Problems during the initial branch length optimization process
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Eun Jee
Oct 12, 2023, 1:30:16 AM10/12/23
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Hello everyone,
RAxML-NG v. 1.2.0 released on 09.05.2023 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
System: 13th Gen Intel(R) Core(TM) i9-13900KF, 16 cores, 31 GB RAM
RAxML-NG was called at 12-Oct-2023 09:22:36 as follows:
/home/infectiouslab/workspace/software/raxml-ng/raxml-ng --msa /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas --all --bs-trees 500 --log PROGRESS --model GTR+G4 --threads 20
Analysis options:
run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
start tree(s): random (10) + parsimony (10)
bootstrap replicates: parsimony (500)
random seed: 1697070156
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
fast spr radius: AUTO
spr subtree cutoff: 1.000000
fast CLV updates: ON
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (20 threads), thread pinning: OFF
[00:00:00] Reading alignment from file: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas
[00:00:00] Loaded alignment with 88 taxa and 11673 sites
WARNING: Sequences LC426670_PyV23-FCC16__Hipposideros_larvatus_China_2016 and LC426689_PyV23-DXC17_Rhinolophus_affinis_China_2016 are exactly identical!
WARNING: Sequences FJ188392_VM-2008_14_Myotis_lucifugus_Canada_2007 and NC_011310_VM-2008_Myotis_lucifugus_Canada_2007 are exactly identical!
WARNING: Duplicate sequences found: 2
NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed)
NOTE: was saved to: /mnt/d/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.reduced.phy
Alignment comprises 1 partitions and 8529 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 11673 / 8529
Gaps: 56.29 %
Invariant sites: 24.01 %
NOTE: Binary MSA file created: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.rba
Parallelization scheme autoconfig: 4 worker(s) x 5 thread(s)
[00:00:00] Generating 10 random starting tree(s) with 88 taxa
[00:00:00] Generating 10 parsimony starting tree(s) with 88 taxa
Parallel parsimony with 20 threads
Parallel reduction/worker buffer size: 1 KB / 0 KB
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 1706 / 27296
[00:00:00] Data distribution: max. searches per worker: 130
Starting ML tree search with 20 distinct starting trees
[00:00:00 -489913.674434] Initial branch length optimization
[00:00:00 -447372.210502] Model parameter optimization (eps = 10.000000)
RAxML-NG v. 1.2.0 released on 09.05.2023 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
System: 13th Gen Intel(R) Core(TM) i9-13900KF, 16 cores, 31 GB RAM
RAxML-NG was called at 12-Oct-2023 11:48:41 as follows:
/home/infectiouslab/workspace/software/raxml-ng/raxml-ng --all --msa /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas --model GTR+G4 --bs-trees 200 --tree pares{10} --threads 20
Analysis options:
run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
start tree(s): user
bootstrap replicates: parsimony (200)
random seed: 1697078921
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
fast spr radius: AUTO
spr subtree cutoff: 1.000000
fast CLV updates: ON
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (20 threads), thread pinning: OFF
WARNING: The model you specified on the command line (GTR+G4) will be ignored
since the binary MSA file already contains a model definition.
If you want to change the model, please re-run RAxML-NG
with the original PHYLIP/FASTA alignment and --redo option.
[00:00:00] Loading binary alignment from file: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.rba
[00:00:00] Alignment comprises 88 taxa, 1 partitions and 8529 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 11673 / 8529
Gaps: 56.29 %
Invariant sites: 24.01 %
Parallelization scheme autoconfig: 4 worker(s) x 5 thread(s)
Parallel reduction/worker buffer size: 1 KB / 0 KB
[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -447372.21, ML trees: 0, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 1706 / 27296
[00:00:00] Data distribution: max. searches per worker: 55
Starting ML tree search with 20 distinct starting trees
I have problems in running RaxML-ng and I don't really don't know how to solve it.
I used the latest version, RAxML-NG v. 1.2.0. I ran the program in window terminal.
I always encounter issues during the initial branch length optimization process. The process keeps getting interrupted with an error message that says "terminate called recursively, aborted." or "segmentation fault".
