Comments (2)
ctSkennerton
commented on August 16, 2024
Hello Branden,
There are multiple software packages on pip with checkm in the name. I think that you may have downloaded a different one. I think that you actually got this one, which is "text-based file manifest format". make sure that use used the command pip install checkm-genome, the latest version is 1.0.3
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brandentimm
commented on August 16, 2024
Ah, indeed. Thanks!
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Related Issues (20)
- 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
- NameError: free variable 'mask' referenced before assignment in enclosing scope
- Having trouble interpreting the meaning of "root" as a marker lineage HOT 1
- Make sure pplacer is on your system path. HOT 1
- Having trouble running CheckM: Models must be parsed before identifying HMM hits.
- Unexpected error: <class 'FileNotFoundError'> HOT 1
- question：Anaconda ——conda install pytorch==1.10.1 torchvision==0.11.2 torchaudio==0.10.1 cudatoolkit=11.3 -c pytorch -c conda-forge
- No space left on device error in HMM step not caught HOT 2
- For a specific bin, why is the Marker lineage in lineage.ms different with it in quality report?
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