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

Commands in mothur
1

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.

2

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…

summary.seqs(fasta= stability.trim.contigs.good.unique.align)
3

Dear Pat,
this is the result of the command

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

4

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I’d also suggest using the most recent version of mothur as 1.43 is quite out of date.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

5

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