Error with screen.seqs removing all sequences

Commands in mothur
1

Hello! I am having an issue with the second screen.seqs step. It has been removing all of my reads. I have tried changing the start and end parameters to 1 and 43116 which I got from the summary. My server also dumped the core at the end. Here’s what I have:

mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)

Using 24 processors.

            Start   End     NBases  Ambigs  Polymer NumSeqs

Minimum: 0 0 0 0 1 1
2.5%-tile: 11895 14961 1 0 1 30635
25%-tile: 11895 25318 57 0 3 306348
Median: 11895 25318 292 0 4 612695
75%-tile: 11895 25318 292 0 4 919042
97.5%-tile: 43116 43116 292 0 6 1194755
Maximum: 43116 43116 300 0 40 1225389
Mean: 17783 27340 207 0 3

of unique seqs: 440136

total # of seqs: 1225389

It took 110 secs to summarize 1225389 sequences.

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

mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, criteria=90, start=1,end=43116)

Using 24 processors.

It took 110 secs to screen 440136 sequences, removed 440136.

//
Running command: remove.seqs(accnos=stability.trim.contigs.good.unique.bad.accnos.temp, count=stability.trim.contigs.good.count_table)
Your file contains only sequences from the .accnos file.
//

You can see it removes every unique sequence I have. Can anyone help me out? Thank you so much!

2

I also have the log file if that would be helpful in diagnosing the issue. Thanks!

3

The start parameter is used to remove sequences that start after the given location. When start=1, mothur will remove any read that starts after 1. The end parameter is used to remove sequences that end before a given location. When end=43116, mothur will remove any sequence that ends before 43116.

I think you want:

mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, criteria=90, start=11895,end=14961)

4

Thank you! I tried this and it worked!

1 Like
5

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