Windows version

Running 64Bit Version

mothur v.1.39.5
Last updated: 3/20/2017

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://www.mothur.org/forum

Type 'quit()' to exit program
Interactive Mode


mothur >
help()
For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.

mothur >
help(summary.seqs)
The summary.seqs command reads a fastafile and summarizes the sequences.
The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.
The name parameter allows you to enter a name file associated with your fasta file.
The count parameter allows you to enter a count file associated with your fasta file.
The summary.seqs command should be in the following format:
summary.seqs(fasta=yourFastaFile, processors=2)
Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.

mothur >
summary.seqs(help)
The summary.seqs command reads a fastafile and summarizes the sequences.
The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.
The name parameter allows you to enter a name file associated with your fasta file.
The count parameter allows you to enter a count file associated with your fasta file.
The summary.seqs command should be in the following format:
summary.seqs(fasta=yourFastaFile, processors=2)
Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).

mothur >
set.dir(input='test')
Mothur's directories:
inputDir=test\

mothur >
help()
inputdir=test\ is not a valid command in Mothur.  Valid commands are align.check, align.seqs, amova, anosim, bin.seqs, biom.info, catchall, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, classify.otu, classify.seqs, classify.svm, classify.tree, 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, heatmap.bin, heatmap.sim, help, homova, indicator, kruskal.wallis, lefse, libshuff, list.otulabels, list.otus, list.seqs, make.biom, make.contigs, make.fastq, make.file, make.group, make.lefse, make.lookup, make.shared, make.sra, make.table, mantel, merge.count, 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, pre.cluster, primer.design, quit, rarefaction.shared, rarefaction.single, remove.dists, remove.groups, remove.lineage, remove.otulabels, remove.otus, remove.rare, remove.seqs, rename.file, 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,
[ERROR]: inputdir=test\ is not a valid command.

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.

mothur >
help(summary.seqs)
summary.seqs, inputdir=test\ is not a valid command in Mothur.  Valid commands are align.check, align.seqs, amova, anosim, bin.seqs, biom.info, catchall, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, classify.otu, classify.seqs, classify.svm, classify.tree, 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, heatmap.bin, heatmap.sim, help, homova, indicator, kruskal.wallis, lefse, libshuff, list.otulabels, list.otus, list.seqs, make.biom, make.contigs, make.fastq, make.file, make.group, make.lefse, make.lookup, make.shared, make.sra, make.table, mantel, merge.count, 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, pre.cluster, primer.design, quit, rarefaction.shared, rarefaction.single, remove.dists, remove.groups, remove.lineage, remove.otulabels, remove.otus, remove.rare, remove.seqs, rename.file, 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,
[ERROR]: summary.seqs, inputdir=test\ is not a valid command.

For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs@gmail.com.

mothur >
summary.seqs(help)
help is not a valid parameter.
The valid parameters are: fasta, name, count, processors, seed, inputdir, and outputdir.
You have no current fastafile and the fasta parameter is required.

Using 1 processors.
[ERROR]: did not complete summary.seqs.

mothur >
quit()


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Detected 3 [ERROR] messages, please review.
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