The production of *peaks_rmBlacklist.narrowPeak files

[tan200000000]

Hi, when I check the pepatac log, I find this command: bedtools intersect -a /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/peak_calling_mm10/mas1_peaks_normalized.narrowPeak -b /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/raw/mm10_blacklist.bed -v > /data3/01.projects/GROUP01043/10.ATAC_seq_test/poj5/pepatac/mas1/peak_calling_mm10/mas1_peaks_rmBlacklist.narrowPeak, but I find the size of the *_peaks_rmBlacklist.narrowPeak file in my result is actully larger than the *_peaks_normalized.narrowPeak file:

Then I rerun the command independently I found the size of rmBlacklist.narrowPeak file become smaller, and factually become the same as the *_peaks_normalized.narrowPeak file and they have the same md5.
I dont know why this happened, thanks very much if anybody could answer me.

[tan200000000]

this picture is from a parllel project becuse I change some files of the origin project