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 05-Jul-2021 13:47:47 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/2_msa/O60812_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/2_msa/O60812_trimmed_msa.fasta
[00:00:00] Loaded alignment with 702 taxa and 220 sites

WARNING: Sequences tr_B4QKF1_B4QKF1_DROSI_7240 and tr_B4HV72_B4HV72_DROSE_7238 are exactly identical!
WARNING: Sequences sp_Q9Z204_HNRPC_MOUSE_10090 and tr_G3HWP9_G3HWP9_CRIGR_10029 are exactly identical!
WARNING: Sequences sp_Q9Z204_HNRPC_MOUSE_10090 and tr_A0A1U8D1D9_A0A1U8D1D9_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_Q3SX47_Q3SX47_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_L5K6X3_L5K6X3_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_M3WLJ6_M3WLJ6_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_A0A2U3W2H8_A0A2U3W2H8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_A0A2U3XJA6_A0A2U3XJA6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_A0A2Y9QN19_A0A2Y9QN19_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_A0A2Y9K3C1_A0A2Y9K3C1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XM61_M3XM61_MUSPF_9669 and tr_A0A384DRF0_A0A384DRF0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_J3KK95_J3KK95_COCIM_246410 and tr_A0A0J6Y013_A0A0J6Y013_COCIT_404692 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2I3SDH2_A0A2I3SDH2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and sp_Q86SE5_RALYL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2I3MLH1_A0A2I3MLH1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2K5NN80_A0A2K5NN80_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2K6C597_A0A2K6C597_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2K5ZKA0_A0A2K5ZKA0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Z435_A0A2I2Z435_GORGO_9595 and tr_A0A2R9BYG3_A0A2R9BYG3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and sp_Q5RA82_HNRPC_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and tr_A0A2I3SF05_A0A2I3SF05_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and sp_P07910_HNRPC_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and tr_U3DFP3_U3DFP3_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and tr_A0A0D9RVK4_A0A0D9RVK4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAL3_A0A2I2ZAL3_GORGO_9595 and tr_A0A2K5ZY30_A0A2K5ZY30_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3S2S1_G3S2S1_GORGO_9595 and tr_H2P1P5_H2P1P5_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3S2S1_G3S2S1_GORGO_9595 and tr_H2R916_H2R916_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3S2S1_G3S2S1_GORGO_9595 and tr_A0A2R9B3Y0_A0A2R9B3Y0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A179UED3_A0A179UED3_BLAGS_559298 and tr_A0A179TXC1_A0A179TXC1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_E2RLQ4_E2RLQ4_CANLF_9615 and tr_G3T3J4_G3T3J4_LOXAF_9785 are exactly identical!
WARNING: Sequences tr_E2RLQ4_E2RLQ4_CANLF_9615 and tr_G1LIT5_G1LIT5_AILME_9646 are exactly identical!
WARNING: Sequences tr_F6SNV2_F6SNV2_HORSE_9796 and tr_I3LK71_I3LK71_PIG_9823 are exactly identical!
WARNING: Sequences tr_F6SNV2_F6SNV2_HORSE_9796 and tr_A0A2Y9S9W7_A0A2Y9S9W7_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A158NFN6_A0A158NFN6_ATTCE_12957 and tr_A0A195AXI4_A0A195AXI4_9HYME_520822 are exactly identical!
