (autodetect)
[00:03:43 -34399.732182] Model parameter optimization (eps = 3.000000)
[00:03:52 -34281.788146] FAST spr round 1 (radius: 25)
[00:04:30 -31969.938866] FAST spr round 2 (radius: 25)
[00:05:02 -31824.142401] FAST spr round 3 (radius: 25)
[00:05:31 -31808.951203] FAST spr round 4 (radius: 25)
[00:05:53 -31803.470472] FAST spr round 5 (radius: 25)
[00:06:15 -31800.425148] FAST spr round 6 (radius: 25)
[00:06:36 -31800.421329] Model parameter optimization (eps = 1.000000)
[00:06:43 -31798.818604] SLOW spr round 1 (radius: 5)
[00:07:17 -31785.249476] SLOW spr round 2 (radius: 5)
[00:07:50 -31780.804155] SLOW spr round 3 (radius: 5)
[00:08:22 -31780.066136] SLOW spr round 4 (radius: 5)
[00:08:53 -31780.066114] SLOW spr round 5 (radius: 10)
[00:09:25 -31779.899974] SLOW spr round 6 (radius: 5)
[00:10:05 -31779.897408] SLOW spr round 7 (radius: 10)
[00:10:42 -31779.897264] SLOW spr round 8 (radius: 15)
[00:11:30 -31779.649394] SLOW spr round 9 (radius: 5)
[00:12:12 -31779.648966] SLOW spr round 10 (radius: 10)
[00:12:51 -31779.648945] SLOW spr round 11 (radius: 15)
[00:13:39 -31779.648936] SLOW spr round 12 (radius: 20)
[00:15:00 -31779.648930] SLOW spr round 13 (radius: 25)
[00:15:12] [worker #1] ML tree search #2, logLikelihood: -31802.610678
[00:16:18] [worker #2] ML tree search #3, logLikelihood: -31787.575615
[00:16:31 -31779.648924] Model parameter optimization (eps = 0.100000)

[00:16:36] [worker #0] ML tree search #1, logLikelihood: -31779.375584

[00:16:36 -82961.895419] Initial branch length optimization
[00:16:37 -67156.718174] Model parameter optimization (eps = 10.000000)
[00:16:55 -66857.650650] AUTODETECT spr round 1 (radius: 5)
[00:17:21 -49343.598604] AUTODETECT spr round 2 (radius: 10)
[00:17:51 -42567.753916] AUTODETECT spr round 3 (radius: 15)
[00:18:29 -37556.891835] AUTODETECT spr round 4 (radius: 20)
[00:19:25 -34878.858049] AUTODETECT spr round 5 (radius: 25)
[00:20:32 -34267.256413] SPR radius for FAST iterations: 25 (autodetect)
[00:20:32 -34267.256413] Model parameter optimization (eps = 3.000000)
[00:20:45 -34151.803747] FAST spr round 1 (radius: 25)
[00:21:21 -32027.661185] FAST spr round 2 (radius: 25)
[00:21:48 -31842.635308] FAST spr round 3 (radius: 25)
[00:22:15 -31829.834412] FAST spr round 4 (radius: 25)
[00:22:38 -31825.495337] FAST spr round 5 (radius: 25)
[00:23:01 -31822.015798] FAST spr round 6 (radius: 25)
[00:23:23 -31822.015718] Model parameter optimization (eps = 1.000000)
[00:23:26 -31821.518766] SLOW spr round 1 (radius: 5)
[00:24:00 -31815.499411] SLOW spr round 2 (radius: 5)
[00:24:34 -31815.388693] SLOW spr round 3 (radius: 5)
[00:25:07 -31815.388645] SLOW spr round 4 (radius: 10)
[00:25:40 -31809.904949] SLOW spr round 5 (radius: 5)
[00:26:22 -31805.559529] SLOW spr round 6 (radius: 5)
[00:26:57 -31805.557442] SLOW spr round 7 (radius: 10)
[00:27:31 -31804.686514] SLOW spr round 8 (radius: 5)
[00:28:13 -31799.998079] SLOW spr round 9 (radius: 5)
[00:28:48 -31799.997579] SLOW spr round 10 (radius: 10)
[00:29:22 -31799.480683] SLOW spr round 11 (radius: 5)
[00:30:01 -31799.480661] SLOW spr round 12 (radius: 10)
[00:30:14] [worker #1] ML tree search #5, logLikelihood: -31775.512030
[00:30:37 -31799.480649] SLOW spr round 13 (radius: 15)
[00:31:25 -31799.480638] SLOW spr round 14 (radius: 20)
[00:32:41 -31799.480626] SLOW spr round 15 (radius: 25)
[00:34:11 -31799.480614] Model parameter optimization (eps = 0.100000)

