{"id":1437,"date":"2022-02-17T16:04:29","date_gmt":"2022-02-17T16:04:29","guid":{"rendered":"https:\/\/www.aassie.net\/Pro\/?p=1437"},"modified":"2022-02-17T16:04:30","modified_gmt":"2022-02-17T16:04:30","slug":"facepalm-thursdays","status":"publish","type":"post","link":"https:\/\/www.aassie.net\/Pro\/facepalm-thursdays\/","title":{"rendered":"Facepalm Thursdays&#8230;"},"content":{"rendered":"\n<p>I was trying to build a Cazy reference database to explore the carbohydrate profiles of the genomes in our microbial laboratory collection. I have a parallel script downloading the proteins sequences from NCBI then aligning and creating a hmm profile for later use. <\/p>\n\n\n\n<p>This morning I am looking through the process that ran overnight and spotted some alignment that didn&#8217;t work. Trying to reproduce the error:<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-large\"><a href=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM.png\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"504\" src=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM-1024x504.png\" alt=\"\" class=\"wp-image-1438\" srcset=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM-1024x504.png 1024w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM-300x148.png 300w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM-768x378.png 768w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.44-AM.png 1086w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/><\/a><figcaption>An offending O appears to be in my alignment&#8230;<\/figcaption><\/figure><\/div>\n\n\n\n<p>Ok let&#8217;s have a look at sequence 3205 in our fasta file<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-full\"><a href=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.22-AM.png\"><img loading=\"lazy\" decoding=\"async\" width=\"1006\" height=\"338\" src=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.22-AM.png\" alt=\"\" class=\"wp-image-1439\" srcset=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.22-AM.png 1006w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.22-AM-300x101.png 300w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.22-AM-768x258.png 768w\" sizes=\"(max-width: 1006px) 100vw, 1006px\" \/><\/a><figcaption>Common now, another error? What&#8217;s that&#8230;<\/figcaption><\/figure><\/div>\n\n\n\n<p>Trying to figure out what was happening there for a good 15 minutes until suddenly&#8230;<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-full\"><a href=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.29-AM.png\"><img loading=\"lazy\" decoding=\"async\" width=\"694\" height=\"66\" src=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.29-AM.png\" alt=\"\" class=\"wp-image-1440\" srcset=\"https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.29-AM.png 694w, https:\/\/www.aassie.net\/Pro\/wp-content\/uploads\/2022\/02\/Screen-Shot-2022-02-17-at-9.50.29-AM-300x29.png 300w\" sizes=\"(max-width: 694px) 100vw, 694px\" \/><\/a><figcaption>:facepalm:<\/figcaption><\/figure><\/div>\n\n\n\n<p>Turns out the NCBI download fail a couple of times during the night and just added the error message to the fasta file&#8230;<\/p>\n\n\n\n<p>Oh well&#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I was trying to build a Cazy reference database to explore the carbohydrate profiles of the genomes in our microbial laboratory collection. I have a parallel script downloading the proteins sequences from NCBI then aligning and creating a hmm profile for later use. This morning I am looking through the&#8230;<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,58],"tags":[105,103,102,104],"_links":{"self":[{"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/posts\/1437"}],"collection":[{"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/comments?post=1437"}],"version-history":[{"count":1,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/posts\/1437\/revisions"}],"predecessor-version":[{"id":1441,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/posts\/1437\/revisions\/1441"}],"wp:attachment":[{"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/media?parent=1437"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/categories?post=1437"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.aassie.net\/Pro\/wp-json\/wp\/v2\/tags?post=1437"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}