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 01-Jul-2021 08:45:10 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/2_msa/Q14533_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/3_mltree/Q14533 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/2_msa/Q14533_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 283 sites WARNING: Sequences tr_A0A146F0A0_A0A146F0A0_CHICK_9031 and sp_O93532_K2CO_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1D5PXP0_A0A1D5PXP0_CHICK_9031 and tr_G1NER8_G1NER8_MELGA_9103 are exactly identical! WARNING: Sequences sp_P97861_KRT86_MOUSE_10090 and sp_Q9ERE2_KRT81_MOUSE_10090 are exactly identical! WARNING: Sequences sp_Q9DCV7_K2C7_MOUSE_10090 and sp_Q6IG12_K2C7_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y7A1_M3Y7A1_MUSPF_9669 and tr_A0A2U3VZ44_A0A2U3VZ44_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y7A1_M3Y7A1_MUSPF_9669 and tr_A0A2Y9KMA6_A0A2Y9KMA6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GD99_A0A2I3GD99_NOMLE_61853 and sp_P02538_K2C6A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GD99_A0A2I3GD99_NOMLE_61853 and tr_A0A2R9B125_A0A2R9B125_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S7P4_G1S7P4_NOMLE_61853 and tr_G3QMP7_G3QMP7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7P4_G1S7P4_NOMLE_61853 and tr_H2NHE7_H2NHE7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7P4_G1S7P4_NOMLE_61853 and tr_H2Q605_H2Q605_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_G3QKU2_G3QKU2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_H2NHD7_H2NHD7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and sp_A5A6M8_K2C5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and tr_H2Q5Z8_H2Q5Z8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7Q6_G1S7Q6_NOMLE_61853 and sp_P13647_K2C5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S7R5_G1S7R5_NOMLE_61853 and tr_H2NHD4_H2NHD4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7S0_G1S7S0_NOMLE_61853 and tr_G1S7S2_G1S7S2_NOMLE_61853 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_H2NHD3_H2NHD3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_H2Q5Z3_H2Q5Z3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A1D5QLK5_A0A1D5QLK5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A096MW83_A0A096MW83_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A2K5P6H0_A0A2K5P6H0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A2K6B230_A0A2K6B230_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A2K5XMZ6_A0A2K5XMZ6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QJY7_G3QJY7_GORGO_9595 and tr_A0A2R9BCT3_A0A2R9BCT3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and tr_H2Q5Z9_H2Q5Z9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and sp_Q3SY84_K2C71_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QKU5_G3QKU5_GORGO_9595 and tr_A0A2R9B4E9_A0A2R9B4E9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QLP7_G3QLP7_GORGO_9595 and tr_H2R1Z0_H2R1Z0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QLP7_G3QLP7_GORGO_9595 and sp_P04264_K2C1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_H2NHF0_H2NHF0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2J8KDC3_A0A2J8KDC3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and sp_P05787_K2C8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFE7_G3RFE7_GORGO_9595 and tr_A0A2R9A6T6_A0A2R9A6T6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RNS3_G3RNS3_GORGO_9595 