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 15:56:29 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/2_msa/P98088_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088 --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/P98088/2_msa/P98088_trimmed_msa.fasta
[00:00:00] Loaded alignment with 934 taxa and 193 sites

WARNING: Sequences tr_A0A286YAF1_A0A286YAF1_DANRE_7955 and tr_A0A2R8QKW8_A0A2R8QKW8_DANRE_7955 are exactly identical!
WARNING: Sequences tr_A0A1D5NVH7_A0A1D5NVH7_CHICK_9031 and tr_G1N8Z1_G1N8Z1_MELGA_9103 are exactly identical!
WARNING: Sequences tr_A0A1D5P623_A0A1D5P623_CHICK_9031 and sp_Q2PC93_SSPO_CHICK_9031 are exactly identical!
WARNING: Sequences tr_A0A1D5PCH3_A0A1D5PCH3_CHICK_9031 and sp_F1NBL0_MUC6_CHICK_9031 are exactly identical!
WARNING: Sequences tr_F1NZY2_F1NZY2_CHICK_9031 and sp_Q98UI9_MUC5B_CHICK_9031 are exactly identical!
WARNING: Sequences tr_F1NZY2_F1NZY2_CHICK_9031 and tr_A0A226MF19_A0A226MF19_CALSU_9009 are exactly identical!
WARNING: Sequences tr_F1NZY2_F1NZY2_CHICK_9031 and tr_A0A226NZ44_A0A226NZ44_COLVI_9014 are exactly identical!
WARNING: Sequences tr_M3Z187_M3Z187_MUSPF_9669 and tr_A0A2Y9IRS1_A0A2Y9IRS1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3R9F3_G3R9F3_GORGO_9595 and sp_Q9HC84_MUC5B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R9F3_G3R9F3_GORGO_9595 and tr_A0A2R9B1M7_A0A2R9B1M7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RIY5_G3RIY5_GORGO_9595 and tr_H2RBG8_H2RBG8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RIY5_G3RIY5_GORGO_9595 and tr_A0A2R8ZW83_A0A2R8ZW83_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2NCD3_H2NCD3_PONAB_9601 and sp_Q02817_MUC2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1K2B9_G1K2B9_CANLF_9615 and sp_Q28295_VWF_CANLF_9615 are exactly identical!
WARNING: Sequences tr_H9GWA1_H9GWA1_CANLF_9615 and tr_J9P8V9_J9P8V9_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3SAQ5_A0A2I3SAQ5_PANTR_9598 and tr_A0A2R9AZ47_A0A2R9AZ47_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3SPJ6_A0A2I3SPJ6_PANTR_9598 and tr_A0A2R8ZIX8_A0A2R8ZIX8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q597_H2Q597_PANTR_9598 and sp_P04275_VWF_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q597_H2Q597_PANTR_9598 and tr_A0A2R8ZVE3_A0A2R8ZVE3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2Q6J1_H2Q6J1_PANTR_9598 and sp_Q3ZCN5_OTOGL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q6J1_H2Q6J1_PANTR_9598 and tr_A0A2R8ZEC9_A0A2R8ZEC9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5QFA8_W5QFA8_SHEEP_9940 and tr_F1MGF6_F1MGF6_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5QFC6_A0A3B5QFC6_XIPMA_8083 and tr_A0A3B5R5B8_A0A3B5R5B8_XIPMA_8083 are exactly identical!
WARNING: Sequences tr_A0A1D5QE93_A0A1D5QE93_MACMU_9544 and tr_A0A096N285_A0A096N285_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QE93_A0A1D5QE93_MACMU_9544 and tr_A0A0D9RCJ6_A0A0D9RCJ6_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QE93_A0A1D5QE93_MACMU_9544 and tr_A0A2K6CY65_A0A2K6CY65_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7CZT4_F7CZT4_MACMU_9544 and tr_A0A2K6E324_A0A2K6E324_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7CZT4_F7CZT4_MACMU_9544 and tr_A0A2K5ZUE8_A0A2K5ZUE8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7H681_F7H681_MACMU_9544 and tr_A0A0D9QV97_A0A0D9QV97_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F7H681_F7H681_MACMU_9544 and tr_A0A2K6CEY3_A0A2K6CEY3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H681_F7H681_MACMU_9544 and tr_A0A2K5ZYP8_A0A2K5ZYP8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3Q5M1_G3Q5M1_GASAC_69293 and tr_G3Q5Q0_G3Q5Q0_GASAC_69293 are exactly identical!
