# Problem with filter.seqs - Length of filtered alignment: 0

**URL:** <https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840>\
**Category:** Commands in mothur\
**Created:** [June 3, 2023, 5:42pm UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840 "2023-06-03T17:42:28Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Matteo](https://avatars.discourse-cdn.com/v4/letter/m/f9ae1b/32.png) [@Matteo](https://forum.mothur.org/u/Matteo)\
**Post date:** [June 3, 2023, 5:42pm UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840/1 "2023-06-03T17:42:28Z")

</div>

Dears all,

I used mothur(1.43) to process several sequences from a single set of samples. However, one of the files is giving me problems. When I run the filter.seq command I always get the following message:

Length of filtered alignment: 0  
Number of columns removed: 7682  
Length of the original alignment: 7682  
Number of sequences used to construct filter: 56544

Since I read that the problem could be in the previous command (sceen.seqs) I tried to modify the end parameter, using various lengths as end (465, 451 etc).  
Below is the screen.seqs command, the summary and the filter.seqs command.

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 1 253 253 0 3 1  
2.5%-tile: 1 440 440 0 4 5965  
25%-tile: 1 443 443 0 5 59650  
Median: 1 460 460 0 5 119299  
75%-tile: 1 460 460 0 6 178948  
97.5%-tile: 1 465 465 0 8 232632  
Maximum: 1 465 465 0 66 238596  
Means: 1 451 451 0 5

# of unique sequences: 93897

total # of seqs: 238596

screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count\_table, summary=stability.trim.contigs.good.unique.summary, start=1, end= 451, maxhomop=8)

filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)

I can’t figure out what the problem is.

Thanks in advance.

---

<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:** [June 6, 2023, 6:45pm UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840/2 "2023-06-06T18:45:54Z")

</div>

Is the `summary.seqs` output you showed from `stability.trim.contigs.good.unique.align` or `stability.trim.contigs.good.unique.fasta`? Can you post the output of…

```auto
summary.seqs(fasta= stability.trim.contigs.good.unique.align)

```

---

<div class="post-metadata">

**Author:** ![Matteo](https://avatars.discourse-cdn.com/v4/letter/m/f9ae1b/32.png) [@Matteo](https://forum.mothur.org/u/Matteo)\
**Post date:** [June 8, 2023, 11:59am UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840/3 "2023-06-08T11:59:48Z")

</div>

Dear Pat,  
this is the result of the command

```auto
summary.seqs(fasta= stability.trim.contigs.good.unique.align)

```

```
	Start	End	NBases	Ambigs	Polymer	NumSeqs

```

Minimum: 0 0 0 0 1 1  
2.5%-tile: 1873 4088 440 0 4 2348  
25%-tile: 1873 4088 443 0 5 23475  
Median: 1873 4088 460 0 5 46949  
75%-tile: 1873 4088 461 0 6 70423  
97.5%-tile: 1873 4088 465 0 10 91550  
Maximum: 6856 6867 465 0 66 93897  
Mean: 1881 4088 452 0 5

# of Seqs: 93897

It took 6 secs to summarize 93897 sequences.

Output File Names:  
stability.trim.contigs.good.unique.summary

Thank you

---

<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:** [June 12, 2023, 2:53pm UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840/4 "2023-06-12T14:53:06Z")

</div>

You likely want to use `start=1873` and `end=4088` when you run `screen.seqs` with `stability.trim.contigs.good.unique.align`.

I’d also suggest using the most recent version of mothur as 1.43 is quite out of date.

Pat

---

<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [June 22, 2023, 2:53pm UTC](https://forum.mothur.org/t/problem-with-filter-seqs-length-of-filtered-alignment-0/21840/5 "2023-06-22T14:53:52Z")

</div>

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.