filter.seqs removes every columns

Commands in mothur
1

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?

2

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