{"action":"created","issue":{"url":"https://api.github.com/repos/jsh58/DMRfinder/issues/1","repository_url":"https://api.github.com/repos/jsh58/DMRfinder","labels_url":"https://api.github.com/repos/jsh58/DMRfinder/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/jsh58/DMRfinder/issues/1/comments","events_url":"https://api.github.com/repos/jsh58/DMRfinder/issues/1/events","html_url":"https://github.com/jsh58/DMRfinder/issues/1","id":265077690,"number":1,"title":"combine_CpG_sites.py issue","user":{"login":"svrever","id":31775519,"avatar_url":"https://avatars3.githubusercontent.com/u/31775519?v=4","gravatar_id":"","url":"https://api.github.com/users/svrever","html_url":"https://github.com/svrever","followers_url":"https://api.github.com/users/svrever/followers","following_url":"https://api.github.com/users/svrever/following{/other_user}","gists_url":"https://api.github.com/users/svrever/gists{/gist_id}","starred_url":"https://api.github.com/users/svrever/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/svrever/subscriptions","organizations_url":"https://api.github.com/users/svrever/orgs","repos_url":"https://api.github.com/users/svrever/repos","events_url":"https://api.github.com/users/svrever/events{/privacy}","received_events_url":"https://api.github.com/users/svrever/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2017-10-12T20:37:23Z","updated_at":"2017-10-17T17:08:16Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nI am trying to analyse Xenopus methylome with the DMRfinder package. Everything worked fine with the .cov files generated (Bismark) for the subset of genome (just one chromosome). When I switched to the whole genome, python script combine_CpG_sites.py  fails after about 25-30 hours. It appears it is being terminated by the kernel OOM  killer. Memory usage is very high and reaches 97% in about 20 min after script starts (computer has 48G RAM).  Interestingly the top process monitor shows the python process to exist in a  D state (uninterruptable sleep) all the way till it is killed. Can you please help?\r\n\r\nBest,\r\nSergei"},"comment":{"url":"https://api.github.com/repos/jsh58/DMRfinder/issues/comments/337300153","html_url":"https://github.com/jsh58/DMRfinder/issues/1#issuecomment-337300153","issue_url":"https://api.github.com/repos/jsh58/DMRfinder/issues/1","id":337300153,"user":{"login":"jsh58","id":4921955,"avatar_url":"https://avatars3.githubusercontent.com/u/4921955?v=4","gravatar_id":"","url":"https://api.github.com/users/jsh58","html_url":"https://github.com/jsh58","followers_url":"https://api.github.com/users/jsh58/followers","following_url":"https://api.github.com/users/jsh58/following{/other_user}","gists_url":"https://api.github.com/users/jsh58/gists{/gist_id}","starred_url":"https://api.github.com/users/jsh58/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsh58/subscriptions","organizations_url":"https://api.github.com/users/jsh58/orgs","repos_url":"https://api.github.com/users/jsh58/repos","events_url":"https://api.github.com/users/jsh58/events{/privacy}","received_events_url":"https://api.github.com/users/jsh58/received_events","type":"User","site_admin":false},"created_at":"2017-10-17T17:08:16Z","updated_at":"2017-10-17T17:08:16Z","author_association":"OWNER","body":"Sergei,\r\n\r\nIf you had a `file` listing the ordered chromosome/scaffold names, comma-separated (on one line, no spaces), you could probably use command substitution: `-e $(< file)` or `-e $(cat file)`.  Hopefully your shell won't choke on the length of the command...\r\n\r\nJohn Gaspar"}}
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