[00:34:14] [worker #0] ML tree search #4, logLikelihood: -31799.421216

[00:34:14 -82897.547596] Initial branch length optimization
[00:34:15 -68300.758002] Model parameter optimization (eps = 10.000000)
[00:34:36 -67916.362495] AUTODETECT spr round 1 (radius: 5)
[00:35:02 -49369.503252] AUTODETECT spr round 2 (radius: 10)
[00:35:33 -38425.974469] AUTODETECT spr round 3 (radius: 15)
[00:36:14 -34941.944199] AUTODETECT spr round 4 (radius: 20)
[00:37:00 -34520.801902] AUTODETECT spr round 5 (radius: 25)
[00:37:48 -34395.886941] SPR radius for FAST iterations: 25 (autodetect)
[00:37:48 -34395.886941] Model parameter optimization (eps = 3.000000)
[00:38:00 -34268.981712] FAST spr round 1 (radius: 25)
[00:38:35 -32189.724808] FAST spr round 2 (radius: 25)
[00:39:04 -31837.994261] FAST spr round 3 (radius: 25)
[00:39:31 -31802.625835] FAST spr round 4 (radius: 25)
[00:39:53 -31801.835788] FAST spr round 5 (radius: 25)
[00:40:14 -31801.835564] Model parameter optimization (eps = 1.000000)
[00:40:22 -31799.936190] SLOW spr round 1 (radius: 5)
[00:40:56 -31791.008532] SLOW spr round 2 (radius: 5)
[00:41:29 -31788.749039] SLOW spr round 3 (radius: 5)
[00:42:01 -31786.361344] SLOW spr round 4 (radius: 5)
[00:42:34 -31785.471848] SLOW spr round 5 (radius: 5)
[00:43:06 -31784.347592] SLOW spr round 6 (radius: 5)
[00:43:37 -31784.346365] SLOW spr round 7 (radius: 10)
[00:43:40] [worker #2] ML tree search #6, logLikelihood: -31791.271013
[00:44:09 -31783.972772] SLOW spr round 8 (radius: 5)
[00:44:19] [worker #1] ML tree search #8, logLikelihood: -31788.098488
[00:44:50 -31783.972469] SLOW spr round 9 (radius: 10)
[00:45:28 -31780.276011] SLOW spr round 10 (radius: 5)
[00:46:07 -31779.217025] SLOW spr round 11 (radius: 5)
[00:46:41 -31779.216997] SLOW spr round 12 (radius: 10)
[00:47:16 -31779.216983] SLOW spr round 13 (radius: 15)
[00:48:09 -31776.699277] SLOW spr round 14 (radius: 5)
[00:48:52 -31776.266254] SLOW spr round 15 (radius: 5)
[00:49:29 -31776.265527] SLOW spr round 16 (radius: 10)
[00:50:06 -31775.895767] SLOW spr round 17 (radius: 5)
[00:50:45 -31775.893366] SLOW spr round 18 (radius: 10)
[00:51:22 -31775.893029] SLOW spr round 19 (radius: 15)
[00:52:15 -31775.765796] SLOW spr round 20 (radius: 5)
[00:52:58 -31775.142513] SLOW spr round 21 (radius: 5)
[00:53:35 -31775.142171] SLOW spr round 22 (radius: 10)
[00:54:10 -31775.142154] SLOW spr round 23 (radius: 15)
[00:55:02 -31775.142144] SLOW spr round 24 (radius: 20)
[00:56:27 -31775.142135] SLOW spr round 25 (radius: 25)
[00:57:58 -31775.142127] Model parameter optimization (eps = 0.100000)

