ERROR in SPR round
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scott small
Jan 17, 2018, 1:30:49 PM1/17/18
to raxml
Hi,
I seem to be having an intermittent error running raxml_ng v0.5.1b.
command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -27.193683 units
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
:
system msg for write_line failure : Bad file descriptor
If I run the command 10 times this error will appear 9/10. I have copied the log file output in DEBUG mode for the error and successful runs.
Any ideas?
thanks,
scott
p.s. The '--threads 1' was something I tried after reading another post about MPI issues
LOG FILE OUTPUT in DEBUG for ERROR RUN:
RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
WARNING: This is a BETA release, please use at your own risk!
RAxML-NG was called as follows:
raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --redo --log DEBUG --threads 1
Analysis options:
run mode: ML tree search
start tree(s): random
random seed: 1516213645
tip-inner: ON
pattern compression: ON
per-rate scalers: OFF
site repeats: OFF
fast spr radius: AUTO
spr subtree cutoff: 1.000000
branch lengths: ML estimate (linked)
SIMD kernels: AVX
parallelization: NONE/sequential
WARNING: Running in REDO mode: existing checkpoints are ignored, and all result files will be overwritten!
|noname| |GTR+FO+G4m| ||
[00:00:00] Reading alignment from file: X.filtered.3722.aln
Failed to load as IPHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
Failed to load as PHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
[00:00:00] Loaded alignment with 42 taxa and 1000 sites
[00:00:00] Extracting partitions...
[00:00:00] Validating alignment...
[00:00:00] Checking the alignment...
WARNING: Duplicate sequences found: 5
WARNING: Sequences funestus_MozF123 and funestus_MozF260 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF561 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF601 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_Zam281 are exactly identical!
WARNING: Sequences funestus_MozF29 and funestus_MozF35 are exactly identical!
[00:00:00] Compressing alignment patterns...
Alignment comprises 1 partitions and 192 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 1000 / 192
Gaps: 1.72 %
Invariant sites: 77.70 %
Parallel reduction buffer size: 1 KB
Generating a random starting tree with 42 taxa
[00:00:00] Generating random starting tree(s) with 42 taxa
Generating a random starting tree with 42 taxa
Initial model parameters:
Partition: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1.000000 (ML), weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
[00:00:00] Data distribution: partitions/thread: 1-1, patterns/thread: 192-192
thread# part# start length
0 0 0 192
Starting ML tree search with 1 distinct starting trees
[00:00:00 -6816.301820] Initial branch length optimization
- after brlen: logLH = -5170.768105
[00:00:00 -5170.768105] Model parameter optimization (eps = 10.000000)
- after rates: logLH = -5040.150912
- after freqs: logLH = -5033.575696
- after alpha: logLH = -4673.262632
- after p-inv: logLH = -4673.262632
- after freeR: logLH = -4673.262632
- after brlen: logLH = -4411.083724
- after rates: logLH = -4408.060893
- after freqs: logLH = -4402.890051
- after alpha: logLH = -4344.122440
- after p-inv: logLH = -4344.122440
- after freeR: logLH = -4344.122440
- after brlen: logLH = -4312.022134
- after rates: logLH = -4311.078989
- after freqs: logLH = -4309.648910
- after alpha: logLH = -4298.969291
- after p-inv: logLH = -4298.969291
