Please add ERROR and WARNING to output messages where something has gone wrong, not just “please correct”. It would be easier to grep on these.
Eh? I’m not sure what you mean. Can you provide more details, please?
No problem. I was just looking for some keyword in the mother.logfile for which I can grep, to automatically pull out errors and warnings. For example, in response to
mothur > read.otu(list=0.11B.unique.filter.fn.list, group=milk.groups, label=unique-0.03)
instead of:
Your group file contains 379933 sequences and list file contains 4772 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to 0.11B.unique.filter.fn.missing.name.
something like this:
Warning: Your group file contains 379933 sequences and list file contains 4772 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to 0.11B.unique.filter.fn.missing.name.
or “Error:”, as appropriate.
Just a small change anytime you say “Please correct.”