Comments (2)
gruppy is part of pplacer, which needs to be installed on your system separately. You will also need HMMER and prodigal on your system, see the wiki for extra info
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I've update the CheckM documentation along with the error message provided when guppy is missing in order to make it clear that it is part of the pplacer package.
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Related Issues (20)
- Placing 3 bins into the genome tree with pplacer Killed HOT 4
- AttributeError: 'Namespace' when running 'checkm coverage' HOT 1
- bin_qa_plot
- Customizing CheckM Dataset & Gene Marker Selection for a Species
- Reference data is missing HOT 1
- don't find Strain heterogeneity info
- FileNotFoundError: [Errno 2] No such file or directory: 'checkm_folder/storage/tree/concatenated.tre' HOT 8
- IndexError: list index out of range HOT 1
- Understanding contamination value HOT 2
- ERROR conda.core.link:_execute(952): An error occurred while installing package 'bioconda::checkm-genome-1.2.2-pyhdfd78af_1'. HOT 1
- Unexpected error: <class 'KeyError'>
- FileNotFoundError: [Errno 2] No such file or directory: '/home/majorram/anaconda3/envs/checkm/hmms/phylo.hmm' HOT 3
- Chekm test: line 1: 16491 Bus error (core dumped) pplacer -j 1 HOT 2
- maximum number of genomes/MAGs to run checkm HOT 2
- WARNING: Expected all files to contain sequences in amino acid space. HOT 1
- local variable 'seqId' referenced before assignment
- 'utf-8' codec can't decode byte 0xb0 in position 37: invalid start byte HOT 1
- checkm ssu_finder HOT 2
- Fatal exception (source file p7_hmmfile.c, line 2095): hmm write failed. system error: No space left on device HOT 2
- checkm_coverage dropped some bins
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