Error in HicPro's normalization in the last step

[gaoyuanccc]

I completed the HIC installation using sample files ：dixon_2M\dixon_2M_2 The rest of the steps are basically done, but when the last step is normalized, an error occurs Run ICE Normalization ... Logs: logs/dixon_2M/ice_20000.log make: *** [/home/gaoyuan/HiC/HiC-Pro_3.0.0/bin/../scripts//Makefile:194: ice_norm] Error 1

I reinstall iced,but It's the same mistake How should i solve this problem?

Many thanks

[nservant]

Hi Could you have a look into logs/dixon_2M/ice_20000.log if you have any error message ? thanks

[gaoyuanccc]

Thank you very much for your reply！！ logs/dixon_2M/ice_20000.log's all content:

ice --results_filename hic_results/matrix/dixon_2M/iced/20000/dixon_2M_20000_iced.matrix --filter_low_counts_perc 0.02 --filter_high_counts_perc 0 --max_iter 100 --eps 0.1 --remove-all-zeros-loci --output-bias 1 hic_results/matrix//dixon_2M/raw/20000/dixon_2M_20000.matrix /home/gaoyuan/anaconda3/bin/ice:65: SyntaxWarning: "is" with a literal. Did you mean "=="? if "--filtering_perc" is None and "--filter_low_counts_perc" not in sys.argv: /home/gaoyuan/anaconda3/lib/python3.9/site-packages/iced/normalization/_ca_utils.py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes warnings.warn( Assuming the file is 1-based. If this is not the desired option, set option --base to 0 Traceback (most recent call last): File "/home/gaoyuan/anaconda3/bin/ice", line 82, in counts = load_counts(filename, base=base) File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/iced/io/_io_pandas.py", line 34, in load_counts dataframe = pd.read_csv(filename, sep="\t", comment="#", header=None) File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/pandas/io/parsers.py", line 610, in read_csv return _read(filepath_or_buffer, kwds) File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/pandas/io/parsers.py", line 462, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/pandas/io/parsers.py", line 819, in init self._engine = self._make_engine(self.engine) File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/pandas/io/parsers.py", line 1050, in _make_engine return mapping[engine](self.f, self.options) # type: ignore[call-arg] File "/home/gaoyuan/anaconda3/lib/python3.9/site-packages/pandas/io/parsers.py", line 1898, in init self._reader = parsers.TextReader(self.handles.handle, **kwds) File "pandas/_libs/parsers.pyx", line 521, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

My pandas was installed Requirement already satisfied: pandas in ./anaconda3/envs/python_3.7.2/lib/python3.7/site-packages (1.2.4)

But when I use ICE, it returns this error (python_3.7.2) [gaoyuan@localhost ~]$ ice -h File "/home/gaoyuan/anaconda3/envs/python_3.7.2/bin/ice", line 58 print "--filtering_perc is deprecated. Please use filter_low_counts_perc" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("--filtering_perc is deprecated. Please use filter_low_counts_perc")?

How should I solve this problem of my ICE? Many thanks!

[gaoyuanccc]

when I import iced in my python,it is appear these error

(python_3.7.2) [gaoyuan@localhost example]$ python Python 3.7.2 (default, Dec 29 2018, 06:19:36) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

import iced /home/gaoyuan/anaconda3/envs/python_3.7.2/lib/python3.7/site-packages/iced/normalization/_ca_utils.py:9: UserWarning: The API of this module is likely to change. Use only for testing purposes "The API of this module is likely to change. "

[nservant]

Hi The latter is just a warning. But it seems that there is something wrong with python3 and iced. You should use HiC-Pro version > 3.0.0 and python3 with the latest iced version. Could you check that please ?

[gaoyuanccc]

Thank you very much for your reply！！

(python_3.7.2) [gaoyuan@localhost example]$ /home/gaoyuan/HiC/HiC-Pro_3.0.0/bin/HiC-Pro -v HiC-Pro version 3.0.0

this is my HiC-Pro and python version

[gaoyuanccc]

but my raw matrix is empty. I don't know if that's the problem

[nservant]

:) indeed ! if the matrix is empty the normalization can not work ! Could you look at logs downstream to see why your matrix is empty ?

[gaoyuanccc]

I'm sorry to have disturbed you!!

I found that there was an error in generating the file SIZES, all because of my carelessness.

I'm sorry to disturb you again. Wish you happiness