Closed Matt-BF closed 6 months ago
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
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
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?
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
Can you post the crisps_all.tab file here?
Had to rename it to .txt so github would allow me to post it crisprs_all.txt
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.
Yeah, removing the sequence from the original FASTA file solved it! Thanks for your help debugging!
Hi! Great program, has been helping me a lot! I've been running cctyper for metagenomes and it has been working for the most part. For one of my FASTA files it has been erroring with XGBoost model incompatible. I am using cctyper v 1.8.0 via mamba on a fresh environment, created as instructed on the README
Thanks for any help in this situation!