Im now unable to run CRAFT using your test data now earlier it was running fine with these following contents

[SREERAMIISERB]

Im a root user, in which i have a directory called test, inside which i have another directory called input. T he contents of the directories are as follows:

1.) root
1.A.) test/ :
a) list_backsplice.txt : 4:143543509-143543972 +
11:33286413-33287511 +
15:64499292-64500166 +
b) params.txt : MO
hsa

hg38

score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10
score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10, voteFrac_RBP=0.3.

c) path_files.txt :
/data/input/HG38.gtf
/data/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa

1.B) input/ :

a) AGO2_binding_sites.bed
b) backsplice_gene_name.txt
c) hg38.02.idx
d) hg38.nin
e) hg38.nto
f) HG38.gtf
g) bigWigToWig
h) hg38.fa
i) hg38.not
j)hg38.shd
k)Homo_sapiens.GRCh38.104.gtf
l) hg38.00.idx
m) hg38.ndb
n) hg38.nsq
o) Homo_sapiens.GRCh38.dna.primary_assembly.fa
p) hg38.01.idx
q) hg38.nhr
r) hg38.ntf