bokulich-lab/q2-checkm

QIIME 2 plugin for assessing the quality of (meta)genomes using CheckM.

q2-checkm's Issues

BUG: gsl library missing

I followed the installation instructions and tried to run the following:

cd download_here
curl -L -o checkm-db.tar.gz https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
mkdir checkm_db
tar -xzf checkm-db.tar.gz -C checkm_db
rm checkm-db.tar.gz
wget https://polybox.ethz.ch/index.php/s/slGyW1uQbyxmyb9/download -O mags.qza

qiime checkm evaluate-bins \
  --i-bins mags.qza \
  --p-db-path ./checkm_db \
  --p-reduced-tree \
  --p-threads 8 \
  --p-pplacer-threads 6 \
  --o-visualization mags.qzv \
  --verbose

I get the following error:

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: checkm lineage_wf --reduced_tree --threads 7 --pplacer_threads 6 -x fasta /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/qiime2/santiago/data/fd55c63f-10a5-4c5a-827f-3a071bea4c10/data/sample1 /var/fold
ers/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1

[2024-06-28 13:02:48] INFO: CheckM v1.2.3
[2024-06-28 13:02:48] INFO: checkm lineage_wf --reduced_tree --threads 7 --pplacer_threads 6 -x fasta /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/qiime2/santiago/data/fd55c63f-10a5-4c5a-827f-3a071bea4c10/dat
a/sample1 /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1
[2024-06-28 13:02:48] INFO: CheckM data: ./checkm_db
[2024-06-28 13:02:48] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-06-28 13:02:48] INFO: Identifying marker genes in 2 bins with 7 threads:
[2024-06-28 13:03:22] INFO: Saving HMM info to file.
[2024-06-28 13:03:22] INFO: Calculating genome statistics for 2 bins with 7 threads:
[2024-06-28 13:03:24] INFO: Extracting marker genes to align.
[2024-06-28 13:03:24] INFO: Parsing HMM hits to marker genes:
    Finished parsing hits for 2 of 2 (100.00%) bins.
[2024-06-28 13:03:24] INFO: Extracting 43 HMMs with 7 threads:
[2024-06-28 13:03:27] INFO: Aligning 43 marker genes with 7 threads:
[2024-06-28 13:03:29] INFO: Reading marker alignment files.
[2024-06-28 13:03:29] INFO: Concatenating alignments.
[2024-06-28 13:03:29] INFO: Placing 2 bins into the genome tree with pplacer (be patient).
dyld[55892]: Library not loaded: /usr/local/lib/libgsl.0.dylib
  Referenced from: <0D61E9B0-4DB5-3D60-99A8-F091685CDB35> /Users/santiago/mambaforge/envs/q2-checkm/bin/pplacer
  Reason: tried: '/usr/local/lib/libgsl.0.dylib' (errno=62), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libgsl.0.dylib' (no such file), '/usr/local/lib/libgsl.0.dylib' (errno=62), '/usr/lib/libgsl.0.dyli
b' (no such file, not in dyld cache)
sh: line 1: 55892 Abort trap: 6           pplacer -j 6 -c ./checkm_db/genome_tree/genome_tree_reduced.refpkg -o /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1/storage/tree/concatenat
ed.pplacer.json /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1/storage/tree/concatenated.fasta > /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1/storage/
tree/pplacer.out
[2024-06-28 13:03:29] ERROR: pplacer exited with code: 34304

  Controlled exit resulting from an unrecoverable error or warning.
Traceback (most recent call last):
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/q2cli/commands.py", line 520, in __call__
    results = self._execute_action(
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
    results = action(**arguments)
  File "<decorator-gen-26>", line 2, in evaluate_bins
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
    outputs = self._callable_executor_(
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/qiime2/sdk/action.py", line 615, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/q2_checkm/checkm.py", line 272, in evaluate_bins
    reports = _evaluate_bins(results_dir, bins, db_path, common_args)
  File "/Users/santiago/mambaforge/envs/q2-checkm/lib/python3.8/site-packages/q2_checkm/checkm.py", line 65, in _evaluate_bins
    raise FileNotFoundError(f"CheckM stats file {stats_fp} could not be found.")
FileNotFoundError: CheckM stats file /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1/storage/bin_stats_ext.tsv could not be found.

Plugin error from checkm:

  CheckM stats file /var/folders/6p/vfbtsnkn1x738nqkqzcprf5w0000gn/T/tmpolikwe3x/results/sample1/storage/bin_stats_ext.tsv could not be found.

See above for debug info.

Apparently, I was missing the gsl library. So I brew install gsl it. The installed version was 2.8 and pplacer was still looking explicitly for version 0 (which is not even available in the ftp server, the earliest available is 1.0). So I cheated and made a file /usr/local/lib/libgsl.0.dylib with a symlink to /usr/local/lib/libgsl.28.dylib and then it worked ✅ 🥳 .

Just a workaround, I guess we need to find a way to install gsl.v0

MAINT: Change imports from q2-types-genomics to q2-types.

• q2-types-genomics will be deprecated with the next qiime distro.
• All imports from q2-types-genomics have to be changed to q2-types.
  qiime2/q2-types#309 (comment)

CheckM results are being saved into a (potentially) read-only directory

That happens in at least two places:

q2-checkm/q2_checkm/checkm.py

Lines 282 to 284 in c959c21

	_zip_checkm_plots(
	plots_per_sample, os.path.join(TEMPLATES, "checkm", "checkm_plots.zip")
	)

and

q2-checkm/q2_checkm/checkm.py

Lines 291 to 295 in c959c21

	checkm_results.to_csv(
	os.path.join(TEMPLATES, "checkm", "results.tsv"),
	sep="\t",
	index=False,
	)

This can lead to issues when the TEMPLATES directory is in a read-only location, eg. when executing from within a Singularity container. The results could be directly written to the output_dir instead.

CI: migrate the GitHub workflow to the new version

See q2-moshpit or q2-assembly for reference.