# missing.group **URL:** \ **Category:** Commands in mothur\ **Created:** [January 22, 2010, 6:46pm UTC](https://forum.mothur.org/t/missing-group/105 "2010-01-22T18:46:29Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![sapeura](https://avatars.discourse-cdn.com/v4/letter/s/dfb087/32.png) [@sapeura](https://forum.mothur.org/u/sapeura)\ **Post date:** [January 22, 2010, 6:46pm UTC](https://forum.mothur.org/t/missing-group/105/1 "2010-01-22T18:46:29Z")
Hi! I’m a new user but I have managed to struggle with my 454-data all the way until clustering is done. But now I don’t know what to do. When doing otu reading, Mothur says that my groups- and list-files have a different number of sequences. The missing sequences should be in missing.group-file and I even got the file, but IT IS EMPTY. So does anybody know how to make those files mach??? ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [January 25, 2010, 2:30pm UTC](https://forum.mothur.org/t/missing-group/105/2 "2010-01-25T14:30:15Z")
This can occur if you do not have unique sequence names. mothur requires sequence names to be unique. ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [January 26, 2010, 3:49am UTC](https://forum.mothur.org/t/missing-group/105/3 "2010-01-26T03:49:49Z")
You might also try following the Costello Stool analysis I provide in the analysis examples page of the wiki. Unfortunately, the names for each file get confusing and its easy to get them messed up, which can cause problems. ---
**Author:** ![sapeura](https://avatars.discourse-cdn.com/v4/letter/s/dfb087/32.png) [@sapeura](https://forum.mothur.org/u/sapeura)\ **Post date:** [January 26, 2010, 7:34am UTC](https://forum.mothur.org/t/missing-group/105/4 "2010-01-26T07:34:08Z")
So far I’ve been following the Sogin-analysis, but I’ll try to change to Costello analysis. I figured out what caused the problem (but don’t yet have the final solution…) At least part of the problem was, that when collecting the original sequence data, I had somehow manage to add 160 sequences twice. Now I removed the duplicates, did it all over again, and ended up again with different number of sequences in .list and .group files. And the missign.group is still empty… ---
**Author:** ![verenastarke](https://avatars.discourse-cdn.com/v4/letter/v/8e8cbc/32.png) [@verenastarke](https://forum.mothur.org/u/verenastarke)\ **Post date:** [January 28, 2010, 9:43pm UTC](https://forum.mothur.org/t/missing-group/105/5 "2010-01-28T21:43:11Z")
Hi there, I had a similar problem. My message said “Your group file contains 41375 sequences and list file contains 41195 sequences”… In my analysis I am using several sequencing files from different samples, which I combined in one big file as described in the Sogin-analysis example…which results in a new fasta-file and a groups-file. When I was using the new fasta-file for downstream analysis (such as screen.seqs) I forgot to change the groups-file accordingly. Every time you are removing sequences from your fasta-file you also need to change the groups-file (and name-file when using unique sequences). Hope this helps. Cheers, V ---
**Author:** ![sapeura](https://avatars.discourse-cdn.com/v4/letter/s/dfb087/32.png) [@sapeura](https://forum.mothur.org/u/sapeura)\ **Post date:** [January 29, 2010, 7:31am UTC](https://forum.mothur.org/t/missing-group/105/6 "2010-01-29T07:31:48Z")
The problem was, that I had accidentaly added 160 sequences twice into the original fasta-file and when trying to remove those, I apparently used a command in BioEdit, that removed all exact duplicate seqs :oops: . However some of the duplicate names were still left (no idea how that’s even possible; duplicate names should have had exactly the same seqs :shock: ). So ones I manually removed the duplicate names, it all went smoothly.