WARNING: Sequences tr_H0UWA3_H0UWA3_CAVPO_10141 and tr_A0A091DXM3_A0A091DXM3_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_A0A0G2JPF8_A0A0G2JPF8_HUMAN_9606 and sp_B7ZW38_HNRC3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A0G2JPF8_A0A0G2JPF8_HUMAN_9606 and sp_P0DMR1_HNRC4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6ZHY1_F6ZHY1_MACMU_9544 and tr_A0A2I3MSZ3_A0A2I3MSZ3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6ZHY1_F6ZHY1_MACMU_9544 and tr_A0A2I3NI48_A0A2I3NI48_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7EG42_F7EG42_MACMU_9544 and tr_G7PGK5_G7PGK5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7EG42_F7EG42_MACMU_9544 and tr_A0A2K6E9N6_A0A2K6E9N6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_I1NWQ8_I1NWQ8_ORYGL_4538 and tr_Q6Z725_Q6Z725_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4WEI0_F4WEI0_ACREC_103372 and tr_N6TQV6_N6TQV6_DENPD_77166 are exactly identical!
WARNING: Sequences tr_F4WEI0_F4WEI0_ACREC_103372 and tr_A0A195E834_A0A195E834_9HYME_471704 are exactly identical!
WARNING: Sequences tr_G1LR44_G1LR44_AILME_9646 and tr_A0A384D3P5_A0A384D3P5_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M7ZKS9_M7ZKS9_TRIUA_4572 and tr_A0A3B6KVD5_A0A3B6KVD5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A096NUT9_A0A096NUT9_PAPAN_9555 and tr_A0A2K5LRM1_A0A2K5LRM1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NUT9_A0A096NUT9_PAPAN_9555 and tr_A0A2K5Y1L5_A0A2K5Y1L5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A094DUA0_A0A094DUA0_9PEZI_1420912 and tr_A0A1B8GFR6_A0A1B8GFR6_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A151NZM1_A0A151NZM1_ALLMI_8496 and tr_A0A3Q0H7W1_A0A3Q0H7W1_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0R3RL82_A0A0R3RL82_9BILA_1147741 and tr_A0A1I7VMJ2_A0A1I7VMJ2_LOALO_7209 are exactly identical!
WARNING: Sequences tr_A0A091EGX9_A0A091EGX9_CORBR_85066 and tr_A0A093QA29_A0A093QA29_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091EGX9_A0A091EGX9_CORBR_85066 and tr_A0A087QVT0_A0A087QVT0_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091EGX9_A0A091EGX9_CORBR_85066 and tr_A0A093I864_A0A093I864_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_A0A091JP71_A0A091JP71_EGRGA_188379 and tr_A0A091UNS0_A0A091UNS0_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JP71_A0A091JP71_EGRGA_188379 and tr_A0A091G0J5_A0A091G0J5_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A091JP71_A0A091JP71_EGRGA_188379 and tr_A0A0A0AXV0_A0A0A0AXV0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091WZ78_A0A091WZ78_NIPNI_128390 and tr_A0A087RB75_A0A087RB75_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A1S3KGA3_A0A1S3KGA3_LINUN_7574 and tr_A0A1S3KHH1_A0A1S3KHH1_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3N973_A0A1S3N973_SALSA_8030 and tr_B5X3G1_B5X3G1_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3N973_A0A1S3N973_SALSA_8030 and tr_A0A060XEV9_A0A060XEV9_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1S3P7T0_A0A1S3P7T0_SALSA_8030 and tr_B5X1C7_B5X1C7_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A226MUK0_A0A226MUK0_CALSU_9009 and tr_A0A226PNC8_A0A226PNC8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QEP9_A0A2D0QEP9_ICTPU_7998 and tr_A0A2D0QH61_A0A2D0QH61_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2I1GMZ6_A0A2I1GMZ6_9GLOM_588596 and tr_A0A2H5RI54_A0A2H5RI54_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2U3V591_A0A2U3V591_TURTR_9739 and tr_A0A2U3V5A4_A0A2U3V5A4_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U3V591_A0A2U3V591_TURTR_9739 and tr_A0A2U4BBZ0_A0A2U4BBZ0_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U3V591_A0A2U3V591_TURTR_9739 and tr_A0A2U4BC22_A0A2U4BC22_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U3V591_A0A2U3V591_TURTR_9739 and tr_A0A2Y9PBF3_A0A2Y9PBF3_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U3VGQ8_A0A2U3VGQ8_ODORO_9708 and tr_A0A2U3X6W2_A0A2U3X6W2_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9RQT9_A0A2Y9RQT9_TRIMA_127582 and tr_A0A383ZYL1_A0A383ZYL1_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 71

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/O60812/3_mltree/O60812.raxml.reduced.phy

