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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
89 stars 16 forks source link

Problems running the program #24

Closed JavierFFavieres closed 2 years ago

JavierFFavieres commented 2 years ago

First of all I have to say the program is great. Easy to use and the output is very comprehensive. However, recently I have been having this error:

/Users/JFF/opt/miniconda3/envs/cctyper/lib/python3.9/site-packages/xgboost/compat.py:36: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import MultiIndex, Int64Index [2022-04-04 14:29:15] INFO: Running CRISPRCasTyper version 1.3.0 [2022-04-04 14:29:15] INFO: Predicting ORFs with prodigal [2022-04-04 14:29:15] INFO: Running HMMER against Cas profiles 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 691/691 [00:14<00:00, 48.44it/s] [2022-04-04 14:29:31] INFO: Parsing HMMER output [2022-04-04 14:29:31] INFO: Subtyping putative operons /Users/JFF/opt/miniconda3/envs/cctyper/lib/python3.9/site-packages/cctyper/castyping.py:294: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. single_effector_hmms = self.scores[self.scores['Hmm'].isin(list(specifics))].drop('Hmm', 1) [2022-04-04 14:29:31] INFO: Predicting CRISPR arrays with minced [2022-04-04 14:29:31] INFO: No CRISPRs found. [2022-04-04 14:29:31] INFO: Plotting map of CRISPR-Cas loci [2022-04-04 14:29:31] INFO: Removing temporary files

It's strange because I have run this same sequence on other occasions with the program and I am sure there are CRISPRs. Do you know what might be causing this?

Kind regards, Javier

Russel88 commented 2 years ago

Dear Javier

There should not be differences between runs of the same cctyper versions. Could you have run it with another version of cctyper? I can see you're using an older CCTyper version.

Also, CRISPR arrays or cas operons that are different between occasions?

Best, Jakob

JavierFFavieres commented 2 years ago

Thank you, updating the program did the trick. I still get the message "FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead" but the program works without issue.

Best, Javier

Russel88 commented 2 years ago

Great. Thank you for reporting this.