checkchrom issue

[Huxiaowei1997]

I use the command below to do the intron clustering
python leafcutter_cluster.py -j juncfile.txt -m 50 -o test -l 500000 –checkchrom

It should not contain any chromosome except 1,2,3, but in the sorted file i see
zless junc.test.gz
NKLS02001165.1:10184:11584:clu_1_NA 0/0
NKLS02001165.1:10184:18597:clu_1_NA 0/0
NKLS02001165.1:10184:21384:clu_1_NA 0/0
NKLS02001165.1:12986:14390:clu_1_NA 0/0
NKLS02001165.1:12986:18597:clu_1_NA 0/0
And I feel like this makes the whole process super slow, is this right format for the -checkchrom flag and right output?