Alignment comprises 1 partitions and 220 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 220 / 220
Gaps: 18.78 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.rba

Parallelization scheme autoconfig: 4 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 702 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 220 / 17600
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -226938.929894] Initial branch length optimization
[00:00:06 -179264.781179] Model parameter optimization (eps = 10.000000)
[00:00:42 -178043.714440] AUTODETECT spr round 1 (radius: 5)
[00:02:18 -137269.491267] AUTODETECT spr round 2 (radius: 10)
[00:04:10 -107733.721286] AUTODETECT spr round 3 (radius: 15)
[00:06:14 -86532.782117] AUTODETECT spr round 4 (radius: 20)
[00:08:39 -77734.690828] AUTODETECT spr round 5 (radius: 25)
[00:11:03 -76677.628351] SPR radius for FAST iterations: 25 (autodetect)
[00:11:03 -76677.628351] Model parameter optimization (eps = 3.000000)
[00:11:36 -76119.512496] FAST spr round 1 (radius: 25)
[00:13:59 -67887.234998] FAST spr round 2 (radius: 25)
[00:15:55 -65888.478364] FAST spr round 3 (radius: 25)
[00:17:36 -64999.963773] FAST spr round 4 (radius: 25)
[00:19:02 -64885.374224] FAST spr round 5 (radius: 25)
[00:20:21 -64873.697814] FAST spr round 6 (radius: 25)
[00:21:37 -64873.115487] FAST spr round 7 (radius: 25)
[00:22:51 -64871.040299] FAST spr round 8 (radius: 25)
[00:24:03 -64871.040226] Model parameter optimization (eps = 1.000000)
[00:24:17 -64859.966318] SLOW spr round 1 (radius: 5)
[00:25:58 -64848.311952] SLOW spr round 2 (radius: 5)
[00:27:35 -64847.922020] SLOW spr round 3 (radius: 5)
[00:29:10 -64846.851405] SLOW spr round 4 (radius: 5)
[00:30:43 -64846.851081] SLOW spr round 5 (radius: 10)
[00:32:27 -64845.753076] SLOW spr round 6 (radius: 5)
[00:34:27 -64845.751073] SLOW spr round 7 (radius: 10)
[00:36:27 -64845.750981] SLOW spr round 8 (radius: 15)
[00:39:25 -64845.164470] SLOW spr round 9 (radius: 5)
[00:41:30 -64845.163965] SLOW spr round 10 (radius: 10)
[00:43:37 -64845.163933] SLOW spr round 11 (radius: 15)
[00:45:21] [worker #3] ML tree search #4, logLikelihood: -64835.566258
[00:46:31 -64844.903035] SLOW spr round 12 (radius: 5)
[00:48:36 -64844.902992] SLOW spr round 13 (radius: 10)
[00:50:43 -64844.902991] SLOW spr round 14 (radius: 15)
[00:53:38 -64843.003558] SLOW spr round 15 (radius: 5)
[00:55:03] [worker #2] ML tree search #3, logLikelihood: -65816.255516
[00:55:43 -64843.003541] SLOW spr round 16 (radius: 10)
[00:57:49 -64842.687133] SLOW spr round 17 (radius: 5)
[00:59:46 -64842.172857] SLOW spr round 18 (radius: 5)
[01:01:30 -64842.172339] SLOW spr round 19 (radius: 10)
[01:03:18 -64842.172286] SLOW spr round 20 (radius: 15)
[01:06:11 -64842.172279] SLOW spr round 21 (radius: 20)
[01:06:57] [worker #1] ML tree search #2, logLikelihood: -64852.521419
[01:09:59 -64842.172277] SLOW spr round 22 (radius: 25)
[01:14:44 -64840.258240] SLOW spr round 23 (radius: 5)
[01:16:57 -64840.256486] SLOW spr round 24 (radius: 10)
[01:19:09 -64840.256453] SLOW spr round 25 (radius: 15)
[01:21:57 -64840.256452] SLOW spr round 26 (radius: 20)
[01:25:54 -64840.256451] SLOW spr round 27 (radius: 25)
[01:30:46 -64840.256450] Model parameter optimization (eps = 0.100000)

