I use rfam_scan.pl to annotate the RNA-seq raw reads. But after run that there is nothing in the results file.

The code:

perl rfam_scan.pl_v_1.0.4 -o rfam.out.gff3 -blastdb Rfam.fasta Rfam.cm 1.fa -v
read fasta file
read CM library
run blast pre-filter
parse blast results
run infernal search
searching [FCC4T3HACXX:5:1101:2926:2243#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2213:2225#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2380:2217#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2003:2178#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2878:2174#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2600:2204#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2839:2176#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2329:2204#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:2998:2154#GCAGTTCG/1/1-22] with [let-7]
searching [FCC4T3HACXX:5:1101:1698:2163#GCAGTTCG/1/1-23] with [let-7]
searching [FCC4T3HACXX:5:1101:2611:2227#GCAGTTCG/1/1-23] with [mir-320]
searching [FCC4T3HACXX:5:1101:2922:2196#GCAGTTCG/1/1-22] with [mir-140]
searching [FCC4T3HACXX:5:1101:3152:2236#GCAGTTCG/1/1-22] with [mir-140]

The rfam.out.gff3 file only contain that:

##gff-version 3
# rfam_scan.pl (v1.0)
# command line:     rfam_scan.pl_v_1.0.4 -o rfam.out.gff3 -blastdb Rfam.fasta Rfam.cm 1.fa -v
# CM file:          Rfam.cm
# query FASTA file: 1.fa
# start time:       2014  11  17  Mon 15:50:54 CST
# end time:         2014  11  17  Mon 15:50:56 CST