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 03-Jul-2021 14:12:39 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/2_msa/P30531_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531 --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/P30531/2_msa/P30531_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 506 sites WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and sp_Q7K4Y6_DAT_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and tr_B4HSZ4_B4HSZ4_DROSE_7238 are exactly identical! WARNING: Sequences sp_P31648_SC6A1_MOUSE_10090 and sp_P23978_SC6A1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61327_SC6A3_MOUSE_10090 and sp_P23977_SC6A3_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_E2RKV9_E2RKV9_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2I2UPJ1_A0A2I2UPJ1_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2U3YMF9_A0A2U3YMF9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z0N5_M3Z0N5_MUSPF_9669 and tr_A0A2U3VL81_A0A2U3VL81_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z0N5_M3Z0N5_MUSPF_9669 and tr_A0A2Y9J8H8_A0A2Y9J8H8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3FZC9_A0A2I3FZC9_NOMLE_61853 and tr_G3RC38_G3RC38_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3FZC9_A0A2I3FZC9_NOMLE_61853 and tr_A0A2I3SWR4_A0A2I3SWR4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3HE37_G3HE37_CRIGR_10029 and sp_P58295_SC6A5_RAT_10116 are exactly identical! WARNING: Sequences tr_G3HE37_G3HE37_CRIGR_10029 and tr_A0A1U8CFY0_A0A1U8CFY0_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2PA22_H2PA22_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2QM23_H2QM23_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and sp_P30531_SC6A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6WVM8_F6WVM8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_G7NYT4_G7NYT4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A096NQ20_A0A096NQ20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A0D9RC09_A0A0D9RC09_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K5KZH8_A0A2K5KZH8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6BVQ8_A0A2K6BVQ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6A0C9_A0A2K6A0C9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2R9CH47_A0A2R9CH47_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_G1SE03_G1SE03_RABIT_9986 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F1P8R8_F1P8R8_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F6WCP2_F6WCP2_HORSE_9796 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F7F7H9_F7F7H9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A287AMT4_A0A287AMT4_PIG_9823 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_G7PQK0_G7PQK0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A096NG10_A0A096NG10_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A0D9QYL3_A0A0D9QYL3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K6ECY9_A0A2K6ECY9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K5YI07_A0A2K5YI07_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2Y9JTR3_A0A2Y9JTR3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A2I0MHT3_A0A2I0MHT3_COLLI_8932 are exactly identical! WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A1V4JPB2_A0A1V4JPB2_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A226MWW0_A0A226MWW0_CALSU_9009 are exactly identical! WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and sp_Q9Y345_SC6A5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and tr_A0A2R9AHV1_A0A2R9AHV1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QQL1_H2QQL1_PANTR_9598 and tr_A0A2R8ZUK6_A0A2R8ZUK6_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7DP91_K7DP91_PANTR_9598 and sp_P48029_SC6A8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7DP91_K7DP91_PANTR_9598 and