Error in pre.cluster command

mothur bugs
1

Hello,

I am using the executable version 1.26.0 for Windows to analyze 4 different sets of sequences that I have merged together. However, when I reach the pre.cluster command I am getting the following: “[ERROR] Your name file contains 6887 valid sequences and your groupfile contains 11789, please correct.”

Here is what I did in more detail:

mothur > sffinfo(sff=13Bac.sff, flow=T)
mothur > summary.seqs(fasta=13Bac.fasta)
mothur > trim.flows(flow=13Bac.flow, oligos=13Bac.oligos, pdiffs=2, bdiffs=1, processors=2)
mothur > shhh.flows(file=13Bac.flow.files, processors=2)
mothur > trim.seqs(fasta=13Bac.shhh.fasta, name=13Bac.shhh.names, oligos=13Bac.oligos, pdiffs=2, bdiffs=1, maxhomop=8, minlength=200, processors=2)
mothur > summary.seqs(fasta=13Bac.shhh.trim.fasta, name=13Bac1.shhh.trim.names)

Completed the 3 other libraries similarly and then merged as follows:

mothur > merge.files(input=13Bac.shhh.trim.fasta-14Bac.shhh.trim.fasta-15Bac.shhh.trim.fasta-16Bac.shhh.trim.fasta, output=SedAnalysis.shhh.trim.fasta)
mothur > merge.files(input=13Bac.shhh.trim.names-14Bac.shhh.trim.names-15Bac.shhh.trim.names-16Bac.shhh.trim.names, output=SedAnalysis.shhh.trim.names)
mothur > merge.files(input=Bac13.shhh.groups-Bac14.shhh.groups-Bac15.shhh.groups-Bac16.shhh.groups, output=SedAnalysis.shhh.groups)

After merging, I continued with the Schloss SOP tutorial:
mothur > unique.seqs(fasta=SedAnalysis.shhh.trim.fasta, name=SedAnalysis.shhh.trim.names)
mothur > summary.seqs(fasta=SedAnalysis.shhh.trim.unique.fasta, name=SedAnalysis.shhh.trim.unique.names)
mothur > align.seqs(fasta=SedAnalysis.shhh.trim.unique.fasta, reference=silva.bacteria.fasta, processors=2)
mothur > summary.seqs(fasta=SedAnalysis.shhh.trim.unique.align, name=SedAnalysis.shhh.trim.unique.names)
mothur > screen.seqs(fasta=SedAnalysis.shhh.trim.unique.align, name=SedAnalysis.shhh.trim.unique.names, group=SedAnalysis.shhh.groups, end=6098, optimize=start, criteria=95, processors=2)
mothur > summary.seqs(fasta= SedAnalysis.shhh.trim.unique.good.align, name= SedAnalysis.shhh.trim.unique.good.names)
mothur > filter.seqs(fasta=SedAnalysis.shhh.trim.unique.good.align, vertical=T, trump=., processors=2)
unique.seqs(fasta=SedAnalysis.shhh.trim.unique.good.filter.fasta, name=SedAnalysis.shhh.trim.unique.good.names)
pre.cluster(fasta=SedAnalysis.shhh.trim.unique.good.filter.unique.fasta, name=SedAnalysis.shhh.trim.unique.good.filter.names, group=SedAnalysis.shhh.good.groups, diffs=2)

I have repeated these analyses multiple times thinking I may have missed something and each time I received “[ERROR] Your name file contains 6887 valid sequences and your groupfile contains 11789, please correct”

I would greatly appreciate any assistance in how to rectify this problem :slight_smile: .

Thanks,
Tamar

2

Could you send your logfile and input files from after the merge steps to mothur.bugs@gmail.com?