When I run a command with files that do not match (e.g. list file has more sequences than group file) then mothur will consume all free memory and for a very long time is just frozen. If it could give an error message right away then I would know that I inserted a wrong filename and don’t have to wait so long for the computer to be responsive again.
Which command were you running?
That moment I was running make.shared, but the same thing has happened when running other commands that takes list file (remove.lineage from list file).
Hmm… I am not seeing that. What version of mothur and OS?
mothur > make.shared(list=final.an.list, group=final.subsample.groups)
[ERROR]: GQY1XT001B2SG4 is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001BRMUT is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001BSHTZ is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001DXZ7B is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001EL7UI is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001A3NTP is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001E4GVL is in your listfile and not in your groupfile. Please correct.
…
[ERROR]: GQY1XT001CXUVC is in your listfile and not in your groupfile. Please correct.
[ERROR]: GQY1XT001DJY6M is in your listfile and not in your groupfile. Please correct.
Your group file contains 48455 sequences and list file contains 58562 sequences. Please correct.