Question: CheckM and pplacer error
0
gravatar for shibl_a
9 months ago by
shibl_a20
shibl_a20 wrote:

I installed checkm using bioconda and downloaded pplacer from its site. I then moved all the pplacer executables into the checkm bin.

When I run this command:

$ checkm lineage_wf --pplacer_threads 2 checkm_input checkm_output

I get this output:

*******************************************************************************
 [CheckM - tree] Placing bins in reference genome tree.
*******************************************************************************
  Identifying marker genes in 10 bins with 1 threads:
    Finished processing 10 of 10 (100.00%) bins.
  Saving HMM info to file.
  Calculating genome statistics for 10 bins with 1 threads:
    Finished processing 10 of 10 (100.00%) bins.
  Extracting marker genes to align.
  Parsing HMM hits to marker genes:
    Finished parsing hits for 10 of 10 (100.00%) bins.
  Extracting 43 HMMs with 1 threads:
    Finished extracting 43 of 43 (100.00%) HMMs.
  Aligning 43 marker genes with 1 threads:
    Finished aligning 43 of 43 (100.00%) marker genes.
  [Error] Make sure pplacer is on your system path.
  Controlled exit resulting from an unrecoverable error or warning.

Please note that when I run this:

$ which pplacer

I get this location, where all checkm executables are:

~/miniconda3/envs/checkm2/bin/pplacer

Any ideas/ suggestions?

ADD COMMENTlink modified 9 months ago • written 9 months ago by shibl_a20

Why didn't you install pplacer from bioconda as well? Could you try installing both from bioconda and give it a try?

ADD REPLYlink written 8 months ago by h.mon27k

That was the first thing I tried but this is what the conda command returns

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pplacer

Current channels:

  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/osx-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.
ADD REPLYlink written 8 months ago by shibl_a20
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