ERROR in SPR round (LIBPLL-2240)

[D T Singh]

Hi Alexey,

I was running RAXML_NG in the following environment:

JobId: 973410.wlm01  

Project: 21120233 

Exit Status: 0

NCPUs Requested: 192 NCPUs Used: 192

CPU Time Used: 178:09:13

Memory Requested: 384gb Memory Used: 7693424kb

Vmem Used: 25764156kb

Walltime requested: 24:00:00 Walltime Used: 07:26:06

Execution Nodes Used: (std0407:ncpus=24:mem=50331648kb)+(std0410:ncpus=24:mem=50331648kb)+(std0412:ncpus=24:mem=50331648kb)+(std0426:ncpus=24:mem=50331648kb)+(std0433:ncpus=24:mem=50331648kb)+(std0441:ncpus=24:mem=50331648kb)+(std0452:ncpus=24:mem=50331648kb)+(std0466:ncpus=24:mem=50331648kb)

 cat Cor_Chn_Gen_16-20.raxml.log 

RAxML-NG v. 0.9.0git released on 26.11.2019 by The Exelixis Lab.

Developed by: Alexey M. Kozlov and Alexandros Stamatakis.

Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.

Latest version: https://github.com/amkozlov/raxml-ng

Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

RAxML-NG was called at 19-Jun-2020 12:00:48 as follows:

raxml-ng-mpi --all --msa /home/projects/21120233/data/input/Corona2_Gen_Chn_16-20.phy --model GTR+G --prefix /home/projects/21120233/data/output/Cor_Chn_Gen_16-20 --tree pars {10} --bs-trees 200 --force

Analysis options:

  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)

  start tree(s): parsimony (10)

  bootstrap replicates: 200

  random seed: 1592568049

  tip-inner: OFF

  pattern compression: ON

  per-rate scalers: OFF

  site repeats: ON

  branch lengths: proportional (ML estimate, algorithm: NR-FAST)

  SIMD kernels: AVX2

  parallelization: MPI (96 ranks)

WARNING: Running in FORCE mode: all safety checks are disabled!

[00:00:01] Reading alignment from file: /home/projects/21120233/data/input/Corona2_Gen_Chn_16-20.phy

[00:00:01] Loaded alignment with 315 taxa and 46365 sites

Alignment comprises 1 partitions and 31359 patterns

Partition 0: noname

Model: GTR+FO+G4m

Alignment sites / patterns: 46365 / 31359

Gaps: 38.94 %

Invariant sites: 27.84 %

All was well till it reached bootstrap tree#113...then I get this error:

[11:11:32] Bootstrap tree #112, logLikelihood: -885022.318987

[11:16:48] Bootstrap tree #113, logLikelihood: -876314.225361

ERROR: ERROR in SPR round (LIBPLL-2240): BL opt converged to a worse likelihood score by -65.995181635487825 units

I got the same error twice despite changing the alignment tool from Muscle to MAFFT

Can you please help to resolve this?

I see that many others reported same error and you have suggested changing some params like --model etc.

Thanks,

DT

[Alexey Kozlov]

Hi

could you please try to reproduce with the latest version available here:

https://github.com/amkozlov/raxml-ng/wiki/installation#building-coarse-grained-parallelization-branch

(also, just restarting from a checkpoint might solve the problem)

Best,
Alexey

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[D T Singh]

Hi Alexey,

Thanks for the prompt reply. I was away and just back. Hence the delay in replying...sry for that. 

Sure, I will check and get back. Btw, just noticed that it restarted by itself from some checkpoint and completed the run!!

Thanks..:)!!

DT