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Russel88 avatar Russel88 commented on June 12, 2024

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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Matt-BF avatar Matt-BF commented on June 12, 2024

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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Russel88 avatar Russel88 commented on June 12, 2024

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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Matt-BF avatar Matt-BF commented on June 12, 2024

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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Russel88 avatar Russel88 commented on June 12, 2024

Can you post the crisps_all.tab file here?

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Matt-BF avatar Matt-BF commented on June 12, 2024

Had to rename it to .txt so github would allow me to post it
crisprs_all.txt

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Russel88 avatar Russel88 commented on June 12, 2024

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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Matt-BF avatar Matt-BF commented on June 12, 2024

Yeah, removing the sequence from the original FASTA file solved it! Thanks for your help debugging!

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