view test-data/test_15.out @ 0:6d930f037fea draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122

******************** CONCATENATION ********************

Process nucleotides concatenation:
	Number of taxa aligned = 9
	Number of loci concatenated = 178

	Total length of the concatenated sequences [All codon positions] = 41262
		Total length of the concatenated sequences [Codon positions 1 & 2] = 27508
		Total length of the concatenated sequences [Codon position 3] = 13754



******************** RAxML RUN ********************



Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" 



This is RAxML version 8.2.9 released by Alexandros Stamatakis on July 20 2016.

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 564 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 76.95%

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
GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 564
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

raxmlHPC -n galaxy_run -s ./03_Concatenation_nuc.phy -m GTRGAMMA -p 1234567890 -N 100 -f d -x 123456789 



Time for BS model parameter optimization 0.210613
Bootstrap[0]: Time 1.048781 seconds, bootstrap likelihood -75932.545350, best rearrangement setting 15
Bootstrap[1]: Time 0.370352 seconds, bootstrap likelihood -76007.537590, best rearrangement setting 11
Bootstrap[2]: Time 0.349113 seconds, bootstrap likelihood -75997.035876, best rearrangement setting 12
Bootstrap[3]: Time 0.485543 seconds, bootstrap likelihood -76139.230321, best rearrangement setting 12
Bootstrap[4]: Time 0.448112 seconds, bootstrap likelihood -76104.701291, best rearrangement setting 6
Bootstrap[5]: Time 0.491783 seconds, bootstrap likelihood -75911.379318, best rearrangement setting 13
Bootstrap[6]: Time 0.529860 seconds, bootstrap likelihood -76170.094697, best rearrangement setting 15
Bootstrap[7]: Time 0.497637 seconds, bootstrap likelihood -76207.588083, best rearrangement setting 14
Bootstrap[8]: Time 0.522369 seconds, bootstrap likelihood -75549.145357, best rearrangement setting 14
Bootstrap[9]: Time 0.562428 seconds, bootstrap likelihood -76015.528837, best rearrangement setting 11
Bootstrap[10]: Time 0.608720 seconds, bootstrap likelihood -76082.832555, best rearrangement setting 11
Bootstrap[11]: Time 0.584563 seconds, bootstrap likelihood -76301.435377, best rearrangement setting 11
Bootstrap[12]: Time 0.557597 seconds, bootstrap likelihood -76014.755388, best rearrangement setting 12
Bootstrap[13]: Time 0.564486 seconds, bootstrap likelihood -75987.806027, best rearrangement setting 9
Bootstrap[14]: Time 0.310805 seconds, bootstrap likelihood -75952.764120, best rearrangement setting 12
Bootstrap[15]: Time 0.551613 seconds, bootstrap likelihood -76248.341862, best rearrangement setting 13
Bootstrap[16]: Time 0.517321 seconds, bootstrap likelihood -76433.446646, best rearrangement setting 7
Bootstrap[17]: Time 0.499398 seconds, bootstrap likelihood -75691.661860, best rearrangement setting 12
Bootstrap[18]: Time 0.521698 seconds, bootstrap likelihood -75894.741916, best rearrangement setting 6
Bootstrap[19]: Time 0.589791 seconds, bootstrap likelihood -76096.718199, best rearrangement setting 7
Bootstrap[20]: Time 0.696489 seconds, bootstrap likelihood -76159.792619, best rearrangement setting 5
Bootstrap[21]: Time 0.563807 seconds, bootstrap likelihood -76066.699952, best rearrangement setting 15
Bootstrap[22]: Time 0.546471 seconds, bootstrap likelihood -76047.310226, best rearrangement setting 5
Bootstrap[23]: Time 0.565515 seconds, bootstrap likelihood -76209.137153, best rearrangement setting 9
Bootstrap[24]: Time 0.595023 seconds, bootstrap likelihood -76036.982097, best rearrangement setting 12
Bootstrap[25]: Time 0.631842 seconds, bootstrap likelihood -76202.050921, best rearrangement setting 6
Bootstrap[26]: Time 0.552071 seconds, bootstrap likelihood -76282.428248, best rearrangement setting 9
