Hi,
I’m currently using mothur v.1.42.0 on Linux-ubunto
Sometimes I face errors because of invalid commands and then I check for the right one (for example chimera.vseach>>> chimera.uchime) and the error would be solved
My question is, is the following list is the only valid command by the latest mothur version (as stated by mothur when encountering an error):
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.file,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,set.seed,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,
because the Miseq SOP, mothur command list on mothur wiki page and mothur manual have so many many commands other than those listed above.
Thanks a lot!