# Trouble with Miseq SOP Example Analysis

**URL:** https://forum.mothur.org/t/trouble-with-miseq-sop-example-analysis/21487
**Category:** Uncategorized
**Created:** [July 19, 2022, 5:30pm UTC](https://forum.mothur.org/t/trouble-with-miseq-sop-example-analysis/21487 "2022-07-19T17:30:32Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![HasanM](https://avatars.discourse-cdn.com/v4/letter/h/f6c823/32.png) [@HasanM](https://forum.mothur.org/u/HasanM)
#### Post date: [July 19, 2022, 5:30pm UTC](https://forum.mothur.org/t/trouble-with-miseq-sop-example-analysis/21487/1 "2022-07-19T17:30:32Z")

</div>

Hello,

Going through the Miseq SOP example ([MiSeq SOP](https://mothur.org/wiki/miseq_sop/)) and am having issues with a step:

After running this step:

```auto
mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_table, start=1969, end=11551)

```

The results that I should have seen are:

```auto
mothur > summary.seqs(fasta=current, count=current)

Using stability.trim.contigs.good.count_table as input file for the count parameter.
Using stability.trim.contigs.unique.good.align as input file for the fasta parameter.

Using 16 processors.
 
       Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1966	11551	250	0	3	1
2.5%-tile:	1969	11551	252	0	3	3217
25%-tile:	1969	11551	252	0	4	32165
Median: 1969	11551	252	0	4	64329
75%-tile:	1969	11551	253	0	5	96493
97.5%-tile:	1969	11551	253	0	6	125440
Maximum:	1969	13401	270	0	8	128656
Mean:	1968	11551	252	0	4
# of unique seqs:	16299
total # of seqs:	128656

```

Instead, I saw:

```auto
mothur > summary.seqs(fasta=current, count=current)
Using stability.trim.contigs.good.count_table as input file for the count parameter.
Using stability.trim.contigs.unique.good.align as input file for the fasta parameter.

Using 16 processors.

                Start End NBases Ambigs Polymer NumSeqs
Minimum: 1965 11552 251 0 3 1
2.5%-tile: 1965 11552 251 0 3 1
25%-tile: 1967 11552 252 0 4 7
Median: 1967 11552 252 0 4 13
75%-tile: 1968 11552 253 0 5 19
97.5%-tile: 1968 13400 270 0 8 24
Maximum: 1968 13400 270 0 8 24
Mean: 1967 11629 252 0 4
# of unique seqs: 23
total # of seqs: 24

```

Don’t know what went wrong in this step, as everything I had before was matching up with the example.

Specifically, what went wrong was that the unique seqs decreased immensely:

```auto
# of unique seqs: 23
total # of seqs: 24

```

Thanks for any help.

---

<div class="post-metadata">

### 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: [August 16, 2022, 5:42pm UTC](https://forum.mothur.org/t/trouble-with-miseq-sop-example-analysis/21487/2 "2022-08-16T17:42:02Z")

</div>

This isn’t anythign to worry about. There are subtle differences between versions of mothur and the output from running mothur on different operating systems. I don’t always have the time to update the output of the SOP.

pat