{"action":"created","issue":{"url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/4","repository_url":"https://api.github.com/repos/YangLab/CIRCexplorer2","labels_url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/4/comments","events_url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/4/events","html_url":"https://github.com/YangLab/CIRCexplorer2/issues/4","id":197632955,"number":4,"title":"can't continue 'Annotating'","user":{"login":"gnilihzeux","id":4859358,"avatar_url":"https://avatars.githubusercontent.com/u/4859358?v=3","gravatar_id":"","url":"https://api.github.com/users/gnilihzeux","html_url":"https://github.com/gnilihzeux","followers_url":"https://api.github.com/users/gnilihzeux/followers","following_url":"https://api.github.com/users/gnilihzeux/following{/other_user}","gists_url":"https://api.github.com/users/gnilihzeux/gists{/gist_id}","starred_url":"https://api.github.com/users/gnilihzeux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gnilihzeux/subscriptions","organizations_url":"https://api.github.com/users/gnilihzeux/orgs","repos_url":"https://api.github.com/users/gnilihzeux/repos","events_url":"https://api.github.com/users/gnilihzeux/events{/privacy}","received_events_url":"https://api.github.com/users/gnilihzeux/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-27T01:46:14Z","updated_at":"2016-12-28T02:50:46Z","closed_at":"2016-12-28T02:50:46Z","body":"I followed the manual and couldn't continue the 'Annotating' with a reply from the error file:\r\n`Usage: CIRCexplorer2 annotate [options] -r REF -g GENOME <circ_dir>`\r\n\r\nThen I checked my input and found no incompatibility.\r\n\r\nThe `REF` is from Ensembl GRCh38 gtf consistent with Ref_genome by using `gtfToGenePred` . The header is:\r\n\r\n```\r\nTSPAN6  ENST00000373020 X       -       100628669       100636806       100630797       100636694       8  100628669,100630758,100632484,100633404,100633930,100635177,100635557,100636607, 100629986,100630866,100632568,100633539,100634029,100635252,100635746,100636806,\r\nTSPAN6  ENST00000494424 X       -       100633441       100639991       100639991       100639991       6  100633441,100633930,100635177,100635557,100636792,100639944,     100633539,100634029,100635252,100635746,100637104,100639991,\r\nTSPAN6  ENST00000496771 X       -       100632540       100636689       100636689       100636689       6  100632540,100633404,100633930,100635177,100635557,100636190,     100632568,100633539,100634029,100635252,100635746,100636689,\r\nTSPAN6  ENST00000612152 X       -       100627108       100637104       100630797       100635569       7  100627108,100630758,100633404,100633930,100635177,100635557,100636792,   100629986,100630866,100633539,100634029,100635252,100635746,100637104,\r\nTSPAN6  ENST00000614008 X       -       100632062       100637104       100632062       100635569       7  100632062,100632484,100633404,100633930,100635177,100635557,100636792,   100632068,100632568,100633539,100634029,100635252,100635746,100637104,\r\nTNMD    ENST00000373031 X       +       100584801       100599885       100585018       100599717       7  100584801,100585230,100593894,100594260,100597503,100599015,100599507,   100585066,100585362,100594035,100594362,100597657,100599182,100599885,\r\nTNMD    ENST00000485971 X       +       100593623       100597531       100597531       100597531       3  100593623,100594260,100597503,   100594035,100594362,100597531,\r\nDPM1    ENST00000371582 20      -       50934866        50958555        50935131        50958523        10 50934866,50936147,50940864,50941128,50942030,50945736,50945846,50948628,50955185,50958362,       50935236,50936262,50940933,50941209,50942126,50945762,50945923,50948662,50955285,50958555,\r\nDPM1    ENST00000371584 