WARNING: Sequences tr_H0ZBH9_H0ZBH9_TAEGU_59729 and tr_A0A091F883_A0A091F883_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZGW8_H0ZGW8_TAEGU_59729 and tr_A0A218USV6_A0A218USV6_9PASE_299123 are exactly identical!
WARNING: Sequences tr_F6RM96_F6RM96_XENTR_8364 and tr_F7D6C7_F7D6C7_XENTR_8364 are exactly identical!
WARNING: Sequences tr_F1SL22_F1SL22_PIG_9823 and sp_Q28833_VWF_PIG_9823 are exactly identical!
WARNING: Sequences tr_B3RQT5_B3RQT5_TRIAD_10228 and tr_A0A369RVP1_A0A369RVP1_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PNU9_G7PNU9_MACFA_9541 and tr_A0A2K6DZI7_A0A2K6DZI7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PQM3_G7PQM3_MACFA_9541 and tr_A0A2I3N413_A0A2I3N413_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PQM3_G7PQM3_MACFA_9541 and tr_A0A2K5MLT3_A0A2K5MLT3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PQM3_G7PQM3_MACFA_9541 and tr_A0A2K6DHQ3_A0A2K6DHQ3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PQM3_G7PQM3_MACFA_9541 and tr_A0A2K5XV09_A0A2K5XV09_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NC21_A0A096NC21_PAPAN_9555 and tr_A0A0D9RD96_A0A0D9RD96_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NC21_A0A096NC21_PAPAN_9555 and tr_A0A2K5LE70_A0A2K5LE70_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0N8JVG1_A0A0N8JVG1_9TELE_113540 and tr_A0A0P7UG38_A0A0P7UG38_9TELE_113540 are exactly identical!
WARNING: Sequences tr_A0A151MCC7_A0A151MCC7_ALLMI_8496 and tr_A0A3Q0GZT6_A0A3Q0GZT6_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151P452_A0A151P452_ALLMI_8496 and tr_A0A1U7SIG9_A0A1U7SIG9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091UXT2_A0A091UXT2_NIPNI_128390 and tr_A0A087RD08_A0A087RD08_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091VYG4_A0A091VYG4_NIPNI_128390 and tr_A0A087QKQ1_A0A087QKQ1_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2I0MHR4_A0A2I0MHR4_COLLI_8932 and tr_A0A1V4JPT2_A0A1V4JPT2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3KS48_A0A1S3KS48_SALSA_8030 and tr_A0A1S3QR93_A0A1S3QR93_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3MYI5_A0A1S3MYI5_SALSA_8030 and tr_A0A1S3MZV5_A0A1S3MZV5_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3PE24_A0A1S3PE24_SALSA_8030 and tr_A0A1S3QJE6_A0A1S3QJE6_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3QCU3_A0A1S3QCU3_SALSA_8030 and tr_A0A1S3QUM9_A0A1S3QUM9_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3QG78_A0A1S3QG78_SALSA_8030 and tr_A0A1S3QL74_A0A1S3QL74_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3QGI2_A0A1S3QGI2_SALSA_8030 and tr_A0A1S3QSA0_A0A1S3QSA0_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3QGI2_A0A1S3QGI2_SALSA_8030 and tr_A0A1S3QYM8_A0A1S3QYM8_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A1S3QRQ6_A0A1S3QRQ6_SALSA_8030 and tr_A0A1S3QSI8_A0A1S3QSI8_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A226ME51_A0A226ME51_CALSU_9009 and tr_A0A226P1B0_A0A226P1B0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226MES1_A0A226MES1_CALSU_9009 and tr_A0A226NZI6_A0A226NZI6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U3WT42_A0A2U3WT42_ODORO_9708 and tr_A0A2U3Z4X3_A0A2U3Z4X3_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9MZ31_A0A2Y9MZ31_DELLE_9749 and tr_A0A383Z087_A0A383Z087_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 62