tr_A0A2K5KJE1_A0A2K5KJE1_CERAT_9531 are exactly identical! WARNING: Sequences tr_K7DP91_K7DP91_PANTR_9598 and tr_A0A2K6APW9_A0A2K6APW9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FWA1_F7FWA1_MONDO_13616 and tr_G3WUU1_G3WUU1_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6Z3A6_F6Z3A6_HORSE_9796 and tr_F1SQA4_F1SQA4_PIG_9823 are exactly identical! WARNING: Sequences tr_F6Z3A6_F6Z3A6_HORSE_9796 and tr_A0A1U7TXN5_A0A1U7TXN5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_W5PDT2_W5PDT2_SHEEP_9940 and tr_F1N5R0_F1N5R0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3ZTE1_M3ZTE1_XIPMA_8083 and tr_A0A096M316_A0A096M316_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NPD8_A0A158NPD8_ATTCE_12957 and tr_F4WH84_F4WH84_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NQQ9_A0A158NQQ9_ATTCE_12957 and tr_F4WBV1_F4WBV1_ACREC_103372 are exactly identical! WARNING: Sequences tr_I3MA19_I3MA19_ICTTR_43179 and tr_H0X8A1_H0X8A1_OTOGA_30611 are exactly identical! WARNING: Sequences tr_I3MA19_I3MA19_ICTTR_43179 and tr_F6ZPU5_F6ZPU5_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_G7PIL7_G7PIL7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A096NC41_A0A096NC41_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A0D9RAK2_A0A0D9RAK2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K5L7Z6_A0A2K5L7Z6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K6DHL4_A0A2K6DHL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HEB3_F7HEB3_MACMU_9544 and tr_A0A2K5ZYU9_A0A2K5ZYU9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZQY1_H0ZQY1_TAEGU_59729 and tr_A0A218V974_A0A218V974_9PASE_299123 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A096MN61_A0A096MN61_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A0D9RXR1_A0A0D9RXR1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5KJJ7_A0A2K5KJJ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K6C6Z6_A0A2K6C6Z6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5Z263_A0A2K5Z263_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3WZR1_M3WZR1_FELCA_9685 and tr_A0A2Y9FHD2_A0A2Y9FHD2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3WZR1_M3WZR1_FELCA_9685 and tr_A0A383ZIE6_A0A383ZIE6_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091ENZ6_A0A091ENZ6_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091VHN5_A0A091VHN5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A093H772_A0A093H772_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A093G6B4_A0A093G6B4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3KDU8_U3KDU8_FICAL_59894 and tr_A0A091I6F5_A0A091I6F5_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3ITL2_U3ITL2_ANAPL_8839 and tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3ITL2_U3ITL2_ANAPL_8839 and tr_A0A087RH38_A0A087RH38_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3ITL2_U3ITL2_ANAPL_8839 and tr_A0A091WBW6_A0A091WBW6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3ITL2_U3ITL2_ANAPL_8839 and tr_A0A099ZE46_A0A099ZE46_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3ITL2_U3ITL2_ANAPL_8839 and tr_A0A0A0ATB2_A0A0A0ATB2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087XTR0_A0A087XTR0_POEFO_48698 and tr_A0A087YDV2_A0A087YDV2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096MYM4_A0A096MYM4_PAPAN_9555 and tr_A0A2K5LFH9_A0A2K5LFH9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MYM4_A0A096MYM4_PAPAN_9555 and tr_A0A2K6BIP4_A0A2K6BIP4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N2F3_A0A096N2F3_PAPAN_9555 and tr_A0A2K6BWY5_A0A2K6BWY5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151MK13_A0A151MK13_ALLMI_8496 and tr_A0A1U8CTU6_A0A1U8CTU6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151MS82_A0A151MS82_ALLMI_8496 and tr_A0A1U8CYT6_A0A1U8CYT6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NIH4_A0A151NIH4_ALLMI_8496 