SAM Header is present Error

[jbrabec]

Hello Everyone!

I am new to SEQanswers so not quite sure how to phrase my question but here goes:

I am trying to run the command

rsem-calculate-expression --bowtie2 --paired-end ~/Striata/cKO02/cKO02_R1.fastq ~/Striata/cKO02/cKO02_R2.fastq ~/rsem_reference/rsem_references ~/rsem_outputs/cKO02_counted

And I get an error that reads
[samopen] SAM header is present: 63759 sequences
The program then stops at that point. Is there something wrong with my reference files that would be giving this error?

Thanks in advance for your help. Let me know if you need more information!