{"action":"created","issue":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/45","repository_url":"https://api.github.com/repos/DerrickWood/kraken","labels_url":"https://api.github.com/repos/DerrickWood/kraken/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/DerrickWood/kraken/issues/45/comments","events_url":"https://api.github.com/repos/DerrickWood/kraken/issues/45/events","html_url":"https://github.com/DerrickWood/kraken/issues/45","id":162047583,"number":45,"title":"Kraken Standard Database","user":{"login":"gkarthik","id":798263,"avatar_url":"https://avatars.githubusercontent.com/u/798263?v=3","gravatar_id":"","url":"https://api.github.com/users/gkarthik","html_url":"https://github.com/gkarthik","followers_url":"https://api.github.com/users/gkarthik/followers","following_url":"https://api.github.com/users/gkarthik/following{/other_user}","gists_url":"https://api.github.com/users/gkarthik/gists{/gist_id}","starred_url":"https://api.github.com/users/gkarthik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gkarthik/subscriptions","organizations_url":"https://api.github.com/users/gkarthik/orgs","repos_url":"https://api.github.com/users/gkarthik/repos","events_url":"https://api.github.com/users/gkarthik/events{/privacy}","received_events_url":"https://api.github.com/users/gkarthik/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-06-23T23:44:47Z","updated_at":"2016-06-28T20:51:18Z","closed_at":null,"body":"Hello,\r\nI'm trying to build the standard kraken database. I gave the job a memory of 140gb and running on 16 threads. \r\n\r\nI get this error after kraken has downloaded the gi to taxid mapping file and the taxonomy dump from NCBI.  \r\n\r\n```\r\nFound jellyfish v1.1.11\r\n--2016-06-23 16:32:01--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz\r\n           => “gi_taxid_nucl.dmp.gz.2”\r\nResolving ftp.ncbi.nih.gov... 130.14.250.10, 2607:f220:41e:250::12\r\nConnecting to ftp.ncbi.nih.gov|130.14.250.10|:21... connected.\r\nLogging in as anonymous ... Logged in!\r\n==> SYST ... done.    ==> PWD ... done.\r\n==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.\r\n==> SIZE gi_taxid_nucl.dmp.gz ... 1405001825\r\n==> PASV ... done.    ==> RETR gi_taxid_nucl.dmp.gz ... done.\r\nLength: 1405001825 (1.3G) (unauthoritative)\r\n\r\n100%[=================================================================>] 1,405,001,825 7.42M/s   in 4m 42s  \r\n\r\n2016-06-23 16:36:45 (4.74 MB/s) - “gi_taxid_nucl.dmp.gz.2” saved [1405001825]\r\n\r\nDownloaded GI to taxon map\r\n--2016-06-23 16:36:45--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz\r\n           => “taxdump.tar.gz”\r\nResolving ftp.ncbi.nih.gov... 130.14.250.12, 2607:f220:41e:250::12\r\nConnecting to ftp.ncbi.nih.gov|130.14.250.12|:21... connected.\r\nLogging in as anonymous ... Logged in!\r\n==> SYST ... done.    ==> PWD ... done.\r\n==> TYPE I ... done.  ==> CWD (1) /pub/taxonomy ... done.\r\n==> SIZE taxdump.tar.gz ... 36397155\r\n==> PASV ... done.    ==> RETR taxdump.tar.gz ... done.\r\nLength: 36397155 (35M) (unauthoritative)\r\n\r\n100%[===================================================================>] 36,397,155  10.2M/s   in 5.2s    \r\n\r\n2016-06-23 16:36:51 (6.62 MB/s) - “taxdump.tar.gz” saved [36397155]\r\n\r\nDownloaded taxonomy tree data\r\n\r\ngzip: gi_taxid_nucl.dmp.gz: unexpected end of file\r\n```\r\n\r\nIs there something I'm missing? \r\n\r\nThanks. "},"comment":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/comments/229179269","html_url":"https://github.com/DerrickWood/kraken/issues/45#issuecomment-229179269","issue_url":"https://api.github.com/repos/DerrickWood/kraken/issues/45","id":229179269,"user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"created_at":"2016-06-28T20:51:18Z","updated_at":"2016-06-28T20:51:18Z","body":"Looks like your download was incomplete or corrupt.\r\n\r\nTry downloading the `.md5` file from `ftp://ftp.ncbi.nih.gov/pub/taxonomy/` and check it was downloaded correctly.\r\n"}}
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