Comments (6)
and also the HMM is created using sequences that ultimately do not pass the length cutoff
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and also the HMM is not dereplicated at the genus level, which would be a nice feature. I'm working on create now so leave this one to me.
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and also the duplicates are included in the diamond db, so it is possible to map to a read that is in the diamond database, but is not in the tree.
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One might argue that diamond sequences shouldn't be deduplicated, because the deduplication happens only for those positions aligned to the HMM, and diamond doesn't care about HMMs. What do you think @geronimp ?
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@wwood Yes I dont think we should de-duplicate the diamond sequences. The branch I'm working on now includes sequences that have not been deduplicated, but it ""doesn't"" remove those which did not pass the min percent align filter.
imo i think this is the best way.
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this issue seems to be fixed now thanks to Joel
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Related Issues (20)
- graftM create_why error in building tree? HOT 6
- Install Error using pip install
- LookupError: unknown encoding: utf8 HOT 3
- Input Reads or Bins HOT 3
- Combined alignment file intermittently produced HOT 15
- KeyError on split sequence?
- search_only mode does not pair reads HOT 2
- Can't find FastTreeMP HOT 4
- graft_package_version error on custom GraftM package HOT 10
- graftM create error while creating package HOT 3
- Error: TC bit thresholds unavailable on model graftmrzdqhx.aln HOT 2
- graftM create error HOT 6
- graftM create failed to root the tree HOT 9
- error using decoy_database with hmmsearch+diamond
- Issue running graftm create using docker HOT 6
- working with non-gene sequences
- What does 'Root' classification refer to? HOT 2
- Getting ZeroDivisionError when running with sample data HOT 7
- GraftM graft on big metagenome error HOT 4
- An error was found that was difficult to resolve after manually reroot HOT 5
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