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/P98088/3_mltree/P98088.raxml.reduced.phy

Alignment comprises 1 partitions and 193 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 193 / 193
Gaps: 6.65 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088.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 934 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 193 / 15440
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -312617.038403] Initial branch length optimization
[00:00:05 -265821.585475] Model parameter optimization (eps = 10.000000)
[00:00:38 -265760.099824] AUTODETECT spr round 1 (radius: 5)
[00:03:20 -187956.867655] AUTODETECT spr round 2 (radius: 10)
[00:06:14 -137132.414108] AUTODETECT spr round 3 (radius: 15)
[00:09:25 -111282.156301] AUTODETECT spr round 4 (radius: 20)
[00:13:58 -97559.120403] AUTODETECT spr round 5 (radius: 25)
[00:18:21 -95197.593674] SPR radius for FAST iterations: 25 (autodetect)
[00:18:21 -95197.593674] Model parameter optimization (eps = 3.000000)
[00:18:52 -95045.900674] FAST spr round 1 (radius: 25)
[00:21:47 -81020.347980] FAST spr round 2 (radius: 25)
[00:24:09 -79873.065522] FAST spr round 3 (radius: 25)
[00:26:13 -79790.849363] FAST spr round 4 (radius: 25)
[00:28:10 -79754.545753] FAST spr round 5 (radius: 25)
[00:29:58 -79697.376250] FAST spr round 6 (radius: 25)
[00:31:43 -79694.671814] FAST spr round 7 (radius: 25)
[00:33:26 -79694.671496] Model parameter optimization (eps = 1.000000)
[00:33:36 -79693.321576] SLOW spr round 1 (radius: 5)
[00:35:49 -79660.558511] SLOW spr round 2 (radius: 5)
[00:38:03 -79657.585215] SLOW spr round 3 (radius: 5)
[00:40:15 -79657.583070] SLOW spr round 4 (radius: 10)
[00:42:27 -79656.561392] SLOW spr round 5 (radius: 5)
[00:45:16 -79653.033706] SLOW spr round 6 (radius: 5)
[00:47:51 -79649.819415] SLOW spr round 7 (radius: 5)
[00:50:11 -79649.818665] SLOW spr round 8 (radius: 10)
[00:52:24 -79649.818455] SLOW spr round 9 (radius: 15)
[00:56:09 -79646.392301] SLOW spr round 10 (radius: 5)
[00:59:05 -79646.385135] SLOW spr round 11 (radius: 10)
[01:01:38 -79646.382101] SLOW spr round 12 (radius: 15)
[01:05:05 -79646.380722] SLOW spr round 13 (radius: 20)
[01:10:58 -79645.905188] SLOW spr round 14 (radius: 5)
[01:13:56 -79645.904527] SLOW spr round 15 (radius: 10)
[01:16:36 -79645.114235] SLOW spr round 16 (radius: 5)
[01:19:20 -79645.112002] SLOW spr round 17 (radius: 10)
[01:21:43 -79645.111685] SLOW spr round 18 (radius: 15)
[01:25:20 -79645.111635] SLOW spr round 19 (radius: 20)
[01:31:23 -79645.111627] SLOW spr round 20 (radius: 25)
[01:36:11] [worker #2] ML tree search #3, logLikelihood: -79659.315663
[01:38:45 -79642.212526] SLOW spr round 21 (radius: 5)
[01:41:45 -79642.177078] SLOW spr round 22 (radius: 10)
[01:44:27 -79642.048609] SLOW spr round 23 (radius: 5)
[01:47:09 -79642.043493] SLOW spr round 24 (radius: 10)
[01:49:32 -79642.042484] SLOW spr round 25 (radius: 15)
[01:53:06 -79642.042259] SLOW spr round 26 (radius: 20)
[01:59:06 -79642.042205] SLOW spr round 27 (radius: 25)
[02:00:52] [worker #1] ML tree search #2, logLikelihood: -79629.197507
[02:06:33 -79640.995563] SLOW spr round 28 (radius: 5)
[02:09:32 -79640.989476] SLOW spr round 29 (radius: 10)
[02:12:12 -79640.988007] SLOW spr round 30 (radius: 15)
[02:15:44 -79640.987310] SLOW spr round 31 (radius: 20)
[02:21:20] [worker #3] ML tree search #4, logLikelihood: -79619.042287
[02:21:52 -79640.987246] SLOW spr round 32 (radius: 25)
[02:29:15 -79640.987202] Model parameter optimization (eps = 0.100000)

