RNA-SeQC - rRNA BWA error

I am trying to RNA-SeQC. It seems to be mostly working. However, it is not generating rRNA stats. I think the problem may be with the BWA rRNA alignment. This is the relevant section of the output:

BWA on end 1
Running BWA on RNA-SeQC/Ctl-2/dSample.bam
Command: [bwa, aln, /ifs/home/i/ref/rRNA/mouse_all_rRNA.fasta, -b1, RNA-SeQC/Ctl-2/dSample.bam]
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... Call to BWA complete
BWA on end 2
Running BWA on RNA-SeQC/Ctl-2/dSample.bam
Command: [bwa, aln, /ifs/home/i/ref/rRNA/mouse_all_rRNA.fasta, -b2, RNA-SeQC/Ctl-2/dSample.bam]
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... Call to BWA complete
Running BWA sampe
Command: [bwa, sampe, /ifs/home/i/ref/rRNA/mouse_all_rRNA.fasta, RNA-SeQC/Ctl-2/end1.sai, RNA-SeQC/Ctl-2/end2.sai, RNA-SeQC/Ctl-2/dSample.bam, RNA-SeQC/Ctl-2/dSample.bam]
[fread] Unexpected end of file
Call to BWA complete

Is "[fread] Unexpected end of file" to be expected? I am guessing that may be the issue. Is that right? How should I resolve this problem?

Thank you.