chimera.uchime not creating a new countfile

mothur bugs
1

Hi, I am a new Mothur user, hopefully this isn’t redundant, but I could not find anything about this by searching the forum.

When running chimera.uchime it does not make an updated count file:

mothur > chimera.uchime(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)

It took 21038 secs to check 53609 sequences. 21571 chimeras were found.

Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras
stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos


To remedy I've run the following:

mothur > remove.seqs(fasta=current, accnos=current, count=current)
Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos as input file for the accnos parameter.
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.fasta 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 21571 sequences from your fasta file.
Removed 32634 sequences from your count file.

Output File Names:
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table.


I am following the commands on the SOP so I'm not sure why it isn't creating the count file. I have run through this process twice and it produced the same results. It does seem that the remove.seqs command removes the chimeras from the count file and thus it would be safe to proceed with data analysis.

When using the count file made this way, it does not produce group information in the count file and then will not work with downstream analysis:


mothur > make.shared(list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.list, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table, label=0.03)

[ERROR]: Your count file does not have group info, aborting.
[ERROR]: did not complete make.shared.

How do I get my count file to contain group information? I’m sorry if these two questions could be contained in different posts. I cannot figure out of the root of the problem is in chimera.uchime or somewhere else upstream with the count table.



Thanks, Tim
2

The chimera.uchime command will only create an updated count table if your inputted count table contains group information and dereplicate=t. When dereplicate=T mothur only flags a sequence as a chimera within the group it was found to be chimeric. The chimera.uchime command must then create a new count table because it knows which groups identified the sequences as chimeric and which did not. If your count table does not contain group information there is no need to process by group or create a revised count table.

It sounds like the issue is when your count table was created the group file was not included. The count file can be created two ways:

mothur > count.seqs(name=yourNameFile) - creates a table with sequenceName and totalAbundance

or

mothur > count.seqs(name=yourNameFile, group=yourGroupFile) - creates a table with sequenceName, totalAbundance, list of abundances per group

1 Like
3

Hi, Thanks for the response. After examining my logfiles and my notes I found that I had made a mistake upstream that had created a countfile without group information and that was the root of the problem. Sorry for not looking harder before posting!