[02:29:26] [worker #0] ML tree search #1, logLikelihood: -79640.836495

[02:29:26 -313192.567977] Initial branch length optimization
[02:29:30 -266493.359043] Model parameter optimization (eps = 10.000000)
[02:30:05 -266399.546567] AUTODETECT spr round 1 (radius: 5)
[02:32:48 -188547.000911] AUTODETECT spr round 2 (radius: 10)
[02:35:44 -134405.078349] AUTODETECT spr round 3 (radius: 15)
[02:38:54 -111018.855784] AUTODETECT spr round 4 (radius: 20)
[02:43:19 -97136.938050] AUTODETECT spr round 5 (radius: 25)
[02:47:53 -94218.485080] SPR radius for FAST iterations: 25 (autodetect)
[02:47:53 -94218.485080] Model parameter optimization (eps = 3.000000)
[02:48:17 -94057.231852] FAST spr round 1 (radius: 25)
[02:51:12 -80660.426332] FAST spr round 2 (radius: 25)
[02:53:32 -79849.856226] FAST spr round 3 (radius: 25)
[02:55:37 -79749.543005] FAST spr round 4 (radius: 25)
[02:57:31 -79734.418820] FAST spr round 5 (radius: 25)
[02:59:18 -79730.803659] FAST spr round 6 (radius: 25)
[03:01:02 -79730.803577] Model parameter optimization (eps = 1.000000)
[03:01:10 -79730.129008] SLOW spr round 1 (radius: 5)
[03:03:22 -79704.514029] SLOW spr round 2 (radius: 5)
[03:05:38 -79702.972836] SLOW spr round 3 (radius: 5)
[03:07:54 -79701.959797] SLOW spr round 4 (radius: 5)
[03:10:05 -79701.959254] SLOW spr round 5 (radius: 10)
[03:12:22 -79698.021107] SLOW spr round 6 (radius: 5)
[03:15:10 -79698.020968] SLOW spr round 7 (radius: 10)
[03:17:43 -79697.945863] SLOW spr round 8 (radius: 15)
[03:21:20 -79692.763186] SLOW spr round 9 (radius: 5)
[03:24:22 -79686.025807] SLOW spr round 10 (radius: 5)
[03:27:03 -79683.299150] SLOW spr round 11 (radius: 5)
[03:28:25] [worker #2] ML tree search #7, logLikelihood: -79632.952536
[03:29:27 -79681.513545] SLOW spr round 12 (radius: 5)
[03:31:43 -79681.513374] SLOW spr round 13 (radius: 10)
[03:33:59 -79681.513324] SLOW spr round 14 (radius: 15)
[03:37:46 -79681.513302] SLOW spr round 15 (radius: 20)
[03:43:59 -79681.027196] SLOW spr round 16 (radius: 5)
[03:47:00 -79681.026736] SLOW spr round 17 (radius: 10)
[03:47:25] [worker #1] ML tree search #6, logLikelihood: -79626.611209
[03:49:46 -79681.026707] SLOW spr round 18 (radius: 15)
[03:53:17 -79681.026700] SLOW spr round 19 (radius: 20)
[03:59:35 -79681.026696] SLOW spr round 20 (radius: 25)
[03:59:53] [worker #3] ML tree search #8, logLikelihood: -79637.235700
[04:07:11 -79680.813270] SLOW spr round 21 (radius: 5)
[04:10:13 -79680.805529] SLOW spr round 22 (radius: 10)
[04:13:00 -79680.802099] SLOW spr round 23 (radius: 15)
[04:16:34 -79677.914727] SLOW spr round 24 (radius: 5)
[04:19:34 -79628.379595] SLOW spr round 25 (radius: 5)
[04:22:08 -79628.378143] SLOW spr round 26 (radius: 10)
[04:24:30 -79628.377778] SLOW spr round 27 (radius: 15)
[04:28:11 -79628.377685] SLOW spr round 28 (radius: 20)
[04:34:31 -79628.377666] SLOW spr round 29 (radius: 25)
[04:42:30 -79628.377655] Model parameter optimization (eps = 0.100000)

