Error with Ice normalization when running HiC-Pro

Question

[Amina]

I am trying to run HiC-Pro to analyze HiChIP data. The software is running fine until the ice normalization step, where I get this error:

Run ICE Normalization ...
Logs: logs/data/ice_10000.log
make: *** [/dfs3b/mbt/aminaoh/hic-pro/bin/../scripts//Makefile:194: ice_norm] Error 1

This is what is the ice_10000.log:

/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/bin/python /data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/HiC-Pro_3.1.0/scripts/ice --results_filename hic_results/matrix/data/iced/10000/data_10000_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//data/raw/10000/data_10000.matrix
/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/HiC-Pro_3.1.0/scripts/ice:65: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if "--filtering_perc" is None and "--filter_low_counts_perc" not in sys.argv:
/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/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 "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/HiC-Pro_3.1.0/scripts/ice", line 82, in <module>
    counts = load_counts(filename, base=base)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/iced/io/_io_pandas.py", line 34, in load_counts
    dataframe = pd.read_csv(filename, sep="\t", comment="#", header=None)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 69, in __init__
    self._reader = parsers.TextReader(self.handles.handle, **kwds)
  File "pandas/_libs/parsers.pyx", line 549, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file

Has anyone encountered this error before? I am not sure how to fix it.

[GenoMax]

Can you add the exact command you are running when you get this message (remove any identifying names if you want to). Keep the options you are using.

[Amina]

This is the script I am using to run:

#!/bin/bash
#SBATCH -A aminaoh
#SBATCH -J hic_pro_workflow
#SBATCH -p standard
#SBATCH --nodes=1 ##number of nodes to use
#SBATCH --cpus-per-task=30 ##number of cores to use per node
#SBATCH -error=slurm-%J.err ##Error file

/dfs3b/aminaoh/hic-pro/bin/HiC-Pro  -i /dfs3b/mbt/aminaoh/data  -o hic_test -c /dfs3b/aminaoh/hic-pro/config-hicpro.txt

I activate the HiC-Pro_v3.1.0 conda environment (downloaded from the environment.yml file here) before running the script above.

[Cibo]

Hi. In your script (/data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0/HiC-Pro_3.1.0/scripts/ice), there is a function load_counts used. Before using it, there is a command from iced.io import load_counts. Your results seem to import this function successfully. But when I run HiC-Pro, it always reports there is no module named load_counts. And I really didn't find this function in iced.io. I wonder whether you encountered this problem, too. Thanks.