Count and fasta file mismatch

Commands in mothur
1

Hi, can somebody help me with this?. After running chimera.vsearch and remove.seqs I tried running the command summary.seqs following the MiSeq SOP and keep getting an error. How do I fix this? Thanks

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

Using stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta as input file for the fasta parameter.

Using 4 processors.
[ERROR]: Your count file contains 151475 unique sequences, but your fasta file contains 120068. File mismatch detected, quitting command.

2

Hi there!!!
Please try the following command:
`

mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table)`

I think you are getting the error because you are not using the count_table file that was generated after the “chimera.vsearch” step.
For summary in this case, you should take chimera search and removal steps altogether. I think you should use the fasta file that was generated after the “remove.seqs” step and the count_table file that was generated after the “chimera.vsearch” step.

Please inform me if the error is fixed.

1 Like
3

Yes! The error is fixed, many thanks!

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4

sorry… but I was wrong, I don’t have count_table after running chimera.vsearch just those files: Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos

5

Look, first try to understand what these “chimera.vsearch” and “remove.seqs” commands do.
“chimera.vsearch” doesn’t remove any chimeric sequences from the fasta file but it removes from the count_table file. And produces an accnos file which contains all the removed chimeric sequences only. Now, in the next step you will use this accnos file together with the fasta file so that the fasta file can understand which sequences have to be removed.
so, you have to consider these two steps altogether as an unit.
Let me know if you understand.

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6

did you include your count file in the vsearch line?

Could you write your command line for vsearch?

7

chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

8

I compared to my scripts, but I use name and group still at vsearch. I only make the count table at the end since I found often this problem.

After chimera.search, do you include the count file also to remove.seqs? Could you write that line of code too?

If different to what you have, give a shot to

chimera.vsearch(chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)
remove.seqs(fasta=current, accnos=current, count=current, dups=t)

1 Like
9

@Ecompanymaso98 what version of mothur are you using? can you post your commands before the error?

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