[04:42:39] [worker #0] ML tree search #5, logLikelihood: -79628.340791

[04:42:39 -312133.879294] Initial branch length optimization
[04:42:46 -267064.689957] Model parameter optimization (eps = 10.000000)
[04:43:32 -266967.899871] AUTODETECT spr round 1 (radius: 5)
[04:44:09] [worker #2] ML tree search #11, logLikelihood: -79913.452731
[04:46:07 -185354.651003] AUTODETECT spr round 2 (radius: 10)
[04:49:00 -129988.215100] AUTODETECT spr round 3 (radius: 15)
[04:52:16 -106299.684827] AUTODETECT spr round 4 (radius: 20)
[04:56:00 -95617.776145] AUTODETECT spr round 5 (radius: 25)
[05:00:27 -92834.265203] SPR radius for FAST iterations: 25 (autodetect)
[05:00:28 -92834.265203] Model parameter optimization (eps = 3.000000)
[05:00:51 -92665.938576] FAST spr round 1 (radius: 25)
[05:03:47 -80476.024717] FAST spr round 2 (radius: 25)
[05:06:09 -79804.702002] FAST spr round 3 (radius: 25)
[05:08:14 -79710.256621] FAST spr round 4 (radius: 25)
[05:10:10 -79700.311237] FAST spr round 5 (radius: 25)
[05:12:02 -79699.852680] FAST spr round 6 (radius: 25)
[05:13:48 -79699.852109] Model parameter optimization (eps = 1.000000)
[05:14:01 -79693.414000] SLOW spr round 1 (radius: 5)
[05:16:23 -79674.719041] SLOW spr round 2 (radius: 5)
[05:18:42 -79668.577424] SLOW spr round 3 (radius: 5)
[05:19:23] [worker #3] ML tree search #12, logLikelihood: -79646.413334
[05:21:03 -79663.654254] SLOW spr round 4 (radius: 5)
[05:23:17 -79663.596614] SLOW spr round 5 (radius: 10)
[05:25:33 -79663.133670] SLOW spr round 6 (radius: 5)
[05:28:25 -79662.825797] SLOW spr round 7 (radius: 5)
[05:30:57 -79662.824375] SLOW spr round 8 (radius: 10)
[05:33:18 -79662.282810] SLOW spr round 9 (radius: 5)
[05:36:08 -79659.807087] SLOW spr round 10 (radius: 5)
[05:38:37 -79659.806963] SLOW spr round 11 (radius: 10)
[05:40:58 -79659.625836] SLOW spr round 12 (radius: 5)
[05:43:46 -79659.621734] SLOW spr round 13 (radius: 10)
[05:44:00] [worker #1] ML tree search #10, logLikelihood: -79617.447697
[05:46:17 -79659.544908] SLOW spr round 14 (radius: 15)
[05:49:59 -79655.942954] SLOW spr round 15 (radius: 5)
[05:52:57 -79655.922315] SLOW spr round 16 (radius: 10)
[05:55:36 -79655.920842] SLOW spr round 17 (radius: 15)
[05:59:08 -79655.919892] SLOW spr round 18 (radius: 20)
[06:05:20 -79655.919053] SLOW spr round 19 (radius: 25)
[06:13:30 -79651.316531] SLOW spr round 20 (radius: 5)
[06:16:32 -79651.315923] SLOW spr round 21 (radius: 10)
[06:19:16 -79651.315534] SLOW spr round 22 (radius: 15)
[06:22:49 -79651.315161] SLOW spr round 23 (radius: 20)
[06:29:05 -79651.314798] SLOW spr round 24 (radius: 25)
[06:37:21 -79651.314443] Model parameter optimization (eps = 0.100000)

