rsem-run-em failed!

[Khadija Wilson]

Hi, 

I am trying to perform rsem-calculate-expression using STAR aligned .bam files - I generated a reference genome (X.laevis) however I keep getting the following error: 

The alignment of read NS500234:1145:HCKWWBGXJ:3:12610:16742:11968 to transcript 31198 starts at -69 from the forward direction, which should be a non-negative number! It is possible that the aligner you use gave different read lengths for a same read in SAM file.

"rsem-run-em /home/wilsonkh/9.2Index/RSEMref 1 Control_1 Control_1.temp/Control_1 Control_1.stat/Control_1 -p 16 -b Control_1Aligned.toTranscriptome.out.bam 0" failed! Plase check if you provide correct parameters/options for the pipeline!

The code I used was: 

~/bin/RSEM-1.3.3/rsem-calculate-expression -p 16 --bam --alignments Control_1Aligned.toTranscriptome.out.bam ~/9.2Index/RSEMref Control_1

Is this a problem with my input files? my reference genome? or is something wrong in my code. 

thank you,

Khadija W