qual length error when run tophat

[HSV-1]

Hi, All,
I am using tophat to process RNA-seq data from Illumunia genome analyzer IIx. I get the error when I treat one in a fastq data set while the other one in the same dataset is fine. I use the same parameter. I really don't undertant why! Could anyone help? Error is below(I have put --solex--qual parameter in my command line.) :

[2012-07-17 19:25:28] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-17 19:25:28] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.8.0
[2012-07-17 19:25:28] Checking for Samtools
Samtools version: 0.1.13.0
[2012-07-17 19:25:28] Checking for Bowtie index files
[2012-07-17 19:25:28] Checking for reference FASTA file
[2012-07-17 19:25:28] Generating SAM header for mm9
format: fastq
quality scale: solexa33 (reads generated with GA pipeline version < 1.3)
[2012-07-17 19:27:10] Reading known junctions from GTF file
[2012-07-17 19:27:22] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: qual length (0) differs from seq length (36) for fastq record SRR390298.!

[Richard Barker]

I'm having a similar issue, one of my files worked fine then when i tried the next i got this error...
Error: qual length (121) differs from seq length (87) for fastq record !

The fastq files were unzipped and then had the first 15 bases trimmed off, could this have caused the quality score to differ from the sequence length?