[06:37:27] [worker #0] ML tree search #9, logLikelihood: -79651.270736

[06:37:27 -312811.188446] Initial branch length optimization
[06:37:32 -265225.358100] Model parameter optimization (eps = 10.000000)
[06:38:11 -265045.766623] AUTODETECT spr round 1 (radius: 5)
[06:40:49 -181267.202306] AUTODETECT spr round 2 (radius: 10)
[06:43:45 -124100.006882] AUTODETECT spr round 3 (radius: 15)
[06:46:45 -101383.166935] AUTODETECT spr round 4 (radius: 20)
[06:48:03] [worker #2] ML tree search #15, logLikelihood: -79633.844691
[06:49:12] [worker #3] ML tree search #16, logLikelihood: -79637.123324
[06:50:28 -91597.058364] AUTODETECT spr round 5 (radius: 25)
[06:55:09 -90791.723937] SPR radius for FAST iterations: 25 (autodetect)
[06:55:09 -90791.723937] Model parameter optimization (eps = 3.000000)
[06:55:17] [worker #1] ML tree search #14, logLikelihood: -79629.934842
[06:55:32 -90632.064148] FAST spr round 1 (radius: 25)
[06:58:35 -80185.774842] FAST spr round 2 (radius: 25)
[07:00:47 -79767.762421] FAST spr round 3 (radius: 25)
[07:02:46 -79746.182484] FAST spr round 4 (radius: 25)
[07:04:37 -79743.836884] FAST spr round 5 (radius: 25)
[07:06:24 -79743.835826] Model parameter optimization (eps = 1.000000)
[07:06:35 -79742.763331] SLOW spr round 1 (radius: 5)
[07:08:51 -79708.027171] SLOW spr round 2 (radius: 5)
[07:11:09 -79701.340833] SLOW spr round 3 (radius: 5)
[07:13:27 -79700.444651] SLOW spr round 4 (radius: 5)
[07:15:41 -79700.443699] SLOW spr round 5 (radius: 10)
[07:17:59 -79696.078117] SLOW spr round 6 (radius: 5)
[07:20:51 -79694.480833] SLOW spr round 7 (radius: 5)
[07:23:24 -79692.908777] SLOW spr round 8 (radius: 5)
[07:25:45 -79692.905813] SLOW spr round 9 (radius: 10)
[07:28:01 -79692.736705] SLOW spr round 10 (radius: 5)
[07:30:50 -79692.731788] SLOW spr round 11 (radius: 10)
[07:33:19 -79692.731764] SLOW spr round 12 (radius: 15)
[07:36:54 -79688.457847] SLOW spr round 13 (radius: 5)
[07:39:57 -79687.585193] SLOW spr round 14 (radius: 5)
[07:42:34 -79687.583924] SLOW spr round 15 (radius: 10)
[07:44:58 -79687.583824] SLOW spr round 16 (radius: 15)
[07:48:47 -79687.583782] SLOW spr round 17 (radius: 20)
[07:54:50 -79628.574126] SLOW spr round 18 (radius: 5)
[07:57:55 -79628.401897] SLOW spr round 19 (radius: 5)
[08:00:32 -79628.400885] SLOW spr round 20 (radius: 10)
[08:02:55 -79628.400376] SLOW spr round 21 (radius: 15)
[08:06:36 -79628.400086] SLOW spr round 22 (radius: 20)
[08:12:26 -79628.362905] SLOW spr round 23 (radius: 25)
[08:14:00] [worker #2] ML tree search #19, logLikelihood: -79645.802076
[08:16:22] [worker #1] ML tree search #18, logLikelihood: -79625.335953
[08:19:36 -79628.361942] Model parameter optimization (eps = 0.100000)

