As a trial I successfully carried out the Miseq SOP on 10 of the 86 samples we have. It worked beautifully!
I then decided to push all 86 samples through and this is when things suffered a set back.
The set back occurred in the section of the miseq SOP headed: Processing improved sequences.
After, unique.seqs(fasta=stability.trim.contigs.good.fasta) I move onto count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups).
This is where the problem occurs I receive the error message:
[ERROR]: processes reported processing 3808225 sequences, but group file indicates you have 3808234 sequences. Could you have a file mismatch?
Things grind to a halt.
Any help would be fantastic and much appreciated,