leafcutter_norm output produce data that should not be there

[hsun3163]

after running leafcutter on the STAR_output of xqtl_protocol_data, the output is:

hs3163@node74:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing$ cat output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz_phenotype_file_list.txt
#chr    #dir
chr12   output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr12
chr16   output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr16
chr21   output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr21
chr7    output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr7
chr22   output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr22
chr14   output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr14
chr1    output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr1
chr2    output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr2

However, the bam file should only contains reads from chr21 and chr22. It is unknown whether this is a leafcutter issue or a alignment issue or a subsetting issue. Will need to see after post processing the rnaseqc output.