[01:30:52] [worker #0] ML tree search #1, logLikelihood: -64840.179363

[01:30:52 -225470.556127] Initial branch length optimization
[01:30:56 -178748.419566] Model parameter optimization (eps = 10.000000)
[01:31:46 -177480.890877] AUTODETECT spr round 1 (radius: 5)
[01:33:22 -139381.220194] AUTODETECT spr round 2 (radius: 10)
[01:35:17 -110260.766780] AUTODETECT spr round 3 (radius: 15)
[01:37:21 -89185.350638] AUTODETECT spr round 4 (radius: 20)
[01:39:51 -78455.439303] AUTODETECT spr round 5 (radius: 25)
[01:42:26 -76110.990054] SPR radius for FAST iterations: 25 (autodetect)
[01:42:26 -76110.990054] Model parameter optimization (eps = 3.000000)
[01:42:55 -75586.258270] FAST spr round 1 (radius: 25)
[01:45:13 -65334.638564] FAST spr round 2 (radius: 25)
[01:46:52 -64943.814363] FAST spr round 3 (radius: 25)
[01:48:19 -64892.187208] FAST spr round 4 (radius: 25)
[01:49:37 -64891.053105] FAST spr round 5 (radius: 25)
[01:50:52 -64891.052040] Model parameter optimization (eps = 1.000000)
[01:51:08 -64871.120194] SLOW spr round 1 (radius: 5)
[01:52:51 -64853.500737] SLOW spr round 2 (radius: 5)
[01:53:46] [worker #2] ML tree search #7, logLikelihood: -64855.004141
[01:54:31 -64847.023183] SLOW spr round 3 (radius: 5)
[01:56:08 -64846.162506] SLOW spr round 4 (radius: 5)
[01:57:41 -64842.992458] SLOW spr round 5 (radius: 5)
[01:59:13 -64842.992355] SLOW spr round 6 (radius: 10)
[02:00:56 -64840.696178] SLOW spr round 7 (radius: 5)
[02:03:01 -64835.895291] SLOW spr round 8 (radius: 5)
[02:04:47 -64835.823273] SLOW spr round 9 (radius: 10)
[02:06:34 -64835.823255] SLOW spr round 10 (radius: 15)
[02:09:25 -64835.122983] SLOW spr round 11 (radius: 5)
[02:11:33 -64835.117100] SLOW spr round 12 (radius: 10)
[02:13:37 -64835.116623] SLOW spr round 13 (radius: 15)
[02:14:22] [worker #3] ML tree search #8, logLikelihood: -64945.902174
[02:16:24 -64834.241564] SLOW spr round 14 (radius: 5)
[02:18:34 -64832.513561] SLOW spr round 15 (radius: 5)
[02:20:25 -64832.513493] SLOW spr round 16 (radius: 10)
[02:22:14 -64832.513489] SLOW spr round 17 (radius: 15)
[02:25:05 -64832.513485] SLOW spr round 18 (radius: 20)
[02:28:59 -64832.363374] SLOW spr round 19 (radius: 5)
[02:31:08 -64832.363295] SLOW spr round 20 (radius: 10)
[02:33:18 -64832.363290] SLOW spr round 21 (radius: 15)
[02:36:03 -64832.363287] SLOW spr round 22 (radius: 20)
[02:39:59 -64832.363278] SLOW spr round 23 (radius: 25)
[02:44:32 -64832.251675] SLOW spr round 24 (radius: 5)
[02:45:59] [worker #1] ML tree search #6, logLikelihood: -64844.536740
[02:46:45 -64831.958291] SLOW spr round 25 (radius: 5)
[02:48:39 -64831.958057] SLOW spr round 26 (radius: 10)
[02:50:32 -64831.958051] SLOW spr round 27 (radius: 15)
[02:53:20 -64831.958048] SLOW spr round 28 (radius: 20)
[02:57:13 -64831.958045] SLOW spr round 29 (radius: 25)
[03:01:48 -64831.958042] Model parameter optimization (eps = 0.100000)