- after freeR: logLH = -4298.969291
- after brlen: logLH = -4269.840070
- after rates: logLH = -4269.476666
- after freqs: logLH = -4269.457569
- after alpha: logLH = -4265.804047
- after p-inv: logLH = -4265.804047
- after freeR: logLH = -4265.804047
- after brlen: logLH = -4263.522560
[00:00:00 -4263.522560] AUTODETECT spr round 1 (radius: 5)
[00:00:01 -3518.426295] AUTODETECT spr round 2 (radius: 10)
[00:00:01 -3283.382011] AUTODETECT spr round 3 (radius: 15)
[00:00:01 -3283.172213] AUTODETECT spr round 4 (radius: 20)
[00:00:01 -3281.503032] AUTODETECT spr round 5 (radius: 25)
[00:00:01 -3281.502179] SPR radius for FAST iterations: 20 (autodetect)
[00:00:01 -3281.502179] Model parameter optimization (eps = 3.000000)
- after rates: logLH = -3279.362471
- after freqs: logLH = -3274.575618
- after alpha: logLH = -3274.486340
- after p-inv: logLH = -3274.486340
- after freeR: logLH = -3274.486340
- after brlen: logLH = -3274.383242
- after rates: logLH = -3274.038095
- after freqs: logLH = -3274.007316
- after alpha: logLH = -3273.952234
- after p-inv: logLH = -3273.952234
- after freeR: logLH = -3273.952234
- after brlen: logLH = -3273.896104
[00:00:02 -3273.896104] FAST spr round 1 (radius: 20)
- after brlen: logLH = -3171.467705
[00:00:02 -3171.467705] FAST spr round 2 (radius: 20)
- after brlen: logLH = -3171.043723
[00:00:02 -3171.043723] FAST spr round 3 (radius: 20)
- after brlen: logLH = -3170.756603
[00:00:03 -3170.756603] FAST spr round 4 (radius: 20)
- after brlen: logLH = -3170.754071
[00:00:03 -3170.754071] Model parameter optimization (eps = 1.000000)
- after rates: logLH = -3170.539514
- after freqs: logLH = -3170.450146
- after alpha: logLH = -3170.427676
- after p-inv: logLH = -3170.427676
- after freeR: logLH = -3170.427676
- after brlen: logLH = -3170.408638
[00:00:03 -3170.408638] SLOW spr round 1 (radius: 5)
ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -34.376174 units
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
:
system msg for write_line failure : Bad file descriptor
LOG FILE OUTPUT in DEBUG for SUCCESSFUL RUN:
RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
WARNING: This is a BETA release, please use at your own risk!
RAxML-NG was called as follows:
raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --redo --log DEBUG --threads 1
Analysis options:
run mode: ML tree search
start tree(s): random
random seed: 1516213607
tip-inner: ON
pattern compression: ON
per-rate scalers: OFF
site repeats: OFF
fast spr radius: AUTO
spr subtree cutoff: 1.000000
branch lengths: ML estimate (linked)
SIMD kernels: AVX
parallelization: NONE/sequential
WARNING: Running in REDO mode: existing checkpoints are ignored, and all result files will be overwritten!
|noname| |GTR+FO+G4m| ||
[00:00:00] Reading alignment from file: X.filtered.3722.aln
Failed to load as IPHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
Failed to load as PHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
[00:00:00] Loaded alignment with 42 taxa and 1000 sites
[00:00:00] Extracting partitions...
[00:00:00] Validating alignment...
[00:00:00] Checking the alignment...
WARNING: Duplicate sequences found: 5
WARNING: Sequences funestus_MozF123 and funestus_MozF260 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF561 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF601 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_Zam281 are exactly identical!
WARNING: Sequences funestus_MozF29 and funestus_MozF35 are exactly identical!
[00:00:00] Compressing alignment patterns...
