Bowtie error - FASTQ reads are too long

[oabudayyeh]

Hi,

I'm just aligning a MiSeq fastq run to a custom index and am getting the following error:

FASTQ read name is too long; read names must be 1022 characters or fewer.
Beginning of bad read name:
terminate called after throwing an instance of 'int'
/local/scratch/1426970873.9330346: line 8: 25641 Aborted

I cant find anything online and am not sure how to fix this. Any thoughts?

[dpryan]

It's likely that your fastq file is corrupt. I've never heard of a read having a name that would be longer than ~50 characters, let alone 1022.