{"action":"created","issue":{"url":"https://api.github.com/repos/lh3/rtgeval/issues/1","repository_url":"https://api.github.com/repos/lh3/rtgeval","labels_url":"https://api.github.com/repos/lh3/rtgeval/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/lh3/rtgeval/issues/1/comments","events_url":"https://api.github.com/repos/lh3/rtgeval/issues/1/events","html_url":"https://github.com/lh3/rtgeval/issues/1","id":143926514,"number":1,"title":"Fail to open the file in hapdip.js for allele evaluation (rtg vcfeval)","user":{"login":"andreas-wilm","id":1095945,"avatar_url":"https://avatars.githubusercontent.com/u/1095945?v=3","gravatar_id":"","url":"https://api.github.com/users/andreas-wilm","html_url":"https://github.com/andreas-wilm","followers_url":"https://api.github.com/users/andreas-wilm/followers","following_url":"https://api.github.com/users/andreas-wilm/following{/other_user}","gists_url":"https://api.github.com/users/andreas-wilm/gists{/gist_id}","starred_url":"https://api.github.com/users/andreas-wilm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andreas-wilm/subscriptions","organizations_url":"https://api.github.com/users/andreas-wilm/orgs","repos_url":"https://api.github.com/users/andreas-wilm/repos","events_url":"https://api.github.com/users/andreas-wilm/events{/privacy}","received_events_url":"https://api.github.com/users/andreas-wilm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-03-28T08:30:02Z","updated_at":"2016-03-30T15:49:03Z","closed_at":null,"body":"Hi Heng,\r\n\r\nI would really like to this gives a try, however releases/download/v0.1/rtgevalkit-0.1_x64-linux.tar.bz2 (and the current commit) keep failing on the data-sets I've tried. The weird thing is that the first commands seem to work okay and I made sure all input files exist. The command line in all cases was:\r\n\r\n    /rtgeval.kit/run-eval -s ref/human_g1k_v37.sdf -b $bed $truth $test\r\n\r\n`$truth` and `$test` are tabix indexed (bgzipped) vcf files.\r\n\r\nThe error is as follows:\r\n\r\n```\r\nRunning position-based evaluaton (hapdip distEval)...\r\nNormalizing the truth VCF...\r\nNormalizing the test VCF...\r\nRunning allele evaluation (rtg vcfeval --squash-ploidy)...\r\nRunning allele evaluation (rtg vcfeval)...\r\n./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file\r\n\tvar file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();\r\n                                                   ^\r\nError: [File] Fail to open the file\r\n    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)\r\n    at main (./rtgeval.kit/hapdip.js:1636:26)\r\n    at ./rtgeval.kit/hapdip.js:1650:1\r\n./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file\r\n\tvar file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();\r\n                                                   ^\r\nError: [File] Fail to open the file\r\n    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)\r\n    at main (./rtgeval.kit/hapdip.js:1636:26)\r\n    at ./rtgeval.kit/hapdip.js:1650:1\r\n./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file\r\n\tvar file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();\r\n                                                   ^\r\nError: [File] Fail to open the file\r\n    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)\r\n    at main (./rtgeval.kit/hapdip.js:1636:26)\r\n    at ./rtgeval.kit/hapdip.js:1650:1\r\n./rtgeval.kit/hapdip.js:472: Error: [File] Fail to open the file\r\n\tvar file = args.length > getopt.ind? new File(args[getopt.ind]) : new File();\r\n                                                   ^\r\nError: [File] Fail to open the file\r\n    at b8_qst1 (./rtgeval.kit/hapdip.js:472:52)\r\n    at main (./rtgeval.kit/hapdip.js:1636:26)\r\n    at ./rtgeval.kit/hapdip.js:1650:1\r\n```\r\n\r\nAny idea what might be going wrong?\r\n\r\nThanks,\r\nAndreas"},"comment":{"url":"https://api.github.com/repos/lh3/rtgeval/issues/comments/203497871","html_url":"https://github.com/lh3/rtgeval/issues/1#issuecomment-203497871","issue_url":"https://api.github.com/repos/lh3/rtgeval/issues/1","id":203497871,"user":{"login":"lh3","id":480346,"avatar_url":"https://avatars.githubusercontent.com/u/480346?v=3","gravatar_id":"","url":"https://api.github.com/users/lh3","html_url":"https://github.com/lh3","followers_url":"https://api.github.com/users/lh3/followers","following_url":"https://api.github.com/users/lh3/following{/other_user}","gists_url":"https://api.github.com/users/lh3/gists{/gist_id}","starred_url":"https://api.github.com/users/lh3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lh3/subscriptions","organizations_url":"https://api.github.com/users/lh3/orgs","repos_url":"https://api.github.com/users/lh3/repos","events_url":"https://api.github.com/users/lh3/events{/privacy}","received_events_url":"https://api.github.com/users/lh3/received_events","type":"User","site_admin":false},"created_at":"2016-03-30T15:49:03Z","updated_at":"2016-03-30T15:49:03Z","body":"I see. That is a bug. I will have a look. Thanks for reporting."}}