Alignment comprises 1 partitions and 192 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 1000 / 192
Gaps: 1.72 %
Invariant sites: 77.70 %
Parallel reduction buffer size: 1 KB
Generating a random starting tree with 42 taxa
[00:00:00] Generating random starting tree(s) with 42 taxa
Generating a random starting tree with 42 taxa
Initial model parameters:
Partition: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1.000000 (ML), weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
[00:00:00] Data distribution: partitions/thread: 1-1, patterns/thread: 192-192
thread# part# start length
0 0 0 192
Starting ML tree search with 1 distinct starting trees
[00:00:00 -6866.401780] Initial branch length optimization
- after brlen: logLH = -5247.712411
[00:00:00 -5247.712411] Model parameter optimization (eps = 10.000000)
- after rates: logLH = -5114.358493
- after freqs: logLH = -5104.480404
- after alpha: logLH = -4736.727629
- after p-inv: logLH = -4736.727629
- after freeR: logLH = -4736.727629
- after brlen: logLH = -4487.693907
- after rates: logLH = -4484.029063
- after freqs: logLH = -4478.879665
- after alpha: logLH = -4423.108095
- after p-inv: logLH = -4423.108095
- after freeR: logLH = -4423.108095
- after brlen: logLH = -4399.194335
- after rates: logLH = -4398.205490
- after freqs: logLH = -4397.705174
- after alpha: logLH = -4388.266748
- after p-inv: logLH = -4388.266748
- after freeR: logLH = -4388.266748
- after brlen: logLH = -4383.188065
- after rates: logLH = -4383.079583
- after freqs: logLH = -4383.036527
- after alpha: logLH = -4380.722074
- after p-inv: logLH = -4380.722074
- after freeR: logLH = -4380.722074
- after brlen: logLH = -4379.137806
[00:00:00 -4379.137806] AUTODETECT spr round 1 (radius: 5)
[00:00:01 -3522.698627] AUTODETECT spr round 2 (radius: 10)
[00:00:01 -3293.091256] AUTODETECT spr round 3 (radius: 15)
[00:00:01 -3287.125175] AUTODETECT spr round 4 (radius: 20)
[00:00:01 -3287.097361] SPR radius for FAST iterations: 15 (autodetect)
[00:00:01 -3287.097361] Model parameter optimization (eps = 3.000000)
- after rates: logLH = -3285.803498
- after freqs: logLH = -3284.160625
- after alpha: logLH = -3284.044672
- after p-inv: logLH = -3284.044672
- after freeR: logLH = -3284.044672
- after brlen: logLH = -3283.953023
- after rates: logLH = -3283.796571
- after freqs: logLH = -3283.776370
- after alpha: logLH = -3283.698639
- after p-inv: logLH = -3283.698639
- after freeR: logLH = -3283.698639
- after brlen: logLH = -3283.631533
[00:00:02 -3283.631533] FAST spr round 1 (radius: 15)
- after brlen: logLH = -3249.481756
[00:00:02 -3249.481756] FAST spr round 2 (radius: 15)
- after brlen: logLH = -3171.554561
[00:00:02 -3171.554561] FAST spr round 3 (radius: 15)
- after brlen: logLH = -3171.554478
[00:00:03 -3171.554478] Model parameter optimization (eps = 1.000000)
- after rates: logLH = -3171.072384
- after freqs: logLH = -3170.997379
- after alpha: logLH = -3170.978181
- after p-inv: logLH = -3170.978181
- after freeR: logLH = -3170.978181
- after brlen: logLH = -3170.944242
[00:00:03 -3170.944242] SLOW spr round 1 (radius: 5)
- after brlen: logLH = -3169.123440
[00:00:04 -3169.123440] SLOW spr round 2 (radius: 5)
- after brlen: logLH = -3168.993851
[00:00:04 -3168.993851] SLOW spr round 3 (radius: 5)
- after brlen: logLH = -3168.768513
[00:00:05 -3168.768513] SLOW spr round 4 (radius: 5)
- after brlen: logLH = -3168.768410
[00:00:06 -3168.768410] SLOW spr round 5 (radius: 10)
- after brlen: logLH = -3168.768410
[00:00:06 -3168.768410] SLOW spr round 6 (radius: 15)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] SLOW spr round 7 (radius: 20)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] SLOW spr round 8 (radius: 25)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] Model parameter optimization (eps = 0.100000)
- after rates: logLH = -3168.736451
- after freqs: logLH = -3168.734472
- after alpha: logLH = -3168.711629
- after p-inv: logLH = -3168.711629
- after freeR: logLH = -3168.711629
- after brlen: logLH = -3168.693184
[00:00:08] ML tree search #1, logLikelihood: -3168.693184
Optimized model parameters:
Partition 0: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.077884 (ML), weights&rates: (0.250000,0.000000) (0.250000,0.000151) (0.250000,0.041501) (0.250000,3.958347)
Base frequencies (ML): 0.264743 0.235238 0.225568 0.274451
Substitution rates (ML): 1.143011 2.302345 0.837022 0.387131 4.506063 1.000000
Final LogLikelihood: -3168.693184
Best ML tree saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.bestTree
Optimized model saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.bestModel
Execution log saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.log
Analysis started: 17-Jan-2018 13:26:47 / finished: 17-Jan-2018 13:26:55
Elapsed time: 8.033 seconds
I seem to be having an intermittent error running raxml_ng v0.5.1b.
command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -27.193683 units
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
:
system msg for write_line failure : Bad file descriptor
If I run the command 10 times this error will appear 9/10. I have copied the log file output in DEBUG mode for the error and successful runs.