Bootstrap[27]: Time 0.567584 seconds, bootstrap likelihood -76167.644169, best rearrangement setting 8
Bootstrap[28]: Time 0.309510 seconds, bootstrap likelihood -76352.659658, best rearrangement setting 14
Bootstrap[29]: Time 0.509756 seconds, bootstrap likelihood -75634.879367, best rearrangement setting 14
Bootstrap[30]: Time 0.600830 seconds, bootstrap likelihood -75902.069529, best rearrangement setting 14
Bootstrap[31]: Time 0.582872 seconds, bootstrap likelihood -75907.870884, best rearrangement setting 8
Bootstrap[32]: Time 0.516745 seconds, bootstrap likelihood -76141.122211, best rearrangement setting 7
Bootstrap[33]: Time 0.295958 seconds, bootstrap likelihood -75699.432027, best rearrangement setting 5
Bootstrap[34]: Time 0.288135 seconds, bootstrap likelihood -76179.780099, best rearrangement setting 10
Bootstrap[35]: Time 0.603329 seconds, bootstrap likelihood -76033.328115, best rearrangement setting 8
Bootstrap[36]: Time 0.572087 seconds, bootstrap likelihood -76301.850307, best rearrangement setting 9
Bootstrap[37]: Time 0.560764 seconds, bootstrap likelihood -75849.124257, best rearrangement setting 13
Bootstrap[38]: Time 0.539320 seconds, bootstrap likelihood -76022.450184, best rearrangement setting 5
Bootstrap[39]: Time 0.546802 seconds, bootstrap likelihood -75813.344550, best rearrangement setting 6
Bootstrap[40]: Time 0.609194 seconds, bootstrap likelihood -76436.765766, best rearrangement setting 10
Bootstrap[41]: Time 0.583296 seconds, bootstrap likelihood -75997.559122, best rearrangement setting 8
Bootstrap[42]: Time 0.560753 seconds, bootstrap likelihood -76239.614653, best rearrangement setting 14
Bootstrap[43]: Time 0.517432 seconds, bootstrap likelihood -75955.941647, best rearrangement setting 6
Bootstrap[44]: Time 0.510632 seconds, bootstrap likelihood -75937.030077, best rearrangement setting 15
Bootstrap[45]: Time 0.555368 seconds, bootstrap likelihood -76124.330062, best rearrangement setting 5
Bootstrap[46]: Time 0.578972 seconds, bootstrap likelihood -76371.369232, best rearrangement setting 12
Bootstrap[47]: Time 0.519948 seconds, bootstrap likelihood -75917.775923, best rearrangement setting 14
Bootstrap[48]: Time 0.537641 seconds, bootstrap likelihood -75993.293598, best rearrangement setting 9
Bootstrap[49]: Time 0.570051 seconds, bootstrap likelihood -76138.715931, best rearrangement setting 7
Bootstrap[50]: Time 0.559163 seconds, bootstrap likelihood -76059.959334, best rearrangement setting 7
Bootstrap[51]: Time 0.499943 seconds, bootstrap likelihood -75692.497159, best rearrangement setting 7
Bootstrap[52]: Time 0.555316 seconds, bootstrap likelihood -75995.458937, best rearrangement setting 12
Bootstrap[53]: Time 0.579144 seconds, bootstrap likelihood -75912.810781, best rearrangement setting 12
Bootstrap[54]: Time 0.538008 seconds, bootstrap likelihood -75961.061510, best rearrangement setting 9
Bootstrap[55]: Time 0.298026 seconds, bootstrap likelihood -76259.944659, best rearrangement setting 9
Bootstrap[56]: Time 0.558566 seconds, bootstrap likelihood -76079.378672, best rearrangement setting 6
Bootstrap[57]: Time 0.590322 seconds, bootstrap likelihood -75749.862721, best rearrangement setting 6
Bootstrap[58]: Time 0.538738 seconds, bootstrap likelihood -76029.413379, best rearrangement setting 5
Bootstrap[59]: Time 0.510509 seconds, bootstrap likelihood -75894.234449, best rearrangement setting 5
Bootstrap[60]: Time 0.513843 seconds, bootstrap likelihood -76154.981497, best rearrangement setting 7
Bootstrap[61]: Time 0.502247 seconds, bootstrap likelihood -76133.712435, best rearrangement setting 11
Bootstrap[62]: Time 0.563201 seconds, bootstrap likelihood -76218.876369, best rearrangement setting 5
Bootstrap[63]: Time 0.522544 seconds, bootstrap likelihood -75774.986219, best rearrangement setting 13
Bootstrap[64]: Time 0.532345 seconds, bootstrap likelihood -75990.492502, best rearrangement setting 13
