# Unique.seqs is removing a lot of sequences
**URL:** https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861
**Category:** Commands in mothur
**Created:** [February 2, 2021, 9:57am UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861 "2021-02-02T09:57:49Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@ds1405](https://forum.mothur.org/u/ds1405)
#### Post date: [February 2, 2021, 9:57am UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/1 "2021-02-02T09:57:50Z")
I this normal? It seems to be removing a lot of my sequences…
```
summary.seqs(fasta=stability.trim.contigs.trim.good.fasta, processors=5)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 150 150 0 3 1
2.5%-tile: 1 177 177 0 3 447237
25%-tile: 1 177 177 0 4 4472366
Median: 1 178 178 0 5 8944732
75%-tile: 1 197 197 0 5 13417097
97.5%-tile: 1 202 202 0 6 17442226
Maximum: 1 220 220 0 52 17889462
Mean: 1 186 186 0 4
# of Seqs: 17889462
It took 320 secs to summarize 17889462 sequences.
unique.seqs(fasta=stability.trim.contigs.trim.good.fasta, processors=6)
stability.trim.contigs.trim.good.names
stability.trim.contigs.trim.good.unique.fasta
summary.seqs(fasta=stability.trim.contigs.trim.good.unique.fasta, processors=1)
Using 5 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 150 150 0 3 1
2.5%-tile: 1 177 177 0 3 252900
25%-tile: 1 177 177 0 4 2528993
Median: 1 178 178 0 5 5057986
75%-tile: 1 197 197 0 5 7586979
97.5%-tile: 1 202 202 0 6 9863072
Maximum: 1 220 220 0 52 10115971
Mean: 1 184 184 0 4
# of Seqs: 10115971
It took 48 secs to summarize 10115971 sequences.
```
I am now trying to run `count.seqs(name=stability.trim.contigs.trim.good.names, group=stability.contigs.good.groups)` and it is doing nothing (has been for the last 10 minutes).
Is this normal?
Edit: formatting
---
### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [February 2, 2021, 2:36pm UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/2 "2021-02-02T14:36:29Z")
If you run `summary.seqs` like this…
`summary.seqs(fasta=stability.trim.contigs.trim.good.unique.fasta, name=stability.trim.contigs.trim.good.names, processors=1)`
You should get a line at the bottom that says something like…
```auto
Total: 17889462
```
You have a lot of unique sequences and I suspect that is what is causing `count.seqs` to take so long to run. Can you also let us know what region you are sequencing and with what chemistry? That looks like a short region.
Pat
---
### Author:  [@ds1405](https://forum.mothur.org/u/ds1405)
#### Post date: [February 3, 2021, 5:13pm UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/3 "2021-02-03T17:13:23Z")
> [@pschloss](#):
>
> summary.seqs(fasta=stability.trim.contigs.trim.good.unique.fasta, name=stability.trim.contigs.trim.good.names, processors=1)
Hi Pat
`mothur > summary.seqs(fasta=stability.trim.contigs.trim.good.unique.fasta, name=stability.trim.contigs.trim.good.names, processors=1)`
```
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 150 150 0 3 1
2.5%-tile: 1 177 177 0 3 447237
25%-tile: 1 177 177 0 4 4472366
Median: 1 178 178 0 5 8944732
75%-tile: 1 197 197 0 5 13417097
97.5%-tile: 1 202 202 0 6 17442226
Maximum: 1 220 220 0 52 17889462
Mean: 1 186 186 0 4
# of unique seqs: 10115971
total # of seqs: 17889462
It took 247 secs to summarize 17889462 sequences.
Output File Names:
stability.trim.contigs.trim.good.unique.summary
```
So I guess that’s okay, right? I am looking at the V3 region which is about 180bp using Illumina MiSeq (is that the right sort of answer? I’m very new to this…)
---
### Author:  [@leocadio](https://forum.mothur.org/u/leocadio)
#### Post date: [February 3, 2021, 8:05pm UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/4 "2021-02-03T20:05:01Z")
> [@ds1405](#):
>
> `889`
Looks a bit noisy to me (more than half uniques)… Which parameters you used in the make.contigs?
---
### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [February 4, 2021, 9:55pm UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/5 "2021-02-04T21:55:32Z")
Did you do 2x250 or 2x150 reads? If you’re doing 2x250 then there can be a problem with sequencing too much generating a higher error rate. If you’re doing 2x150 then you aren’t going to have fully overlapping reads, which could also be causing problems.
Pat
---
### Author:  [@system](https://forum.mothur.org/u/system)
#### Post date: [February 14, 2021, 9:55pm UTC](https://forum.mothur.org/t/unique-seqs-is-removing-a-lot-of-sequences/20861/6 "2021-02-14T21:55:53Z")
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