and tr_A0A1U7SBY4_A0A1U7SBY4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PBK1_A0A151PBK1_ALLMI_8496 and tr_A0A1U7SB16_A0A1U7SB16_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087RH37_A0A087RH37_APTFO_9233 and tr_A0A0A0ATJ6_A0A0A0ATJ6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093I2B1_A0A093I2B1_STRCA_441894 and tr_A0A226N140_A0A226N140_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A093I2B1_A0A093I2B1_STRCA_441894 and tr_A0A226P2N5_A0A226P2N5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A091W8F8_A0A091W8F8_OPIHO_30419 and tr_A0A218VCV3_A0A218VCV3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I0LVM4_A0A2I0LVM4_COLLI_8932 and tr_A0A1V4JII7_A0A1V4JII7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RRC9_A0A0V0RRC9_9BILA_6336 and tr_A0A0V1CJ51_A0A0V1CJ51_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RRC9_A0A0V0RRC9_9BILA_6336 and tr_A0A0V0WXY8_A0A0V0WXY8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RRC9_A0A0V0RRC9_9BILA_6336 and tr_A0A0V0VPP5_A0A0V0VPP5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1L239_A0A0V1L239_9BILA_6335 and tr_A0A0V1NLY7_A0A0V1NLY7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0ZD68_A0A0V0ZD68_9BILA_990121 and tr_A0A0V1MYG8_A0A0V1MYG8_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0ZD68_A0A0V0ZD68_9BILA_990121 and tr_A0A0V1H1N0_A0A0V1H1N0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226MXQ4_A0A226MXQ4_CALSU_9009 and tr_A0A226PLR4_A0A226PLR4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NG47_A0A226NG47_CALSU_9009 and tr_A0A226PF47_A0A226PF47_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RWR4_A0A2D0RWR4_ICTPU_7998 and tr_A0A2D0RYA2_A0A2D0RYA2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T468_A0A2D0T468_ICTPU_7998 and tr_A0A2D0T472_A0A2D0T472_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 100 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/P30531/3_mltree/P30531.raxml.reduced.phy Alignment comprises 1 partitions and 506 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 506 / 506 Gaps: 0.64 % Invariant sites: 0.99 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 253 / 20240 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -680378.846411] Initial branch length optimization [00:00:13 -577301.250839] Model parameter optimization (eps = 10.000000) [00:01:13 -575068.092107] AUTODETECT spr round 1 (radius: 5) [00:04:56 -358776.113007] AUTODETECT spr round 2 (radius: 10) [00:08:51 -249392.443674] AUTODETECT spr round 3 (radius: 15) [00:13:00 -198010.066641] AUTODETECT spr round 4 (radius: 20) [00:17:47 -173645.037253] AUTODETECT spr round 5 (radius: 25) [00:24:44 -164798.203415] SPR radius for FAST iterations: 25 (autodetect) [00:24:44 -164798.203415] Model parameter optimization (eps = 3.000000) [00:25:16 -164683.258153] FAST spr round 1 (radius: 25) [00:28:51 -140698.776028] FAST spr round 2 (radius: 25) [00:31:33 -139632.076731] FAST spr round 3 (radius: 25) [00:33:56 -139538.554057] FAST spr round 4 (radius: 25) [00:36:04 -139536.506799] FAST spr round 5 (radius: 25) [00:38:07 -139535.739642] FAST spr round 6 (radius: 25) [00:40:06 -139535.378608] FAST spr round 7 (radius: 25) [00:42:04 -139535.378605] Model parameter optimization (eps = 1.000000) [00:42:34 -139525.181049] SLOW spr round 1 (radius: 5) [00:45:25 -139499.076782] SLOW spr round 2 (radius: 5) [00:48:15 -139493.737557] SLOW spr round 3 (radius: 5) [00:50:59 -139493.737425] SLOW spr round 4 (radius: 10) [00:53:52 -139490.372965] SLOW spr round 5 (radius: 5) [00:57:32 -139489.689707] SLOW spr round 6 (radius: 5) [01:00:39 -139489.689685] SLOW spr round 7 (radius: 10) [01:03:34 -139489.689676] SLOW spr round 8 (radius: 15) [01:08:05 -139489.689676] SLOW spr round 9 (radius: 20) [01:16:10] [worker #2] ML tree search #3, logLikelihood: -139497.529900 [01:16:45 -139489.689676] SLOW spr round 10 (radius: 25) [01:21:04] [worker #1] ML tree search #2, logLikelihood: -139495.298036 [01:28:57 -139489.689676] Model parameter optimization (eps = 0.100000) [01:29:11] [worker #0] ML tree search #1, logLikelihood: -139489.596677 [01:29:11 -677098.198718] Initial branch length optimization [01:29:21 -573572.226856] Model parameter optimization (eps = 10.000000) [01:30:19 -571389.578298] AUTODETECT spr round 1 (radius: 5) [01:33:56 -356261.374146] AUTODETECT spr round 2 (radius: 10) [01:37:41 -231626.662167] AUTODETECT spr round 3 (radius: 15) [01:41:35 -196585.729193] AUTODETECT spr round 4 (radius: 20) [01:46:11 -179524.605646] AUTODETECT spr round 5 (radius: 25) [01:51:18 -167140.372274] SPR radius for FAST iterations: 25 (autodetect) [01:51:18 -167140.372274] Model parameter optimization (eps = 3.000000) [01:51:59 -167005.746371] FAST spr round 1 (radius: 25) [01:55:20 -140989.537945] FAST spr round 2 (radius: 25) [01:58:05 -139668.247608] FAST spr round 3 (radius: 25) [02:00:27 -139558.111162] FAST spr round 4 (radius: 25) [02:02:37 -139553.487534] FAST spr round 5 (radius: 25) [02:04:39 -139553.486937] Model parameter optimization (eps = 1.000000) [02:05:04 -139546.315650] SLOW spr round 1 (radius: 5) [02:08:03 -139494.385629] SLOW spr round 2 (radius: 5) [02:10:46 -139494.385373] SLOW spr round 3 (radius: 10) [02:13:35 -139494.385335] SLOW spr round 4 (radius: 15) [02:18:04 -139494.216147] SLOW spr round 5 (radius: 5) [02:21:54 -139494.216144] SLOW spr round 6 (radius: 10) [02:25:10 -139494.216144] SLOW spr round 7 (radius: 15) [02:29:29 -139494.216144] SLOW spr round 8 (radius: 20) [02:37:43 -139494.216144] SLOW spr round 9 (radius: 25) [02:41:10] [worker #2] ML tree search #6, logLikelihood: -139508.193952 [02:49:01 -139494.216144] Model parameter optimization (eps = 0.100000) [02:49:08] [worker #0] ML tree search #4, logLikelihood: -139494.174939 [02:49:08 -680586.032084] Initial branch length optimization [02:49:15 -577185.750105] Model parameter optimization (eps = 10.000000) [02:50:12 -574914.186557] AUTODETECT spr round 1 (radius: 5) [02:53:40 -346639.848030] AUTODETECT spr round 2 (radius: 10) [02:55:01] [worker #1] ML tree search #5, logLikelihood: -139482.922190 [02:57:24 -225548.729210] AUTODETECT spr round 3 (radius: 15) [03:01:14 -188019.176287] AUTODETECT spr round 4 (radius: 20) [03:05:52 -164262.444235] AUTODETECT spr round 5 (radius: 25) [03:11:02 -162293.857738] SPR radius for FAST iterations: 25 (autodetect) [03:11:02 -162293.857738] Model parameter optimization (eps = 3.000000) [03:11:29 -162157.601132] FAST spr round 1 (radius: 25) [03:14:57 -140869.986264] FAST spr round 2 (radius: 25) [03:17:35 -139711.215945] FAST spr round 3 (radius: 25) [03:19:57 -139546.658777] FAST spr round 4 (radius: 25) [03:22:06 -139541.773142] FAST spr round 5 (radius: 25) [03:24:09 -139541.772714] Model parameter optimization (eps = 1.000000) [03:24:31 -139534.718518] SLOW spr round 1 (radius: 5) [03:27:24 -139496.214163] SLOW spr round 2 (radius: 5) [03:30:11 -139495.325163] SLOW spr round 3 (radius: 5) [03:32:52 -139495.323517] SLOW spr round 4 (radius: 10) [03:35:41 -139495.323195] SLOW spr round 5 (radius: 15) [03:40:17 -139495.323140] SLOW spr round 6 (radius: 20) [03:48:58 -139495.323131] SLOW spr round 7 (radius: 25) [04:01:05 -139495.323129] Model parameter optimization (eps = 0.100000) [04:01:21] [worker #0] ML tree search #7, logLikelihood: -139494.912516 [04:01:21 -680844.482587] Initial branch length optimization [04:01:34 -578222.767163] Model parameter optimization (eps = 10.000000) [04:02:43 -576066.272754] AUTODETECT spr round 1 (radius: 5) [04:03:59] [worker #2] ML tree search #9, logLikelihood: -139513.551075 [04:06:16 -353949.231499] AUTODETECT spr round 2 (radius: 