Bootstrap[65]: Time 0.535124 seconds, bootstrap likelihood -76306.072449, best rearrangement setting 12
Bootstrap[66]: Time 0.554829 seconds, bootstrap likelihood -76332.253655, best rearrangement setting 6
Bootstrap[67]: Time 0.520356 seconds, bootstrap likelihood -76129.398815, best rearrangement setting 8
Bootstrap[68]: Time 0.558836 seconds, bootstrap likelihood -76254.564769, best rearrangement setting 15
Bootstrap[69]: Time 0.550105 seconds, bootstrap likelihood -76046.944289, best rearrangement setting 5
Bootstrap[70]: Time 0.566401 seconds, bootstrap likelihood -76189.196831, best rearrangement setting 6
Bootstrap[71]: Time 0.508642 seconds, bootstrap likelihood -75960.712756, best rearrangement setting 6
Bootstrap[72]: Time 0.526512 seconds, bootstrap likelihood -76210.045656, best rearrangement setting 13
Bootstrap[73]: Time 0.515909 seconds, bootstrap likelihood -76169.812350, best rearrangement setting 9
Bootstrap[74]: Time 0.579022 seconds, bootstrap likelihood -76025.554093, best rearrangement setting 7
Bootstrap[75]: Time 0.570090 seconds, bootstrap likelihood -75655.041599, best rearrangement setting 5
Bootstrap[76]: Time 0.487730 seconds, bootstrap likelihood -75829.406474, best rearrangement setting 13
Bootstrap[77]: Time 0.254941 seconds, bootstrap likelihood -75860.607115, best rearrangement setting 14
Bootstrap[78]: Time 0.298414 seconds, bootstrap likelihood -76055.311793, best rearrangement setting 11
Bootstrap[79]: Time 0.588599 seconds, bootstrap likelihood -75915.374846, best rearrangement setting 6
Bootstrap[80]: Time 0.667347 seconds, bootstrap likelihood -76261.543583, best rearrangement setting 13
Bootstrap[81]: Time 0.612976 seconds, bootstrap likelihood -76174.874698, best rearrangement setting 5
Bootstrap[82]: Time 0.531991 seconds, bootstrap likelihood -75793.101339, best rearrangement setting 5
Bootstrap[83]: Time 0.585576 seconds, bootstrap likelihood -75938.639400, best rearrangement setting 8
Bootstrap[84]: Time 0.627221 seconds, bootstrap likelihood -75996.185152, best rearrangement setting 10
Bootstrap[85]: Time 0.560480 seconds, bootstrap likelihood -76154.783869, best rearrangement setting 10
Bootstrap[86]: Time 0.596546 seconds, bootstrap likelihood -76215.777177, best rearrangement setting 6
Bootstrap[87]: Time 0.589085 seconds, bootstrap likelihood -76233.616897, best rearrangement setting 12
Bootstrap[88]: Time 0.291329 seconds, bootstrap likelihood -75804.735625, best rearrangement setting 6
Bootstrap[89]: Time 0.553877 seconds, bootstrap likelihood -76026.236128, best rearrangement setting 12
Bootstrap[90]: Time 0.679948 seconds, bootstrap likelihood -76296.463995, best rearrangement setting 15
Bootstrap[91]: Time 0.543307 seconds, bootstrap likelihood -76001.064460, best rearrangement setting 15
Bootstrap[92]: Time 0.624406 seconds, bootstrap likelihood -76140.644926, best rearrangement setting 7
Bootstrap[93]: Time 0.331340 seconds, bootstrap likelihood -76002.798476, best rearrangement setting 15
Bootstrap[94]: Time 0.333815 seconds, bootstrap likelihood -75909.186324, best rearrangement setting 14
Bootstrap[95]: Time 0.317092 seconds, bootstrap likelihood -76442.785521, best rearrangement setting 14
Bootstrap[96]: Time 0.598750 seconds, bootstrap likelihood -76081.323369, best rearrangement setting 12
Bootstrap[97]: Time 0.313615 seconds, bootstrap likelihood -75913.019207, best rearrangement setting 5
Bootstrap[98]: Time 0.620730 seconds, bootstrap likelihood -76178.332365, best rearrangement setting 10
Bootstrap[99]: Time 0.607763 seconds, bootstrap likelihood -76031.354102, best rearrangement setting 11


Overall Time for 100 Rapid Bootstraps 52.903293 seconds
Average Time per Rapid Bootstrap 0.529033 seconds
All 100 bootstrapped trees written to: /tmp/tmpo3fKpd/job_working_directory/000/3/working/RAxML_bootstrap.galaxy_run