"size of sequence does not equal size of quality" problem

Question

[Len]

Dear all,

I am seeking some help as I am still a novice with genomics. I am running an analysis using pool-sequencing data with the software Popoolation1 to calculate basic pop gen statistics. It requires an mpileup file to run the script; however, I keep getting an error that says "size of sequence does not equal size of quality" when the script is running. I have used this same mpileup file with other scripts from Popoolation2, and it works fine.

Can anyone please advise of what may be the error?

Advance apologies if this question is too general or specific.

Best, L

[Pierre Lindenbaum]

see length of quality sequence and length of read do not match in fastq