# filter.seqs removes every columns

**URL:** <https://forum.mothur.org/t/filter-seqs-removes-every-columns/2693>\
**Category:** Commands in mothur\
**Created:** [February 5, 2016, 10:20am UTC](https://forum.mothur.org/t/filter-seqs-removes-every-columns/2693 "2016-02-05T10:20:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lgoetghe](https://avatars.discourse-cdn.com/v4/letter/l/bb73d2/32.png) [@lgoetghe](https://forum.mothur.org/u/lgoetghe)\
**Post date:** [February 5, 2016, 10:20am UTC](https://forum.mothur.org/t/filter-seqs-removes-every-columns/2693/1 "2016-02-05T10:20:29Z")

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Hi,

Sorry in advance, i’m a novice with mothur…I encounter some problems with the filter.seqs command  
I have run the screen.seqs command and obtained :

summary.seqs(fasta=all.trim.unique.good.align)

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs  
Minimum: 1045 5331 195 0 3 1  
2.5%-tile: 1046 5339 224 0 3 1312  
25%-tile: 1046 5459 253 0 4 13112  
Median: 1046 5711 262 0 5 26224  
75%-tile: 1046 6098 269 0 5 39336  
97.5%-tile: 1046 6324 282 0 6 51136  
Maximum: 1046 6428 314 0 8 52447  
Mean: 1045.99 5770.99 259.602 0 4.72832

# of Seqs: 52447

Output File Names:  
all.trim.unique.good.summary

  
Then I run the filter.seqs command, and seems like all the columns have been removed...

filter.seqs(fasta=all.trim.unique.good.align-silva.gold.align, trump=., vertical=T, processors=2)

Using 2 processors.  
Creating Filter…

  
Running Filter...  
  
Length of filtered alignment: 0 Number of columns removed: 50000 Length of the original alignment: 50000 Number of sequences used to construct filter: 57628

Output File Names:  
allsilva.filter  
all.trim.unique.good.filter.fasta  
silva.gold.filter.fasta

  
  
mothur \> summary.seqs(fasta=all.trim.unique.good.filter.fasta)

Using 2 processors.

Start End NBases Ambigs Polymer NumSeqs  
Minimum: -1 -1 0 0 1 1  
2.5%-tile: 0 0 0 0 1 1312  
25%-tile: 0 0 0 0 1 13112  
Median: 0 0 0 0 1 26224  
75%-tile: 0 0 0 0 1 39336  
97.5%-tile: 0 0 0 0 1 51136  
Maximum: -1 -1 0 0 1 52447  
Mean: 0 0 0 0 1

# of Seqs: 52447

Output File Names:  
all.trim.unique.good.filter.summary

Any help?

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<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:** [February 8, 2016, 12:29pm UTC](https://forum.mothur.org/t/filter-seqs-removes-every-columns/2693/2 "2016-02-08T12:29:11Z")

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I haven’t done it in a while, but what happens when you run summary.seqs on silva.gold.align? I suspect you need to run screen.seqs on silva.gold.align using the same parameters as you did with your file.

Pat