RAxML-NG v. 1.2.0 released on 09.05.2023 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
System: 13th Gen Intel(R) Core(TM) i9-13900KF, 16 cores, 31 GB RAM
RAxML-NG was called at 12-Oct-2023 09:22:36 as follows:
/home/infectiouslab/workspace/software/raxml-ng/raxml-ng --msa /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas --all --bs-trees 500 --log PROGRESS --model GTR+G4 --threads 20
Analysis options:
run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
start tree(s): random (10) + parsimony (10)
bootstrap replicates: parsimony (500)
random seed: 1697070156
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
fast spr radius: AUTO
spr subtree cutoff: 1.000000
fast CLV updates: ON
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (20 threads), thread pinning: OFF
[00:00:00] Reading alignment from file: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas
[00:00:00] Loaded alignment with 88 taxa and 11673 sites
WARNING: Sequences LC426670_PyV23-FCC16__Hipposideros_larvatus_China_2016 and LC426689_PyV23-DXC17_Rhinolophus_affinis_China_2016 are exactly identical!
WARNING: Sequences FJ188392_VM-2008_14_Myotis_lucifugus_Canada_2007 and NC_011310_VM-2008_Myotis_lucifugus_Canada_2007 are exactly identical!
WARNING: Duplicate sequences found: 2
NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed)
NOTE: was saved to: /mnt/d/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.reduced.phy
Alignment comprises 1 partitions and 8529 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 11673 / 8529
Gaps: 56.29 %
Invariant sites: 24.01 %
NOTE: Binary MSA file created: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.rba
Parallelization scheme autoconfig: 4 worker(s) x 5 thread(s)
[00:00:00] Generating 10 random starting tree(s) with 88 taxa
[00:00:00] Generating 10 parsimony starting tree(s) with 88 taxa
Parallel parsimony with 20 threads
Parallel reduction/worker buffer size: 1 KB / 0 KB
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 1706 / 27296
[00:00:00] Data distribution: max. searches per worker: 130
Starting ML tree search with 20 distinct starting trees
[00:00:00 -489913.674434] Initial branch length optimization
[00:00:00 -447372.210502] Model parameter optimization (eps = 10.000000)
RAxML-NG v. 1.2.0 released on 09.05.2023 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
System: 13th Gen Intel(R) Core(TM) i9-13900KF, 16 cores, 31 GB RAM
RAxML-NG was called at 12-Oct-2023 11:48:41 as follows:
/home/infectiouslab/workspace/software/raxml-ng/raxml-ng --all --msa /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas --model GTR+G4 --bs-trees 200 --tree pares{10} --threads 20
Analysis options:
run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
start tree(s): user
bootstrap replicates: parsimony (200)
random seed: 1697078921
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000
fast spr radius: AUTO
spr subtree cutoff: 1.000000
fast CLV updates: ON
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (20 threads), thread pinning: OFF
WARNING: The model you specified on the command line (GTR+G4) will be ignored
since the binary MSA file already contains a model definition.
If you want to change the model, please re-run RAxML-NG
with the original PHYLIP/FASTA alignment and --redo option.
[00:00:00] Loading binary alignment from file: /home/infectiouslab/workspace/bat_virome/alignment/polyomavirus/polyomavirus_align_muscle_rename.fas.raxml.rba
[00:00:00] Alignment comprises 88 taxa, 1 partitions and 8529 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 11673 / 8529
Gaps: 56.29 %
Invariant sites: 24.01 %
Parallelization scheme autoconfig: 4 worker(s) x 5 thread(s)
Parallel reduction/worker buffer size: 1 KB / 0 KB
[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -447372.21, ML trees: 0, bootstraps: 0)
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 1706 / 27296
[00:00:00] Data distribution: max. searches per worker: 55
Starting ML tree search with 20 distinct starting trees
Best regard,
Eun Jee
Oleksiy Kozlov
Oct 12, 2023, 5:39:07 AM10/12/23
to ra...@googlegroups.com
Hi Eun Jee,
please send me your MSA and I will have a look.
Best,
Oleksiy
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please send me your MSA and I will have a look.
Best,
Oleksiy
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Oleksiy Kozlov
Oct 13, 2023, 5:04:18 PM10/13/23
to ra...@googlegroups.com
Hi Eun Jee,
thanks for sending the input files. I could not reproduce the problem on mu machine.
So probably it is specific to the novel Intel CPU that you have. It could be that pre-compiled
version does not work anymore.
So please try to compile raxml-ng from scratch:
https://github.com/amkozlov/raxml-ng/wiki/Installation#building-from-source
Best,
Oleksiy
On 12.10.23 07:30, Eun Jee wrote:
thanks for sending the input files. I could not reproduce the problem on mu machine.
So probably it is specific to the novel Intel CPU that you have. It could be that pre-compiled
version does not work anymore.
So please try to compile raxml-ng from scratch:
https://github.com/amkozlov/raxml-ng/wiki/Installation#building-from-source
Best,
Oleksiy
On 12.10.23 07:30, Eun Jee wrote:
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