Any ideas?
thanks,
scott
p.s. The '--threads 1' was something I tried after reading another post about MPI issues
LOG FILE OUTPUT in DEBUG for ERROR RUN:
RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
WARNING: This is a BETA release, please use at your own risk!
RAxML-NG was called as follows:
raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --redo --log DEBUG --threads 1
Analysis options:
run mode: ML tree search
start tree(s): random
random seed: 1516213645
tip-inner: ON
pattern compression: ON
per-rate scalers: OFF
site repeats: OFF
fast spr radius: AUTO
spr subtree cutoff: 1.000000
branch lengths: ML estimate (linked)
SIMD kernels: AVX
parallelization: NONE/sequential
WARNING: Running in REDO mode: existing checkpoints are ignored, and all result files will be overwritten!
|noname| |GTR+FO+G4m| ||
[00:00:00] Reading alignment from file: X.filtered.3722.aln
Failed to load as IPHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
Failed to load as PHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
[00:00:00] Loaded alignment with 42 taxa and 1000 sites
[00:00:00] Extracting partitions...
[00:00:00] Validating alignment...
[00:00:00] Checking the alignment...
WARNING: Duplicate sequences found: 5
WARNING: Sequences funestus_MozF123 and funestus_MozF260 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF561 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF601 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_Zam281 are exactly identical!
WARNING: Sequences funestus_MozF29 and funestus_MozF35 are exactly identical!
[00:00:00] Compressing alignment patterns...
Alignment comprises 1 partitions and 192 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 1000 / 192
Gaps: 1.72 %
Invariant sites: 77.70 %
Parallel reduction buffer size: 1 KB
Generating a random starting tree with 42 taxa
[00:00:00] Generating random starting tree(s) with 42 taxa
Generating a random starting tree with 42 taxa
Initial model parameters:
Partition: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1.000000 (ML), weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
[00:00:00] Data distribution: partitions/thread: 1-1, patterns/thread: 192-192
thread# part# start length
0 0 0 192
Starting ML tree search with 1 distinct starting trees
[00:00:00 -6816.301820] Initial branch length optimization
- after brlen: logLH = -5170.768105
[00:00:00 -5170.768105] Model parameter optimization (eps = 10.000000)
- after rates: logLH = -5040.150912
- after freqs: logLH = -5033.575696
- after alpha: logLH = -4673.262632
- after p-inv: logLH = -4673.262632
- after freeR: logLH = -4673.262632
- after brlen: logLH = -4411.083724
- after rates: logLH = -4408.060893
- after freqs: logLH = -4402.890051
- after alpha: logLH = -4344.122440
- after p-inv: logLH = -4344.122440
- after freeR: logLH = -4344.122440
- after brlen: logLH = -4312.022134
- after rates: logLH = -4311.078989
- after freqs: logLH = -4309.648910
- after alpha: logLH = -4298.969291
- after p-inv: logLH = -4298.969291
- after freeR: logLH = -4298.969291
- after brlen: logLH = -4269.840070
- after rates: logLH = -4269.476666
- after freqs: logLH = -4269.457569
- after alpha: logLH = -4265.804047
- after p-inv: logLH = -4265.804047
- after freeR: logLH = -4265.804047
- after brlen: logLH = -4263.522560
