报错：two mates are aligned to two different transcripts! failed! Plase check if you provide correct parameters/options for the pipeline

跑以下命令时出现的报错：two mates are aligned to two different transcripts!…… failed! Plase check if you provide correct parameters/options for the pipeline

while read line
do        
     nohup rsem-calculate-expression -p 8 --paired-end --append-names --seed 0 --estimate-rspd --sampling-for-bam --output-genome-bam --alignments ${line}Aligned.toTranscriptome.out.bam rsem_ref ${line} &
done < sampleid

用的rsem版本为v1.3.3，降级为v1.3.1后重新跑就没有报错了