{"id":3851,"date":"2019-09-02T11:42:57","date_gmt":"2019-09-02T10:42:57","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=3851"},"modified":"2019-09-02T15:20:51","modified_gmt":"2019-09-02T14:20:51","slug":"mothur","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/mothur\/","title":{"rendered":"Mothur"},"content":{"rendered":"

Overview<\/h2>\n

Mothur<\/a> mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes. mothur is capable of processing data generated from several DNA sequencing methods including 454 pyrosequencing, Illumina HiSeq and MiSeq, Sanger, PacBio, and IonTorrent<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing this software.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

module load apps\/binapps\/mothur\/1.42.3\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run Mothur on the login node. Jobs should be run interactively on the backend nodes (via qrsh<\/code>) or submitted to the compute nodes via batch.<\/p>\n
Batch usage<\/h3>\n
The majority of jobs should be run in batch.
\n
\nVarious mothur commands can take advantage of multiple processors. To specify multiple processors, add the processors option to a command. Once a mothur command has had the processors option set it is persistent therefore subsequent multi-processor commands will inherit the original processor option. This applies to both single node (smp) and multi-node (mpi) multi core jobs. <\/p>\n
In batch mode you can supply a file with a list of mothur commands that you want mothur to run. For example the batch file could look like:<\/p>\n
\r\n#Create mothur input file using txt editor of your choice\r\n$ vim stability.batch\r\n\r\n#Enter the following (example usage)\r\npcr.seqs(fasta=silva.bacteria.fasta, start=11894, end=25319, keepdots=F)\r\nsystem(mv silva.bacteria.pcr.fasta silva.v4.fasta)\r\n\r\n#change the name of the file from stability.files to whatever suits your study\r\nmake.contigs(file=stability.files, processors=8)\r\nscreen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)\r\nunique.seqs()\r\ncount.seqs(name=current, group=current)\r\nalign.seqs(fasta=current, reference=silva.v4.fasta)\r\nscreen.seqs(fasta=current, count=current, start=1968, end=11550, maxhomop=8)\r\nfilter.seqs(fasta=current, vertical=T, trump=.)\r\nunique.seqs(fasta=current, count=current)\r\npre.cluster(fasta=current, count=current, diffs=2)\r\nchimera.uchime(fasta=current, count=current, dereplicate=t)\r\nremove.seqs(fasta=current, accnos=current)\r\nclassify.seqs(fasta=current, count=current, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)\r\nremove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)\r\nremove.groups(count=current, fasta=current, taxonomy=current, groups=Mock)\r\ncluster.split(fasta=current, count=current, taxonomy=current, splitmethod=classify, taxlevel=4, cutoff=0.15)\r\nmake.shared(list=current, count=current, label=0.03)\r\nclassify.otu(list=current, count=current, taxonomy=current, label=0.03)\r\nphylotype(taxonomy=current)\r\nmake.shared(list=current, count=current, label=1)\r\nclassify.otu(list=current, count=current, taxonomy=current, label=1)\r\n<\/pre>\n
Submit this job using a suitable job script. *** Please Note***<\/strong> In the above example the mothur input file (stability.batch) file requires 8 processors therefore job script must also request at least 8 processors:<\/p>\n
#!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 8      \r\n\r\n# Load any required modulefiles\r\nmodule load apps\/binapps\/mothur\/1.42.3\r\n\r\n\r\nmothur stability.batch\r\n<\/pre>\n
Submit the jobscript using<\/p>\n
\r\nqsub jobscript<\/em>\r\n<\/pre>\n
where jobscript<\/em><\/code> is the name of your jobscript file (not your mothur input file!)<\/p>\n
Interactive usage<\/h3>\n
Interactive jobs should be primarily used for debugging purposes. <\/p>\n
To schedule a multi-core interactive job run the following command on the login node:<\/p>\n
\r\nqrsh -l short -pe smp.pe 2\r\n                         #\r\n                         # Number of required cores\r\n<\/pre>\n
You will be logged in to a compute node and will have access to 2 CPU cores (in this example) and 4GB per core. You should ensure  you run use only the number of cores reserved for you.<\/p>\n
\r\n# Once logged onto a node you run mothur interactively \r\n$ module load apps\/binapps\/mothur\/1.42.3\r\n$ mothur\r\n\r\nLinux version\r\n\r\nUsing ReadLine,Boost,HDF5\r\nmothur v.1.42.3\r\nLast updated: 8\/20\/19\r\nby\r\nPatrick D. Schloss\r\n\r\nDepartment of Microbiology & Immunology\r\n\r\nUniversity of Michigan\r\nhttp:\/\/www.mothur.org\r\n\r\nWhen using, please cite:\r\nSchloss, 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.\r\n\r\nDistributed under the GNU General Public License\r\n\r\nType 'help()' for information on the commands that are available\r\n\r\nFor questions and analysis support, please visit our forum at https:\/\/forum.mothur.org\r\n\r\nType 'quit()' to exit program\r\n\r\n[NOTE]: Setting random seed to 19760620.\r\n\r\nInteractive Mode\r\n\r\n\r\n\r\nmothur > make.contigs(file=stability.files, processors=2)\r\n\r\n... omitted for clarity ...\r\n\r\nmothur > summary.seqs(fasta=stability.trim.contigs.fasta)\r\n\r\nUsing 2 processors.\r\n\r\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\r\nMinimum:\t1\t248\t248\t0\t3\t1\r\n2.5%-tile:\t1\t252\t252\t0\t3\t3810\r\n25%-tile:\t1\t252\t252\t0\t4\t38091\r\nMedian: \t1\t252\t252\t0\t4\t76181\r\n75%-tile:\t1\t253\t253\t0\t5\t114271\r\n97.5%-tile:\t1\t253\t253\t6\t6\t148552\r\nMaximum:\t1\t502\t502\t249\t243\t152360\r\nMean:\t1\t252\t252\t0\t4\r\n# of Seqs:\t152360\r\n\r\nIt took 2 secs to summarize 152360 sequences.\r\n\r\nOutput File Names:\r\nstability.trim.contigs.summary\r\n\r\n\r\nmothur > quit()\r\n<\/pre>\n
Further info<\/h2>\n