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RAxML_ONLY-500M5-16.o9561503
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----------------------------------------
Begin Torque Prologue (Sat Sep 21 17:23:47 2019)
Job ID: 9561503.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M5-16
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Job Queue: secondary
Account: tallis
Nodes: golub037
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
RAxML output files with the run ID <bestml> already exist
in directory /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R16/ ...... exiting
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 SG and SEGE are exactly identical
IMPORTANT WARNING: Sequences SBAH and SEFD are exactly identical
IMPORTANT WARNING: Sequences SCEG and SIB are exactly identical
IMPORTANT WARNING
Found 3 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/500M5/R17/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: 1
This is RAxML Worker Pthread Number: 2
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 1302 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 33.58%
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: 1302
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/500M5/R17/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R17/ -m GTRGAMMA -T 3 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.259 0.224 0.242 0.275
Inference[0]: Time 677.836839 GAMMA-based likelihood -231872.088590, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -231871.830367 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R17/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -231871.830367 ....
Final GAMMA-based Score of best tree -231871.830367
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R17/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R17/RAxML_bestTree.bestml
Overall execution time: 882.946479 secs or 0.245263 hours or 0.010219 days
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 SBGG and SBA are exactly identical
IMPORTANT WARNING: Sequences SCHG and SEJ are exactly identical
IMPORTANT WARNING: Sequences SBHA and SBD are exactly identical
IMPORTANT WARNING: Sequences SCHB and SEIG are exactly identical
IMPORTANT WARNING: Sequences SBGF and SDBD are exactly identical
IMPORTANT WARNING
Found 5 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/500M5/R18/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: 1
This is RAxML Worker Pthread Number: 2
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 1408 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 41.96%
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: 1408
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/500M5/R18/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R18/ -m GTRGAMMA -T 3 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.274 0.229 0.232 0.266
Inference[0]: Time 531.464786 GAMMA-based likelihood -264591.786397, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -264591.783176 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R18/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -264591.783176 ....
Final GAMMA-based Score of best tree -264591.783176
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R18/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R18/RAxML_bestTree.bestml
Overall execution time: 717.161820 secs or 0.199212 hours or 0.008300 days
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 SEGC and SEJI are exactly identical
IMPORTANT WARNING: Sequences SJG and SCJJ are exactly identical
IMPORTANT WARNING: Sequences SCJG and SCGD are exactly identical
IMPORTANT WARNING
Found 3 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/500M5/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: 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 1180 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 25.40%
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: 1180
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/500M5/R19/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R19/ -m GTRGAMMA -T 2 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.257 0.242 0.233 0.268
Inference[0]: Time 616.983441 GAMMA-based likelihood -199650.943721, best rearrangement setting 5
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -199650.943543 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R19/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -199650.943543 ....
Final GAMMA-based Score of best tree -199650.943543
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R19/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M5/R19/RAxML_bestTree.bestml
Overall execution time: 874.415701 secs or 0.242893 hours or 0.010121 days
----------------------------------------
Begin Torque Epilogue (Sat Sep 21 18:05:07 2019)
Job ID: 9561503.cc-mgmt1.campuscluster.illinois.edu
Username: binghui2
Group: tallis
Job Name: RAxML_ONLY-500M5-16
Session: 10315
Limits: nodes=1:ppn=12,walltime=04:00:00,neednodes=1:ppn=12
Resources: cput=01:49:16,vmem=249172kb,walltime=00:41:20,mem=118324kb,energy_used=0
Job Queue: secondary
Account: tallis
Nodes: golub037
End Torque Epilogue
----------------------------------------