{"id":4060,"date":"2019-09-26T14:24:56","date_gmt":"2019-09-26T13:24:56","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4060"},"modified":"2019-09-26T15:11:22","modified_gmt":"2019-09-26T14:11:22","slug":"repeatmasker","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/repeatmasker\/","title":{"rendered":"RepeatMasker"},"content":{"rendered":"<h2><span id=\"Overview\">Overview<\/span><\/h2>\n<p>RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.<\/p>\n<p>Version 4.0.9 (patch 2) is available on the CSF3.<\/p>\n<h2><span id=\"Restrictions_on_use\">Restrictions on use<\/span><\/h2>\n<p>This software is opensource.<\/p>\n<h2><span id=\"Set_up_procedure\">Set up procedure<\/span><\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<p><code>module load apps\/gcc\/repeatmasker\/4.0.9.p2<\/code><\/p>\n<h2><span id=\"Running_the_application\">Running the application<\/span><\/h2>\n<p>Please do not run RepeatMasker on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3><span id=\"Parallel_batch_job_submission\">Parallel batch job submission<\/span><\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre><span class=\"shebang\">#!\/bin\/bash<\/span>\r\n<span class=\"sge\">#$ -S \/bin\/bash<\/span>\r\n<span class=\"sge\">#$ -V<\/span>\r\n<span class=\"sge\">#$ -cwd<\/span>\r\n<span class=\"sge\">#$ -pe smp.pe 4<\/span>\r\n\r\nRepeatMasker -pa $[NSLOTS \/ 2] sample.fas\r\n<\/pre>\n<p><strong>Important notes:<\/strong><\/p>\n<ul>\n<li>By default, RepeatMasker will start 2 threads for every CPU in the node resulting in <b>badly overloaded nodes<\/b> which will cause your jobs and those of others running on the same node to run inefficiently. Users must prevent this behavior by setting <tt>-pa N<\/tt> where <tt>N<\/tt> is equal to the number of allocated CPUs divided by 2. <\/li>\n<li>In <tt>-pa N<\/tt>, &#8220;<tt>N<\/tt>&#8221; must always be greater than or equal to 2; <tt>-pa 1<\/tt> causes RepeatMasker to run as though the <tt>-pa<\/tt> option was not specified and to start 2 threads for each CPU.<\/li>\n<li>In the above example we use <code>$[NSLOTS \/ 2]<\/code> which automatically take the number specified on the smp.pe line and divides it by two.<\/li>\n<\/ul>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2><span id=\"Further_info\">Further info<\/span><\/h2>\n<p><a href=\"http:\/\/repeatmasker.org\/\">repeatmasker.org<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Version 4.0.9 (patch 2) is available on the CSF3. Restrictions on use This software is opensource. Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/repeatmasker\/4.0.9.p2 Running the application Please do not run RepeatMasker on the login node. Jobs should be submitted to the compute nodes via batch. Parallel batch job submission.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/repeatmasker\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":12,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4060","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4060","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4060"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4060\/revisions"}],"predecessor-version":[{"id":4070,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4060\/revisions\/4070"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4060"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}