Hello, I was running this command of gsnapl: gsnapl -t 12 -d CSPSE -D ~/zav/ S1.trimmed-paired-1.fq S1.trimmed-paired-2.fq S2.trimmed-paired-1.fq S2.trimmed-paired-2.fq S3.trimmed-paired-1.fq S3.trimmed-paired-2.fq > S.sam
and I get this error message:
"Paired-end accessions HWI-D00525:193:C6DFKANXX:2:1101:1233:2170 and @HWI-D00525:193:C6DFKANXX:2:1101:1233:2170 do not match"
As you can see, they do match, except for the "@" at the first line. However, the "@" is present in the fastq file.
I got this message twice, each time on different file, and in both cases, these were the first lines of the file.
Thank you for your help.