--- a/test-data/RAxML_parsimonyTree.galaxy.multi	Mon Nov 30 22:03:09 2015 -0500
+++ b/test-data/RAxML_parsimonyTree.galaxy.multi	Sat Jun 25 19:34:35 2016 -0400
@@ -45,43 +45,43 @@
 
 RAxML was called as follows:
 
-raxmlHPC -s /tmp/tmp_D_Wx1/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 
+raxmlHPC -s /tmp/tmpS1corm/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 
 
 
 Partition: 0 with name: No Name Provided
 Base frequencies: 0.325 0.288 0.168 0.218 
 
-Inference[0]: Time 0.384667 CAT-based likelihood -318.296661, best rearrangement setting 5
-alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.921091 909.963678 698.791844 49.826026 1853.987180 1.000000 
-Inference[1]: Time 0.312805 CAT-based likelihood -320.216685, best rearrangement setting 5
-alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.966228 1693.994555 1327.595110 133.225736 5344.810756 1.000000 
-Inference[2]: Time 0.310104 CAT-based likelihood -317.720602, best rearrangement setting 5
-alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.622832 1755.681465 1079.971295 84.603657 3889.976834 1.000000 
-Inference[3]: Time 0.361859 CAT-based likelihood -320.856853, best rearrangement setting 5
-alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.251278 1754.861720 1010.715785 104.248328 4976.318155 1.000000 
-Inference[4]: Time 0.365067 CAT-based likelihood -320.068835, best rearrangement setting 5
-alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.935051 2115.369469 1728.113008 157.211587 6783.037433 1.000000 
+Inference[0]: Time 0.216205 CAT-based likelihood -318.296661, best rearrangement setting 5
+alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.924095 909.973305 698.798586 49.826281 1854.008494 1.000000 
+Inference[1]: Time 0.156515 CAT-based likelihood -320.216706, best rearrangement setting 5
+alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.611489 1694.475132 1327.909793 133.166551 5344.045057 1.000000 
+Inference[2]: Time 0.168518 CAT-based likelihood -317.720618, best rearrangement setting 5
+alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.628294 1755.581565 1080.117186 84.613232 3889.913949 1.000000 
+Inference[3]: Time 0.151635 CAT-based likelihood -320.856852, best rearrangement setting 5
+alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.225250 1754.836760 1010.717630 104.250644 4976.305821 1.000000 
+Inference[4]: Time 0.148819 CAT-based likelihood -320.068842, best rearrangement setting 5
+alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.938988 2115.384600 1728.203983 157.161613 6782.996281 1.000000 
 
 
 Conducting final model optimizations on all 5 trees under GAMMA-based models ....
 
-Inference[0] final GAMMA-based Likelihood: -378.273623 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.0
-Inference[1] final GAMMA-based Likelihood: -378.202275 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.1
-Inference[2] final GAMMA-based Likelihood: -377.272786 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.2
-Inference[3] final GAMMA-based Likelihood: -377.004344 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.3
-Inference[4] final GAMMA-based Likelihood: -378.202275 tree written to file /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_result.galaxy.RUN.4
+Inference[0] final GAMMA-based Likelihood: -378.273666 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.0
+Inference[1] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.1
+Inference[2] final GAMMA-based Likelihood: -377.272824 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.2
+Inference[3] final GAMMA-based Likelihood: -377.004321 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.3
+Inference[4] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.4
 
 
-Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004344 .... 
+Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004321 .... 
 
-Final GAMMA-based Score of best tree -377.004344
+Final GAMMA-based Score of best tree -377.004321
 
-Program execution info written to /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_info.galaxy
-Best-scoring ML tree written to: /tmp/tmp_D_Wx1/job_working_directory/000/4/RAxML_bestTree.galaxy
+Program execution info written to /tmp/tmpS1corm/job_working_directory/000/4/RAxML_info.galaxy
+Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy
 
-Overall execution time: 1.829373 secs or 0.000508 hours or 0.000021 days
+Overall execution time: 0.917038 secs or 0.000255 hours or 0.000011 days
 
 
 OM: CLI options DEBUG START:
-<Values at 0x7fd1fab4d518: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmp_D_Wx1/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}>
+<Values at 0x7f8e104919e0: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmpS1corm/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}>
 OM: CLI options DEBUG END