[00:00:00 -4263.522560] AUTODETECT spr round 1 (radius: 5)
[00:00:01 -3518.426295] AUTODETECT spr round 2 (radius: 10)
[00:00:01 -3283.382011] AUTODETECT spr round 3 (radius: 15)
[00:00:01 -3283.172213] AUTODETECT spr round 4 (radius: 20)
[00:00:01 -3281.503032] AUTODETECT spr round 5 (radius: 25)
[00:00:01 -3281.502179] SPR radius for FAST iterations: 20 (autodetect)
[00:00:01 -3281.502179] Model parameter optimization (eps = 3.000000)
- after rates: logLH = -3279.362471
- after freqs: logLH = -3274.575618
- after alpha: logLH = -3274.486340
- after p-inv: logLH = -3274.486340
- after freeR: logLH = -3274.486340
- after brlen: logLH = -3274.383242
- after rates: logLH = -3274.038095
- after freqs: logLH = -3274.007316
- after alpha: logLH = -3273.952234
- after p-inv: logLH = -3273.952234
- after freeR: logLH = -3273.952234
- after brlen: logLH = -3273.896104
[00:00:02 -3273.896104] FAST spr round 1 (radius: 20)
- after brlen: logLH = -3171.467705
[00:00:02 -3171.467705] FAST spr round 2 (radius: 20)
- after brlen: logLH = -3171.043723
[00:00:02 -3171.043723] FAST spr round 3 (radius: 20)
- after brlen: logLH = -3170.756603
[00:00:03 -3170.756603] FAST spr round 4 (radius: 20)
- after brlen: logLH = -3170.754071
[00:00:03 -3170.754071] Model parameter optimization (eps = 1.000000)
- after rates: logLH = -3170.539514
- after freqs: logLH = -3170.450146
- after alpha: logLH = -3170.427676
- after p-inv: logLH = -3170.427676
- after freeR: logLH = -3170.427676
- after brlen: logLH = -3170.408638
[00:00:03 -3170.408638] SLOW spr round 1 (radius: 5)
ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -34.376174 units
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
:
system msg for write_line failure : Bad file descriptor
LOG FILE OUTPUT in DEBUG for SUCCESSFUL RUN:
RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
WARNING: This is a BETA release, please use at your own risk!
RAxML-NG was called as follows:
raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --redo --log DEBUG --threads 1
Analysis options:
run mode: ML tree search
start tree(s): random
random seed: 1516213607
tip-inner: ON
pattern compression: ON
per-rate scalers: OFF
site repeats: OFF
fast spr radius: AUTO
spr subtree cutoff: 1.000000
branch lengths: ML estimate (linked)
SIMD kernels: AVX
parallelization: NONE/sequential
WARNING: Running in REDO mode: existing checkpoints are ignored, and all result files will be overwritten!
|noname| |GTR+FO+G4m| ||
[00:00:00] Reading alignment from file: X.filtered.3722.aln
Failed to load as IPHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
Failed to load as PHYLIP: Unable to parse PHYLIP file: X.filtered.3722.aln
[00:00:00] Loaded alignment with 42 taxa and 1000 sites
[00:00:00] Extracting partitions...
[00:00:00] Validating alignment...
[00:00:00] Checking the alignment...
WARNING: Duplicate sequences found: 5
WARNING: Sequences funestus_MozF123 and funestus_MozF260 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF561 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_TanF601 are exactly identical!
WARNING: Sequences funestus_MozF123 and funestus_Zam281 are exactly identical!
WARNING: Sequences funestus_MozF29 and funestus_MozF35 are exactly identical!
[00:00:00] Compressing alignment patterns...
