failed to generate SAM/BAM FILES

[Sneha Bhat]

I am getting this error while running command for calculate expression for strand specific expression analysis. please help me if anybody can.

(ERR): bowtie2-align exited with value 139

The SAM/BAM file declares less than one reference sequence!
"rsem-parse-alignments /home/snehabhat/sneha/HM1_Genome_ref /home/snehabhat/sneha/ORF1_AS_Rep1_rev-expression.temp/ORF1_AS_Rep1_rev-expression /home/snehabhat/sneha/ORF1_AS_Rep1_rev-expression.stat/ORF1_AS_Rep1_rev-expression /home/snehabhat/sneha/ORF1_AS_Rep1_rev-expression.temp/ORF1_AS_Rep1_rev-expression.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!