Chimera.vsearch command not valid?

Please report bugs you encounter in mothur using this forum.
Post Reply
adanni01
Posts: 1
Joined: Thu Jul 13, 2017 12:12 pm

Chimera.vsearch command not valid?

Post by adanni01 » Thu Jul 13, 2017 12:24 pm

Hi,

I am a very beginner user trying to go through the MiSeq_SOP tutorial and when I try to execute

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

I get the error: Invalid command.
Valid commands are: align.check,align.seqs,amova,anosim,bin.seqs,catchall,chimera.bellerophon,chimera.ccode,chimera.check,chimera.perseus,chimera.pintail,chimera.slayer,chimera.uchime,chop.seqs,classify.otu,classify.rf,classify.seqs,classify.svm,classify.tree,clear.memory,clearcut,cluster,cluster.classic,cluster.fragments,cluster.split,collect.shared,collect.single,consensus.seqs,cooccurrence,corr.axes,count.groups,count.seqs,create.database,degap.seqs,deunique.seqs,deunique.tree,dist.seqs,dist.shared,fastq.info,filter.seqs,filter.shared,get.commandinfo,get.communitytype,get.coremicrobiome,get.current,get.dists,get.group,get.groups,get.label,get.lineage,get.mimarkspackage,get.otulabels,get.otulist,get.oturep,get.otus,get.rabund,get.relabund,get.sabund,get.seqs,get.sharedseqs,hcluster,heatmap.bin,heatmap.sim,help,homova,indicator,kruskal.wallis,lefse,libshuff,list.otulabels,list.seqs,load.logfile,make.biom,make.contigs,make.fastq,make.group,make.lefse,make.lookup,make.shared,make.sra,make.table,mantel,merge.files,merge.groups,merge.sfffiles,merge.taxsummary,metastats,mgcluster,mimarks.attributes,nmds,normalize.shared,otu.association,otu.hierarchy,pairwise.seqs,parse.list,parsimony,pca,pcoa,pcr.seqs,phylo.diversity,phylotype,pipeline.pds,pre.cluster,primer.design,quit,rarefaction.shared,rarefaction.single,remove.dists,remove.groups,remove.lineage,remove.otulabels,remove.otus,remove.rare,remove.seqs,rename.seqs,reverse.seqs,screen.seqs,sens.spec,seq.error,set.current,set.dir,set.logfile,sff.multiple,sffinfo,shhh.flows,shhh.seqs,sort.seqs,sparcc,split.abund,split.groups,sub.sample,summary.qual,summary.seqs,summary.shared,summary.single,summary.tax,system,tree.shared,trim.flows,trim.seqs,unifrac.unweighted,unifrac.weighted,unique.seqs,venn.


Why isn't chimera.vsearch listed as a "valid command"? Am I missing something? I am following the tutorial word-for-word with the data provided in the tutorial.

dwaite
Posts: 252
Joined: Tue Sep 13, 2011 3:54 am

Re: Chimera.vsearch command not valid?

Post by dwaite » Sun Jul 16, 2017 3:05 am

Which version of mothur are you using? Chimera.vsearch was only added in 1.38.0 (1.39.0 for Windows) so an older version of mothur is the most likely reason it's not in the list of valid commands.

Post Reply

Who is online

Users browsing this forum: No registered users and 1 guest