pplacer on CentOS 7.0

[Igor Tolstoy]

Hello everybody,
It looks like pplacer is not working on CentOS 7.0

problem located in multiprocessing.ml which heavily rely on Unix module

pplacer_run.ml :

 Multiprocessing.try_fork
      (Prefs.children prefs)
      (new pplacer_process partial gotfunc nextfunc)
      Progressfunc


pplacer -j 30 -c /usr/local/checkm/1.0.5/data/genome_tree/genome_tree_full.refpkg -o x
concatenated.fasta
Running pplacer unknown analysis on concatenated.fasta...
Didn't find any reference sequences in given alignment file. Using
supplied reference alignment.
Pre-masking sequences... sequence length cut from 6988 to 6687.
Warning: pplacer results make the most sense when the given tree is
multifurcating at the root. See manual for details.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree... done.
Pulling exponents... done.
Preparing the edges for baseball... done.
working on 9968 (1/1)...
Uncaught exception: Multiprocessing.Child_error(_)
Fatal error: exception Multiprocessing.Child_error(_)

 any help will be appreciated.

[Erick Matsen]

Hello Igor--

Sorry to hear you're having issues. 

Just to make sure, it's working with one thread (-j 1)? What about just with two threads (-j 2)?

Thanks,

Erick

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[Igor Tolstoy]

It doesn't work with -j 1 : same error.
 -j 2 I don't check.

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[Erick Matsen]

Igor--

I'm afraid we don't have a CentOS machine nor a whole lot of time to look into this.

If you are determined, take a look at https://github.com/matsen/pplacer-build-env/blob/master/Dockerfile for a complete environment setup for compiling pplacer-- ideally you will be able to replace the apt-get commands with the equivalent yum commands.

Erick

Erick

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[Marc C]

Hi all--

This is longggggg after the fact, but I ran into the same error and found a fix.

After a bit of debugging I found it was due to my reference tree. Branch lengths were very large, and some began with '0'. (this was done by accidentally removing all \. characters). Fixing this allowed for pplacer to run smoothly. Tested on 1.7alpha and 1.9alpha. So, check your branch lengths?

--MC

Erick

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[Marc C]

NOTE: My fix above was tested on Ubuntu 16 LTE, not centos. Same goes for my error, though it seems exactly the same issue.