Problem with sub.sample

Commands in mothur
1

Dear all,

I decided to combine my samples in groups, but when I run the command sub.sample I obtain the following error:

[ERROR]: your fasta file contains 567577 sequences, and your groupfile contains 228995, please correct.

Before the clustering phase, I would like to group my samples in 3 groups. This is the sequence of commands I executed:

split.groups(fasta files, name and groups): in order to separate my samples
merge.files for each group with fasta and names files: I obtained 3 fasta and 3 names files
merge file with my 3 fasta groups and names in order to obtain a single fasta and a single names file
make.groups with my 3 fasta files

So the problem is that I only have unique sequences in my group files (because it was created from the fasta file), so the standardisation does not work.

Any help is appreciated. Thanks in advance.

2

You can run the deunique.seqs command before the make.group to make sure your fasta files contains all the sequences.


split.groups(fasta files, name and groups): in order to separate my samples merge.files for each group with fasta and names files: I obtained 3 fasta and 3 names files deunique.seqs(fasta=fasta1, name=name1) deunique.seqs(fasta=fasta2, name=name2) deunique.seqs(fasta=fasta3, name=name3) merge file with my 3 deuniqued fasta groups in order to obtain a single fasta make.groups with my 3 deuniqued fasta files unique.seqs(fasta=combinedFastaFile) - create unique fasta and names files

This should get you what you are looking for.

3

Hi Westcott!

It worked! Thank you for your valuable help!