{"action":"created","issue":{"url":"https://api.github.com/repos/ncbi/sra-tools/issues/26","repository_url":"https://api.github.com/repos/ncbi/sra-tools","labels_url":"https://api.github.com/repos/ncbi/sra-tools/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/ncbi/sra-tools/issues/26/comments","events_url":"https://api.github.com/repos/ncbi/sra-tools/issues/26/events","html_url":"https://github.com/ncbi/sra-tools/issues/26","id":133339955,"number":26,"title":"vdb-dump for complete genomics reads is extremely slow","user":{"login":"lilit-nersisyan","id":7588977,"avatar_url":"https://avatars.githubusercontent.com/u/7588977?v=3","gravatar_id":"","url":"https://api.github.com/users/lilit-nersisyan","html_url":"https://github.com/lilit-nersisyan","followers_url":"https://api.github.com/users/lilit-nersisyan/followers","following_url":"https://api.github.com/users/lilit-nersisyan/following{/other_user}","gists_url":"https://api.github.com/users/lilit-nersisyan/gists{/gist_id}","starred_url":"https://api.github.com/users/lilit-nersisyan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lilit-nersisyan/subscriptions","organizations_url":"https://api.github.com/users/lilit-nersisyan/orgs","repos_url":"https://api.github.com/users/lilit-nersisyan/repos","events_url":"https://api.github.com/users/lilit-nersisyan/events{/privacy}","received_events_url":"https://api.github.com/users/lilit-nersisyan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-12T20:47:35Z","updated_at":"2016-02-12T20:51:35Z","closed_at":null,"body":"It's already two weeks I'm trying to dump a single SRA file from Complete Genomics WGS data: SRR833540. The .sra file size is 180 Gb, and the number of reads is about 3 bln. I'm using Linux machine, with 16 Gb of RAM and 7 cores, and the vdb-dump program. \r\n\r\nThere are two main issues here: \r\n1. The process is extremely slow: if run in one thread, it will take 75 weeks to dump this single run. \r\n2. Dumping the file simultaneosly from different regions is also an issue, since vdb-dump is memory-intensive, and it consumes more than 2-4 Gb RAM per dump. Also, memory consumption is not constant during time. \r\n3. And lastly, a question: vdb-dump performs slow in the beginning of the file, but is much faster when performed on the second part of the file. What can be the reason? \r\n\r\nIs there any solution to this issue? \r\nThanks! \r\nLilit"},"comment":{"url":"https://api.github.com/repos/ncbi/sra-tools/issues/comments/183484430","html_url":"https://github.com/ncbi/sra-tools/issues/26#issuecomment-183484430","issue_url":"https://api.github.com/repos/ncbi/sra-tools/issues/26","id":183484430,"user":{"login":"kwrodarmer","id":8517690,"avatar_url":"https://avatars.githubusercontent.com/u/8517690?v=3","gravatar_id":"","url":"https://api.github.com/users/kwrodarmer","html_url":"https://github.com/kwrodarmer","followers_url":"https://api.github.com/users/kwrodarmer/followers","following_url":"https://api.github.com/users/kwrodarmer/following{/other_user}","gists_url":"https://api.github.com/users/kwrodarmer/gists{/gist_id}","starred_url":"https://api.github.com/users/kwrodarmer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kwrodarmer/subscriptions","organizations_url":"https://api.github.com/users/kwrodarmer/orgs","repos_url":"https://api.github.com/users/kwrodarmer/repos","events_url":"https://api.github.com/users/kwrodarmer/events{/privacy}","received_events_url":"https://api.github.com/users/kwrodarmer/received_events","type":"User","site_admin":false},"created_at":"2016-02-12T20:51:35Z","updated_at":"2016-02-12T20:51:35Z","body":"Can you give an example of the command line?"}}