rsem-calculate expression

[Naveen prasath]

#!/bin/bash
GTF="/home/student/UCD1.2.99.gtf"
FNA="/home/student/UCD1.2.dna.toplevel.fa"
INDEX="/home/student/cell/rsem/star"
Read="/home/student/sort"

rsem-prepare-reference --gtf $GTF $FNA --star -p 8 $INDEX/stind

for i in $Read/*.fq.gz

do
R2=$(echo $R1|sed 's/_1.fq/_2.fq/')
Out=$(basename $R1|sed 's/-sortmerna_1.fq.gz//')
echo $R1 $R2 $Out

rrsem-calculate-expression --forward-prob 1 -p 8 --paired-end --star --strandedness reverse $R1 $R2 $INDEX/stind $Out

when I am using this i am getting the error of 

Oct 18 04:35:16 ..... started STAR run
Oct 18 04:35:16 ..... loading genome
Oct 18 04:35:33 ..... started mapping

ReadAlignChunk_processChunks.cpp:177:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID should start with @ or >

Oct 18 04:35:33 ...... FATAL ERROR, exiting

But I have succesfully got the *genes.results and *isoforms.results for option Bowtie