Alignment comprises 1 partitions and 192 patterns
Partition 0: noname
Model: GTR+FO+G4m
Alignment sites / patterns: 1000 / 192
Gaps: 1.72 %
Invariant sites: 77.70 %
Parallel reduction buffer size: 1 KB
Generating a random starting tree with 42 taxa
[00:00:00] Generating random starting tree(s) with 42 taxa
Generating a random starting tree with 42 taxa
Initial model parameters:
Partition: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1.000000 (ML), weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294)
Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000
Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
[00:00:00] Data distribution: partitions/thread: 1-1, patterns/thread: 192-192
thread# part# start length
0 0 0 192
Starting ML tree search with 1 distinct starting trees
[00:00:00 -6866.401780] Initial branch length optimization
- after brlen: logLH = -5247.712411
[00:00:00 -5247.712411] Model parameter optimization (eps = 10.000000)
- after rates: logLH = -5114.358493
- after freqs: logLH = -5104.480404
- after alpha: logLH = -4736.727629
- after p-inv: logLH = -4736.727629
- after freeR: logLH = -4736.727629
- after brlen: logLH = -4487.693907
- after rates: logLH = -4484.029063
- after freqs: logLH = -4478.879665
- after alpha: logLH = -4423.108095
- after p-inv: logLH = -4423.108095
- after freeR: logLH = -4423.108095
- after brlen: logLH = -4399.194335
- after rates: logLH = -4398.205490
- after freqs: logLH = -4397.705174
- after alpha: logLH = -4388.266748
- after p-inv: logLH = -4388.266748
- after freeR: logLH = -4388.266748
- after brlen: logLH = -4383.188065
- after rates: logLH = -4383.079583
- after freqs: logLH = -4383.036527
- after alpha: logLH = -4380.722074
- after p-inv: logLH = -4380.722074
- after freeR: logLH = -4380.722074
- after brlen: logLH = -4379.137806
[00:00:00 -4379.137806] AUTODETECT spr round 1 (radius: 5)
[00:00:01 -3522.698627] AUTODETECT spr round 2 (radius: 10)
[00:00:01 -3293.091256] AUTODETECT spr round 3 (radius: 15)
[00:00:01 -3287.125175] AUTODETECT spr round 4 (radius: 20)
[00:00:01 -3287.097361] SPR radius for FAST iterations: 15 (autodetect)
[00:00:01 -3287.097361] Model parameter optimization (eps = 3.000000)
- after rates: logLH = -3285.803498
- after freqs: logLH = -3284.160625
- after alpha: logLH = -3284.044672
- after p-inv: logLH = -3284.044672
- after freeR: logLH = -3284.044672
- after brlen: logLH = -3283.953023
- after rates: logLH = -3283.796571
- after freqs: logLH = -3283.776370
- after alpha: logLH = -3283.698639
- after p-inv: logLH = -3283.698639
- after freeR: logLH = -3283.698639
- after brlen: logLH = -3283.631533
[00:00:02 -3283.631533] FAST spr round 1 (radius: 15)
- after brlen: logLH = -3249.481756
[00:00:02 -3249.481756] FAST spr round 2 (radius: 15)
- after brlen: logLH = -3171.554561
[00:00:02 -3171.554561] FAST spr round 3 (radius: 15)
- after brlen: logLH = -3171.554478
[00:00:03 -3171.554478] Model parameter optimization (eps = 1.000000)
- after rates: logLH = -3171.072384
- after freqs: logLH = -3170.997379
- after alpha: logLH = -3170.978181
- after p-inv: logLH = -3170.978181
- after freeR: logLH = -3170.978181
- after brlen: logLH = -3170.944242
[00:00:03 -3170.944242] SLOW spr round 1 (radius: 5)
- after brlen: logLH = -3169.123440
[00:00:04 -3169.123440] SLOW spr round 2 (radius: 5)
- after brlen: logLH = -3168.993851
[00:00:04 -3168.993851] SLOW spr round 3 (radius: 5)
- after brlen: logLH = -3168.768513
[00:00:05 -3168.768513] SLOW spr round 4 (radius: 5)
- after brlen: logLH = -3168.768410
[00:00:06 -3168.768410] SLOW spr round 5 (radius: 10)
- after brlen: logLH = -3168.768410
[00:00:06 -3168.768410] SLOW spr round 6 (radius: 15)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] SLOW spr round 7 (radius: 20)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] SLOW spr round 8 (radius: 25)
- after brlen: logLH = -3168.768410
[00:00:07 -3168.768410] Model parameter optimization (eps = 0.100000)
- after rates: logLH = -3168.736451
- after freqs: logLH = -3168.734472
- after alpha: logLH = -3168.711629
- after p-inv: logLH = -3168.711629
- after freeR: logLH = -3168.711629
- after brlen: logLH = -3168.693184
[00:00:08] ML tree search #1, logLikelihood: -3168.693184
Optimized model parameters:
Partition 0: noname
Rate heterogeneity: GAMMA (4 cats, mean), alpha: 0.077884 (ML), weights&rates: (0.250000,0.000000) (0.250000,0.000151) (0.250000,0.041501) (0.250000,3.958347)
Base frequencies (ML): 0.264743 0.235238 0.225568 0.274451
Substitution rates (ML): 1.143011 2.302345 0.837022 0.387131 4.506063 1.000000
Final LogLikelihood: -3168.693184
Best ML tree saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.bestTree
Optimized model saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.bestModel
Execution log saved to: /scratch365/ssmall2/anop_fun/AnopSG_align/subgroup_align/X/X_fasta/X.filtered.3722.aln.raxml.log
Analysis started: 17-Jan-2018 13:26:47 / finished: 17-Jan-2018 13:26:55
Elapsed time: 8.033 seconds
Alexey Kozlov
Jan 18, 2018, 7:27:28 AM1/18/18
to ra...@googlegroups.com
Hi Scott,
could you please send me the alignment?