[08:19:48] [worker #0] ML tree search #13, logLikelihood: -79627.698562

[08:19:49 -314198.131635] Initial branch length optimization
[08:19:52 -267724.777409] Model parameter optimization (eps = 10.000000)
[08:20:37 -267595.631583] AUTODETECT spr round 1 (radius: 5)
[08:23:17 -183358.726413] AUTODETECT spr round 2 (radius: 10)
[08:26:11 -129716.097820] AUTODETECT spr round 3 (radius: 15)
[08:29:15 -105488.082006] AUTODETECT spr round 4 (radius: 20)
[08:33:24 -93550.545319] AUTODETECT spr round 5 (radius: 25)
[08:37:59 -92093.388888] SPR radius for FAST iterations: 25 (autodetect)
[08:37:59 -92093.388888] Model parameter optimization (eps = 3.000000)
[08:38:22 -91912.975380] FAST spr round 1 (radius: 25)
[08:41:19 -80332.237239] FAST spr round 2 (radius: 25)
[08:43:35 -79758.106711] FAST spr round 3 (radius: 25)
[08:45:36 -79682.807928] FAST spr round 4 (radius: 25)
[08:47:25 -79679.792057] FAST spr round 5 (radius: 25)
[08:49:09 -79679.770126] Model parameter optimization (eps = 1.000000)
[08:49:16 -79678.930266] SLOW spr round 1 (radius: 5)
[08:51:28 -79652.767587] SLOW spr round 2 (radius: 5)
[08:53:43 -79643.647975] SLOW spr round 3 (radius: 5)
[08:55:59 -79640.478050] SLOW spr round 4 (radius: 5)
[08:58:10 -79640.331764] SLOW spr round 5 (radius: 5)
[09:00:19 -79640.331726] SLOW spr round 6 (radius: 10)
[09:02:34 -79639.268301] SLOW spr round 7 (radius: 5)
[09:05:23 -79636.982746] SLOW spr round 8 (radius: 5)
[09:07:51 -79636.978938] SLOW spr round 9 (radius: 10)
[09:10:10 -79636.977390] SLOW spr round 10 (radius: 15)
[09:13:53 -79636.520895] SLOW spr round 11 (radius: 5)
[09:16:49 -79636.495863] SLOW spr round 12 (radius: 10)
[09:19:28 -79636.057951] SLOW spr round 13 (radius: 5)
[09:22:10 -79635.749376] SLOW spr round 14 (radius: 5)
[09:24:36 -79635.745260] SLOW spr round 15 (radius: 10)
[09:26:52 -79635.745260] SLOW spr round 16 (radius: 15)
[09:30:35 -79635.745260] SLOW spr round 17 (radius: 20)
[09:36:29 -79635.745260] SLOW spr round 18 (radius: 25)
[09:36:46] [worker #3] ML tree search #20, logLikelihood: -79633.391214
[09:44:01 -79634.711476] SLOW spr round 19 (radius: 5)
[09:47:01 -79634.550766] SLOW spr round 20 (radius: 5)
[09:49:37 -79634.539058] SLOW spr round 21 (radius: 10)
[09:51:58 -79634.538536] SLOW spr round 22 (radius: 15)
[09:55:37 -79634.538079] SLOW spr round 23 (radius: 20)
[10:01:34 -79634.537709] SLOW spr round 24 (radius: 25)
[10:09:05 -79634.537328] Model parameter optimization (eps = 0.100000)

[10:09:20] [worker #0] ML tree search #17, logLikelihood: -79634.109348


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.197109,0.380429) (0.216262,0.681904) (0.394326,1.015946) (0.192302,1.960089) 
   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: -79617.447697

AIC score: 162976.895394 / AICc score: 7168000.895394 / BIC score: 169081.388738
Free parameters (model + branch lengths): 1871

WARNING: Number of free parameters (K=1871) is larger than alignment size (n=193).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P98088/3_mltree/P98088.raxml.log

Analysis started: 05-Jul-2021 15:56:29 / finished: 06-Jul-2021 02:05:50

Elapsed time: 36560.665 seconds

Consumed energy: 3012.904 Wh (= 15 km in an electric car, or 75 km with an e-scooter!)