shahab-sarmashghi / RESPECT

Estimating repeat spectra and genome length from low-coverage genome skims

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with the hist file input,I got a IndexError

helan-1997 opened this issue · comments

the code I used is as follows:
respect -i Unknown_AL483-01R0001-01-R00_good_10w.hist -I hist-info.txt IndexError: single positional indexer is out-of-bounds

Is hist-info.txt formatted as described in the documentation? See example.

If both .hist and info file have the right format and you still get an error, try to run the command with --debug option and paste the error here please.

yes,there is a problem with the info format.then I still run this code:
respect -i Unknown_AL483-01R0001-01-R00_good_10w.hist -I hist-info.txt
then:
/home/user/miniconda3/envs/respect_env/lib/python3.10/site-packages/respect-1.3.0-py3.10.egg/respect/optimizer.py:234: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self._parameters_dataframe = self._parameters_dataframe.append( /home/user/miniconda3/envs/respect_env/lib/python3.10/site-packages/respect-1.3.0-py3.10.egg/respect/optimizer.py:241: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self._spectra_dataframe = self._spectra_dataframe.append(pd.Series([iteration] + list(self.repeat_spectra),
keep circulating.

These are warnings that you can ignore. Do you still get an error (other than these warnings)?

No problem, thank you.