Comments (8)
It's probably because of the XGboost version. I would fix the py-xgboost to version 1.7.1 and probably also Biopython to 1.76 to avoid those warnings.
Looks like I have to update the version requirements
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It's probably because of the XGboost version. I would fix the py-xgboost to version 1.7.1 and probably also Biopython to 1.76 to avoid those warnings.
Looks like I have to update the version requirements
Hi, thanks for the quick response! I downgraded py-xgboost to 1.7.1 in my env and Biopython 1.76, but still get the same incompatible model error (albeit without the deprecation warnings).
It's strange because I have 528 of these FASTA, all apparently ran successfully, and only one gave me this error
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That's strange. It could be weird characters in your fasta headers for that single fasta, or maybe lower case nucleotides. Is any output produced at all?
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Yes, from what I can see I have most files, except Crispr_Cas.tab, and the crisprs_all.tab does not have the prediction, subtype or subtype probability columns. Everything else seem the same
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Can you post the crisps_all.tab file here?
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Had to rename it to .txt so github would allow me to post it
crisprs_all.txt
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Aha, it's probably the following repeat that's the problem: GGGGGGGGGGGGGGGGGGNNNNN - which also looks super weird.
I don't think the repeat classifier can handle N's, usually CRISPRs do not span across N's.
A quick fix for you would be to remove that contig from the fasta file.
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Yeah, removing the sequence from the original FASTA file solved it! Thanks for your help debugging!
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Related Issues (20)
- FileNotFoundError: blast.tab HOT 3
- Complete genome and draft genome HOT 2
- A complement to CRISRPRCasFinder or its own thing? HOT 1
- Execution against protein fasta and gff HOT 2
- Different results from CRISPR Cas typer web server and standalone version HOT 5
- Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied HOT 2
- ![image](https://user-images.githubusercontent.com/121949837/212599561-d771b233-4bde-4850-8e5f-98a4164f78cb.png)
- Option to use Prodigal-gv
- Meaning of asterisk at the end of protein sequence HOT 1
- Creating empty files when there's no data HOT 1
- castyping.py having an issue with positional arguments. HOT 2
- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
- (Question) provide GFF file for pre computed gene calls? HOT 5
- If minced detects a CRISPR with N's in the repeat sequence
- (Question) How can I plot svg post-hoc after a run? HOT 1
- ValueError: invalid literal for int() with base 10: 'lengt' HOT 2
- access to sequences that used to geenrate Cas profiles
- access to sequences that used to geenrate Cas profiles HOT 1
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