and sp_P78385_KRT83_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SY72_G1SY72_RABIT_9986 and sp_Q29426_K2C3_RABIT_9986 are exactly identical! WARNING: Sequences tr_F1PTY1_F1PTY1_CANLF_9615 and sp_Q6EIY9_K2C1_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3TV17_A0A2I3TV17_PANTR_9598 and sp_P12035_K2C3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TV17_A0A2I3TV17_PANTR_9598 and tr_A0A2R9A6B3_A0A2R9A6B3_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5Q671_W5Q671_SHEEP_9940 and sp_Q148H5_K2C71_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q9NSB4_KRT82_HUMAN_9606 and tr_A0A2R9AZX5_A0A2R9AZX5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RKK9_A0A1D5RKK9_MACMU_9544 and tr_A0A2K6DEK3_A0A2K6DEK3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A096MVH8_A0A096MVH8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A2K6DMD1_A0A2K6DMD1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VKQ3_F6VKQ3_MACMU_9544 and tr_A0A2K5ZK75_A0A2K5ZK75_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7AEN7_F7AEN7_MACMU_9544 and tr_A0A2K6BPE2_A0A2K6BPE2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A096NAU0_A0A096NAU0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A2K5MDQ1_A0A2K5MDQ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B786_F7B786_MACMU_9544 and tr_A0A2K6CZV9_A0A2K6CZV9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BW59_F7BW59_MACMU_9544 and tr_A0A096N7Y8_A0A096N7Y8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BW59_F7BW59_MACMU_9544 and tr_A0A2K5NJ30_A0A2K5NJ30_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BW59_F7BW59_MACMU_9544 and tr_A0A2K6E7G3_A0A2K6E7G3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BW59_F7BW59_MACMU_9544 and tr_A0A2K5XF23_A0A2K5XF23_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7E526_F7E526_MACMU_9544 and tr_G7PIC9_G7PIC9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E5G2_F7E5G2_MACMU_9544 and tr_A0A2K5NRP9_A0A2K5NRP9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E5G2_F7E5G2_MACMU_9544 and tr_A0A2K6AAG1_A0A2K6AAG1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_G7PIC5_G7PIC5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A096ML93_A0A096ML93_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K5KH39_A0A2K5KH39_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K6B509_A0A2K6B509_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E5G8_F7E5G8_MACMU_9544 and tr_A0A2K6AJ14_A0A2K6AJ14_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HGY2_F7HGY2_MACMU_9544 and tr_A0A2K6CR37_A0A2K6CR37_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HIB9_F7HIB9_MACMU_9544 and tr_A0A096ML94_A0A096ML94_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HIB9_F7HIB9_MACMU_9544 and tr_A0A2K5MGV5_A0A2K5MGV5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HIB9_F7HIB9_MACMU_9544 and tr_A0A2K5N3F0_A0A2K5N3F0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HIB9_F7HIB9_MACMU_9544 and tr_A0A2K6BGC6_A0A2K6BGC6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A096MSQ9_A0A096MSQ9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K5N2V1_A0A2K5N2V1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HME7_F7HME7_MACMU_9544 and tr_A0A2K6BED4_A0A2K6BED4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PIC7_G7PIC7_MACFA_9541 and tr_A0A2K5MWZ1_A0A2K5MWZ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PIC7_G7PIC7_MACFA_9541 and