[03:01:56] [worker #0] ML tree search #5, logLikelihood: -64831.777144

[03:01:56 -228725.441249] Initial branch length optimization
[03:02:00 -181167.826064] Model parameter optimization (eps = 10.000000)
[03:02:36 -179932.210701] AUTODETECT spr round 1 (radius: 5)
[03:03:57] [worker #3] ML tree search #12, logLikelihood: -64910.350211
[03:04:11 -135612.646561] AUTODETECT spr round 2 (radius: 10)
[03:05:10] [worker #2] ML tree search #11, logLikelihood: -64845.489031
[03:06:01 -107159.782595] AUTODETECT spr round 3 (radius: 15)
[03:08:00 -87374.920514] AUTODETECT spr round 4 (radius: 20)
[03:10:25 -79057.131003] AUTODETECT spr round 5 (radius: 25)
[03:13:22 -76813.564572] SPR radius for FAST iterations: 25 (autodetect)
[03:13:22 -76813.564572] Model parameter optimization (eps = 3.000000)
[03:13:55 -76262.468301] FAST spr round 1 (radius: 25)
[03:16:01 -66231.827996] FAST spr round 2 (radius: 25)
[03:17:33 -65014.660693] FAST spr round 3 (radius: 25)
[03:18:53 -64894.676910] FAST spr round 4 (radius: 25)
[03:20:07 -64887.657616] FAST spr round 5 (radius: 25)
[03:21:15 -64887.656614] Model parameter optimization (eps = 1.000000)
[03:21:30 -64883.621570] SLOW spr round 1 (radius: 5)
[03:23:06 -64855.438166] SLOW spr round 2 (radius: 5)
[03:24:38 -64848.336748] SLOW spr round 3 (radius: 5)
[03:26:04 -64848.336429] SLOW spr round 4 (radius: 10)
[03:27:37 -64847.191099] SLOW spr round 5 (radius: 5)
[03:29:31 -64846.420651] SLOW spr round 6 (radius: 5)
[03:31:08 -64846.420625] SLOW spr round 7 (radius: 10)
[03:32:45 -64846.420618] SLOW spr round 8 (radius: 15)
[03:35:24 -64844.707224] SLOW spr round 9 (radius: 5)
[03:37:20 -64841.817007] SLOW spr round 10 (radius: 5)
[03:39:04 -64839.727839] SLOW spr round 11 (radius: 5)
[03:40:34 -64839.727837] SLOW spr round 12 (radius: 10)
[03:42:09 -64839.727837] SLOW spr round 13 (radius: 15)
[03:44:47 -64839.727836] SLOW spr round 14 (radius: 20)
[03:48:16 -64838.506790] SLOW spr round 15 (radius: 5)
[03:50:13 -64838.506786] SLOW spr round 16 (radius: 10)
[03:52:07 -64838.506785] SLOW spr round 17 (radius: 15)
[03:54:37 -64838.506785] SLOW spr round 18 (radius: 20)
[03:58:08 -64838.506785] SLOW spr round 19 (radius: 25)
[04:00:30] [worker #2] ML tree search #15, logLikelihood: -65476.947868
[04:01:50] [worker #1] ML tree search #10, logLikelihood: -64842.124736
[04:02:09 -64838.506784] Model parameter optimization (eps = 0.100000)

