Modeltest was unexpectedly killed

[TANGLi83-star]

I was running the modeltest-ng with the concated single copy gene as input, using the following command

modeltest-ng -d aa -i all.mafft.aln.trimmed.fa -o all_model -T raxml -p 136

However, the modeltest program was killed suddenly, and the output info as follow

                            | |    | | |          | |    | \ | |/ ____|
         _ __ ___   ___   __| | ___| | |_ ___  ___| |_   |  \| | |  __ 
        | '_ ` _ \ / _ \ / _` |/ _ \ | __/ _ \/ __| __|  | . ` | | |_ |
        | | | | | | (_) | (_| |  __/ | ||  __/\__ \ |_   | |\  | |__| |
        |_| |_| |_|\___/ \__,_|\___|_|\__\___||___/\__|  |_| \_|\_____|
--------------------------------------------------------------------------------
ModelTest-NG v0.1.7 released on 17.03.2021 by The Exelixis Lab.
Written by Diego Darriba.
Contributors: Tomas Flouri, Alexey Kozlov, Benoit Morel, David Posada, 
              Alexandros Stamatakis.
Latest version: https://github.com/ddarriba/modeltest
--------------------------------------------------------------------------------

Physical cores: 136
Logical cores:  272
Memory:         16GB
Extensions:     AVX

WARNING: Partition DATA: Sequences Streptomyces_caniscabiei_ND05-01C and Streptomyces_caniscabiei_ND05-3B are identical
WARNING: Partition DATA: Sequences Streptomyces_caniscabiei_ND05-01C and Streptomyces_caniscabiei_NE06-02F are identical
WARNING: Partition DATA: Sequences Streptomyces_fulvoviridis_NRRL_ISP-5210 and Streptomyces_olivaceus_NRRL_B-1125 are identical
WARNING: Partition DATA: Sequences Streptomyces_scabiei_LBUM_1477 and Streptomyces_scabiei_LBUM_1487 are identical
WARNING: Partition DATA: Sequences Streptomyces_galilaeus_ATCC_14969 and Streptomyces_galilaeus_JCM_4757 are identical

WARNING: MSA has not enough sites to infer reliable results
Creating new checkpoint file: all_model.ckp
--------------------------------------------------------------------------------
ModelTest-NG v0.1.7

Input data:
  MSA:        all.fa.sort
  Tree:       Maximum parsimony
    file:           -
  #taxa:            151
  #sites:           40352
  #patterns:        20019
  Max. thread mem:  3245 MB

Output:
  Log:           all_model.log
  Starting tree: all_model.tree
  Results:       all_model.out

Selection options:
  # protein matrices: 19
  # protein models:   57
  include model parameters:
    Uniform:         false
    p-inv (+I):      true
    gamma (+G):      true
    both (+I+G):     true
    free rates (+R): false
    fixed freqs:     true
    estimated freqs: false
    #categories:     4
  gamma rates mode:   mean
  asc bias:           none
  epsilon (opt):      0.01
  epsilon (par):      0.05
  keep branches:      false

Additional options:
  verbosity:        very low
  threads:          136/136
  RNG seed:         12345
  subtree repeats:  enabled
--------------------------------------------------------------------------------
modeltest-ng was called as follows: 
>> modeltest-ng -d aa -i all.fa.sort -o all_model -T raxml -p 136 

Partition 1/1

Killed

[TANGLi83-star]

Please help me out, thanks!

[stamatak]

Please read the warning message, something is wrong with your MSA:

WARNING: Partition DATA: Sequences Streptomyces_caniscabiei_ND05-01C and Streptomyces_caniscabiei_ND05-3B are identical WARNING: Partition DATA: Sequences Streptomyces_caniscabiei_ND05-01C and Streptomyces_caniscabiei_NE06-02F are identical WARNING: Partition DATA: Sequences Streptomyces_fulvoviridis_NRRL_ISP-5210 and Streptomyces_olivaceus_NRRL_B-1125 are identical WARNING: Partition DATA: Sequences Streptomyces_scabiei_LBUM_1477 and Streptomyces_scabiei_LBUM_1487 are identical WARNING: Partition DATA: Sequences Streptomyces_galilaeus_ATCC_14969 and Streptomyces_galilaeus_JCM_4757 are identical

WARNING: MSA has not enough sites to infer reliable results

On 11.04.23 10:39, TANGLi83 wrote:

Please help me out, thanks!

— Reply to this email directly, view it on GitHub https://github.com/ddarriba/modeltest/issues/63#issuecomment-1502841317, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGXB6URH34OAHYJF5XW5NDXAUDCZANCNFSM6AAAAAAWZ4O6SY. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and Technology - Hellas Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab) www.exelixis-lab.org (Heidelberg lab)

[ddarriba]

I believe it is a memory error. According to the execution details, each thread could require a maximum of 3 GBytes of memory, so you should not run more than 4 or 5 threads in your machine (if the log information is correct and you have 16 GB).