{"action":"created","issue":{"url":"https://api.github.com/repos/charite/jannovar/issues/106","labels_url":"https://api.github.com/repos/charite/jannovar/issues/106/labels{/name}","comments_url":"https://api.github.com/repos/charite/jannovar/issues/106/comments","events_url":"https://api.github.com/repos/charite/jannovar/issues/106/events","html_url":"https://github.com/charite/jannovar/issues/106","id":56154478,"number":106,"title":"Database downloading does not work for ftp:// URLs","user":{"login":"buske","id":4251264,"avatar_url":"https://avatars.githubusercontent.com/u/4251264?v=3","gravatar_id":"","url":"https://api.github.com/users/buske","html_url":"https://github.com/buske","followers_url":"https://api.github.com/users/buske/followers","following_url":"https://api.github.com/users/buske/following{/other_user}","gists_url":"https://api.github.com/users/buske/gists{/gist_id}","starred_url":"https://api.github.com/users/buske/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/buske/subscriptions","organizations_url":"https://api.github.com/users/buske/orgs","repos_url":"https://api.github.com/users/buske/repos","events_url":"https://api.github.com/users/buske/events{/privacy}","received_events_url":"https://api.github.com/users/buske/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/charite/jannovar/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/charite/jannovar/milestones/5","html_url":"https://github.com/charite/jannovar/milestones/0.13.0","labels_url":"https://api.github.com/repos/charite/jannovar/milestones/5/labels","id":936699,"number":5,"title":"0.13.0","description":"","creator":{"login":"holtgrewe","id":521780,"avatar_url":"https://avatars.githubusercontent.com/u/521780?v=3","gravatar_id":"","url":"https://api.github.com/users/holtgrewe","html_url":"https://github.com/holtgrewe","followers_url":"https://api.github.com/users/holtgrewe/followers","following_url":"https://api.github.com/users/holtgrewe/following{/other_user}","gists_url":"https://api.github.com/users/holtgrewe/gists{/gist_id}","starred_url":"https://api.github.com/users/holtgrewe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/holtgrewe/subscriptions","organizations_url":"https://api.github.com/users/holtgrewe/orgs","repos_url":"https://api.github.com/users/holtgrewe/repos","events_url":"https://api.github.com/users/holtgrewe/events{/privacy}","received_events_url":"https://api.github.com/users/holtgrewe/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":10,"state":"open","created_at":"2015-01-15T12:25:47Z","updated_at":"2015-04-01T10:02:17Z","due_on":"2015-02-27T23:00:00Z","closed_at":null},"comments":8,"created_at":"2015-02-01T06:36:58Z","updated_at":"2015-04-01T10:02:17Z","closed_at":"2015-04-01T10:02:17Z","body":"Just did a `mvn clean install` from the latest pull from `master`, and am trying to set up the annotation databases. URLs that start with `http://` seem to download fine, while URLs that start with `ftp://` fail with an error such as:\r\n```ERROR: ERROR: problem downloading file Could not open connection for file chr_accessions_GRCh37.p13```\r\n\r\nCalling `wget <URL>` with the console-logged URL works fine, so I was able to download each file and then re-run.\r\n\r\nFor example:\r\n```\r\n[01:29:52] (buske@combine-102:jannovar)$ java -jar jannovar-cli-0.11.jar download hg19/refseq\r\nOptions\r\ndataSourceFiles: [bundle:///default_sources.ini]\r\ndataSourceNames: [hg19/refseq]\r\ndownloadPathdata\r\nHTTP proxy: null\r\nHTTPS proxy: null\r\nFTP proxy: null\r\nDownloading/parsing for data source \"hg19/refseq\"\r\nDownloading data...\r\nDownloading ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz\r\nCreating directory data/hg19/refseq\r\n(server did not tell us the file size, no progress bar)\r\nERROR: ERROR: problem downloading file Could not open connection for file ref_GRCh37.p13_top_level.gff3.gz\r\n\r\n[01:30:04] (buske@combine-102:jannovar)$ wget ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz\r\n--2015-02-01 01:30:18--  ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz\r\n           => `ref_GRCh37.p13_top_level.gff3.gz'\r\nResolving ftp.ncbi.nlm.nih.gov... 130.14.250.13, 2607:f220:41e:250::10\r\nConnecting to ftp.ncbi.nlm.nih.gov|130.14.250.13|:21... connected.\r\nLogging in as anonymous ... Logged in!\r\n==> SYST ... done.    ==> PWD ... done.\r\n==> TYPE I ... done.  ==> CWD (1) /genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF ... done.\r\n==> SIZE ref_GRCh37.p13_top_level.gff3.gz ... 24904770\r\n==> PASV ... done.    ==> RETR ref_GRCh37.p13_top_level.gff3.gz ... done.\r\nLength: 24904770 (24M) (unauthoritative)\r\n\r\n100%[===========================================================================================================================================================================================>] 24,904,770  25.4M/s   in 0.9s    \r\n\r\n2015-02-01 01:30:19 (25.4 MB/s) - `ref_GRCh37.p13_top_level.gff3.gz' saved [24904770]\r\n```\r\n\r\nand to show that it worked fine for `http://` files:\r\n\r\n```\r\n[01:31:14] (buske@combine-102:jannovar)$ java -jar jannovar-cli-0.11.jar download hg19/refseq\r\nOptions\r\ndataSourceFiles: [bundle:///default_sources.ini]\r\ndataSourceNames: [hg19/refseq]\r\ndownloadPathdata\r\nHTTP proxy: null\r\nHTTPS proxy: null\r\nFTP proxy: null\r\nDownloading/parsing for data source \"hg19/refseq\"\r\nDownloading data...\r\nDownloading ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz\r\nDownloading ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz\r\nDownloading http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz\r\n[==================================================]   100%     \r\nDownloading ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13\r\n(server did not tell us the file size, no progress bar)\r\nERROR: ERROR: problem downloading file Could not open connection for file chr_accessions_GRCh37.p13\r\n```"},"comment":{"url":"https://api.github.com/repos/charite/jannovar/issues/comments/88423011","html_url":"https://github.com/charite/jannovar/issues/106#issuecomment-88423011","issue_url":"https://api.github.com/repos/charite/jannovar/issues/106","id":88423011,"user":{"login":"visze","id":9267120,"avatar_url":"https://avatars.githubusercontent.com/u/9267120?v=3","gravatar_id":"","url":"https://api.github.com/users/visze","html_url":"https://github.com/visze","followers_url":"https://api.github.com/users/visze/followers","following_url":"https://api.github.com/users/visze/following{/other_user}","gists_url":"https://api.github.com/users/visze/gists{/gist_id}","starred_url":"https://api.github.com/users/visze/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/visze/subscriptions","organizations_url":"https://api.github.com/users/visze/orgs","repos_url":"https://api.github.com/users/visze/repos","events_url":"https://api.github.com/users/visze/events{/privacy}","received_events_url":"https://api.github.com/users/visze/received_events","type":"User","site_admin":false},"created_at":"2015-04-01T10:02:16Z","updated_at":"2015-04-01T10:02:16Z","body":"I think this bug is fixed!"}}