pplacer error during test

[corkdagga]

Hi,

I just installed checkm on my macbook and downloaded the database as described in the instructions. When running the checkm test, I run into the following error.

(checkm) 13:23:40 p@NABI-MAC001:/Volumes/pmi23/tools_databases/checkm$ checkm test test_run
[2025-03-05 13:24:20] INFO: CheckM v1.2.3
[2025-03-05 13:24:20] INFO: checkm test test_run
[2025-03-05 13:24:20] INFO: CheckM data: /Volumes/pmi23/tools_databases/checkm/DB
[2025-03-05 13:24:20] INFO: [CheckM - Test] Processing E.coli K12-W3310 to verify operation of CheckM.
[2025-03-05 13:24:20] INFO: [Step 1]: Verifying tree command.
[2025-03-05 13:24:20] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2025-03-05 13:24:20] INFO: Identifying marker genes in 1 bins with 1 threads:
[2025-03-05 13:24:32] INFO: Saving HMM info to file.
[2025-03-05 13:24:32] INFO: Calculating genome statistics for 1 bins with 1 threads:
[2025-03-05 13:24:32] INFO: Extracting marker genes to align.
[2025-03-05 13:24:32] INFO: Parsing HMM hits to marker genes:
    Finished parsing hits for 1 of 1 (100.00%) bins.
[2025-03-05 13:24:32] INFO: Extracting 43 HMMs with 1 threads:
[2025-03-05 13:24:34] INFO: Aligning 43 marker genes with 1 threads:
[2025-03-05 13:24:43] INFO: Reading marker alignment files.
[2025-03-05 13:24:43] INFO: Concatenating alignments.
[2025-03-05 13:24:43] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
dyld[47698]: Library not loaded: @rpath/libgsl.25.dylib
  Referenced from: <0D61E9B0-4DB5-3D60-99A8-F091685CDB35> /opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/pplacer
  Reason: tried: '/opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/../lib/libgsl.25.dylib' (no such file), '/opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/../lib/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file, not in dyld cache)
sh: line 1: 47698 Abort trap: 6           pplacer -j 1 -c /Volumes/pmi23/tools_databases/checkm/DB/genome_tree/genome_tree_reduced.refpkg -o test_run/results/storage/tree/concatenated.pplacer.json test_run/results/storage/tree/concatenated.fasta > test_run/results/storage/tree/pplacer.out
[2025-03-05 13:24:43] ERROR: pplacer exited with code: 34304

  Controlled exit resulting from an unrecoverable error or warning.

When I simply run pplacer within the checkm conda environment I also get a similar error:

(checkm) 13:39:46 p@NABI-MAC001:/Volumes/pmi23/tools_databases/checkm$ pplacer
dyld[49847]: Library not loaded: @rpath/libgsl.25.dylib
  Referenced from: <0D61E9B0-4DB5-3D60-99A8-F091685CDB35> /opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/pplacer
  Reason: tried: '/opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/../lib/libgsl.25.dylib' (no such file), '/opt/homebrew/Caskroom/mambaforge/base/envs/checkm/bin/../lib/libgsl.25.dylib' (no such file), '/usr/local/lib/libgsl.25.dylib' (no such file), '/usr/lib/libgsl.25.dylib' (no such file, not in dyld cache)
Abort trap: 6

I saw several people had this issue due to gsl and I tried to implement those but without success

[donovan-h-parks]

Hi. Most likely issue is that your laptop does not have sufficient memory to run pplacer. You can find the CheckM system requirements here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements. Also, you might be interested in considering CheckM v2: https://github.com/chklovski/CheckM2.