tr_A0A2K6AJW7_A0A2K6AJW7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PID6_G7PID6_MACFA_9541 and tr_A0A096N9P6_A0A096N9P6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PID6_G7PID6_MACFA_9541 and tr_A0A2K6D660_A0A2K6D660_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PID6_G7PID6_MACFA_9541 and tr_A0A2K6AE66_A0A2K6AE66_MANLE_9568 are exactly identical! WARNING: Sequences tr_A5D7M6_A5D7M6_BOVIN_9913 and sp_Q5XQN5_K2C5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MPX0_A0A096MPX0_PAPAN_9555 and tr_A0A2K5LH62_A0A2K5LH62_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4V8_A0A096N4V8_PAPAN_9555 and tr_A0A2K5N3I3_A0A2K5N3I3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N4V8_A0A096N4V8_PAPAN_9555 and tr_A0A2K6A0H6_A0A2K6A0H6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QZY9_A0A0D9QZY9_CHLSB_60711 and tr_A0A2K5ZTU8_A0A2K5ZTU8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091IPJ1_A0A091IPJ1_EGRGA_188379 and tr_A0A091VPR9_A0A091VPR9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091VSH3_A0A091VSH3_NIPNI_128390 and tr_A0A087QJT4_A0A087QJT4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VK76_A0A091VK76_OPIHO_30419 and tr_A0A0A0A888_A0A0A0A888_CHAVO_50402 are exactly identical! WARNING: Sequences tr_B5X320_B5X320_SALSA_8030 and tr_A0A060X772_A0A060X772_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MNG6_A0A226MNG6_CALSU_9009 and tr_A0A226PU49_A0A226PU49_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5MSX8_A0A2K5MSX8_CERAT_9531 and tr_A0A2K6CHM8_A0A2K6CHM8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5MSX8_A0A2K5MSX8_CERAT_9531 and tr_A0A2K5YI70_A0A2K5YI70_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5P4N6_A0A2K5P4N6_CERAT_9531 and tr_A0A2K6BQ53_A0A2K6BQ53_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5P4N6_A0A2K5P4N6_CERAT_9531 and tr_A0A2K5XFB0_A0A2K5XFB0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3VZ03_A0A2U3VZ03_ODORO_9708 and tr_A0A2U3VZ04_A0A2U3VZ04_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2U3WCU6_A0A2U3WCU6_ODORO_9708 and tr_A0A2U3YQ66_A0A2U3YQ66_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3YQ72_A0A2U3YQ72_LEPWE_9713 and tr_A0A2Y9KMG2_A0A2Y9KMG2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3YQ72_A0A2U3YQ72_LEPWE_9713 and tr_A0A384D7D7_A0A384D7D7_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 93 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/Q14533/3_mltree/Q14533.raxml.reduced.phy Alignment comprises 1 partitions and 283 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 283 / 283 Gaps: 0.52 % Invariant sites: 0.71 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/3_mltree/Q14533.raxml.rba Parallelization scheme autoconfig: 6 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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 283 / 22640 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -287041.069621] Initial branch length optimization [00:00:07 -248678.347557] Model parameter optimization (eps = 10.000000) [00:01:09 -247943.266518] AUTODETECT spr round 1 (radius: 5) [00:04:17 -159207.675438] AUTODETECT spr round 2 (radius: 10) [00:07:26 -100751.145734] AUTODETECT spr round 3 (radius: 15) [00:10:55 -83370.485663] AUTODETECT spr round 4 (radius: 20) [00:15:38 -76364.050787] AUTODETECT spr round 5 (radius: 25) [00:20:58 -75065.025633] SPR radius for FAST iterations: 25 (autodetect) [00:20:58 -75065.025633] Model parameter optimization (eps = 3.000000) [00:21:20 -75033.115806] FAST spr round 1 (radius: 25) [00:24:32 -64134.300830] FAST spr round 2 (radius: 25) [00:26:58 -63592.699382] FAST spr round 3 (radius: 25) [00:29:11 -63517.450440] FAST spr round 4 (radius: 25) [00:31:07 -63511.857676] FAST spr round 5 (radius: 25) [00:32:58 -63508.479092] FAST spr round 6 (radius: 25) [00:34:44 -63507.300231] FAST spr round 7 (radius: 25) [00:36:32 -63507.300219] Model parameter optimization (eps = 1.000000) [00:36:46 -63503.058337] SLOW spr round 1 (radius: 5) [00:39:25 -63482.625664] SLOW spr round 2 (radius: 5) [00:42:00 -63478.236382] SLOW spr round 3 (radius: 5) [00:44:29 -63478.236291] SLOW spr round 4 (radius: 10) [00:46:53 -63475.973624] SLOW spr round 5 (radius: 5) [00:50:10 -63475.973595] SLOW spr round 6 (radius: 10) [00:52:51 -63475.973595] SLOW spr round 7 (radius: 15) [00:56:40 -63474.131527] SLOW spr round 8 (radius: 5) [01:00:04 -63474.131404] SLOW spr round 9 (radius: 10) [01:02:53 -63474.131402] SLOW spr round 10 (radius: 15) [01:06:03] [worker #1] ML tree search #2, logLikelihood: -63497.901935 [01:06:39 -63474.131402] SLOW spr round 11 (radius: 20) [01:12:57 -63474.131402] SLOW spr round 12 (radius: 25) [01:20:01 -63472.815868] SLOW spr round 13 (radius: 5) [01:23:30 -63470.115254] SLOW spr round 14 (radius: 5) [01:26:30 -63470.115247] SLOW spr round 15 (radius: 10) [01:29:00 -63470.115247] SLOW spr round 16 (radius: 15) [01:32:55 -63470.115247] SLOW spr round 17 (radius: 20) [01:34:45] [worker #2] ML tree search #3, logLikelihood: -63498.900326 [01:39:06 -63470.115247] SLOW spr round 18 (radius: 25) [01:44:58] [worker #5] ML tree search #6, logLikelihood: -63479.931169 [01:46:11 -63470.115247] Model parameter optimization (eps = 0.100000) [01:46:18] [worker #0] ML tree search #1, logLikelihood: -63470.085840 [01:46:18 -288052.567026] Initial branch length optimization [01:46:26 -248319.672409] Model parameter optimization (eps = 10.000000) [01:47:21 -247574.672853] AUTODETECT spr round 1 (radius: 5) [01:50:30 -150666.179076] AUTODETECT spr round 2 (radius: 10) [01:52:38] [worker #4] ML tree search #5, logLikelihood: -63359.914133 [01:53:30 -100669.456294] AUTODETECT spr round 3 (radius: 15) [01:54:59] [worker #3] ML tree search #4, logLikelihood: -63483.997202 [01:57:20 -77941.614673] AUTODETECT spr round 4 (radius: 20) [02:02:03 -72556.206381] AUTODETECT spr round 5 (radius: 25) [02:08:00 -72109.215833] SPR radius for FAST iterations: 25 (autodetect) [02:08:00 -72109.215833] Model parameter optimization (eps = 3.000000) [02:08:27 -72053.173127] FAST spr round 1 (radius: 25) [02:11:37 -63995.448068] FAST spr round 2 (radius: 25) [02:13:51 -63629.037983] FAST spr round 3 (radius: 25) [02:15:55 -63565.947722] FAST spr round 4 (radius: 25) [02:17:50 -63559.086334] FAST spr round 5 (radius: 25) [02:19:41 -63557.756497] FAST spr round 6 (radius: 25) [02:21:30 -63557.756326] Model parameter optimization (eps = 1.000000) [02:21:57 -63547.972834] SLOW spr round 1 (radius: 5) [02:24:39 -63522.125769] SLOW spr round 2 (radius: 5) [02:27:19 -63514.580378] SLOW spr round 3 (radius: 5) [02:29:55 -63511.642964] SLOW spr round 4 (radius: 5) [02:32:23 -63511.313876] SLOW spr round 5 (radius: 5) [02:34:49 -63511.313830] SLOW spr round 6 (radius: 10) [02:37:15 -63504.164533] SLOW spr round 7 (radius: 5) [02:40:33 -63503.246319] SLOW spr round 8 (radius: 5) [02:42:47] [worker #1] ML tree search #8, logLikelihood: -63360.247746 [02:43:23 -63503.246307] SLOW spr round 9 (radius: 10) [02:45:54 -63494.130228] SLOW spr round 10 (radius: 5) [02:49:08 -63494.129929] SLOW spr round 11 (radius: 10) [02:51:48 -63494.129899] SLOW spr round 12 (radius: 15) [02:55:38 -63492.007521] SLOW spr round 13 (radius: 5) [02:57:50] [worker #4] ML tree search #11, logLikelihood: -63499.041916 [02:59:07 -63459.726924] SLOW spr round 14 (radius: 5) [03:02:04 -63458.239295] SLOW spr round 15 (radius: 5) [03:03:08] [worker #2] ML tree search #9, logLikelihood: -63479.709827 [03:04:50 -63456.028303] SLOW spr round 16 (radius: 5) [03:05:57] [worker #3] ML tree search #10, logLikelihood: -63466.963606 [03:07:22 -63455.176787] SLOW spr round 17 (radius: 5) [03:09:49 -63455.176786] SLOW spr round 18 (radius: 10) [03:12:13 -63455.176786] SLOW spr round 19 (radius: 15) [03:16:23 -63455.176785] SLOW spr round 20 (radius: 20) [03:22:48 -63455.176785] SLOW spr round 21 (radius: 25) [03:26:53] [worker #5] ML tree search #12, logLikelihood: -63418.725161 [03:30:59 -63455.176785] Model parameter optimization (eps = 0.100000) [03:31:25] [worker #0] ML tree search #7, logLikelihood: -63449.156056 [03:31:25 -287796.554826] Initial branch length optimization [03:31:31 -248906.235215] Model parameter optimization (eps = 10.000000) [03:32:18 -248187.274285] AUTODETECT spr round 1 (radius: 5) [03:35:26 -153589.586363] AUTODETECT spr round 2 (radius: 10) [03:38:32 -102312.995819] AUTODETECT spr round 3 (radius: 15) [03:42:11 -79349.395546] AUTODETECT spr round 4 (radius: 20) [03:46:57 -73283.344776] AUTODETECT spr round 5 (radius: 25) [03:51:37 -72791.451419] SPR radius for FAST iterations: 25 (autodetect) [03:51:37 -72791.451419] Model parameter optimization (eps = 3.000000) [03:51:59 -72735.986767] FAST spr round 1 (radius: 25) [03:55:07 -63932.748568] FAST spr round 2 (radius: 25) [03:57:25 -63587.988079] FAST spr round 3 (radius: 25) [03:59:32 -63521.335084] FAST spr round 4 (radius: 25) [04:01:28 -63517.141459] FAST spr round 5 (radius: 25) [04:03:18 -63517.141393] Model parameter optimization (eps = 1.000000) [04:03:48 -63456.243001] SLOW spr round 1 (radius: 5) [04:06:36 -63395.468023] SLOW spr round 2 (radius: 5) [04:09:11] [worker #2] ML tree search #15, logLikelihood: -63481.774079 [04:09:15 -63388.556802] SLOW spr round 3 (radius: 5) [04:10:27] [worker #4] ML tree search #17, logLikelihood: -63363.199532 [04:11:48 -63384.799839] SLOW spr round 4 (radius: 5) [04:14:14 -63384.799834] SLOW spr round 5 (radius: 10) [04:16:44 -63377.206613] SLOW spr round 6 (radius: 5) [04:20:08 -63372.406248] SLOW spr round 7 (radius: 5) [04:23:00 -63372.062357] SLOW spr round 8 (radius: 5) [04:24:34] [worker #1] ML tree search #14, logLikelihood: -63375.766787 [04:25:38 -63372.062357] SLOW spr round 9 (radius: 10) [04:28:04 -63372.062357] SLOW spr round 10 (radius: 15) [04:32:10 -63371.590558] SLOW spr round 11 (radius: 5) [04:35:40 -63366.028352] SLOW spr round 12 (radius: 5) [04:38:42 -63365.595861] SLOW spr round 13 (radius: 5) [04:41:20 -63365.595620] SLOW spr round 14 (radius: 10) [04:41:48] [worker #3] ML tree search #16, logLikelihood: -63479.894597 [04:43:45 -63365.595460] SLOW spr round 15 (radius: 15) [04:47:47 -63362.264130] SLOW spr round 16 (radius: 5) [04:51:18 -63358.676578] SLOW spr round 17 (radius: 5) [04:54:15 -63358.675478] SLOW spr round 18 (radius: 10) [04:56:46 -63358.674752] SLOW spr round 19 (radius: 15) [05:00:43 -63358.674267] SLOW