Error: list index out of range

[die...@nocrotec.com]

Hello Rob and all,
I tried to analyse a little larger MSA (167 sites broad and 1279 sequences long).
Config:
# ALIGNMENT FILE #
alignment = infile.phy;
# BRANCHLENGTHS #
branchlengths = linked;
# MODELS OF EVOLUTION #
models=JC, K80, SYM, F81, HKY, GTR, JC+G, K80+G, SYM+G, F81+G, HKY+G, GTR+G;
model_selection = bic;
# DATA BLOCKS #
[data_blocks]
58S = 1 - 167;
# SCHEMES #
[schemes]
search = all; #I also tried greedy here#

But I experienced an error - the important lines al follows:

Exception in thread Thread-8:
Traceback (most recent call last):
  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run
    cmd, args = self.pool.next_task()
  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task
    task = self.tasks[self.curtask]
IndexError: list index out of range

ERROR    | 2017-12-12 04:09:23,905 | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem
ERROR    | 2017-12-12 04:09:23,906 |
ERROR    | 2017-12-12 04:09:23,906 | .......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename: 7f4a7a49dd5801a1f46e3c62545526b7.phy . Data type: dna . Alphabet size: 4 . Sequence format: interleaved . Number of data sets: 1 . Nb of bootstrapped data sets: 0 . Model name: Custom . Proportion of invariable sites: 0.000000 . Number of subst. rate categs: 4 . Gamma distribution parameter: estimated . 'Middle' of each rate class: mean . Nucleotide equilibrium frequencies: user-defined . Optimise tree topology: no . Evaluated tree: file "user tree (filtered_source.phy_phyml_tree.txt)" . Optimise branch lengths: yes . Optimise substitution model parameters: yes . Run ID: JC+G . Random seed: 1513079883 . Subtree patterns aliasing: no . Version: 20120412 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 92 patterns found (out of a total of 167 sites). . 109 sites without polymorphism (65.27%). . Reading tree...
slurmstepd: Exceeded job memory limit at some point.

What should I do to get it work?
All the best
Dieter

[Rob Lanfear]

Hi Dieter,

The error tells you that PhyML ran out of memory. So you need to allocate more memory to the job somehow. Lots of ways to do this:

1. Use fewer cores on the same computer
2. Use a computer with more memory
3. Allocate more memory to the job (if you're on a cluster)

Rob

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Rob Lanfear
Division of Ecology and Evolution,

Research School of Biology,

The Australian National University,

Canberra

www.robertlanfear.com

[Dieter Waechter]

Hello Rob,

Thank you very much.

I checked with Cipres and they found the problem.

With 4 processors it worked perfectly.

All the best

Dieter

 

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[Rob Lanfear]

Great!

R

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