RAxML_info.result error message

[Harshani Dilrukshika]

Hi,

I am continuously  getting this message in RAxML_info.result;

Kindly let me know the error that I have done in my phylogenetic analysis.

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Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Sarah Lutteropp (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Charlie Taylor (UF) Alignment has 216 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 33.03% RAxML rapid bootstrapping algorithm Using 1 distinct models/data partitions with joint branch length optimization Executing 100 rapid bootstrap inferences All free model parameters will be estimated by RAxML ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units Partition: 0 Alignment Patterns: 216 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: raxmlHPC-HYBRID-AVX -T 4 -s infile -n result -N 100 -k -p 12345 -x 12345 -m GTRCAT -o Outgroup Time for BS model parameter optimization on Process 7: 0.025945 seconds Time for BS model parameter optimization on Process 9: 0.026137 seconds Time for BS model parameter optimization on Process 3: 0.025209 seconds Time for BS model parameter optimization on Process 2: 0.025322 seconds Time for BS model parameter optimization on Process 5: 0.025641 seconds Time for BS model parameter optimization on Process 8: 0.025701 seconds Time for BS model parameter optimization on Process 0: 0.026718 seconds Time for BS model parameter optimization on Process 1: 0.027601 seconds Time for BS model parameter optimization on Process 4: 0.027507 seconds Bootstrap[90]: Time 0.117928 seconds, bootstrap likelihood -2744.490304, best rearrangement setting 12 Bootstrap[20]: Time 0.120444 seconds, bootstrap likelihood -2832.313956, best rearrangement setting 10 Bootstrap[80]: Time 0.124775 seconds, bootstrap likelihood -2861.637894, best rearrangement setting 13 Bootstrap[50]: Time 0.131204 seconds, bootstrap likelihood -2951.791833, best rearrangement setting 6 Bootstrap[0]: Time 0.136242 seconds, bootstrap likelihood -2903.789317, best rearrangement setting 13 Bootstrap[70]: Time 0.166356 seconds, bootstrap likelihood -2820.594738, best rearrangement setting 15 Bootstrap[30]: Time 0.166571 seconds, bootstrap likelihood -2836.423079, best rearrangement setting 9 Bootstrap[40]: Time 0.158237 seconds, bootstrap likelihood -2907.072031, best rearrangement setting 8 Bootstrap[91]: Time 0.090033 seconds, bootstrap likelihood -2902.092872, best rearrangement setting 5 Bootstrap[1]: Time 0.072929 seconds, bootstrap likelihood -2782.110349, best rearrangement setting 13 Bootstrap[21]: Time 0.107545 seconds, bootstrap likelihood -2903.385580, best rearrangement setting 13 Bootstrap[81]: Time 0.100380 seconds, bootstrap likelihood -2859.885635, best rearrangement setting 5 Bootstrap[10]: Time 0.218123 seconds, bootstrap likelihood -2733.197329, best rearrangement setting 12 Bootstrap[51]: Time 0.115780 seconds, bootstrap likelihood -2866.361820, best rearrangement setting 15 Bootstrap[71]: Time 0.092763 seconds, bootstrap likelihood -2944.945350, best rearrangement setting 5 Bootstrap[41]: Time 0.098613 seconds, bootstrap likelihood -2858.608831, best rearrangement setting 14 Bootstrap[31]: Time 0.127856 seconds, bootstrap likelihood -2820.079634, best rearrangement setting 14 Bootstrap[92]: Time 0.097973 seconds, bootstrap likelihood -2873.724801, best rearrangement setting 10 Bootstrap[22]: Time 0.083306 seconds, bootstrap likelihood -2869.027924, best rearrangement setting 14 Bootstrap[2]: Time 0.099605 seconds, bootstrap likelihood -2947.429592, best rearrangement setting 12 Bootstrap[52]: Time 0.118086 seconds, bootstrap likelihood -2933.266020, best rearrangement setting 6 Time for BS model parameter optimization on Process 6: 0.057938 seconds Bootstrap[82]: Time 0.165863 seconds, bootstrap likelihood -2831.853029, best rearrangement setting 9 Bootstrap[32]: Time 0.135858 seconds, bootstrap likelihood -2860.782430, best rearrangement setting 15 Bootstrap[3]: Time 0.109054 seconds, bootstrap likelihood -2775.922369, best rearrangement setting 