10) [04:08:56] [worker #1] ML tree search #8, logLikelihood: -139514.475283 [04:10:04 -239522.501724] AUTODETECT spr round 3 (radius: 15) [04:14:03 -198599.214738] AUTODETECT spr round 4 (radius: 20) [04:19:30 -170022.411337] AUTODETECT spr round 5 (radius: 25) [04:26:02 -166266.845451] SPR radius for FAST iterations: 25 (autodetect) [04:26:02 -166266.845451] Model parameter optimization (eps = 3.000000) [04:26:34 -166110.219811] FAST spr round 1 (radius: 25) [04:29:56 -140551.036644] FAST spr round 2 (radius: 25) [04:32:42 -139567.224093] FAST spr round 3 (radius: 25) [04:35:10 -139534.485788] FAST spr round 4 (radius: 25) [04:37:16 -139530.486810] FAST spr round 5 (radius: 25) [04:39:18 -139530.145764] FAST spr round 6 (radius: 25) [04:41:17 -139530.145755] Model parameter optimization (eps = 1.000000) [04:41:43 -139519.700394] SLOW spr round 1 (radius: 5) [04:44:33 -139495.468787] SLOW spr round 2 (radius: 5) [04:47:16 -139495.194641] SLOW spr round 3 (radius: 5) [04:49:54 -139495.194637] SLOW spr round 4 (radius: 10) [04:52:42 -139495.194358] SLOW spr round 5 (radius: 15) [04:57:08 -139495.018019] SLOW spr round 6 (radius: 5) [05:00:58 -139495.018018] SLOW spr round 7 (radius: 10) [05:04:13 -139495.018018] SLOW spr round 8 (radius: 15) [05:08:35 -139495.018018] SLOW spr round 9 (radius: 20) [05:16:54 -139495.018018] SLOW spr round 10 (radius: 25) [05:19:23] [worker #2] ML tree search #12, logLikelihood: -139504.663138 [05:28:26 -139495.018018] Model parameter optimization (eps = 0.100000) [05:28:32] [worker #0] ML tree search #10, logLikelihood: -139494.940614 [05:28:32 -681093.894111] Initial branch length optimization [05:28:40 -577676.617613] Model parameter optimization (eps = 10.000000) [05:29:43 -575329.972580] AUTODETECT spr round 1 (radius: 5) [05:31:46] [worker #1] ML tree search #11, logLikelihood: -139496.276566 [05:33:18 -355519.037449] AUTODETECT spr round 2 (radius: 10) [05:37:08 -232279.390658] AUTODETECT spr round 3 (radius: 15) [05:40:58 -197708.241175] AUTODETECT spr round 4 (radius: 20) [05:45:43 -169163.237536] AUTODETECT spr round 5 (radius: 25) [05:50:47 -168603.811146] SPR radius for FAST iterations: 25 (autodetect) [05:50:47 -168603.811146] Model parameter optimization (eps = 3.000000) [05:51:13 -168455.281996] FAST spr round 1 (radius: 25) [05:54:26 -140498.388739] FAST spr round 2 (radius: 25) [05:56:50 -139551.386379] FAST spr round 3 (radius: 25) [05:59:05 -139526.859195] FAST spr round 4 (radius: 25) [06:01:06 -139526.225473] FAST spr round 5 (radius: 25) [06:03:04 -139526.225472] Model parameter optimization (eps = 1.000000) [06:03:25 -139518.264549] SLOW spr round 1 (radius: 5) [06:06:17 -139496.165459] SLOW spr round 2 (radius: 5) [06:09:00 -139495.887651] SLOW spr round 3 (radius: 5) [06:11:36 -139495.887643] SLOW spr round 4 (radius: 10) [06:14:21 -139495.887640] SLOW spr round 5 (radius: 15) [06:18:49 -139495.887640] SLOW spr round 6 (radius: 20) [06:26:41 -139495.887640] SLOW spr round 7 (radius: 25) [06:37:52 -139495.887639] Model parameter optimization (eps = 0.100000) [06:38:04] [worker #0] ML tree search #13, logLikelihood: -139495.763421 [06:38:04 -676839.659603] Initial branch length optimization [06:38:13 -575199.023742] Model parameter optimization (eps = 10.000000) [06:39:25 -572971.389558] AUTODETECT spr round 1 (radius: 5) [06:43:02 -347043.609291] AUTODETECT spr round 2 (radius: 10) [06:43:07] [worker #2] ML tree search #15, logLikelihood: -139512.432391 [06:46:53 -233648.123932] AUTODETECT spr round 3 (radius: 15) [06:50:51 -194345.642509] AUTODETECT spr round 4 (radius: 20) [06:56:56 -166531.204615] AUTODETECT spr round 5 (radius: 25) [07:04:51 -163182.563369] SPR radius for FAST iterations: 25 (autodetect) [07:04:51 -163182.563369] Model parameter optimization (eps = 3.000000) [07:05:22 -163037.511437] FAST spr round 1 (radius: 25) [07:08:38 -140373.835929] FAST spr round 2 (radius: 25) [07:11:12 -139633.475829] FAST spr round 3 (radius: 25) [07:13:35 -139555.599483] FAST spr round 4 (radius: 25) [07:15:45 -139547.143839] FAST spr round 5 (radius: 25) [07:17:45 -139546.052999] FAST spr round 6 (radius: 25) [07:19:43 -139546.052440] Model parameter optimization (eps = 1.000000) [07:20:06 -139541.418216] SLOW spr round 1 (radius: 5) [07:22:53 -139520.587002] SLOW spr round 2 (radius: 5) [07:25:31] [worker #1] ML tree search #14, logLikelihood: -139498.487559 [07:25:34 -139519.869484] SLOW spr round 3 (radius: 5) [07:28:13 -139518.771047] SLOW spr round 4 (radius: 5) [07:30:51 -139518.771026] SLOW spr round 5 (radius: 10) [07:33:42 -139510.502679] SLOW spr round 6 (radius: 5) [07:37:23 -139501.368848] SLOW spr round 7 (radius: 5) [07:40:33 -139501.065139] SLOW spr round 8 (radius: 5) [07:43:23 -139501.065138] SLOW spr round 9 (radius: 10) [07:46:14 -139501.065138] SLOW spr round 10 (radius: 15) [07:50:37 -139501.065138] SLOW spr round 11 (radius: 20) [07:57:32 -139501.065138] SLOW spr round 12 (radius: 25) [08:01:44] [worker #2] ML tree search #18, logLikelihood: -139501.532544 [08:09:56 -139501.065138] Model parameter optimization (eps = 0.100000) [08:10:09] [worker #0] ML tree search #16, logLikelihood: -139500.819011 [08:10:09 -678543.020407] Initial branch length optimization [08:10:18 -576551.303619] Model parameter optimization (eps = 10.000000) [08:11:32 -574280.824380] AUTODETECT spr round 1 (radius: 5) [08:15:06 -361909.934076] AUTODETECT spr round 2 (radius: 10) [08:18:54 -246281.596472] AUTODETECT spr round 3 (radius: 15) [08:22:47 -201544.955739] AUTODETECT spr round 4 (radius: 20) [08:27:24 -169180.369093] AUTODETECT spr round 5 (radius: 25) [08:33:19 -165162.569333] SPR radius for FAST iterations: 25 (autodetect) [08:33:19 -165162.569333] Model parameter optimization (eps = 3.000000) [08:33:56 -165027.759349] FAST spr round 1 (radius: 25) [08:37:16 -140712.129225] FAST spr round 2 (radius: 25) [08:39:51 -139636.323138] FAST spr round 3 (radius: 25) [08:42:14 -139555.306225] FAST spr round 4 (radius: 25) [08:44:17 -139549.983187] FAST spr round 5 (radius: 25) [08:44:24] [worker #1] ML tree search #17, logLikelihood: -139496.153091 [08:46:18 -139548.278520] FAST spr round 6 (radius: 25) [08:48:17 -139548.278496] Model parameter optimization (eps = 1.000000) [08:48:39 -139541.205719] SLOW spr round 1 (radius: 5) [08:51:31 -139509.497730] SLOW spr round 2 (radius: 5) [08:54:18 -139507.276000] SLOW spr round 3 (radius: 5) [08:56:57 -139507.275485] SLOW spr round 4 (radius: 10) [08:59:47 -139507.051410] SLOW spr round 5 (radius: 5) [09:03:13 -139507.051408] SLOW spr round 6 (radius: 10) [09:06:06 -139507.051407] SLOW spr round 7 (radius: 15) [09:09:36 -139507.051407] SLOW spr round 8 (radius: 20) [09:17:59 -139507.051407] SLOW spr round 9 (radius: 25) [09:29:58 -139507.051407] Model parameter optimization (eps = 0.100000) [09:30:09] [worker #0] ML tree search #19, logLikelihood: -139506.922624 [10:02:13] [worker #1] ML tree search #20, logLikelihood: -139500.127909 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.314010,0.485491) (0.410499,0.684536) (0.230354,1.767002) (0.045138,3.533951) 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: -139482.922190 AIC score: 282975.844380 / AICc score: 8327035.844380 / BIC score: 291450.050402 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=506). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 168 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P30531/3_mltree/P30531.raxml.log Analysis started: 03-Jul-2021 14:12:39 / finished: 04-Jul-2021 00:14:53 Elapsed time: 36133.797 seconds Consumed energy: 3154.570 Wh (= 16 km in an electric car, or 79 km with an e-scooter!)