the tutorial version of hisat scripts uesage:
./rnaseq_pipeline.sh outputdir
when you run this script ,you may count the problem
[2019-04-24 16:27:41] #> START: ./rnaseq_pipeline.sh outputdir
[2019-04-24 16:27:41] Processing sample: *
[2019-04-24 16:27:41] * Alignment of reads to genome (HISAT2)
the problem was that the data is can not found the right path is BASEDIR="/media/gsadmin/vd2/mysql/chrX_data/chrX_data"