Invalid Command

Hey all,

Working through the MiSeq SOP on a Linux OS. From a terminal window I am unable to execute the make.contigs command (invalid command); however, from the GUI, the command executes just fine. Anyone else have a similar experience?

Many thanks,

Can you post the exact command you are running? I suspect you have an extra space, missing a parenthesis, or some other minor typo.

Hi - please see below.

mothur > make.contigs(file=stability.files, processors=2)

Invalid command.
Valid commands are: align.check,align.seqs,amova,anosim,bin.seqs,bootstrap.shared,catchall,chimera.bellerophon,chimera.ccode,chimera.check,chimera.perseus,chimera.pintail,chimera.slayer,chimera.uchime,chop.seqs,classify.otu,classify.seqs,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,degap.seqs,deunique.seqs,deunique.tree,dist.seqs,dist.shared,,filter.seqs,get.commandinfo,get.current,,get.groups,get.label,get.lineage,get.otulist,get.oturep,get.otus,get.rabund,get.relabund,get.sabund,get.seqs,get.sharedseqs,hcluster,heatmap.bin,heatmap.sim,help,homova,indicator,libshuff,list.seqs,make.fastq,,make.shared,mantel,merge.files,merge.groups,metastats,mgcluster,nmds,normalize.shared,otu.association,otu.hierarchy,pairwise.seqs,parse.list,parsimony,pca,pcoa,phylo.diversity,phylotype,pipeline.pds,pre.cluster,quit,rarefaction.shared,rarefaction.single,read.dist,read.otu,read.tree,remove.groups,remove.lineage,remove.otus,remove.rare,remove.seqs,reverse.seqs,screen.seqs,sens.spec,seq.error,set.current,set.dir,set.logfile,sffinfo,shhh.flows,shhh.seqs,sort.seqs,split.abund,split.groups,sub.sample,summary.qual,summary.seqs,summary.shared,summary.single,,system,tree.shared,trim.flows,trim.seqs,unifrac.unweighted,unifrac.weighted,unique.seqs,venn,

What version are you running? If you open the log file mothur created from this run you will be able to see the version. Could you have an older version of mothur in your path?

Hi westcott

I have same problem. My mothur version is 1.33 and I never install other old version in my computer.
I try to find out “make.contigs” in valid commands, but it’s not in the commands list.

how can I do? thx!

Can you provide us with the actual command syntax you are entering and the exact error message you get back?

Hi pschloss

my command and results is:

mothur > make.contigs(file=stability.files, 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…

and I copy the valid commands list and try to find out “make.contigs”, but I can’t find it.


You’ve got to be using an older version of mothur. If you open the log file and look at the top lines, what version does it say?


I want to analyze 16S Ion Torrent PGM data and I can’t seem to get pass the trim.flows command because of the error “Invalid Command”. The command I’m using is:

trim.flows (flow=March 1.flow, oligos=March.oligos, pdiffs=1, bdiffs=1, order=I, processors=2) and my oligos file looks like this:

barcode CCTGCCATTCGC March Site 1

Any assistance will be greatly appreciated.

Thank you.

When you enter the command, do you have a space between trim.flows and the ( like you do here? Get rid of that space.

I had the same problem as described above (invalid command).
However, I then found out that I did additionally have a much older version of Mothur installed within Qiime, and that I was running Mothur from there…
Once I deleted that one everything went back to normal. I hope this helps.

Deleting QIIME will certainly take care of a lot of other problems too. :slight_smile: