enormous logfile

mothur bugs
1

something goofy happened to my last batch run (possibly due to my server). The last few commands in my batch are

system(mkdir send)
system(cp *shared send)
system(cp *cons.tax* send)
system(cp *pick.tax.summary send)
system(cp *.rep.fasta send)
system(cp *lt.ave.dist send)
system(cp *groups.ave-std.summary send)
system(cp mothur.batch send)
system(rm send/*0.01*)
system(rm send/*0.02*)
system(rm send/*0.04*)
system(rm send/*0.06*)
system(rm send/*0.07*)
system(rm send/*0.08*)

On the last cp, I’m getting this error

mothur > system(cp *
[ERROR]: You are missing )
Invalid.

Then this error repeated so many times that my logfile is 250GB

mothur > 
[ERROR]: You are missing (
Invalid.

running mothur 1.36.1

2

Can you try it without the system(cp *groups.ave-std.summary send) command? I am wondering if the ‘-’ character is causing an issue.

3

I reran it and it was fine. The bug that I think I want to report is actually the repeating error where mothur though that I was entering an empty command over and over.