spr round 20 (radius: 20) [05:07:18 -63355.838349] SLOW spr round 21 (radius: 5) [05:10:45 -63355.837927] SLOW spr round 22 (radius: 10) [05:13:40 -63355.837645] SLOW spr round 23 (radius: 15) [05:17:26 -63355.837458] SLOW spr round 24 (radius: 20) [05:24:11 -63355.837334] SLOW spr round 25 (radius: 25) [05:32:29 -63355.837251] Model parameter optimization (eps = 0.100000) [05:32:41] [worker #0] ML tree search #13, logLikelihood: -63355.634019 [05:32:41 -287046.968062] Initial branch length optimization [05:32:47 -247892.567301] Model parameter optimization (eps = 10.000000) [05:33:33 -247169.979632] AUTODETECT spr round 1 (radius: 5) [05:36:43 -155983.597937] AUTODETECT spr round 2 (radius: 10) [05:39:46 -101454.787305] AUTODETECT spr round 3 (radius: 15) [05:39:58] [worker #1] ML tree search #20, logLikelihood: -63495.757118 [05:43:13 -83768.215243] AUTODETECT spr round 4 (radius: 20) [05:47:14 -76201.767571] AUTODETECT spr round 5 (radius: 25) [05:51:53 -74880.745811] SPR radius for FAST iterations: 25 (autodetect) [05:51:53 -74880.745811] Model parameter optimization (eps = 3.000000) [05:52:22 -74801.751111] FAST spr round 1 (radius: 25) [05:55:25 -64268.437518] FAST spr round 2 (radius: 25) [05:57:44 -63637.960440] FAST spr round 3 (radius: 25) [05:59:51 -63534.529984] FAST spr round 4 (radius: 25) [06:01:52 -63514.541507] FAST spr round 5 (radius: 25) [06:03:40 -63511.648288] FAST spr round 6 (radius: 25) [06:05:25 -63511.648237] Model parameter optimization (eps = 1.000000) [06:05:50 -63411.473587] SLOW spr round 1 (radius: 5) [06:08:28 -63385.453969] SLOW spr round 2 (radius: 5) [06:11:03 -63381.150903] SLOW spr round 3 (radius: 5) [06:13:31 -63380.574881] SLOW spr round 4 (radius: 5) [06:15:56 -63380.573664] SLOW spr round 5 (radius: 10) [06:18:18 -63380.573648] SLOW spr round 6 (radius: 15) [06:20:02] [worker #5] ML tree search #18, logLikelihood: -63554.415519 [06:22:30 -63380.573648] SLOW spr round 7 (radius: 20) [06:29:16 -63380.007150] SLOW spr round 8 (radius: 5) [06:32:44 -63374.595358] SLOW spr round 9 (radius: 5) [06:35:49 -63371.379722] SLOW spr round 10 (radius: 5) [06:38:29 -63366.347021] SLOW spr round 11 (radius: 5) [06:40:58 -63365.171202] SLOW spr round 12 (radius: 5) [06:43:21 -63365.167742] SLOW spr round 13 (radius: 10) [06:45:40 -63365.166959] SLOW spr round 14 (radius: 15) [06:49:44 -63365.166766] SLOW spr round 15 (radius: 20) [06:56:24 -63365.166716] SLOW spr round 16 (radius: 25) [07:05:07 -63365.166703] Model parameter optimization (eps = 0.100000) [07:05:16] [worker #0] ML tree search #19, logLikelihood: -63364.728115 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.274736,0.443747) (0.231080,1.045592) (0.299593,0.726774) (0.194590,2.151876) 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: -63355.634019 AIC score: 130721.268037 / AICc score: 8174781.268037 / BIC score: 138030.389067 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=283). 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/Q14533/3_mltree/Q14533.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/3_mltree/Q14533.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/3_mltree/Q14533.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14533/3_mltree/Q14533.raxml.log Analysis started: 01-Jul-2021 08:45:10 / finished: 01-Jul-2021 15:50:27 Elapsed time: 25517.083 seconds Consumed energy: 2089.148 Wh (= 10 km in an electric car, or 52 km with an e-scooter!)