{"action":"created","issue":{"url":"https://api.github.com/repos/claczny/VizBin/issues/31","labels_url":"https://api.github.com/repos/claczny/VizBin/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/claczny/VizBin/issues/31/comments","events_url":"https://api.github.com/repos/claczny/VizBin/issues/31/events","html_url":"https://github.com/claczny/VizBin/issues/31","id":107922225,"number":31,"title":"where to find the log file?","user":{"login":"yoyohashao","id":7657231,"avatar_url":"https://avatars.githubusercontent.com/u/7657231?v=3","gravatar_id":"","url":"https://api.github.com/users/yoyohashao","html_url":"https://github.com/yoyohashao","followers_url":"https://api.github.com/users/yoyohashao/followers","following_url":"https://api.github.com/users/yoyohashao/following{/other_user}","gists_url":"https://api.github.com/users/yoyohashao/gists{/gist_id}","starred_url":"https://api.github.com/users/yoyohashao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yoyohashao/subscriptions","organizations_url":"https://api.github.com/users/yoyohashao/orgs","repos_url":"https://api.github.com/users/yoyohashao/repos","events_url":"https://api.github.com/users/yoyohashao/events{/privacy}","received_events_url":"https://api.github.com/users/yoyohashao/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"claczny","id":1991960,"avatar_url":"https://avatars.githubusercontent.com/u/1991960?v=3","gravatar_id":"","url":"https://api.github.com/users/claczny","html_url":"https://github.com/claczny","followers_url":"https://api.github.com/users/claczny/followers","following_url":"https://api.github.com/users/claczny/following{/other_user}","gists_url":"https://api.github.com/users/claczny/gists{/gist_id}","starred_url":"https://api.github.com/users/claczny/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/claczny/subscriptions","organizations_url":"https://api.github.com/users/claczny/orgs","repos_url":"https://api.github.com/users/claczny/repos","events_url":"https://api.github.com/users/claczny/events{/privacy}","received_events_url":"https://api.github.com/users/claczny/received_events","type":"User","site_admin":false},"milestone":null,"comments":8,"created_at":"2015-09-23T13:41:58Z","updated_at":"2015-09-24T16:03:17Z","closed_at":"2015-09-24T16:03:17Z","body":"Hi I am very new to this software. I asked the question because when I tried to add the annotation, there was an error and I couldn't locate the log file in my macbook. \r\n\r\nAlso I  wanna know if I can  just label the 1st sequence in my file? I made a quite simple annotation file with only two lines : \r\nisMarker \r\n1\r\n\r\nCould this annotation file cause the error? I am not a man with lots of coding experience. So I decided to not fill the series of 0 after the 1.\r\n\r\nMany thanks"},"comment":{"url":"https://api.github.com/repos/claczny/VizBin/issues/comments/142973622","html_url":"https://github.com/claczny/VizBin/issues/31#issuecomment-142973622","issue_url":"https://api.github.com/repos/claczny/VizBin/issues/31","id":142973622,"user":{"login":"claczny","id":1991960,"avatar_url":"https://avatars.githubusercontent.com/u/1991960?v=3","gravatar_id":"","url":"https://api.github.com/users/claczny","html_url":"https://github.com/claczny","followers_url":"https://api.github.com/users/claczny/followers","following_url":"https://api.github.com/users/claczny/following{/other_user}","gists_url":"https://api.github.com/users/claczny/gists{/gist_id}","starred_url":"https://api.github.com/users/claczny/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/claczny/subscriptions","organizations_url":"https://api.github.com/users/claczny/orgs","repos_url":"https://api.github.com/users/claczny/repos","events_url":"https://api.github.com/users/claczny/events{/privacy}","received_events_url":"https://api.github.com/users/claczny/received_events","type":"User","site_admin":false},"created_at":"2015-09-24T16:03:17Z","updated_at":"2015-09-24T16:03:17Z","body":"> if I only picked sequences longer than 2000nt, I could finally got a nice figure\r\n\r\nGood to hear that. I will consider this issue closed but discussion can continue.\r\n\r\nDid you apply any size selection out of VizBin when using the labels? If so, this is something we are working on, see Issue #3.\r\nIn summary, when using annotation information, the sequence file should only contain the sequences of interest, i.e., it should already be size-selected when loading into VizBin. The annotation file *must* match the sequence file in terms of number and order of the sequences.\r\nAccordingly, please make sure that this is the case as currently *no* automated checks are integrated.\r\n\r\n> all the genomes derived from vizbin contained less than 50 of 107 essential genes\r\n\r\nIn the VizBin manuscript, we used publicly available data and, thus, had no influence on the sequencing depth, assembly, etc. \r\nYou are right that several factors can influence the quality of the reconstruction of population-level genomes from metagenomic data. \r\nYou might also want to have a look at http://www.nature.com/articles/srep04516 (the manuscript describing the methodology underlying VizBin), specifically http://www.nature.com/articles/srep04516/tables/2, to see that indeed highly complete genomes can be recovered, as well as http://www.nature.com/ncomms/2014/141126/ncomms6603/full/ncomms6603.html for more on this.\r\nThe assemblies have to be \"good\" in the first place as otherwise there is no chance of achieving a \"good\" genomic recovery, with VizBin or any other tool :)\r\n\r\nInternally, we routinely assess the completeness of clusters as we are typically interested in recovered genomes that should be as complete as possible. In particular for functional analysis and interpretation it is important to know if one has well \"sampled\" a population-level genome or not, as otherwise any interpretation might simply be based on incomplete information."}}