EMIRGE<\/a> is a program to reconstruct full length ribosomal genes from short read sequencing data. In the process, it also provides estimates of the sequences’ abundances.<\/p>\n Version 0.61.1 is installed on the CSF. This will use python 2.7 provided by Anaconda Python 2.5.0.<\/p>\n EMIRGE will use the There are no restrictions on accessing the software on the CSF. It is released under the GPL v3 license and all usage should fall within that license<\/a>.<\/p>\n Please cite your usage of this software in your research by citing the references listed in the EMIRGE github page<\/a>.<\/p>\n To access the software you must first load one<\/em> of the You may run the following command on the login node to check the flags\/switches that the application requires:<\/p>\n The following executables are available (which all accept the You must<\/em> run the application via a batch script when processing data.<\/p>\n Please do not run emirge on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview EMIRGE is a program to reconstruct full length ribosomal genes from short read sequencing data. In the process, it also provides estimates of the sequences’ abundances. Version 0.61.1 is installed on the CSF. This will use python 2.7 provided by Anaconda Python 2.5.0. EMIRGE will use the usearch application installed on the CSF. Please follow the link to the CSF usearch page to see how to obtain access to this restricted application. Restrictions on.. Read more »<\/a><\/p>\n","protected":false},"author":15,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4678","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4678","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4678"}],"version-history":[{"count":4,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4678\/revisions"}],"predecessor-version":[{"id":4683,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4678\/revisions\/4683"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=4678"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}usearch<\/code> application installed on the CSF. Please follow the link to the CSF usearch page<\/a> to see how to obtain access to this restricted application.<\/p>\nRestrictions on use<\/h2>\n
Set up procedure<\/h2>\n
usearch<\/code> modulefiles and then the emirge modulefile:<\/p>\n\r\n# If using emirge.py or emirge_amplicon.py load one<\/strong> of the usearch modulefiles first:\r\nmodule load apps\/binapps\/usearch\/6.1.544\r\nmodule load apps\/binapps\/usearch\/8.0.1623\r\n\r\n# If using emirge_makedb.py load the vsearch and bowtie modulefiles first:\r\nmodule load apps\/binapps\/vsearch\/1.1.3\r\nmodule load apps\/binapps\/bowtie\/0.12.9\r\n\r\n# Then load the emirge modulefile\r\nmodule load apps\/gcc\/python-packages\/anaconda-2.5.0\/emirge\/0.61.1\r\n<\/pre>\n
\r\nemirge.py --help\r\n<\/pre>\n
--help<\/code> flag):<\/p>\n\r\nemirge_amplicon.py\r\nemirge_makedb.py\r\nemirge.py\r\nemirge_rename_fasta.py\r\n<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n\r\n# $NSLOTS will be set to 1 (for 1 core) in a serial job\r\nemirge.py -a $NSLOTS args...<\/em>\r\nemirge_amplicon.py -a $NSLOTS args...<\/em>\r\nemirge_makedb.py -p $NSLOTS args...<\/em> # Note -p flag (not -a)\r\nemirge_rename_fasta.py args...<\/em> # This is a serial app\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd # Job will run from the current directory\r\n#$ -V # Job will inherit current environment settings\r\n#$ -pe smp.pe 8 # Number of cores (2-24 permitted)\r\n\r\n# $NSLOTS will be set to the number of cores given on the -pe line above:\r\nemirge.py -a $NSLOTS args...<\/em>\r\nemirge_amplicon.py -a $NSLOTS args...<\/em>\r\nemirge_makedb.py -p $NSLOTS args...<\/em> # Note -p flag (not -a)\r\nemirge_rename_fasta.py args...<\/em> # This is a serial app\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
\n
Updates<\/h2>\n