Comments (3)
That is by design. When you call flair 123 each subprogram gets one or two parameters it doesn't understand. It's just a warning.
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from flair.
An easy short-term workaround would have flair 123 set an environment variable that says to ignore invalid parameters.
One would still get confusing warnings with 123, but at least the modules would be robust.
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Related Issues (20)
- Set isoform abundance cutoff to FLAIR quantify HOT 1
- Crash running flair collapse HOT 8
- Gene model naming issue HOT 1
- error in flair quantify HOT 9
- add --split-prefix to collapse minimap command
- Flair collapse issue HOT 13
- flair collapse--NameError: name 'blockcount' is not defined HOT 4
- How to count the isoforms corresponding to each gene. HOT 2
- Incorrectly name flair align options is confusing
- allow flair correct to specify temporary directory HOT 1
- How to concatenate bed files before flair collapse HOT 2
- The naming of my isoforms is different from what is mentioned in your manual.
- Hello, after splitting the BED file by chromosomes, we found that a single chromosome's BED file is 1.03G, which is larger than 1G. Can Flair Collapse currently handle a BED file of 1.03G? HOT 1
- psl_to_sequence command
- flair correct shows FileNotFoundError HOT 1
- flair quantify problem error HOT 3
- ValueError in filter_isoforms_by_proportion_of_gene_expr.py
- Collapse step didn't output a gtf file without a reference annotation
- FLAIR missing isoforms HOT 1
- Process termination at Step 5/5 in flair correct without error messages HOT 1
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from flair.