Chelsea: /* Version */

2024-05-13T18:19:31Z

Version

Keeko at 14:30, 24 February 2022

2022-02-24T14:30:38Z

← Older revision		Revision as of 10:30, 24 February 2022
Line 23:		Line 23:
	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

	The ~~last~~ version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0		The latest version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0

	To use this version, please load the module with		To use this version, please load the module with
Line 43:		Line 43:
	</pre>		</pre>

	~~The~~ following is an example submission script ~~using~~ the above Mother command file.		he following is an example job submission script (sub.sh) running the above Mother command file:

	<pre class="gscript">		<pre class="gscript">
Line 60:		Line 60:

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
	module load ~~mothur~~		module load Mothur/1.47.0-GCCcore-8.3.0"
	mothur Mother_Commandfile.txt		mothur Mother_Commandfile.txt

Keeko: /* Running Program */

2022-02-23T20:54:25Z

Running Program

← Older revision		Revision as of 16:54, 23 February 2022
Line 63:		Line 63:
	mothur Mother_Commandfile.txt		mothur Mother_Commandfile.txt

	</pre>		</pre>

	~~In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.~~

	Here is an example of job submission command:		Here is an example of job submission command:

Keeko: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.43.0,1.45.2,1.47.0 ===..."

2022-02-23T20:42:00Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.43.0,1.45.2,1.47.0 ===..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
1.43.0,1.45.2,1.47.0

=== Author / Distributor ===
Please see [https://mothur.org/wiki/ Mothur]

=== Description ===
"Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. The functionality of different software including dotur, sons, treeclimber, s-libshuff, unifrac, and others have been incorperated in Mothur. In addition to improving the flexibility of these software, a number of other features including calculators and visualization tools are available with Mothur."
More details, documentation and tutorials are at the[https://mothur.org/wiki/ Mothur Wiki]

=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

The last version of this application is at /apps/eb/Mothur/1.47.0-GCCcore-8.3.0

To use this version, please load the module with
<pre class="gscript">
ml Mothur/1.47.0-GCCcore-8.3.0
</pre>
To run mother in "batch mode", collect your Mothur commands into a command file and use that file in a batch job. More information about creating Mothur batch files can be found here: https://mothur.org/wiki/batch_mode/
Some Mothur commands can use multiple cores. To use multiple cores, adjust the processors parameter for each command in the Mothur command file. You must also adjust the --cpus_per_task parameter in your submission script to be equal to the number of processors you request in your Mothur command file.

The following is an example of a Mothur command file requesting use of 8 cpus.This file is called Mother_Commandfile.txt, and assembles pair end reads and prepares them for analysis.

<pre class="gscript">
make.file(inputdir=./MiSeq_SOP, type=gz, prefix=stability)
make.contigs(file=current, processors=8)
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs()
count.seqs(name=current, group=current)
align.seqs(fasta=current, reference=silva.v4.fasta)
</pre>

The following is an example submission script using the above Mother command file.

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=Mothurtest # Job name
#SBATCH --partition=batch # Partition (queue) name
#SBATCH --ntasks=1 # Run on a single CPU
#SBATCH --cpus-per-task=8 # Use 8 cpus
#SBATCH --mem=10gb # Job memory request
#SBATCH --time=02:00:00 # Time limit hrs:min:sec
#SBATCH --output=%x_%j.out # Standard output log
#SBATCH --error=%x_%j.err # Standard error log

#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu # Where to send mail

cd $SLURM_SUBMIT_DIR
module load mothur
mothur Mother_Commandfile.txt

</pre>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml Mothur/1.47.0-GCCcore-8.3.0
mothur --help
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
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://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Script Mode

mothur > help()

NOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.

Clustering commmands include: cluster, cluster.classic, cluster.fit, cluster.split, mgcluster, phylotype

General commmands include: get.current, get.dists, make.biom, make.file, make.group, make.lefse, merge.count, merge.files, merge.groups, remove.dists, rename.file, set.current, set.dir, set.logfile, set.seed, system

Hypothesis Testing commmands include: amova, anosim, clearcut, cooccurrence, corr.axes, deunique.tree, homova, indicator, kruskal.wallis, libshuff, mantel, nmds, otu.association, parsimony, pca, pcoa, phylo.diversity, unifrac.unweighted, unifrac.weighted

OTU-Based Approaches commmands include: biom.info, classify.svm, collect.shared, collect.single, create.database, dist.shared, estimator.single, filter.shared, get.communitytype, get.coremicrobiome, get.group, get.groups, get.label, get.otus, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.sharedseqs, heatmap.bin, heatmap.sim, lefse, list.otus, list.otus, make.clr, make.shared, merge.otus, metastats, normalize.shared, otu.hierarchy, primer.design, rarefaction.shared, rarefaction.single, remove.groups, remove.otus, remove.otus, remove.rare, sens.spec, sparcc, split.abund, summary.shared, summary.single, tree.shared, venn

Phylotype Analysis commmands include: classify.otu, classify.seqs, classify.tree, get.lineage, merge.taxsummary, remove.lineage, summary.tax

Sequence Processing commmands include: align.check, align.seqs, bin.seqs, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, cluster.fragments, consensus.seqs, count.groups, count.seqs, degap.seqs, deunique.seqs, dist.seqs, fastq.info, filter.seqs, get.mimarkspackage, get.seqs, list.seqs, make.contigs, make.fastq, make.lookup, make.sra, count.seqs, merge.sfffiles, pairwise.seqs, pcr.seqs, pre.cluster, remove.seqs, rename.seqs, reverse.seqs, screen.seqs, seq.error, sff.multiple, sff.info, shhh.flows, shhh.seqs, sort.seqs, split.groups, sra.info, sub.sample, summary.qual, summary.seqs, trim.flows, trim.seqs, unique.seqs

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

Common Questions:

1. How do I cite mothur?
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.

2. Do you have an example analysis?
Yes, https://mothur.org/wiki/454_SOP and https://mothur.org/wiki/MiSeq_SOP highlight some of the things you can do with mothur.

3. Do you offer workshops?
Yes! Please see our https://mothur.org/wiki/Workshops page for more information.

4. What are mothur's file types?
Mothur uses and creates many file types. Including fasta, name, group, design, count, list, rabund, sabund, shared, relabund, oligos, taxonomy, constaxonomy, phylip, column, flow, qfile, file, biom and tree. You can find out more about these formats here: https://www.mothur.org/wiki/File_Types.

5. Is there a list of all of mothur's commands?
Yes! You can find it here, http://www.mothur.org/wiki/Category:Commands.

6. Why does the cutoff change when I cluster with average neighbor?
This is a product of using the average neighbor algorithm with a sparse distance matrix. When you run cluster, the algorithm looks for pairs of sequences to merge in the rows and columns that are getting merged together. Let's say you set the cutoff to 0.05. If one cell has a distance of 0.03 and the cell it is getting merged with has a distance above 0.05 then the cutoff is reset to 0.03, because it's not possible to merge at a higher level and keep all the data. All of the sequences are still there from multiple phyla. Incidentally, although we always see this, it is a bigger problem for people that include sequences that do not fully overlap.

</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/mothur/mothur Mothur github]

=== System ===
64-bit Linux

Mothur-Sapelo2 - Revision history

Chelsea: /* Version */

Keeko at 14:30, 24 February 2022

Keeko: /* Running Program */

Keeko: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.43.0,1.45.2,1.47.0 ===..."