[04:02:13] [worker #0] ML tree search #9, logLikelihood: -64838.477963

[04:02:14 -228527.314721] Initial branch length optimization
[04:02:17 -181048.171715] Model parameter optimization (eps = 10.000000)
[04:03:18 -179388.110076] AUTODETECT spr round 1 (radius: 5)
[04:04:28] [worker #3] ML tree search #16, logLikelihood: -64826.986194
[04:04:46 -137182.893152] AUTODETECT spr round 2 (radius: 10)
[04:06:31 -107125.558671] AUTODETECT spr round 3 (radius: 15)
[04:08:25 -91519.247009] AUTODETECT spr round 4 (radius: 20)
[04:10:44 -81403.647958] AUTODETECT spr round 5 (radius: 25)
[04:13:50 -78446.816068] SPR radius for FAST iterations: 25 (autodetect)
[04:13:50 -78446.816068] Model parameter optimization (eps = 3.000000)
[04:14:31 -77121.390785] FAST spr round 1 (radius: 25)
[04:16:42 -65661.564636] FAST spr round 2 (radius: 25)
[04:18:17 -64936.006018] FAST spr round 3 (radius: 25)
[04:19:48 -64892.059768] FAST spr round 4 (radius: 25)
[04:21:08 -64888.465453] FAST spr round 5 (radius: 25)
[04:22:21 -64888.464429] Model parameter optimization (eps = 1.000000)
[04:22:36 -64878.412491] SLOW spr round 1 (radius: 5)
[04:24:13 -64863.343204] SLOW spr round 2 (radius: 5)
[04:25:40 -64861.659158] SLOW spr round 3 (radius: 5)
[04:27:06 -64861.526271] SLOW spr round 4 (radius: 5)
[04:28:30 -64861.525293] SLOW spr round 5 (radius: 10)
[04:30:11 -64861.525208] SLOW spr round 6 (radius: 15)
[04:33:06 -64861.442880] SLOW spr round 7 (radius: 20)
[04:37:05 -64857.614604] SLOW spr round 8 (radius: 5)
[04:39:16 -64856.774803] SLOW spr round 9 (radius: 5)
[04:41:05 -64854.106387] SLOW spr round 10 (radius: 5)
[04:42:44 -64854.106184] SLOW spr round 11 (radius: 10)
[04:44:23 -64847.276331] SLOW spr round 12 (radius: 5)
[04:46:12 -64847.074159] SLOW spr round 13 (radius: 5)
[04:47:49 -64846.294876] SLOW spr round 14 (radius: 5)
[04:48:03] [worker #2] ML tree search #19, logLikelihood: -64833.195848
[04:49:22 -64845.025216] SLOW spr round 15 (radius: 5)
[04:50:50 -64845.025173] SLOW spr round 16 (radius: 10)
[04:52:24 -64845.025168] SLOW spr round 17 (radius: 15)
[04:55:24 -64845.025165] SLOW spr round 18 (radius: 20)
[04:59:15 -64845.025163] SLOW spr round 19 (radius: 25)
[05:03:45 -64845.025161] Model parameter optimization (eps = 0.100000)

