Get split reads ...Error in read.table(file = file, header = header, sep = sep, quote = quote

While running the command I am getting the error:

for i in $(ls $path_to_fq/ | rev | cut -c 14- | rev | sort -u); do

Rscript FuSeq_v1.1.4_linux_x86-64/R/FuSeq.R in=$i txfasta=GRCh37_files/Homo_sapiens.GRCh37.75.cdna.all.fa sqlite=GRCh37_files/Homo_sapiens.GRCh37.75.sqlite txanno=GRCh37_files/Homo_sapiens.GRCh37.75.txAnno.RData out=$folder_name params=FuSeq_v1.1.4_linux_x86-64/R/params.txt

done

FOLDER NAME:  26-R-LU2-LI_S2_trim_L001_out
During startup - Warning message:
Setting LC_CTYPE failed, using "C"

Number of arguments:  6
List of arguments:  in=26-R-LU2-LI_S2_trim_L001 txfasta=GRCh37_files/Homo_sapiens.GRCh37.75.cdna.all.fa sqlite=GRCh37_files/Homo_sapiens.GRCh37.75.sqlite txanno=GRCh37_files/Homo_sapiens.GRCh37.75.txAnno.RData out=26-R-LU2-LI_S2_trim_L001_out params=FuSeq_v1.1.4_linux_x86-64/R/params.txt
-----
Parameter settings:
 readStrands= UN
 chromRef=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
 maxSharedCount= 0.05
 onlyProteinCodingGenes= TRUE
 minGeneDist= 1e+05
 minJunctionDist= 1e+05
 maxInvertedFusionCount= 0
 maxMRfusionFc= 2
 maxMRfusionNum= 2
 sgtMRcount= 10
 minMR= 2
 minNonDupMR= 2
 minSR= 1
 minScore= 3
 exonBoundary= TRUE
 keepRData= TRUE
 exportFasta= FALSE
-------------------------

 ------------------------------------------------------------------
 Processing mapped reads (MR) from dataset:  26-R-LU2-LI_S2_trim_L001  read strands: UN
 Read fusion equivalence classes
 Reading  26-R-LU2-LI_S2_trim_L001/feq_UN.txt
 The total number of fusion equivalence classes:  0
 ------------------------------------------------------------------
 Processing split reads (SR) from dataset:  26-R-LU2-LI_S2_trim_L001  read strands: UN
 Get split reads ...Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
  no lines available in input
Calls: processSplitRead -> read.csv -> read.table
In addition: Warning messages:
1: In max(feqR$Feq) : no non-missing arguments to max; returning -Inf
2: In min(fragRg) : no non-missing arguments to min; returning Inf
3: In max(fragRg) : no non-missing arguments to max; returning -Inf
Execution halted

nghiavtr / FuSeq

Get split reads ...Error in read.table(file = file, header = header, sep = sep, quote = quote #19