No generation of a stability.trim.contigs.good.count_table

1

Hi Everyone,

I was wondering if anyone would be able to help me with a problem I am having. I am using the example data on mothur to work through the MiSeq SOP. Everything has ran smoothly until I have gotten to here:

mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_table, start=1969, end=11551)

It gives me an error that a sequence isn’t in my count table, but when I look in the file that specific sequence is there. I also noticed that I am missing a stability.trim.contigs.good.count_table file which I need for the following line and the sequential ones after it:

mothur > unique.seqs(fasta=stability.trim.contigs.unique.good.filter.fasta, count=stability.trim.contigs.good.count_table)

I’m not sure why this file can’t be generated. If anyone could help me, I would really appreciate it!

2

Hi Nicole - is this with the MiSeq data or your own data? What usually works best is to go back a step or two until you no longer get the error messages and then rerun the following commands. Errors like your typically happen because a file gets left out of a command where sequences are removed. I wonder if you included a count file when you ran unique.seqs

Pat