Error with Ice normalization when running HiC-Pro
0
0
Entering edit mode
2.3 years ago
Amina • 0

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.

Hi-C HiChIP HiC-Pro • 1.2k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1564 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6