# Problem in summary.single file
**URL:** https://forum.mothur.org/t/problem-in-summary-single-file/2096
**Category:** Commands in mothur
**Created:** [October 23, 2014, 12:47pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096 "2014-10-23T12:47:39Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)
#### Post date: [October 23, 2014, 12:47pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/1 "2014-10-23T12:47:39Z")
Hello,
I am getting this result after doing mothur \> summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=14272) [14271 is the no. of sequence of the smallest samlple]
label group method nseqs coverage sobs invsimpson invsimpson\_lci invsimpson\_hci 0.03 Sample1 ave 14742 0.99221 224.895 8.860295 8.640853 9.091174 0.03 Sample12 ave 14742 0.99630 141.139 9.128217 8.969688 9.292452 0.03 Sample13 ave 14742 0.99626 148.776 9.978423 9.793687 10.170263 0.03 Sample18 ave 14742 0.99378 205.971 14.276668 13.974664 14.592015 0.03 Smple1 std 0 0.00062 9.09835 0.103303 0.10143 0.105278 0.03 Sample12 std 0 0.00046 6.498744 0.075838 0.07445 0.077307 0.03 Sample13 std 0 0.00043 6.295222 0.090122 0.088274 0.092076 0.03 Sample18 std 0 0.00056 8.082336 0.139745 0.137408 0.142195
Why am I getting 0 no. of sequences in the std method ?
looking forward.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [October 24, 2014, 7:33pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/2 "2014-10-24T19:33:59Z")
Did you possibly run sub.sample before running summary.single? Do all of your samples have 14742 reads in them?
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### Author:  [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)
#### Post date: [October 27, 2014, 9:56am UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/3 "2014-10-27T09:56:23Z")
Hello Dr. Schloss,
Yes I did sub. sample before summary.single. 14742 is the no. of sequence of my smallest sample (sample with least no.of unique sequences).
looking forward,
Richa
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [October 28, 2014, 3:59pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/4 "2014-10-28T15:59:34Z")
You don’t want to run summary.single on subsampled data. The reason the std (standard deviation) is zero is because there’s no variation since all of the samples have the same number of reads.
pat
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### Author:  [@pdlnn](https://forum.mothur.org/u/pdlnn)
#### Post date: [October 28, 2014, 5:50pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/5 "2014-10-28T17:50:59Z")
> [@pschloss](#):
>
> You don’t want to run summary.single on subsampled data. The reason the std (standard deviation) is zero is because there’s no variation since all of the samples have the same number of reads.
>
> pat
Hi Dr. Schloss,
Do you mean we should remove the subsample=# option from summary.single command? Or using the original (before subsampled) .shared file not the .subsample.shared file?
The sub.sample command will generate a separate .subsample.shared file and the original .shared file is not modified, am I right?
Also, how informative those “std” values are? Can I just use the “ave” values to make a table and put it in my dissertation? Thanks!
Deng Pan
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### Author:  [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)
#### Post date: [October 31, 2014, 12:36pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/6 "2014-10-31T12:36:21Z")
Hello Dr. Schloss,
Thanks for your reply.
I follow Miseq SOP, where I see
“mothur \> summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=2441)”
What is subsample here ? Could you please explain, the correct command line that I should use at summary.single step ??
Thanks
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### Author:  [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)
#### Post date: [November 3, 2014, 5:17pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/7 "2014-11-03T17:17:03Z")
Hello Dr. Schloss,
Thanks for your reply.
I follow Miseq SOP, where I see
“mothur \> summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=2441)”
What is subsample here ? Could you please explain, the correct command line that I should use at summary.single step ??
Thanks and looking forward
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [November 4, 2014, 1:02am UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/8 "2014-11-04T01:02:28Z")
Earlier you said…
> Yes I did sub. sample before summary.single. 14742 is the no. of sequence of my smallest sample (sample with least no.of unique sequences).
Where did you do that?
if you are following the SOP, the correct command is what you posted last:
> summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=2441)
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### Author:  [@Kumari\_Richa](https://forum.mothur.org/u/Kumari_Richa)
#### Post date: [November 4, 2014, 11:53am UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/9 "2014-11-04T11:53:53Z")
Hello
If I understood correctly, in mothur \> summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=2441), 2441 is the total no. of sequences of the smallest sample in SOP.
But you wrote: " You don’t want to run summary.single on subsampled data". Why so ?
Are you suggesting that I should not run summary.single on subsmapled data, if I have to work with Standard deviation values ??
Thanks and looking forward.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [November 11, 2014, 5:59pm UTC](https://forum.mothur.org/t/problem-in-summary-single-file/2096/10 "2014-11-11T17:59:49Z")
> But you wrote: " You don’t want to run summary.single on subsampled data". Why so ?
> Are you suggesting that I should not run summary.single on subsmapled data, if I have to work with Standard deviation values ??
Sorry, I’m lost. you just quoted what I said and asked if that was what I said. The input to summary.single should be the file that is generated by make.shared and should not be subsampled prior to running summary.single.