sokrypton / sokrypton/ColabFold
Two MSA results in --msa-only output
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Expected Behavior
I'm using --msa-only mode to get the MSA file and it runs without issues. However, in the generated *.a3m file, I notice that there are two lines for >101, and it is like there are two different MSA results appended together. For example, when I plot query coverage ordered by lines in the file, the coverage goes down, and then it peaks. (This is the place for the second >101 header).
Current Behavior
x = line number
y = query coverage
The .a3m file is attached as .txt (github doesn't allow loading a3m)
CUTINASE.txt
This is the Fasta file used as input (in .txt format)
1CUS.txt
Command used
colabfold_batch --msa-only 1CUS.fasta <output-directory>
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
Reproduce the report with colabfold_batch --msa-only 1CUS.fasta <output-directory> and inspect the attached CUTINASE.txt and 1CUS.txt files. Trace the --msa-only command path to find why the generated .a3m contains a second >101 header; done means one coherent MSA result is produced without duplicated records.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, cli
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100