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RAxML_ONLY-500M4-19.o9562186
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----------------------------------------
Begin Torque Prologue (Sat Sep 21 20:12:29 2019)
Job ID: 9562186.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M4-19
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Job Queue: secondary
Account: tallis
Nodes: golub004
End Torque Prologue
----------------------------------------
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences SBG and SDIA are exactly identical
IMPORTANT WARNING: Sequences SFB and SJG are exactly identical
IMPORTANT WARNING
Found 2 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M4/R19/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 3
This is RAxML Worker Pthread Number: 2
This is RAxML Worker Pthread Number: 1
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 1541 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 49.74%
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: 1541
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M4/R19/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M4/R19/ -m GTRGAMMA -T 4 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.261 0.237 0.228 0.274
Inference[0]: Time 466.727628 GAMMA-based likelihood -235345.519752, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -235345.506784 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M4/R19/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -235345.506784 ....
Final GAMMA-based Score of best tree -235345.506784
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M4/R19/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M4/R19/RAxML_bestTree.bestml
Overall execution time: 620.243116 secs or 0.172290 hours or 0.007179 days
----------------------------------------
Begin Torque Epilogue (Sat Sep 21 20:22:54 2019)
Job ID: 9562186.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M4-19
Session: 59358
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Resources: cput=00:41:22,vmem=317672kb,walltime=00:10:25,mem=129668kb,energy_used=0
Job Queue: secondary
Account: tallis
Nodes: golub004
End Torque Epilogue
----------------------------------------