RSEM Error - rsem-calculate-expression

[anupullanhi]

Hello I am working on RSEM rsem-calculate-expression:

rsem-calculate-expression --paired-end --bam -p 8 /home/user/data/Rat/***.sorted.bam /home/user/data/RSEM/ rat_paired_end_quals

Error: Warning: The SAM/BAM file declares less reference sequences (955) than RSEM knows (71103)! Please make sure that you aligned your reads against transcript sequences instead of genome. RSEM can not recognize reference sequence name 1! rsem-parse-alignments /home/user/data/RSEM/ rat_paired_end_quals.temp/rat_paired_end_quals rat_paired_end_quals.stat/rat_paired_end_quals /home/user/data/Rat/***.sorted.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!

Any help is appreciated!