error with m6anet dataprep

[mocherry]

Dear all,

after having struggled with m6Anet on Galaxy, where is has been running for days now, I resorted to give it a try on a windows system.

Now when running: m6anet dataprep --eventalign d:\temp\test.txt --out_dir d:\temp\output --n_processes 4

I get the following long error, the indexing... occuring multiple times but at the end this occurs:

**_PerformanceWarning: indexing past lexsort depth may impact performance. pos_end += eventalign_result.loc[_index]['line_length'].sum() Traceback (most recent call last): File "pandas_libs\lib.pyx", line 2280, in pandas._libs.lib.maybe_convert_numeric ValueError: Unable to parse string "97.6604,109.208,107.283,102.632,104.076,104.717,108.406,106.161,104.076,103.755"

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\Scripts\m6anet-script.py", line 9, in sys.exit(main()) File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\lib\site-packages\m6anet__init__.py", line 30, in main args.func(args) File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\lib\site-packages\m6anet\scripts\dataprep.py", line 68, in main parallel_preprocess_tx(args.eventalign, args.out_dir, args.n_processes, File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\lib\site-packages\m6anet\utils\dataprep_utils.py", line 383, in parallel_preprocess_tx data = combine(events_str) File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\lib\site-packages\m6anet\utils\dataprep_utils.py", line 291, in combine eventalign_result.loc[:, 'length'] = pd.to_numeric(eventalign_result['end_idx']) - \ File "C:\Users\kirsch\AppData\Local\miniconda3\envs\m6anet\lib\site-packages\pandas\core\tools\numeric.py", line 217, in to_numeric values, new_mask = lib.maybe_convert_numeric( # type: ignore[call-overload] # noqa File "pandas_libs\lib.pyx", line 2322, in pandas._libs.lib.maybe_convertnumeric ValueError: Unable to parse string "97.6604,109.208,107.283,102.632,104.076,104.717,108.406,106.161,104.076,103.755" at position 0**

Can anyone suggest a solution?

Thanks and best, Matthias

[yuukiiwa]

Hi Matthias (@mocherry),

I think it is specific to pandas' problem in windows.

Thanks!

Best wishes, Yuk Kei