15 Bootstrap[53]: Time 0.094759 seconds, bootstrap likelihood -2874.328944, best rearrangement setting 13 Bootstrap[72]: Time 0.226089 seconds, bootstrap likelihood -2890.915165, best rearrangement setting 8 Bootstrap[93]: Time 0.178131 seconds, bootstrap likelihood -2875.604572, best rearrangement setting 9 Bootstrap[83]: Time 0.148201 seconds, bootstrap likelihood -2719.487741, best rearrangement setting 8 Bootstrap[23]: Time 0.227024 seconds, bootstrap likelihood -2834.738048, best rearrangement setting 8 Bootstrap[33]: Time 0.147702 seconds, bootstrap likelihood -3029.306082, best rearrangement setting 10 Bootstrap[84]: Time 0.066503 seconds, bootstrap likelihood -2795.730656, best rearrangement setting 14 Bootstrap[4]: Time 0.194354 seconds, bootstrap likelihood -2928.651012, best rearrangement setting 10 Bootstrap[54]: Time 0.180779 seconds, bootstrap likelihood -2939.582604, best rearrangement setting 14 Bootstrap[73]: Time 0.184238 seconds, bootstrap likelihood -2902.382796, best rearrangement setting 6 Bootstrap[34]: Time 0.121619 seconds, bootstrap likelihood -2913.458459, best rearrangement setting 10 Bootstrap[24]: Time 0.176451 seconds, bootstrap likelihood -2882.810516, best rearrangement setting 14 Bootstrap[42]: Time 0.465493 seconds, bootstrap likelihood -2829.717932, best rearrangement setting 5 Bootstrap[85]: Time 0.206798 seconds, bootstrap likelihood -2846.161813, best rearrangement setting 8 Bootstrap[11]: Time 0.640410 seconds, bootstrap likelihood -2977.831947, best rearrangement setting 13 Bootstrap[60]: Time 0.740767 seconds, bootstrap likelihood -2934.071890, best rearrangement setting 5 Bootstrap[25]: Time 0.194828 seconds, bootstrap likelihood -2904.433663, best rearrangement setting 12 Bootstrap[35]: Time 0.231216 seconds, bootstrap likelihood -2886.560472, best rearrangement setting 13 Bootstrap[86]: Time 0.127356 seconds, bootstrap likelihood -2878.857134, best rearrangement setting 6 Bootstrap[43]: Time 0.230977 seconds, bootstrap likelihood -2797.123391, best rearrangement setting 11 Bootstrap[5]: Time 0.423862 seconds, bootstrap likelihood -2772.176802, best rearrangement setting 10 Bootstrap[74]: Time 0.382584 seconds, bootstrap likelihood -2950.697868, best rearrangement setting 6 Bootstrap[61]: Time 0.171796 seconds, bootstrap likelihood -2985.503121, best rearrangement setting 15 Bootstrap[26]: Time 0.178272 seconds, bootstrap likelihood -2869.379609, best rearrangement setting 14 Bootstrap[87]: Time 0.148335 seconds, bootstrap likelihood -2949.880872, best rearrangement setting 6 Bootstrap[6]: Time 0.141309 seconds, bootstrap likelihood -2921.826684, best rearrangement setting 6 Bootstrap[44]: Time 0.226450 seconds, bootstrap likelihood -2915.945184, best rearrangement setting 6 Bootstrap[88]: Time 0.127061 seconds, bootstrap likelihood -2854.835262, best rearrangement setting 8 Bootstrap[27]: Time 0.139264 seconds, bootstrap likelihood -2805.404869, best rearrangement setting 15 Bootstrap[62]: Time 0.195761 seconds, bootstrap likelihood -2758.232866, best rearrangement setting 7 Bootstrap[75]: Time 0.208706 seconds, bootstrap likelihood -2958.221716, best rearrangement setting 7 Bootstrap[12]: Time 0.432008 seconds, bootstrap likelihood -2919.585416, best rearrangement setting 13 Bootstrap[28]: Time 0.076335 seconds, bootstrap likelihood -2978.537062, best rearrangement setting 9 Bootstrap[94]: Time 0.845560 seconds, bootstrap likelihood -2921.851063, best rearrangement setting 10 Bootstrap[89]: Time 0.148924 seconds, bootstrap likelihood -2800.344039, best rearrangement setting 5 Bootstrap[45]: Time 0.242102 seconds, bootstrap likelihood -3032.155485, best rearrangement setting 15 Bootstrap[29]: Time 0.159305 seconds, bootstrap likelihood -2946.860043, best rearrangement setting 6 Bootstrap[36]: Time 0.548286 seconds, bootstrap likelihood -2961.698755, best rearrangement setting 7 Bootstrap[63]: Time 0.226290 seconds, bootstrap likelihood -2777.348590, best rearrangement setting 15 Bootstrap[13]: Time 0.219318 seconds, bootstrap likelihood -2823.022553, best rearrangement setting 6 Bootstrap[64]: