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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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an unexpected keyword argument "inplace" and can't out the "results.xlxs" #184

Closed Yovelaaa closed 10 months ago

Yovelaaa commented 11 months ago

2023-07-24 18:54:21 INFO: Predicting AMR resistance phenotypes is enabled. The predictions are for microbiological resistance and not clinical resistance. These results are continually being improved and we welcome any feedback. 2023-07-24 18:54:21 INFO: Writing resfinder to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/resfinder.tsv] 2023-07-24 18:54:21 INFO: --output-dir or --output-pointfinder unset. No pointfinder file will be written 2023-07-24 18:54:21 INFO: Writing plasmidfinder to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/plasmidfinder.tsv] 2023-07-24 18:54:21 INFO: Writing summary to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/summary.tsv] 2023-07-24 18:54:21 INFO: Writing MLST summary to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/mlst.tsv] 2023-07-24 18:54:21 INFO: Writing detailed summary to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/detailed_summary.tsv] 2023-07-24 18:54:21 INFO: Writing settings to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/settings.txt] 2023-07-24 18:54:21 INFO: Writing Excel to [/public/home/2021180/caoyue/20SCAPR/negative/staramr/results.xlsx] 2023-07-24 18:54:21 ERROR: DataFrame.set_axis() got an unexpected keyword argument 'inplace' Traceback (most recent call last): File "/public/home/2021180/miniconda3/envs/staramr/bin/staramr", line 68, in args.run_command(args) File "/public/home/2021180/miniconda3/envs/staramr/lib/python3.11/site-packages/staramr/subcommand/Search.py", line 544, in run settings_dataframe.set_axis(['Value'], axis='columns', inplace=True) TypeError: DataFrame.set_axis() got an unexpected keyword argument 'inplace' 2023-07-24 18:54:22 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases 2023-07-24 18:54:22 INFO: PlasmidFinder database type [enterobacteriaceae] is out of date, switching to [enterobacteriales] 2023-07-24 18:54:22 ERROR: Output directory [/public/home/2021180/caoyue/20SCAPR/negative/staramr/] already exists

apetkau commented 11 months ago

Hello @Yovelaaa, it looks like pandas removed DataFrame.set_axis for version 2.0.0. To get staramr to work, you will have to install a version of pandas < 2.0.0. For example:

conda create --name staramr staramr 'pandas<2'
Yovelaaa commented 11 months ago

Hello @Yovelaaa, it looks like pandas removed DataFrame.set_axis for version 2.0.0. To get staramr to work, you will have to install a version of pandas < 2.0.0. For example:

conda create --name staramr staramr 'pandas<2'

It works! Thank you very much!

apetkau commented 10 months ago

Fixed in #193