{"id":399,"date":"2022-04-13T16:01:16","date_gmt":"2022-04-13T08:01:16","guid":{"rendered":"https:\/\/linguopeng.top\/?p=399"},"modified":"2022-04-13T16:12:17","modified_gmt":"2022-04-13T08:12:17","slug":"pgap","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=399","title":{"rendered":"pgap"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">seq_dir=\/home\/data\/ssy051\/container\/pgap\/input # PGAP-formatted input files<br>out_dir=\/home\/data\/ssy051\/container\/pgap\/output # Output directory (should exist)<br>strains=AHWH11M1+AHWH13M7+AHWH9M5+BJCY3M3+BJSJS1M2+C57BLSB16+CCFM1025+FAHWH21M7+FBJCP1M6+FBJCP2M1+FBJHD5M2+FCQNA20M1+FFJFZ2M5+FFJND11M5+FFJND13M6+FFJND14_L2+FFJND26M5+FFJND6M1+FFJND7M7+FFJXM1M3+FFJXM2M1+FGZ18I1M1+FGZ18I1M6+FGZ18I2M1+FGZ19I1M4+FGZ19I1M6+FGZ19I2M1+FGZ23I1M6+FGZ23I2M1+FGZ35I1M1+FGZ35I2M1+FGZ39I2M1+FGZ39MM6+FGZ3I1M6+FGZ3I2M1+FGZ6I2M1+FGZ9I2M1+FHLJDQ3M5+FHNFQ22M5+FHNFQ23M3+FHNFQ49M1+FHNFQ4M7+FHNXY43M2+FHNXY48M6+FHuNMY8M2+FJND12M6+FJND2M11+FJSSZ5M9+FJSSZ6M10+FJSSZ8M2+FJSWX19M3+FJSWX22M4+FJSWX24M2+FJSWX28M1+FJSWX30M2+FJSWX38M7+FJSWX4M9+FJSWX5M4+FJSWX7M1+FJSZJ1M5+FJSZJ2M2+FNMHLBE8M6+FNMHLBE9M6+FNXHL2M2+FNXHL8M4+FQHXN5M2+FSHMX2M1+FSHXXA1M1+FWX346+FXJCJ32M7+FZJJH10M6+FZJJH9M2+GuXi201667+HeNJZ1M1+HeNJZ2M1+HeNJZ9M1+HNXY26M4+HNXY47M8+HuNan2016415+HuNan2016497+HuNCS1M5+HuNCS3M4+HuNCS6M1+JSSZ7M1+JSWX17M1+JSWX21M5+JSWX23M8+JSWX25M8+JSWX26M5+JSWX39M4+M207F01M63+NMGCF1M12+NMGEL2M1+R2_CDS+SHMX3M1+SXR13+XJCJ1041+XJCJ653+XJCJ951+ZJHZ13M2+ZJHZ24M9+ZJHZ3M2+ZJHZ7M2+ZJHZD20M12<br>nohup docker run &#8211;name=pgap &#8211;restart=always \\<br>-v &#8220;${seq_dir}&#8221;:\/input \\<br>-v &#8220;${out_dir}&#8221;:\/output \\<br>-w \/pgap kastman\/pgap:1.12 \\<br>perl .\/PGAP.pl &#8211;strains $strains \\<br>&#8211;input \/input &#8211;output \/output \\<br>&#8211;cluster -pangenome -method GF &#8211;thread 45 &#8211;bootstrap 500 &amp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>seq_dir=\/home\/data\/ssy051\/container\/pgap\/input # PGAP-f [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-399","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/399","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=399"}],"version-history":[{"count":3,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/399\/revisions"}],"predecessor-version":[{"id":404,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/399\/revisions\/404"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=399"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=399"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=399"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}