Time 0.114284 seconds, bootstrap likelihood -2863.236617, best rearrangement setting 10 Bootstrap[37]: Time 0.148125 seconds, bootstrap likelihood -2945.841379, best rearrangement setting 10 Bootstrap[46]: Time 0.250861 seconds, bootstrap likelihood -2850.765668, best rearrangement setting 11 Bootstrap[14]: Time 0.231073 seconds, bootstrap likelihood -2948.246536, best rearrangement setting 7 Bootstrap[65]: Time 0.178642 seconds, bootstrap likelihood -2986.618396, best rearrangement setting 6 Bootstrap[7]: Time 0.620634 seconds, bootstrap likelihood -2889.737079, best rearrangement setting 14 Bootstrap[47]: Time 0.142044 seconds, bootstrap likelihood -2830.521665, best rearrangement setting 5 Bootstrap[38]: Time 0.281842 seconds, bootstrap likelihood -2899.014359, best rearrangement setting 10 Bootstrap[8]: Time 0.160997 seconds, bootstrap likelihood -2865.605225, best rearrangement setting 5 Bootstrap[66]: Time 0.214036 seconds, bootstrap likelihood -2771.974508, best rearrangement setting 9 Bootstrap[15]: Time 0.225275 seconds, bootstrap likelihood -2915.085475, best rearrangement setting 11 Bootstrap[48]: Time 0.153960 seconds, bootstrap likelihood -2838.390595, best rearrangement setting 12 Bootstrap[55]: Time 1.492395 seconds, bootstrap likelihood -2798.920726, best rearrangement setting 5 Bootstrap[9]: Time 0.162660 seconds, bootstrap likelihood -3007.558453, best rearrangement setting 7 Bootstrap[16]: Time 0.177738 seconds, bootstrap likelihood -3025.286515, best rearrangement setting 10 Bootstrap[39]: Time 0.264233 seconds, bootstrap likelihood -2914.191063, best rearrangement setting 12 Bootstrap[49]: Time 0.180197 seconds, bootstrap likelihood -2794.183425, best rearrangement setting 6 Bootstrap[67]: Time 0.213238 seconds, bootstrap likelihood -3029.324587, best rearrangement setting 5 Bootstrap[17]: Time 0.084516 seconds, bootstrap likelihood -2881.355769, best rearrangement setting 9 Bootstrap[95]: Time 0.951798 seconds, bootstrap likelihood -2985.677911, best rearrangement setting 10 Bootstrap[56]: Time 0.153278 seconds, bootstrap likelihood -2900.695705, best rearrangement setting 5 Bootstrap[76]: Time 1.097454 seconds, bootstrap likelihood -2972.418620, best rearrangement setting 13 Bootstrap[18]: Time 0.170563 seconds, bootstrap likelihood -2951.382458, best rearrangement setting 7 Bootstrap[68]: Time 0.240755 seconds, bootstrap likelihood -2951.615622, best rearrangement setting 15 Bootstrap[57]: Time 0.181294 seconds, bootstrap likelihood -2904.724609, best rearrangement setting 11 Bootstrap[19]: Time 0.155824 seconds, bootstrap likelihood -2997.770519, best rearrangement setting 12 Bootstrap[69]: Time 0.205211 seconds, bootstrap likelihood -2907.178132, best rearrangement setting 6 Bootstrap[58]: Time 0.365913 seconds, bootstrap likelihood -3001.316271, best rearrangement setting 14 Bootstrap[59]: Time 0.182060 seconds, bootstrap likelihood -2892.240683, best rearrangement setting 11 Bootstrap[77]: Time 0.816079 seconds, bootstrap likelihood -2963.763375, best rearrangement setting 11 Bootstrap[78]: Time 0.195081 seconds, bootstrap likelihood -2818.666332, best rearrangement setting 6 Bootstrap[79]: Time 0.199404 seconds, bootstrap likelihood -2810.579011, best rearrangement setting 11 Bootstrap[96]: Time 1.611031 seconds, bootstrap likelihood -2871.202049, best rearrangement setting 10 Bootstrap[97]: Time 0.963781 seconds, bootstrap likelihood -2825.662763, best rearrangement setting 12 Bootstrap[98]: Time 0.217827 seconds, bootstrap likelihood -2914.727063, best rearrangement setting 9 Bootstrap[99]: Time 0.184596 seconds, bootstrap likelihood -2872.613216, best rearrangement setting 11 Overall Time for 100 Rapid Bootstraps 5.374294 seconds Average Time per Rapid Bootstrap 0.053743 seconds All 100 bootstrapped trees written to: /expanse/projects/ngbt/backend/expanse_workspace/NGBW-JOB-RAXMLHPC2BB-D18AE25452CA4294A2EA2700332FBE5E/RAxML_bootstrap.result 

[Mark Miller]

Hi there,

This looks like a pretty normal output file for a successful run.

Can you tell me what concerns you have about the output?

Mark