Hi,
My name is Kasun Bodawatta and I am a masters student at the University of Copenhagen. Currently, I am working with digestive tract gut microbial communities of birds and cockroaches and I am currently trying to analyze my MiSeq data using Mothur. However, I cannot run the chimera.vsearch command and I kept getting an error saying I have been using inaccurate input files. I checked multiple times and my command looks exactly like the one that is suggested in mothur tutorial. Are there substitute commands that I can work with? and how can I face this problem? I am attaching the command that I insert and the error message below. Looking forward to hear back from you. Any help would be greatly appreciated.
Best,
Kasun
This is the command and the error:
mothur > chimera.vsearch(fasta=stability_map_birdstrim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability_map_birdstrim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t, processors=8)
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.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,