[00:58:01] [worker #0] ML tree search #7, logLikelihood: -31775.061443

[00:58:01 -83524.188198] Initial branch length optimization
[00:58:02 -68618.024189] Model parameter optimization (eps = 10.000000)
[00:58:16 -68300.359876] AUTODETECT spr round 1 (radius: 5)
[00:58:43 -50453.951760] AUTODETECT spr round 2 (radius: 10)
[00:59:14 -42153.348373] AUTODETECT spr round 3 (radius: 15)
[00:59:55 -36315.201848] AUTODETECT spr round 4 (radius: 20)
[01:00:50 -34648.149481] AUTODETECT spr round 5 (radius: 25)
[01:00:55] [worker #1] ML tree search #11, logLikelihood: -31786.124994
[01:01:45 -34621.827037] SPR radius for FAST iterations: 25 (autodetect)
[01:01:45 -34621.827037] Model parameter optimization (eps = 3.000000)
[01:01:55 -34528.639880] FAST spr round 1 (radius: 25)
[01:02:33 -32000.305189] FAST spr round 2 (radius: 25)
[01:03:03 -31827.733140] FAST spr round 3 (radius: 25)
[01:03:30 -31794.798744] FAST spr round 4 (radius: 25)
[01:03:56 -31786.023018] FAST spr round 5 (radius: 25)
[01:04:19 -31782.840528] FAST spr round 6 (radius: 25)
[01:04:40 -31782.696444] FAST spr round 7 (radius: 25)
[01:05:02 -31782.693530] Model parameter optimization (eps = 1.000000)
[01:05:08 -31781.273653] SLOW spr round 1 (radius: 5)
[01:05:42 -31778.998609] SLOW spr round 2 (radius: 5)
[01:06:03] [worker #2] ML tree search #9, logLikelihood: -31782.137566
[01:06:17 -31777.719426] SLOW spr round 3 (radius: 5)
[01:06:48 -31777.716187] SLOW spr round 4 (radius: 10)
[01:07:21 -31777.306096] SLOW spr round 5 (radius: 5)
[01:08:00 -31777.305640] SLOW spr round 6 (radius: 10)
[01:08:36 -31777.305430] SLOW spr round 7 (radius: 15)
[01:09:24 -31777.305326] SLOW spr round 8 (radius: 20)
[01:10:39 -31777.305271] SLOW spr round 9 (radius: 25)
[01:12:08 -31777.305240] Model parameter optimization (eps = 0.100000)

[01:12:11] [worker #0] ML tree search #10, logLikelihood: -31777.208335

[01:12:11 -83491.931405] Initial branch length optimization
[01:12:13 -68394.840188] Model parameter optimization (eps = 10.000000)
[01:12:28 -68094.746883] AUTODETECT spr round 1 (radius: 5)
[01:12:54 -49139.164613] AUTODETECT spr round 2 (radius: 10)
[01:13:25 -38940.657661] AUTODETECT spr round 3 (radius: 15)
[01:14:02 -35644.257542] AUTODETECT spr round 4 (radius: 20)
[01:14:55 -34894.062043] AUTODETECT spr round 5 (radius: 25)
[01:15:53 -34474.235283] SPR radius for FAST iterations: 25 (autodetect)
[01:15:53 -34474.235283] Model parameter optimization (eps = 3.000000)
[01:16:06 -34349.855534] FAST spr round 1 (radius: 25)
[01:16:42 -32014.504048] FAST spr round 2 (radius: 25)
[01:17:11 -31833.018901] FAST spr round 3 (radius: 25)
[01:17:38 -31816.850842] FAST spr round 4 (radius: 25)
[01:18:01 -31810.820562] FAST spr round 5 (radius: 25)
[01:18:25 -31797.069812] FAST spr round 6 (radius: 25)
[01:18:48 -31795.532399] FAST spr round 7 (radius: 25)
[01:19:10 -31795.525180] Model parameter optimization (eps = 1.000000)
[01:19:17 -31793.649056] SLOW spr round 1 (radius: 5)
[01:19:51 -31785.674939] SLOW spr round 2 (radius: 5)
[01:20:25 -31783.229275] SLOW spr round 3 (radius: 5)
[01:20:58 -31783.228430] SLOW spr round 4 (radius: 10)
[01:21:31 -31782.861087] SLOW spr round 5 (radius: 5)
[01:22:11 -31782.860925] SLOW spr round 6 (radius: 10)
[01:22:48 -31782.860839] SLOW spr round 7 (radius: 15)
[01:23:34 -31782.584615] SLOW spr round 8 (radius: 5)
[01:24:18 -31782.361975] SLOW spr round 9 (radius: 5)
[01:24:55 -31782.360603] SLOW spr round 10 (radius: 10)
[01:25:13] [worker #2] ML tree search #12, logLikelihood: -31780.892717
[01:25:30 -31782.360412] SLOW spr round 11 (radius: 15)
[01:25:37] [worker #1] ML tree search #14, logLikelihood: -31777.547193
[01:26:17 -31782.360364] SLOW spr round 12 (radius: 20)
[01:27:28 -31782.360342] SLOW spr round 13 (radius: 25)
[01:28:51 -31782.360328] Model parameter optimization (eps = 0.100000)

