{"id":267,"date":"2013-10-28T15:25:50","date_gmt":"2013-10-28T15:25:50","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=267"},"modified":"2013-10-28T15:35:48","modified_gmt":"2013-10-28T15:35:48","slug":"hpc-lampredi-software-update-polymutt-0-15","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/igmit\/?p=267","title":{"rendered":"HPC \u2013 Lampredi \u2013 software update \u2013 Polymutt 0.15"},"content":{"rendered":"<p>Polymutt 0.15 has been added to lampredi2. Details are:<\/p>\n<p><code>$ module load apps\/polymutt<br \/>\napps\/polymutt\/0.15\/gcc-4.4.6<br \/>\n | -- libs\/gcc\/system<br \/>\n |    * --&gt; OK<br \/>\n |<br \/>\n OK<\/p>\n<p>$ ls -l $POLYMUTTDIR<br \/>\ntotal 12<br \/>\ndrwxr-xr-x 2 root root 4096 Oct 28 14:47 bin<br \/>\ndrwxr-xr-x 2 root root 4096 Oct 28 14:47 doc<br \/>\ndrwxr-xr-x 2 root root 4096 Oct 28 14:47 example<\/p>\n<p>$ polymutt --help<\/p>\n<p>The following parameters are in effect:<br \/>\n                       pedfile :                 (-pname)<br \/>\n                       datfile :                 (-dname)<br \/>\n                  glfIndexFile :                 (-gname)<br \/>\n              posterior cutoff :            0.50 (-c99.999)<\/p>\n<p>Additional Options<br \/>\n   Alternative input file : --in_vcf [], --mixed_vcf_records<br \/>\n     Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]<br \/>\n     Prior of ts\/tv ratio : --poly_tstv [2.00]<br \/>\n      Non-autosome labels : --chrX [X], --chrY [Y], --MT [MT]<br \/>\n         de novo mutation : --denovo, --rate_denovo [1.5e-08],<br \/>\n[snip]<\/p>\n<p>[...@node06(lampredi) ~]$ $POLYMUTTEXAMPLE\/run.sh<\/p>\n<p>The following parameters are in effect:<br \/>\n                       pedfile :        test.ped (-pname)<br \/>\n                       datfile :        test.dat (-dname)<br \/>\n                  glfIndexFile :        test.gif (-gname)<br \/>\n              posterior cutoff :            0.90 (-c99.999)<br \/>\n[snip]<br \/>\nAnalysis started on Mon Oct 28 14:58:35 2013<\/p>\n<p>Summary of reference -- 1<br \/>\nTotal Entry Count:     81016<br \/>\nTotal Base Cout:     81016<br \/>\nNon-Polymorphic Count:     72880<br \/>\nTransition Count:      5373<br \/>\nTransversion Count:      2763<br \/>\nOther Polymorphism Count:         0<br \/>\nFilter counts:<br \/>\n\tminMapQual 0<br \/>\n\tminTotalDepth 0<br \/>\n\tmaxTotalDepth 0<br \/>\nHard to call:         0<br \/>\nSkipped bases: 0<br \/>\nAnalysis ended on Mon Oct 28 14:58:42 2013<\/p>\n<p>Running time is 7 seconds<br \/>\n[snip]<\/p>\n<p><\/code><\/p>\n<p>\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n<p><code>$ module whatis apps\/polymutt<br \/>\napps\/polymutt        : <\/p>\n<p>            Title: Polymutt<br \/>\n          Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data<br \/>\n          License: NONFREE - modification granted; distribution of modifications prohibited<br \/>\n            Group: Bioinformatics<br \/>\n              URL: http:\/\/genome.sph.umich.edu\/wiki\/Polymutt<\/p>\n<p>             Name: polymutt<br \/>\n          Version: 0.15<br \/>\n           Module: apps\/polymutt\/0.15\/gcc-4.4.6<br \/>\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/polymutt\/0.15\/gcc-4.4.6<br \/>\n     Package path: \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6<\/p>\n<p>       Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@ea64008<br \/>\n          Package: apps\/polymutt\/0.15@b8b7f565<br \/>\n      Last update: 2013-10-28<\/p>\n<p>          Builder: root@headnode1.lampredi.cluster.local<br \/>\n       Build date: 2013-10-28T14:47:12<br \/>\n         Compiler: compilers\/gcc\/system<br \/>\n           System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<br \/>\n             Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)<br \/>\n     Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n<p>For further information, execute:<\/p>\n<p>\tmodule help apps\/polymutt\/0.15\/gcc-4.4.6<\/code><\/p>\n<p>\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n<p><code>$ module help apps\/polymutt\/0.15\/gcc-4.4.6<\/p>\n<p>----------- Module Specific Help for 'apps\/polymutt\/0.15\/gcc-4.4.6' ---------------------------<\/p>\n<p>                     ======== Polymutt ========<br \/>\n     Calls single nucleotide variants and detects de novo point<br \/>\n     mutation events in families for next-generation sequencing<br \/>\n                                data<br \/>\n                      =========================                      <\/p>\n<p>This module sets up your environment for the use of the 'polymutt'<br \/>\napplication. This module sets up version '0.15' of the<br \/>\napplication.