tophat error

[muzz56]

Hi,
Am running tophat and this is the first time am seeing this error and I don't know how to correct it. Anyone out there with some ideas how to solve this.
The error is:

[Thu Feb 24 14:16:05 2011] Preparing output location SEQ1/
[Thu Feb 24 14:16:05 2011] Checking for Bowtie index files
[Thu Feb 24 14:16:05 2011] Checking for reference FASTA file
[Thu Feb 24 14:16:05 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Thu Feb 24 14:16:05 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Thu Feb 24 14:16:46 2011] Checking reads

Error encountered parsing file /home/mh/Data/RNA_seq/110213_F/A_S.fq:
Different read ID for sequence and quality (HWI-ST333_0073:2:1:1460:2172#ACCTGA/1 vs HWI-ST333_0073:2:1:1460:2172#gggggg/1)

The code am using is:
tophat -p 4 -o SEQ1 /home/mh/Data/RNA_seq/bowtie_indexes/mm9 /home/mh/Data/RNA_seq/110213_F/A_N.fq

I have used this code before without any problems.