mothur

Error with screen.seqs removing all sequences

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!

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

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)

Thank you! I tried this and it worked!

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