Make.share fail!

Commands in mothur
1

Any suggestions about how to get around this error message. I’ve followed the 454SOP tutorial but I’ve skipped the Error analysis section because I don’t have a mock community… Mothur doesn’t like my group file, but is the one I created after remove.lineage…?

mothur > make.shared(list=/home/zm1/Mothur.cen/mothur/ggfinal.an.list, group=/home/zm1/Mothur.cen/mothur/ggfinal.groups, label=0.03)
[ERROR]: IQ5MJTO02F00CD is in your groupfile and not your listfile. Please correct.

Your group file contains 54533 sequences and list file contains 49161 sequences. Please correct.

2

more details about the error:
mothur > cluster(column=/home/zm1/Mothur.cen/mothur/ggfinal.dist, name=/home/zm1/Mothur.cen/mothur/ggfinal.names)
********************###########
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.0591382

Output File Names:
/home/zm1/Mothur.cen/mothur/ggfinal.an.sabund
/home/zm1/Mothur.cen/mothur/ggfinal.an.rabund
/home/zm1/Mothur.cen/mothur/ggfinal.an.list

It took 373 seconds to cluster

mothur > make.shared(list=/home/zm1/Mothur.cen/mothur/ggfinal.an.list, groups=/home/zm1/Mothur.cen/mothur/ggfinal.groups, label=0.03)
You need to provide a groupfile or countfile if you are going to use the list format.
[ERROR]: did not complete make.shared.

mothur > make.shared(list=/home/zm1/Mothur.cen/mothur/ggfinal.an.list, group=/home/zm1/Mothur.cen/mothur/ggfinal.groups, label=0.03)
[ERROR]: IQ5MJTO02F00CD is in your groupfile and not your listfile. Please correct.

mothur > count.groups(group=/home/zm1/Mothur.cen/012414MCcom519F.shhh.good.pick.pick.groups)
com519Fbar3 contains 5127.
com519bar10 contains 3872.
com519bar11 contains 9347.
com519bar12 contains 688.
com519bar15 contains 6880.
com519bar16 contains 5866.
com519bar19 contains 5368.
com519bar20 contains 7550.
com519bar4 contains 3015.
com519bar9 contains 6820.

Total seqs: 54533.

Output File Names:
/home/zm1/Mothur.cen/012414MCcom519F.shhh.good.pick.pick.count.summary


mothur > count.groups(group=/home/zm1/Mothur.cen/mothur/ggfinal.groups) com519Fbar3 contains 5127. com519bar10 contains 3872. com519bar11 contains 9347. com519bar12 contains 688. com519bar15 contains 6880. com519bar16 contains 5866. com519bar19 contains 5368. com519bar20 contains 7550. com519bar4 contains 3015. com519bar9 contains 6820.

Total seqs: 54533.

THANKS!!!

3

I’m guessing you grabbed the wrong group file (did you include the group file in the remove.lineage command?). Outside of mothur can you run the following from the folder with all of your files?

wc -l *.groups

Is there a groups file with 49161 lines in it?