# Invalid Command
**URL:** https://forum.mothur.org/t/invalid-command/1733
**Category:** Commands in mothur
**Created:** [March 3, 2014, 11:59pm UTC](https://forum.mothur.org/t/invalid-command/1733 "2014-03-03T23:59:38Z")
**Posts on this page:** 12
**Page:** 1
### Author:  [@bhassett](https://forum.mothur.org/u/bhassett)
#### Post date: [March 3, 2014, 11:59pm UTC](https://forum.mothur.org/t/invalid-command/1733/1 "2014-03-03T23:59:38Z")
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,
b
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 4, 2014, 11:58am UTC](https://forum.mothur.org/t/invalid-command/1733/2 "2014-03-04T11:58:36Z")
Can you post the exact command you are running? I suspect you have an extra space, missing a parenthesis, or some other minor typo.
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### Author:  [@bhassett](https://forum.mothur.org/u/bhassett)
#### Post date: [March 4, 2014, 8:05pm UTC](https://forum.mothur.org/t/invalid-command/1733/3 "2014-03-04T20:05:28Z")
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,fastq.info,filter.seqs,get.commandinfo,get.current,get.group,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.group,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,summary.tax,system,tree.shared,trim.flows,trim.seqs,unifrac.unweighted,unifrac.weighted,unique.seqs,venn,
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [March 5, 2014, 12:55pm UTC](https://forum.mothur.org/t/invalid-command/1733/4 "2014-03-05T12:55:11Z")
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?
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### Author:  [@wtlien](https://forum.mothur.org/u/wtlien)
#### Post date: [July 2, 2014, 2:19pm UTC](https://forum.mothur.org/t/invalid-command/1733/5 "2014-07-02T14:19:06Z")
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!
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [July 2, 2014, 6:25pm UTC](https://forum.mothur.org/t/invalid-command/1733/6 "2014-07-02T18:25:35Z")
Can you provide us with the actual command syntax you are entering and the exact error message you get back?
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### Author:  [@wtlien](https://forum.mothur.org/u/wtlien)
#### Post date: [July 3, 2014, 1:22am UTC](https://forum.mothur.org/t/invalid-command/1733/7 "2014-07-03T01:22:58Z")
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.
thx!
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [July 9, 2014, 1:52pm UTC](https://forum.mothur.org/t/invalid-command/1733/8 "2014-07-09T13:52:40Z")
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?
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### Author:  [@tdickerson](https://forum.mothur.org/u/tdickerson)
#### Post date: [July 23, 2014, 3:58pm UTC](https://forum.mothur.org/t/invalid-command/1733/9 "2014-07-23T15:58:45Z")
Hello,
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:
forward GGMTTAGATACCCBDGTA P609D
reverse GGGTTNCGNTCGTTG 1100R
barcode CCTGCCATTCGC March Site 1
Any assistance will be greatly appreciated.
Thank you.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [July 24, 2014, 3:36pm UTC](https://forum.mothur.org/t/invalid-command/1733/10 "2014-07-24T15:36:26Z")
When you enter the command, do you have a space between trim.flows and the ( like you do here? Get rid of that space.
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### Author:  [@Eunde](https://forum.mothur.org/u/Eunde)
#### Post date: [September 15, 2014, 12:15pm UTC](https://forum.mothur.org/t/invalid-command/1733/11 "2014-09-15T12:15:00Z")
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.
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [September 15, 2014, 9:17pm UTC](https://forum.mothur.org/t/invalid-command/1733/12 "2014-09-15T21:17:40Z")
Deleting QIIME will certainly take care of a lot of other problems too. 🙂