Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! IMPORTANT WARNING: Alignment column 99627 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 540593 contains only undetermined values which will be treated as missing data IMPORTANT WARNING: Alignment column 877792 contains only undetermined values which will be treated as missing data IMPORTANT WARNING Found 3 columns that contain only undetermined values which will be treated as missing data. Normally these columns should be excluded from the analysis. Just in case you might need it, an alignment file with undetermined columns removed is printed to file /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph.reduced Alignment has 3 completely undetermined sites that will be automatically removed from the input data This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 This is RAxML Worker Pthread Number: 2 This is RAxML Worker Pthread Number: 3 This is RAxML Worker Pthread Number: 4 This is RAxML Worker Pthread Number: 5 This is RAxML Worker Pthread Number: 6 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 3765 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.75% RAxML rapid hill-climbing mode Using 1 distinct models/data partitions with joint branch length optimization Executing 1 inferences on the original alignment using 1 distinct randomized MP trees All free model parameters will be estimated by RAxML GAMMA model of rate heterogeneity, 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: 3765 Name: No Name Provided DataType: AA Substitution Matrix: AUTO Using fixed base frequencies RAxML was called as follows: /opt/mosga/tools/RAxML/raxmlHPC-PTHREADS-AVX -T 7 -m PROTGAMMAAUTO -s /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph -o a5559a11b7 -n tree-ml -w /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/ -p 31415926535 Partition: 0 with name: No Name Provided Base frequencies: 0.087 0.044 0.039 0.057 0.019 0.037 0.058 0.083 0.024 0.048 0.086 0.062 0.020 0.038 0.046 0.070 0.061 0.014 0.035 0.071 Automatic protein model assignment algorithm using ML criterion: Partition: 0 best-scoring AA model: HIVB likelihood -3425586.032778 with empirical base frequencies Automatic protein model assignment algorithm using ML criterion: Partition: 0 best-scoring AA model: HIVB likelihood -3424440.214369 with empirical base frequencies Automatic protein model assignment algorithm using ML criterion: Partition: 0 best-scoring AA model: HIVB likelihood -3424434.070514 with empirical base frequencies Automatic protein model assignment algorithm using ML criterion: Partition: 0 best-scoring AA model: HIVB likelihood -3424434.036740 with empirical base frequencies Inference[0]: Time 14.307423 GAMMA-based likelihood -3424434.036554, best rearrangement setting 3 Conducting final model optimizations on all 1 trees under GAMMA-based models .... Automatic protein model assignment algorithm using ML criterion: Partition: 0 best-scoring AA model: HIVB likelihood -3424434.036555 with empirical base frequencies Inference[0] final GAMMA-based Likelihood: -3424434.036553 tree written to file /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_result.tree-ml Starting final GAMMA-based thorough Optimization on tree 0 likelihood -3424434.036553 .... Final GAMMA-based Score of best tree -3424434.036553 Program execution info written to /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_info.tree-ml Best-scoring ML tree written to: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_bestTree.tree-ml Overall execution time: 18.569020 secs or 0.005158 hours or 0.000215 days