In the meantime, you can also try to remove duplicates (see WARNINGs in the log), this should help to alleviate the problem.
Best,
Alexey
On 17.01.2018 19:30, scott small wrote:
> Hi,
> I seem to be having an intermittent error running raxml_ng v0.5.1b.
> command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
>
> /ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -27.193683 units
> *LOG FILE OUTPUT in DEBUG for SUCCESSFUL RUN:*
> /
> /
> //
>
>
> --
> You received this message because you are subscribed to the Google Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
could you please send me the alignment?
In the meantime, you can also try to remove duplicates (see WARNINGs in the log), this should help to alleviate the problem.
Best,
Alexey
On 17.01.2018 19:30, scott small wrote:
> Hi,
> I seem to be having an intermittent error running raxml_ng v0.5.1b.
> command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
>
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
> :
> system msg for write_line failure : Bad file descriptor
>
> /If I run the command 10 times this error will appear 9/10. I have copied the log file output in DEBUG mode for the
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
> :
> system msg for write_line failure : Bad file descriptor
>
> error and successful runs.
> Any ideas?
> thanks,
> scott
>
> p.s. The '--threads 1' was something I tried after reading another post about MPI issues
>
> *LOG FILE OUTPUT in DEBUG for ERROR RUN:*
> Any ideas?
> thanks,
> scott
>
> p.s. The '--threads 1' was something I tried after reading another post about MPI issues
>
> /
> //
>
>
> --
> You received this message because you are subscribed to the Google Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
Alexey Kozlov
Jan 20, 2018, 8:26:45 PM1/20/18
to ra...@googlegroups.com
Hi Scott,
> I attached one of the alignments.
thanks, I can reproduce the issue, working on the solution now.
>I would prefer not to remove duplicate sequences as I would like the taxa to be the
> same among all trees for downstream comparisons.
But I assume you do realize that the branching order of duplicate sequences in the inferred tree will be arbitrary?
Is this OK for your application? Or would it make more sense to have multifurcations?
Best,
Alexey
> thanks,
> scott
>
> On Wednesday, January 17, 2018 at 1:30:49 PM UTC-5, scott small wrote:
>
> Hi,
> I seem to be having an intermittent error running raxml_ng v0.5.1b.
> command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
>
> /ERROR: ERROR in SPR round: BL opt converged to a worse likelihood score by -27.193683 units
> *LOG FILE OUTPUT in DEBUG for SUCCESSFUL RUN:*
> I attached one of the alignments.
>I would prefer not to remove duplicate sequences as I would like the taxa to be the
> same among all trees for downstream comparisons.
Is this OK for your application? Or would it make more sense to have multifurcations?
Best,
Alexey
> thanks,
> scott
>
> On Wednesday, January 17, 2018 at 1:30:49 PM UTC-5, scott small wrote:
>
> Hi,
> I seem to be having an intermittent error running raxml_ng v0.5.1b.
> command: raxml-ng-mpi --msa X.filtered.3722.aln --model GTR+G --log DEBUG --threads 1
>
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
> :
> system msg for write_line failure : Bad file descriptor
>
> /If I run the command 10 times this error will appear 9/10. I have copied the log file output in DEBUG mode for the
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1
> :
> system msg for write_line failure : Bad file descriptor
>
> error and successful runs.
> Any ideas?
