{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/31","repository_url":"https://api.github.com/repos/CGATOxford/UMI-tools","labels_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/31/comments","events_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/31/events","html_url":"https://github.com/CGATOxford/UMI-tools/issues/31","id":156548667,"number":31,"title":"dedup dir-adjacency too slow/does not complete","user":{"login":"royfrancis","id":5083500,"avatar_url":"https://avatars.githubusercontent.com/u/5083500?v=3","gravatar_id":"","url":"https://api.github.com/users/royfrancis","html_url":"https://github.com/royfrancis","followers_url":"https://api.github.com/users/royfrancis/followers","following_url":"https://api.github.com/users/royfrancis/following{/other_user}","gists_url":"https://api.github.com/users/royfrancis/gists{/gist_id}","starred_url":"https://api.github.com/users/royfrancis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/royfrancis/subscriptions","organizations_url":"https://api.github.com/users/royfrancis/orgs","repos_url":"https://api.github.com/users/royfrancis/repos","events_url":"https://api.github.com/users/royfrancis/events{/privacy}","received_events_url":"https://api.github.com/users/royfrancis/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":22,"created_at":"2016-05-24T16:12:47Z","updated_at":"2016-06-02T11:52:05Z","closed_at":null,"body":"I started with a 12gb BAM (77 mil reads) using 3 cores and 24GB RAM. It did not complete in 2.5 hours or even close. Output BAM after 2.5 hours was 2.3MB. Then I extracted one chromosome to create a 314MB BAM. Dedup was run on this small BAM for 1 hour and it was still incomplete. A truncated BAM file of 12.4MB was exported. I ran `qualimap bamqc` on both files (1 chromosome bam before dedup and after dedup).\r\n\r\nfile      |before dedup |after dedup\r\n:--------|:------------------|:---------------\r\nreads |5,104,918       |197,280\r\ndup rate| 38.74%      | 2.27%\r\n\r\nSo, I suppose the deduplication must be working.\r\n\r\nExtrapolating from this run time, my 12gb bam would take lot more than 39 hours. Would this be an expected run time? I was wondering if I was doing something wrong or some setting/switches are not optimal. \r\n\r\nThis is my script:\r\n\r\n```\r\numi_tools dedup \\\r\n--method=\"directional-adjacency\" \\\r\n--paired \\\r\n--output-stats=\"file-dedup.stats\" \\\r\n-v 3 \\\r\n-E \"file-dedup.error\" \\\r\n-L \"file-dedup.log\" \\\r\n-I \"file.bam\" \\\r\n-S \"file-dedup.bam\"\r\n```"},"comment":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/comments/223269314","html_url":"https://github.com/CGATOxford/UMI-tools/issues/31#issuecomment-223269314","issue_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/31","id":223269314,"user":{"login":"royfrancis","id":5083500,"avatar_url":"https://avatars.githubusercontent.com/u/5083500?v=3","gravatar_id":"","url":"https://api.github.com/users/royfrancis","html_url":"https://github.com/royfrancis","followers_url":"https://api.github.com/users/royfrancis/followers","following_url":"https://api.github.com/users/royfrancis/following{/other_user}","gists_url":"https://api.github.com/users/royfrancis/gists{/gist_id}","starred_url":"https://api.github.com/users/royfrancis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/royfrancis/subscriptions","organizations_url":"https://api.github.com/users/royfrancis/orgs","repos_url":"https://api.github.com/users/royfrancis/repos","events_url":"https://api.github.com/users/royfrancis/events{/privacy}","received_events_url":"https://api.github.com/users/royfrancis/received_events","type":"User","site_admin":false},"created_at":"2016-06-02T11:52:05Z","updated_at":"2016-06-02T11:52:05Z","body":"I ran my full bam yesterday for 18 hours and it still failed. Is there some way to output the progress, so as to estimate how much of the bam file was completed? "}}
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