# Chimera.vsearch command Error **URL:** \ **Category:** Commands in mothur\ **Created:** [October 9, 2017, 2:57pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416 "2017-10-09T14:57:11Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Kasun\_Bodawatta](https://avatars.discourse-cdn.com/v4/letter/k/c68b51/32.png) [@Kasun\_Bodawatta](https://forum.mothur.org/u/Kasun_Bodawatta)\ **Post date:** [October 9, 2017, 2:57pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/1 "2017-10-09T14:57:11Z")
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, ---
**Author:** ![chloelulu1005](https://avatars.discourse-cdn.com/v4/letter/c/bc8723/32.png) [@chloelulu1005](https://forum.mothur.org/u/chloelulu1005)\ **Post date:** [October 10, 2017, 2:16pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/2 "2017-10-10T14:16:44Z")
Hi, are you using the latest version of mothur? I think the latest version will not have this problem. ---
**Author:** ![Kasun\_Bodawatta](https://avatars.discourse-cdn.com/v4/letter/k/c68b51/32.png) [@Kasun\_Bodawatta](https://forum.mothur.org/u/Kasun_Bodawatta)\ **Post date:** [October 10, 2017, 2:19pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/3 "2017-10-10T14:19:54Z")
I am using the 1.39.5 version. Is that the latest version? Also can I use chimera.uchime command instead of chimera.vesearch command? Will this make a big difference in my data? ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [October 12, 2017, 12:23pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/4 "2017-10-12T12:23:56Z")
It should give the same/similar results. But there shouldn’t be a problem with 1.39.5 - we’ll double check on that. Pat ---
**Author:** ![Kasun\_Bodawatta](https://avatars.discourse-cdn.com/v4/letter/k/c68b51/32.png) [@Kasun\_Bodawatta](https://forum.mothur.org/u/Kasun_Bodawatta)\ **Post date:** [October 13, 2017, 8:48am UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/5 "2017-10-13T08:48:46Z")
Thank you very much! Best, Kasun ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [October 16, 2017, 2:01pm UTC](https://forum.mothur.org/t/chimera-vsearch-command-error/3416/6 "2017-10-16T14:01:41Z")
From the output of the command I suspect you may be accidentally using an older version of mothur. Could you have an older version of mothur in your path? I have a local copy of 1.39.5, but if I run mothur without giving the path the OS will use the version of mothur in my path. 1.39.5 sarahwestcott$ which mothur /Users/sarahwestcott/Desktop/mothur/TARGET\_BUILD\_DIRTARGET\_BUILD\_DIR/mothur \* Gives version information for local copy of mothur 1.39.5 sarahwestcott$ ./mothur --version Mac 64Bit Version Mothur version=1.39.5 Release Date=3/20/2017 \* Gives version information for mothur found in path, in my case this is a pre release version 1.39.5 sarahwestcott$ mothur --version Mac 64Bit Version Mothur version=1.40.0 Release Date=11/20/2017