[01:28:55] [worker #0] ML tree search #13, logLikelihood: -31782.202983

[01:28:55 -83972.070222] Initial branch length optimization
[01:28:56 -68614.482864] Model parameter optimization (eps = 10.000000)
[01:29:09 -68307.048311] AUTODETECT spr round 1 (radius: 5)
[01:29:35 -49385.361543] AUTODETECT spr round 2 (radius: 10)
[01:30:04 -41293.045400] AUTODETECT spr round 3 (radius: 15)
[01:30:40 -35237.485216] AUTODETECT spr round 4 (radius: 20)
[01:31:27 -34721.841728] AUTODETECT spr round 5 (radius: 25)
[01:32:26 -34706.704203] SPR radius for FAST iterations: 25 (autodetect)
[01:32:26 -34706.704203] Model parameter optimization (eps = 3.000000)
[01:32:39 -34613.250572] FAST spr round 1 (radius: 25)
[01:33:14 -31947.376899] FAST spr round 2 (radius: 25)
[01:33:43 -31818.162330] FAST spr round 3 (radius: 25)
[01:34:07 -31811.847402] FAST spr round 4 (radius: 25)
[01:34:31 -31809.219556] FAST spr round 5 (radius: 25)
[01:34:53 -31808.006883] FAST spr round 6 (radius: 25)
[01:35:14 -31808.006803] Model parameter optimization (eps = 1.000000)
[01:35:20 -31806.203691] SLOW spr round 1 (radius: 5)
[01:35:54 -31798.621932] SLOW spr round 2 (radius: 5)
[01:36:27 -31798.620986] SLOW spr round 3 (radius: 10)
[01:37:00 -31798.620829] SLOW spr round 4 (radius: 15)
[01:37:51 -31797.452608] SLOW spr round 5 (radius: 5)
[01:38:12] [worker #1] ML tree search #17, logLikelihood: -31801.579377
[01:38:34 -31797.452589] SLOW spr round 6 (radius: 10)
[01:39:15 -31794.623139] SLOW spr round 7 (radius: 5)
[01:39:54 -31793.567329] SLOW spr round 8 (radius: 5)
[01:40:29 -31793.565292] SLOW spr round 9 (radius: 10)
[01:41:03 -31793.565290] SLOW spr round 10 (radius: 15)
[01:41:13] [worker #2] ML tree search #15, logLikelihood: -31785.649551
[01:41:52 -31793.443325] SLOW spr round 11 (radius: 5)
[01:42:36 -31792.499115] SLOW spr round 12 (radius: 5)
[01:43:12 -31792.496585] SLOW spr round 13 (radius: 10)
[01:43:47 -31792.495955] SLOW spr round 14 (radius: 15)
[01:44:35 -31792.495760] SLOW spr round 15 (radius: 20)
[01:45:50 -31792.495690] SLOW spr round 16 (radius: 25)
[01:47:18 -31792.495662] Model parameter optimization (eps = 0.100000)

