Issue with prep nonpeaks Command - Empty negatives.bed File

[zhenyu7500]

Hi ChromBPNet Developers,

Thank you for creating such a powerful and useful tool!

I am currently encountering an issue with the prep nonpeaks step. Below is the command I am using:

chrombpnet prep nonpeaks -g genome.fa -o non_peak -p bulk_peaks.narrowPeak -c genome.size -fl fold_0.json -br blacklist.bed

The bulk_peaks.narrowPeak file looks like this:
chr1 0 1582 bulk_peak_1a 103 . 3.41016 10.3014 8.5055 55
chr1 0 1582 bulk_peak_1b 108 . 3.50489 10.8932 9.07625 170
chr1 0 1582 bulk_peak_1c 217 . 5.02052 21.7408 19.5926 332
chr1 0 1582 bulk_peak_1d 108 . 3.50489 10.8932 9.07625 460
chr1 0 1582 bulk_peak_1e 97 . 3.31543 9.72138 7.9464 587
chr1 0 1582 bulk_peak_1f 83 . 2.94931 8.3157 6.59649 920
chr1 0 1582 bulk_peak_1g 116 . 3.35476 11.6601 9.81738 1161
chr1 0 1582 bulk_peak_1h 217 . 4.51535 21.7907 19.6411 1331
chr1 0 1582 bulk_peak_1i 28 . 1.79808 2.87629 1.48527 1538
chr1 5584 6169 bulk_peak_2a 134 . 2.93209 13.4059 11.5053 125

the log fie look like:
Traceback (most recent call last):
File "/home/zhenyu/anaconda3/envs/chrombpnet_v2/bin/chrombpnet", line 33, in
sys.exit(load_entry_point('chrombpnet', 'console_scripts', 'chrombpnet')())
File "/home/zhenyu/software/chrombpnet/chrombpnet/CHROMBPNET.py", line 157, in main
negatives = pd.read_csv(args.output_prefix+"_auxiliary/negatives.bed", sep="\t", header=None)
File "/home/zhenyu/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/zhenyu/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/zhenyu/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/home/zhenyu/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
return mapping[engine](f, **self.options)
File "/home/zhenyu/.local/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file

When I checked the output negatives.bed file, I found it to be empty. Could you please help me understand why this file is empty and how I can modify my command to resolve this issue?

Thank you for your support!

Best regards,
zhenyu