With the command mothur > pre.cluster(fasta=merge.good.filter.unique.fasta, count=merge.good.filter.count_table, diffs=2, processors=40) for my 89 samples I’ve obtained the next error for 2 of my samples
Removing group: 2_JOUE_R1 because all sequences have been removed.
Removing group: 2_NEZ_R1 because all sequences have been removed.
And now, when I’ve made the next step to mothur > chimera.uchime(fasta=merge.good.filter.unique.precluster.fasta, count=merge.good.filter.unique.precluster.count_table, dereplicate=t, processors=40)
Hi Rocio,
This is where the problem is stemming from:
5.5 mothur “#count.seqs(name=merge.names, group=merge.groups)”
Output files: merge.count_table #error messages here, check the log #count.seqs() will generate a file called stability.trim.contigs.good.count_table. #In subsequent commands we’ll use it by using the count option
The error messages you are getting are because your group file only contains the unique sequences. When you run the make.group command before this it must be on fasta files that contain all your sequences, i.e. before you run the unique.seqs command on each individual fasta file.