# Get.groups in MiSeq SOP
**URL:** https://forum.mothur.org/t/get-groups-in-miseq-sop/3349
**Category:** Commands in mothur
**Created:** [July 31, 2017, 4:15pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349 "2017-07-31T16:15:34Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@AOFlaherty](https://forum.mothur.org/u/AOFlaherty)
#### Post date: [July 31, 2017, 4:15pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/1 "2017-07-31T16:15:34Z")
Hello all,
I’m following the MiSeq SOP nd all is going well until I get to the assessing error rates of the SOP. When I enter the get.groups command, the following appears:
\_mothur \> get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count\_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, groups=Mock)
[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.
Mock is not a valid group, and will be disregarded.
You provided no valid groups. I will run the command using all the groups in your file.
Selected 116011 sequences from your fasta file.
Selected 662924 sequences from your count file.\_
Could anyone explain to me what the problem is here?
Kind Regards,
Aidan.
---
### Author:  [@dwaite](https://forum.mothur.org/u/dwaite)
#### Post date: [July 31, 2017, 9:54pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/2 "2017-07-31T21:54:26Z")
Did you sequence a mock community as part of your sequencing run? If not, you’ll have to skip this part of the SOP because you don’t have reference data to compare to. If you did sequence a mock community, what name did you give it in your data?
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### Author:  [@skchewning](https://forum.mothur.org/u/skchewning)
#### Post date: [September 1, 2017, 8:06pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/3 "2017-09-01T20:06:58Z")
Hello,
I am encountering the same problem. I am using the subset data provided on the wiki MiSeq SOP page. [https://www.mothur.org/wiki/MiSeq\_SOP](https://www.mothur.org/wiki/MiSeq_SOP). This example data contains mock community fastq files called : Mock\_S280\_L001\_R1\_001.fastq and Mock\_S280\_L001\_R2\_001.fastq
I am using mothur version 1.39.5\_1. My code and output are below:
\_mothur \> get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, groups=Mock)
[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.
Mock is not a valid group, and will be disregarded.
You provided no valid groups. I will run the command using all the groups in your file.
Selected 1342 sequences from your fasta file.
Selected 117930 sequences from your count file.\_[/i]
Many thanks in advance for advice!
Sarah
---
### Author:  [@dwaite](https://forum.mothur.org/u/dwaite)
#### Post date: [September 1, 2017, 11:04pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/4 "2017-09-01T23:04:38Z")
That is strange, because I just downloaded the files and the mock community is definitely in there, under the name ‘Mock’.
What do you see if you run the following command?
```nohighlight
mothur > count.seqs(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count_table)
```
---
### Author:  [@skchewning](https://forum.mothur.org/u/skchewning)
#### Post date: [September 5, 2017, 3:40pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/5 "2017-09-05T15:40:41Z")
My output is below:
mothur \> count.seqs(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table)
count is not a valid parameter.
The valid parameters are: shared, name, group, processors, groups, seed, inputdir, and outputdir.
Using MiSeq\_SOP/stability.trim.contigs.good.names as input file for the name parameter.
Using 8 processors.
[ERROR]: did not complete count.seqs.
---
### Author:  [@dwaite](https://forum.mothur.org/u/dwaite)
#### Post date: [September 5, 2017, 10:03pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/6 "2017-09-05T22:03:59Z")
Damn! Sorry, I always make that mistake. Can you run count.groups() using the same file?
---
### Author:  [@skchewning](https://forum.mothur.org/u/skchewning)
#### Post date: [September 7, 2017, 3:21pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/7 "2017-09-07T15:21:42Z")
No worries! Output is below:
mothur \> count.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table)
Unable to open stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table. Trying default /usr/local/bin/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table
Unable to open /usr/local/bin/mothur/stability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table. Trying mothur’s location /usr/local/bin/mothurstability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table
Unable to open /usr/local/bin/mothurstability.trim.contigs.good.unique.good.filter.unique.precluster.denvo.vsearch.pick.pick.count\_table
You have no current groupfile, countfile or sharedfile and one is required.
[ERROR]: did not complete count.groups.
---
### Author:  [@dwaite](https://forum.mothur.org/u/dwaite)
#### Post date: [September 7, 2017, 9:57pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/8 "2017-09-07T21:57:07Z")
It looks like you’re in the wrong directory for your count table.
---
### Author:  [@skchewning](https://forum.mothur.org/u/skchewning)
#### Post date: [September 11, 2017, 4:18pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/9 "2017-09-11T16:18:47Z")
I agree it appears that way at first. However, I see the file in my current working directory. I received the same error when I ran the command from one directory above.
Do you know what file(s) it is referring to when it says:
“You have no current groupfile, countfile or sharedfile and one is required?”
---
### Author:  [@dwaite](https://forum.mothur.org/u/dwaite)
#### Post date: [September 11, 2017, 11:07pm UTC](https://forum.mothur.org/t/get-groups-in-miseq-sop/3349/10 "2017-09-11T23:07:04Z")
For that message, it just means that if the file you specify isn’t found then it looks for a previous one in the current files cache.
If you’re absolutely sure you’re working from the correct directory, the only other thing I can think of is that there might be spaces in the path name? Sometimes mothur has issues with those.