Count and name file mismatch

Commands in mothur
1

Hi, can somebody help me with this?. After running align.seqs I tried running the command summary.seqs and keep getting an error. How do I fix this? Thanks

mothur > align.seqs(fasta=otus_leq.fasta, reference=silva.bacteria.fasta, flip=t, processors=8)

Output File Names:
otus_leq.align
otus_leq.align.report
otus_leq.flip.accnos

mothur > summary.seqs(fasta=otus_leq.align, count=otus_leq.count_table)

Using 8 processors.
[ERROR]: Your name file contains 5298 unique sequences, but your fasta file contains 4106. File mismatch detected, quitting command.

2

I think you are running in the same problems as before. I run into that problem more often than I like too! So, summary.seqs is actually using your name file. At some point, you cleaned your fasta (or reduced with a unique) and the name file did not got it.

Could you put your full command list? It is very easy at some step to create a mismatch between the fasta/align and the name file

3

mothur > align.seqs(fasta=otus_leq.fasta, reference=silva.bacteria.fasta, flip=t, processors=8)
Reading in the silva.bacteria.fasta template sequences… DONE.
It took 25 to read 14956 sequences.

Aligning sequences from otus_leq.fasta …
530
530
530
530
530
530
530
536
It took 11 secs to align 4246 sequences.

[WARNING]: 19 of your sequences generated alignments that eliminated too many bases, a list is provided in otus_leq.flip.accnos.
[NOTE]: 6 of your sequences were reversed to produce a better alignment.

It took 11 seconds to align 4246 sequences.

Output File Names:
otus_leq.align
otus_leq.align.report
otus_leq.flip.accnos

mothur > summary.seqs(fasta=otus_leq.align, count=otus_leq.count_table)

Using 8 processors.
[ERROR]: Your name file contains 5438 unique sequences, but your fasta file contains 4246. File mismatch detected, quitting command.

mothur > remove.seqs(fasta=current, accnos=otus_leq.flip.accnos, count=current, dups=t)

Using otus_leq.count_table as input file for the count parameter.
Using otus_leq.align as input file for the fasta parameter.

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.

Removed 19 sequences from your fasta file.
[ERROR]: NOT is not in your count table. Please correct.

4

Hi Emma
You have already a problem in the number of sequences before that step. I meant: Could you send all the steps also before that one? (So, your pipeline). Sorry for the misunderstanding.

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1 Like
5

You probably meant to run

align.seqs(fasta=otus_leq.unique.fasta, reference=silva.bacteria.fasta, flip=t, processors=8)
summary.seqs(fasta=otus_leq.unique.align, count=otus_leq.count_table)

As @leocadio mentioned, it would be helpful to see what commands you ran before running align.seqs.
Pat

6

Ok @leocadio and @pschloss! The steps before were made by my partner with Usearch so we are going to check it! Thanks!

7

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