[05:03:50] [worker #0] ML tree search #13, logLikelihood: -64844.996599

[05:03:50 -225523.484717] Initial branch length optimization
[05:03:54 -178371.274194] Model parameter optimization (eps = 10.000000)
[05:04:44 -177037.274358] AUTODETECT spr round 1 (radius: 5)
[05:06:20 -139372.359009] AUTODETECT spr round 2 (radius: 10)
[05:08:15 -110777.084252] AUTODETECT spr round 3 (radius: 15)
[05:09:47] [worker #3] ML tree search #20, logLikelihood: -64849.917872
[05:10:25 -93577.827609] AUTODETECT spr round 4 (radius: 20)
[05:12:47 -82920.852656] AUTODETECT spr round 5 (radius: 25)
[05:14:57] [worker #1] ML tree search #14, logLikelihood: -64835.586911
[05:15:27 -79259.537469] SPR radius for FAST iterations: 25 (autodetect)
[05:15:27 -79259.537469] Model parameter optimization (eps = 3.000000)
[05:16:12 -78704.036502] FAST spr round 1 (radius: 25)
[05:18:33 -65888.453283] FAST spr round 2 (radius: 25)
[05:20:23 -65041.504074] FAST spr round 3 (radius: 25)
[05:21:59 -64977.760278] FAST spr round 4 (radius: 25)
[05:23:18 -64972.637407] FAST spr round 5 (radius: 25)
[05:24:36 -64969.246486] FAST spr round 6 (radius: 25)
[05:25:51 -64969.246255] Model parameter optimization (eps = 1.000000)
[05:26:06 -64964.384780] SLOW spr round 1 (radius: 5)
[05:27:51 -64949.979095] SLOW spr round 2 (radius: 5)
[05:29:26 -64949.979002] SLOW spr round 3 (radius: 10)
[05:31:08 -64946.742685] SLOW spr round 4 (radius: 5)
[05:33:10 -64945.249557] SLOW spr round 5 (radius: 5)
[05:34:55 -64945.249519] SLOW spr round 6 (radius: 10)
[05:36:42 -64945.249517] SLOW spr round 7 (radius: 15)
[05:39:16 -64943.217859] SLOW spr round 8 (radius: 5)
[05:41:14 -64940.275828] SLOW spr round 9 (radius: 5)
[05:42:54 -64939.637656] SLOW spr round 10 (radius: 5)
[05:44:25 -64939.637618] SLOW spr round 11 (radius: 10)
[05:46:02 -64934.580918] SLOW spr round 12 (radius: 5)
[05:47:51 -64923.624437] SLOW spr round 13 (radius: 5)
[05:49:25 -64923.624125] SLOW spr round 14 (radius: 10)
[05:51:05 -64923.624117] SLOW spr round 15 (radius: 15)
[05:53:43 -64922.632090] SLOW spr round 16 (radius: 5)
[05:55:39 -64922.631517] SLOW spr round 17 (radius: 10)
[05:57:34 -64922.631503] SLOW spr round 18 (radius: 15)
[06:00:06 -64922.105547] SLOW spr round 19 (radius: 5)
[06:02:00 -64922.104931] SLOW spr round 20 (radius: 10)
[06:03:55 -64922.104871] SLOW spr round 21 (radius: 15)
[06:06:27 -64922.104864] SLOW spr round 22 (radius: 20)
[06:10:05 -64898.496782] SLOW spr round 23 (radius: 5)
[06:12:08 -64871.648594] SLOW spr round 24 (radius: 5)
[06:13:51 -64871.550612] SLOW spr round 25 (radius: 10)
[06:15:33 -64871.550581] SLOW spr round 26 (radius: 15)
[06:18:07 -64870.814056] SLOW spr round 27 (radius: 5)
[06:20:05 -64867.387539] SLOW spr round 28 (radius: 5)
[06:21:46 -64866.851320] SLOW spr round 29 (radius: 5)
[06:23:17 -64866.850623] SLOW spr round 30 (radius: 10)
[06:24:53 -64866.850616] SLOW spr round 31 (radius: 15)
[06:27:32 -64866.850615] SLOW spr round 32 (radius: 20)
[06:29:07] [worker #1] ML tree search #18, logLikelihood: -64833.108016
[06:31:09 -64866.850614] SLOW spr round 33 (radius: 25)
[06:35:35 -64856.942942] SLOW spr round 34 (radius: 5)
[06:37:53 -64854.156711] SLOW spr round 35 (radius: 5)
[06:39:47 -64854.137062] SLOW spr round 36 (radius: 10)
[06:41:43 -64854.136953] SLOW spr round 37 (radius: 15)
[06:44:33 -64854.136935] SLOW spr round 38 (radius: 20)
[06:48:34 -64854.136932] SLOW spr round 39 (radius: 25)
[06:53:12 -64854.136931] Model parameter optimization (eps = 0.100000)

[06:53:22] [worker #0] ML tree search #17, logLikelihood: -64853.901165


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.127218,0.590412) (0.058370,0.839633) (0.332605,0.706907) (0.481807,1.329908) 
   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: -64826.986194

AIC score: 132467.972387 / AICc score: 4094579.972387 / BIC score: 137242.806345
Free parameters (model + branch lengths): 1407

WARNING: Number of free parameters (K=1407) is larger than alignment size (n=220).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 139 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60812/3_mltree/O60812.raxml.log

Analysis started: 05-Jul-2021 13:47:47 / finished: 05-Jul-2021 20:41:10

Elapsed time: 24802.963 seconds

Consumed energy: 2111.383 Wh (= 11 km in an electric car, or 53 km with an e-scooter!)