donovan-h-parks
commented
4 months ago Hi. Such issues are generally due to CheckM running out of memory. You can check the system requirements here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements
Unexpected error: <class 'FileNotFoundError'> Traceback (most recent call last): File "/Users/zhangluyao/anaconda3/bin/checkm", line 856, in
checkmParser.parseOptions(args)
File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/main.py", line 980, in parseOptions
self.lineageSet(options)
File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/main.py", line 261, in lineageSet
treeParser.getBinMarkerSets(options.tree_dir, options.marker_file,
File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/checkm/treeParser.py", line 485, in getBinMarkerSets
tree = dendropy.Tree.get_from_path(treeFile, schema='newick', rooting="force-rooted", preserve_underscores=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/zhangluyao/anaconda3/lib/python3.11/site-packages/dendropy/datamodel/basemodel.py", line 217, in get_from_path
with open(src, *open_args) as fsrc:
^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/Users/zhangluyao/Downloads/checkm_data_2015_01_16/result/storage/tree/concatenated.tre'