pod5 filter/ subset failed with TypeError: enable_string_cache() missing 1 required positional argument: 'enable'

[jkh00]

Hi,

I am trying to demultiplex my pod5 files using pod5 subset or pod5 filter, however I'm always getting error stating:

TypeError: enable_string_cache() missing 1 required positional argument: 'enable'

The full command used:

POD5_DEBUG=1 pod5 filter PAS86942_375dd100_f2dee0dd_0.pod5 --ids all_ids.txt --output 1k.pod5 --missing-ok

The error output:

Traceback (most recent call last):
File "/home-directory/miniconda3/envs/pod5/bin/pod5", line 8, in
sys.exit(main())
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/main.py", line 60, in main
return run_tool(parser)
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/parsers.py", line 41, in run_tool
raise exc
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/parsers.py", line 38, in run_tool
return tool_func(**kwargs)
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/parsers.py", line 288, in run
from pod5.tools.pod5_filter import filter_pod5
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/pod5_filter.py", line 27, in
from pod5.tools.pod5_subset import (
File "/home-directory/miniconda3/envs/pod5/lib/python3.8/site-packages/pod5/tools/pod5_subset.py", line 43, in
pl.enable_string_cache()
TypeError: enable_string_cache() missing 1 required positional argument: 'enable'

The pod5 version I'm using is v0.3.2 and I have also downgraded my polar version to 0.19 using this command pip install -U polars==0.19 according to suggestion from this issue.

The read ids were obtained using pod5 view and it works perfectly fine. I wonder if this is an issue related to the version of polar I used, but I haven't seen anyone raising the same issue.

Any input will be helpful, thanks!

[HalfPhoton]

Hi @jkh00 ,

Based on the polars enable_string_cache documentation [0.19] there is no required positional argument.
This implies that you don't have the latest polars 0.19 version.

Can you please double check this?

Kind regards,
Rich

[jkh00]

Hi Rich,

I solved the issue by updating polars to 0.19.7, my previous version was 0.19.0 and according to the documentation, updates for enable_string_cache was after 0.19.3 so I guess that was the problem. I am able to run the commands now. Thanks for the help!

Kind regards,
Jin

[HalfPhoton]

Hi @jkh00 ,
Thanks for getting back to us.
We will be releasing an update shortly to support polars 0.20.

Kind regards,
Rich