<\/p>\n<p>&gt;&gt; SYNOPSIS &lt;&gt; LICENSING &lt;&gt; FURTHER INFORMATION &lt;&gt; GET STARTED &lt;&lt;<\/p>\n<p>Please refer to the website for further details on usage of this<br \/>\npackage.<\/code><\/p>\n<p>\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n<p><code>$ module show apps\/polymutt\/0.15\/gcc-4.4.6<\/p>\n<p>\/opt\/gridware\/etc\/modules\/apps\/polymutt\/0.15\/gcc-4.4.6:<\/p>\n<p>module-whatis\t <\/p>\n<p>            Title: Polymutt<br \/>\n          Summary: Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data<br \/>\n          License: NONFREE - modification granted; distribution of modifications prohibited<br \/>\n            Group: Bioinformatics<br \/>\n              URL: http:\/\/genome.sph.umich.edu\/wiki\/Polymutt<\/p>\n<p>             Name: polymutt<br \/>\n          Version: 0.15<br \/>\n           Module: apps\/polymutt\/0.15\/gcc-4.4.6<br \/>\n      Module path: \/opt\/gridware\/etc\/modules\/apps\/polymutt\/0.15\/gcc-4.4.6<br \/>\n     Package path: \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6<\/p>\n<p>       Repository: git+http:\/\/download.alces-software.com\/git\/packager-base@ea64008<br \/>\n          Package: apps\/polymutt\/0.15@b8b7f565<br \/>\n      Last update: 2013-10-28<\/p>\n<p>          Builder: root@headnode1.lampredi.cluster.local<br \/>\n       Build date: 2013-10-28T14:47:12<br \/>\n         Compiler: compilers\/gcc\/system<br \/>\n           System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64<br \/>\n             Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2x4 (b6b89932)<br \/>\n     Dependencies: libs\/gcc\/system (using: libs\/gcc\/system)<\/p>\n<p>For further information, execute:<\/p>\n<p>\tmodule help apps\/polymutt\/0.15\/gcc-4.4.6<\/p>\n<p>module-prereq\t libs\/gcc\/system<br \/>\nmodule-conflict\t apps\/polymutt<br \/>\nsetenv\t\t POLYMUTTDIR \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6<br \/>\nsetenv\t\t POLYMUTTBIN \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6\/bin<br \/>\nsetenv\t\t POLYMUTTDOC \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6\/doc<br \/>\nsetenv\t\t POLYMUTTEXAMPLE \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6\/example<br \/>\nprepend-path\t PATH \/opt\/gridware\/pkg\/apps\/polymutt\/0.15\/gcc-4.4.6\/bin <\/code><\/p>\n<p>\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014\u2014-<\/p>\n<p>Lampredi HPC<br \/>\nigm-lampredi-users@ncl.ac.uk<\/p>\n<p>IGM IT<br \/>\nigmithelp@ncl.ac.uk<br \/>\nx8625<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Polymutt 0.15 has been added to lampredi2. Details are: $ module load apps\/polymutt apps\/polymutt\/0.15\/gcc-4.4.6 | &#8212; libs\/gcc\/system | * &#8211;&gt; OK | OK $ ls -l $POLYMUTTDIR total 12 drwxr-xr-x 2 root root 4096 Oct 28 14:47 bin drwxr-xr-x 2 root root 4096 Oct 28 14:47 doc drwxr-xr-x 2 root root 4096 Oct 28 14:47 <a href='https:\/\/blogs.ncl.ac.uk\/igmit\/?p=267' class='excerpt-more'>[&#8230;]<\/a><\/p>\n","protected":false},"author":1149,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-267","post","type-post","status-publish","format-standard","hentry","category-uncategorized","category-1-id","post-seq-1","post-parity-odd","meta-position-corners","fix"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/267","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/users\/1149"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=267"}],"version-history":[{"count":4,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/267\/revisions"}],"predecessor-version":[{"id":269,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=\/wp\/v2\/posts\/267\/revisions\/269"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=267"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=267"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/igmit\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=267"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}