{"action":"created","issue":{"url":"https://api.github.com/repos/torognes/swarm/issues/57","labels_url":"https://api.github.com/repos/torognes/swarm/issues/57/labels{/name}","comments_url":"https://api.github.com/repos/torognes/swarm/issues/57/comments","events_url":"https://api.github.com/repos/torognes/swarm/issues/57/events","html_url":"https://github.com/torognes/swarm/issues/57","id":86887221,"number":57,"title":"Sequence identifiers format,  abundace annotation not found error","user":{"login":"jenspreem","id":11595638,"avatar_url":"https://avatars.githubusercontent.com/u/11595638?v=3","gravatar_id":"","url":"https://api.github.com/users/jenspreem","html_url":"https://github.com/jenspreem","followers_url":"https://api.github.com/users/jenspreem/followers","following_url":"https://api.github.com/users/jenspreem/following{/other_user}","gists_url":"https://api.github.com/users/jenspreem/gists{/gist_id}","starred_url":"https://api.github.com/users/jenspreem/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jenspreem/subscriptions","organizations_url":"https://api.github.com/users/jenspreem/orgs","repos_url":"https://api.github.com/users/jenspreem/repos","events_url":"https://api.github.com/users/jenspreem/events{/privacy}","received_events_url":"https://api.github.com/users/jenspreem/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-10T08:27:11Z","updated_at":"2015-06-10T13:54:11Z","closed_at":"2015-06-10T12:36:34Z","body":"From Swarm manual pdf. v1.2.19 released October 3, 2014\r\nVersion 1.2.19 fixes a problem related to abundance information when the sequence iden-\r\ntifier includes multiple underscore characters.\r\n\r\nNo-where else in manuals or -h printout is anything mentioned that input fasta should have sequence headers conforming to any standard. As I'm inputing a fasta file I will get Error: Abundance annotation not found for 106167 sequences.\r\nSo it seems that every sequence should have a header that has info on it's abundance? \r\n\r\nFrom manual:\r\nTo speed up the clustering process, strictly identical amplicons should be merged. This step is not mandatory, but it is an important time saver, especially for highly redundant high-throughput sequencing results. \r\n\r\n Swarm can perform a dereplication for you (with options -d 0 -w), or you can use standard command line tools:\r\n\r\nSo will the dereplication command in swarm output fasta file that will be correctly formatted with the abundance annotation? \r\nIt might be good to make a mention of the needed format of fasta files to be inputted as someone might want to do their own de-replication with some other tools or use fasta files as they are.\r\n\r\nEdit: OK, was foolish and missed the description in pdf. If amplicon identifiers end with\r\na \"_\" followed by a positive integer, that value is used as the amplicon copy number in the statistics outputfile .\r\nCan close the issue.\r\n"},"comment":{"url":"https://api.github.com/repos/torognes/swarm/issues/comments/110762729","html_url":"https://github.com/torognes/swarm/issues/57#issuecomment-110762729","issue_url":"https://api.github.com/repos/torognes/swarm/issues/57","id":110762729,"user":{"login":"frederic-mahe","id":2270759,"avatar_url":"https://avatars.githubusercontent.com/u/2270759?v=3","gravatar_id":"","url":"https://api.github.com/users/frederic-mahe","html_url":"https://github.com/frederic-mahe","followers_url":"https://api.github.com/users/frederic-mahe/followers","following_url":"https://api.github.com/users/frederic-mahe/following{/other_user}","gists_url":"https://api.github.com/users/frederic-mahe/gists{/gist_id}","starred_url":"https://api.github.com/users/frederic-mahe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/frederic-mahe/subscriptions","organizations_url":"https://api.github.com/users/frederic-mahe/orgs","repos_url":"https://api.github.com/users/frederic-mahe/repos","events_url":"https://api.github.com/users/frederic-mahe/events{/privacy}","received_events_url":"https://api.github.com/users/frederic-mahe/received_events","type":"User","site_admin":false},"created_at":"2015-06-10T13:54:11Z","updated_at":"2015-06-10T13:54:11Z","body":"Hi @jenspreem. It also works with `;size=` as a sequenceID and abundance value separator (when using the `-z` option)."}}