Bug in ARG + taxonomy merging
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- Nextflow
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Description
Description of the bug
There is a bug in the merging step of hamronization results with the taxonomy results. ARG hits are duplicated in some cases probably because some table joining on the contig names went not correct. The correct hit is always present, but is surrounded by hits of wrong taxa classifications (because wrong contig numbers merged).
This only affects the ARG subworkflow, i.e. the hamronization_complete_summary_taxonomy.tsv.gz file; AMP and BGC subworkflows are fine.
In the below example, the correct contig k141_349539 is assigned to its correct taxid, rank_label etc. but multiple contig IDs starting with the same numbers (but not matching k141_349539) are added to the same ARG hit.
Command used and terminal output
Relevant files
No response
System information
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the ARG subworkflow's merging step that produces hamronization_complete_summary_taxonomy.tsv.gz, using the k141_349539 example and the attached image as the failure case. Inspect how contig names are joined with taxonomy results and verify that only the matching contig is retained while AMP and BGC outputs remain unchanged.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100