[01:47:21] [worker #0] ML tree search #16, logLikelihood: -31792.441933

[01:47:21 -84348.848911] Initial branch length optimization
[01:47:22 -69317.523290] Model parameter optimization (eps = 10.000000)
[01:47:37 -69003.859329] AUTODETECT spr round 1 (radius: 5)
[01:48:03 -50485.894915] AUTODETECT spr round 2 (radius: 10)
[01:48:33 -40929.997491] AUTODETECT spr round 3 (radius: 15)
[01:49:09 -36171.988321] AUTODETECT spr round 4 (radius: 20)
[01:50:00 -34457.947264] AUTODETECT spr round 5 (radius: 25)
[01:50:51 -34433.560789] SPR radius for FAST iterations: 25 (autodetect)
[01:50:51 -34433.560789] Model parameter optimization (eps = 3.000000)
[01:51:03 -34352.173634] FAST spr round 1 (radius: 25)
[01:51:42 -32018.396240] FAST spr round 2 (radius: 25)
[01:52:14 -31846.757372] FAST spr round 3 (radius: 25)
[01:52:41 -31827.828215] FAST spr round 4 (radius: 25)
[01:53:03 -31822.002444] FAST spr round 5 (radius: 25)
[01:53:25 -31822.001557] Model parameter optimization (eps = 1.000000)
[01:53:32 -31812.680399] SLOW spr round 1 (radius: 5)
[01:53:41] [worker #2] ML tree search #18, logLikelihood: -31792.814550
[01:54:07 -31798.889844] SLOW spr round 2 (radius: 5)
[01:54:40 -31795.306783] SLOW spr round 3 (radius: 5)
[01:55:14 -31794.574288] SLOW spr round 4 (radius: 5)
[01:55:47 -31791.494024] SLOW spr round 5 (radius: 5)
[01:56:19 -31791.182989] SLOW spr round 6 (radius: 5)
[01:56:50 -31791.182405] SLOW spr round 7 (radius: 10)
[01:57:21 -31791.182335] SLOW spr round 8 (radius: 15)
[01:58:09 -31789.248507] SLOW spr round 9 (radius: 5)
[01:58:51 -31789.247407] SLOW spr round 10 (radius: 10)
[01:59:29 -31789.009821] SLOW spr round 11 (radius: 5)
[01:59:39] [worker #1] ML tree search #20, logLikelihood: -31781.434456
[02:00:09 -31789.008402] SLOW spr round 12 (radius: 10)
[02:00:43 -31789.008229] SLOW spr round 13 (radius: 15)
[02:01:28 -31789.008182] SLOW spr round 14 (radius: 20)
[02:02:43 -31789.008148] SLOW spr round 15 (radius: 25)
[02:04:13 -31788.699476] SLOW spr round 16 (radius: 5)
[02:04:57 -31788.699465] SLOW spr round 17 (radius: 10)
[02:05:36 -31788.699458] SLOW spr round 18 (radius: 15)
[02:06:21 -31786.445002] SLOW spr round 19 (radius: 5)
[02:07:04 -31785.329327] SLOW spr round 20 (radius: 5)
[02:07:40 -31785.328970] SLOW spr round 21 (radius: 10)
[02:08:13 -31785.328946] SLOW spr round 22 (radius: 15)
[02:08:58 -31785.328938] SLOW spr round 23 (radius: 20)
[02:10:12 -31785.328931] SLOW spr round 24 (radius: 25)
[02:11:42 -31785.328924] Model parameter optimization (eps = 0.100000)

[02:11:47] [worker #0] ML tree search #19, logLikelihood: -31785.206648


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.226707,0.423254) (0.219870,0.505517) (0.302696,1.044086) (0.250727,1.901898) 
   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: -31775.061443

AIC score: 65152.122886 / AICc score: 1349956.122886 / BIC score: 67514.079558
Free parameters (model + branch lengths): 801

WARNING: Number of free parameters (K=801) is larger than alignment size (n=141).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 93 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92802/3_mltree/Q92802.raxml.log

Analysis started: 30-Jun-2021 17:36:17 / finished: 30-Jun-2021 19:48:05

Elapsed time: 7907.969 seconds

Consumed energy: 757.724 Wh (= 4 km in an electric car, or 19 km with an e-scooter!)