Comments (6)
emma-bell
commented on August 10, 2024
1
Thank you @chklovski and @kellikmullane, checkm2 now works for me with the latest release (conda install) :)
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Mass23
commented on August 10, 2024
Having the same errors with my bins and the testrun, using the "run without installation" and "Installation" methods.
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GeoMicroSoares
commented on August 10, 2024
Same here! @chklovski
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emma-bell
commented on August 10, 2024
Me too, did anyone figure it out?
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kellikmullane
commented on August 10, 2024
@emma-bell I never figured it out. Ended up just going with the original CheckM. The CheckM2 documentation suggested for the organisms I was working with (Gammaproteobacteria), CheckM and CheckM2 would provide fairly similar results. Would love to get it working for future projects though, so if anyone is able to fix this issue, please drop the info on how you resolved the issue on this thread!
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chklovski
commented on August 10, 2024
Apologies for the late reply. If you want to try checkm2 again, please install it via bioconda and let me know if the issue persists.
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Related Issues (20)
- Cannot install ChekM2 HOT 1
- Question about Checkm2 Annotation HOT 1
- Checkm2 flags certain species and genera as contaminated on a consistent basis.
- the version checkm2 v1.0.2 was not available on conda HOT 1
- Error in DIAMOND execution HOT 2
- [Feature Request] Use #!/usr/bin/env python instead of hardcoding python path
- AttributeError: 'Predictor' object has no attribute '__set_up_prodigal_thread' HOT 2
- Random errors on clusters HOT 3
- Database update? HOT 2
- TypeError: metaclass conflict HOT 7
- coding density
- Can Checkm2 be fine-tuned for euMAGs? HOT 1
- Got different results of the same genome from the different runs of checkm2 HOT 3
- testrun error: AttributeError: module '__main__' has no attribute '__spec__'
- Testrun ERROR: No DIAMOND annotation was generated. HOT 2
- test run yields different results HOT 1
- Database download failed HOT 3
- Naming Output TSV File
- TypeError: split() error
- AF_UNIX path too long HOT 2
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