CheckM and pplacer correctly installed and in PATH but checkm not running: [Errno 2] No such file or directory: 'ffn_checkM/.../hmmer.tree.txt'/[Error] Make sure pplacer is on your system path. about checkm

[donovan-h-parks]

Hello,

CheckM requires HMMER >=3.1b1. It appears you only have rnammer on your path. Can you confirm that HMMER >= 3.1.b1 is installed and on the path. You can check the version number with:
hmmsearch -h.

Cheers,
Donovan

Thanks for your answer. I have in my PATH hmmser 2.4i.
I will try to get the 3.1 version and see if it works.

hmmsearch -h
hmmsearch - search a sequence database with a profile HMM
HMMER 2.4i (December 2006)
Copyright (C) 1992-2006 HHMI Janelia Farm
Freely distributed under the GNU General Public License (GPL)
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You were completely right!
With hmmer 3.1b1 in the paths everything went perfect.
Thanks very much!