mothur

Summary seq between count table and fasta file resulting in file mismatch

I am running into an error following my align sequences command with the silva.v4 database between my aligned fasta file and my most recent count table.
The error I keep getting is: [ERROR]: Your count file contains 3538449 unique sequences, but your fasta file contains 249941. File mismatch detected, quitting command.
I’ve re-started my run right from make.contigs to ensure that files haven’t somehow gotten mis-aligned. However, I still seem to be coming up with this error… could I have the wrong silva.v4.fasta file perhaps??
The workflow I’ve used and output are as follows:

mothur >
make.contigs(file=stability.file, processors=16)
It took 39 secs to assemble 242886 reads.
Total of all groups is 12486425

mothur >
summary.seqs(fasta=stability.trim.contigs.fasta)
It took 65 secs to summarize 12247832 sequences.

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, minlength=291, maxlength=293)
It took 54 secs to screen 12247832 sequences, removed 2453909.

mothur >
summary.seqs(fasta=stability.trim.contigs.good.fasta, processors=16)
It took 52 secs to summarize 9793923 sequences.

mothur >
unique.seqs(fasta=stability.trim.contigs.good.fasta)

mothur >
count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)

mothur >
summary.seqs(count=stability.trim.contigs.good.count_table)
It took 52 secs to summarize 9793923 sequences.

mothur >
align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference= silva.v4.fasta)
Reading in the silva.v4.fasta template sequences… DONE.
It took 3 to read 14956 sequences.
It took 656 secs to align 3538449 sequences.

mothur >
summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
[ERROR]: Your count file contains 3538449 unique sequences, but your fasta file contains 447516. File mismatch detected, quitting command.

Any insight into code errors would be greatly appreciated.

JM

Hi,

When you ran…

mothur > summary.seqs(count=stability.trim.contigs.good.count_table)
It took 52 secs to summarize 9793923 sequences.

How many unique sequences did it say you had? Also, did you have any error messages when you ran align.seqs?

You might also try going back and rerun align.seqs and then try the summary.seqs command again.

Pat

I personally stay away from count files until the end - it is very easy to have a mismatch when forgetting to call them for any step.

I try to keep using the name file until the very end - then I run the count command.

Leo

1 Like

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