File mismatch after screen.seqs

I started analysing my microbiome data with mothur. I stick closely to the tutorial. However the summary.seqs command after the screen.seqs command (after the alignment has been done) yields a file mismatch error because the count file contains much more sequences than the fasta file. I can not figure out why that is and what I can do about that. Can anyone help me with that issue? I am happy to provide a log file, but can not figure out how to do that in this forum.
Thanks already in advance


Can you copy and paste in the commands you are running along with the error message you are getting?


These are the commands that I used:

make.file(inputdir=data, type=fastq, prefix=stability)

make.contigs(file=stability.files, processors=2)

screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=500, processors=2)

remove.seqs(accnos=current, group=current)

count.seqs(name=stability.trim.contigs.good.names, group=current)


align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.seed_v132.align, processors=2)

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

screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=6330, end=25438, maxhomop=8)

summary.seqs(fasta=current, count=current)

And this is the error message I get:

mothur > summary.seqs(fasta=current, count=current)
Using data/stability.trim.contigs.good.count_table as input file for the count parameter.
Using data/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.

Using 2 processors.
[ERROR]: Your count file contains 160370 unique sequences, but your fasta file contains 2048. File mismatch detected, quitting command.



You have this line…

remove.seqs(accnos=current, group=current)

I’m not sure what you’re trying to remove, but it should likely not be in the pipeline. FWIW, the problem is that you are removing sequences from your group file, but not the fasta or names files. I’m kind of surprised that the following count.seqs command is working. I’d get rid of the remove.seqs line and try again.


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