> thanks,
> scott
>
> p.s. The '--threads 1' was something I tried after reading another post about MPI issues
>
> *LOG FILE OUTPUT in DEBUG for ERROR RUN:*
> Any ideas?
> thanks,
> scott
>
> p.s. The '--threads 1' was something I tried after reading another post about MPI issues
>
> RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
> Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
> Latest version: https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>
> Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
> RAxML-NG v. 0.5.1b BETA released on 01.12.2017 by The Exelixis Lab.
> Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
> Latest version: https://github.com/amkozlov/raxml-ng <https://github.com/amkozlov/raxml-ng>
> Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel.
> Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml
scott small
Jan 21, 2018, 1:51:16 PM1/21/18
to raxml
Hi Alexey,
You are of course correct but I am attempting to use the programs Twisst (https://github.com/simonhmartin/twisst) and TreeScape to visualize different gene trees. Twisst will produce an error if a tip name which is in the groups file does not appear in the tree.
Thank you for checking out the Alignment, I hope it is an easy fix!
-scott
You are of course correct but I am attempting to use the programs Twisst (https://github.com/simonhmartin/twisst) and TreeScape to visualize different gene trees. Twisst will produce an error if a tip name which is in the groups file does not appear in the tree.
Thank you for checking out the Alignment, I hope it is an easy fix!
-scott
scott small
Feb 22, 2018, 6:31:53 PM2/22/18
to raxml
Hi Alexey,
Just wanted to follow-up with this thread. Do you have any recommendations based the alignment file?
thank you,
Just wanted to follow-up with this thread. Do you have any recommendations based the alignment file?
thank you,
scott
On Saturday, January 20, 2018 at 8:26:45 PM UTC-5, Alexey Kozlov wrote:
Alexey Kozlov
Feb 23, 2018, 6:19:37 PM2/23/18
to ra...@googlegroups.com
Hi Scott,
sorry for long silence, the issue turned out to be much harder to fix than I thought.
Now I believe to have it fixed at least on the dataset you sent me, although the fix is only available in the dev branch
for now.
It would be great if you could test it on your side, here is how you can build the dev branch:
git clone --recursive https://github.com/amkozlov/raxml-ng.git .
git checkout dev
git submodule update --recursive
mkdir build && cd build
cmake ..
make
Thanks!
Best,
Alexey
> <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
sorry for long silence, the issue turned out to be much harder to fix than I thought.
Now I believe to have it fixed at least on the dataset you sent me, although the fix is only available in the dev branch
for now.
It would be great if you could test it on your side, here is how you can build the dev branch:
git clone --recursive https://github.com/amkozlov/raxml-ng.git .
git checkout dev
git submodule update --recursive
mkdir build && cd build
cmake ..
make
Thanks!
Best,
Alexey
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
scott small
Mar 29, 2018, 12:33:23 PM3/29/18
to raxml
Thank you Alexey. Everything seems much better now!!
Alexey Kozlov
Mar 29, 2018, 12:44:32 PM3/29/18
to ra...@googlegroups.com
great news, many thanks for confirmation!
On 29.03.2018 18:33, scott small wrote:
>
> Thank you Alexey. Everything seems much better now!!
>
> On Friday, February 23, 2018 at 6:19:37 PM UTC-5, Alexey Kozlov wrote:
>
> Hi Scott,
>
> sorry for long silence, the issue turned out to be much harder to fix than I thought.
>
> Now I believe to have it fixed at least on the dataset you sent me, although the fix is only available in the dev
> branch
> for now.
>
> It would be great if you could test it on your side, here is how you can build the dev branch:
>
> git clone --recursive https://github.com/amkozlov/raxml-ng.git <https://github.com/amkozlov/raxml-ng.git> .
On 29.03.2018 18:33, scott small wrote:
>
> Thank you Alexey. Everything seems much better now!!
>
> On Friday, February 23, 2018 at 6:19:37 PM UTC-5, Alexey Kozlov wrote:
>
> Hi Scott,
>
> sorry for long silence, the issue turned out to be much harder to fix than I thought.
>
> Now I believe to have it fixed at least on the dataset you sent me, although the fix is only available in the dev
> branch
> for now.
>
> It would be great if you could test it on your side, here is how you can build the dev branch:
>
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