20      -       50934944        50958521        50935131        50958521        10 50934944,50936147,50940864,50941104,50942030,50945736,50945846,50948628,50955185,50958362,       50935236,50936262,50940933,50941209,50942126,50945762,50945923,50948662,50955285,50958521,\r\nDPM1    ENST00000371588 20      -       50934866        50958550        50935131        50958523        9  50934866,50936147,50940864,50942030,50945736,50945846,50948628,50955185,50958362,        50935236,50936262,50940933,50942126,50945762,50945923,50948662,50955285,50958550,\r\n```\r\n\r\nAnd my Ref genome is Ensembl GRCh38, headers are:\r\n\r\n```\r\n>1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF\r\n>2 dna:chromosome chromosome:GRCh38:2:1:242193529:1 REF\r\n>3 dna:chromosome chromosome:GRCh38:3:1:198295559:1 REF\r\n>4 dna:chromosome chromosome:GRCh38:4:1:190214555:1 REF\r\n>5 dna:chromosome chromosome:GRCh38:5:1:181538259:1 REF\r\n>6 dna:chromosome chromosome:GRCh38:6:1:170805979:1 REF\r\n>7 dna:chromosome chromosome:GRCh38:7:1:159345973:1 REF\r\n>8 dna:chromosome chromosome:GRCh38:8:1:145138636:1 REF\r\n>9 dna:chromosome chromosome:GRCh38:9:1:138394717:1 REF\r\n>10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF\r\n>11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF\r\n>12 dna:chromosome chromosome:GRCh38:12:1:133275309:1 REF\r\n>13 dna:chromosome chromosome:GRCh38:13:1:114364328:1 REF\r\n>14 dna:chromosome chromosome:GRCh38:14:1:107043718:1 REF\r\n>15 dna:chromosome chromosome:GRCh38:15:1:101991189:1 REF\r\n>16 dna:chromosome chromosome:GRCh38:16:1:90338345:1 REF\r\n>17 dna:chromosome chromosome:GRCh38:17:1:83257441:1 REF\r\n>18 dna:chromosome chromosome:GRCh38:18:1:80373285:1 REF\r\n>19 dna:chromosome chromosome:GRCh38:19:1:58617616:1 REF\r\n>20 dna:chromosome chromosome:GRCh38:20:1:64444167:1 REF\r\n>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF\r\n>22 dna:chromosome chromosome:GRCh38:22:1:50818468:1 REF\r\n>X dna:chromosome chromosome:GRCh38:X:1:156040895:1 REF\r\n>Y dna:chromosome chromosome:GRCh38:Y:2781480:56887902:1 REF\r\n```\r\n\r\nand `<circ_dir>` is directory `circ_out` with file `fusion_junction.bed` and its header is:\r\n ```\r\n15      83885100        83891379        FUSIONJUNC_0/1  0       +\r\n16      15001838        70036578        FUSIONJUNC_1/1  0       +\r\n17      46475199        46694662        FUSIONJUNC_2/1  0       +\r\n19      3586648 14480485        FUSIONJUNC_3/4  0       +\r\n3       73047269        197634612       FUSIONJUNC_4/1  0       +\r\n21      8206731 8433925 FUSIONJUNC_5/1  0       +\r\n21      5121790 44137296        FUSIONJUNC_6/1  0       +\r\n3       158652095       158666386       FUSIONJUNC_7/2  0       +\r\n5       94569462        134924198       FUSIONJUNC_8/15 0       +\r\n5       94569462        134924197       FUSIONJUNC_9/1  0       +\r\n```\r\nThanks for your attention!\r\n"},"comment":{"url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/comments/269416910","html_url":"https://github.com/YangLab/CIRCexplorer2/issues/4#issuecomment-269416910","issue_url":"https://api.github.com/repos/YangLab/CIRCexplorer2/issues/4","id":269416910,"user":{"login":"xingma","id":6956745,"avatar_url":"https://avatars.githubusercontent.com/u/6956745?v=3","gravatar_id":"","url":"https://api.github.com/users/xingma","html_url":"https://github.com/xingma","followers_url":"https://api.github.com/users/xingma/followers","following_url":"https://api.github.com/users/xingma/following{/other_user}","gists_url":"https://api.github.com/users/xingma/gists{/gist_id}","starred_url":"https://api.github.com/users/xingma/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xingma/subscriptions","organizations_url":"https://api.github.com/users/xingma/orgs","repos_url":"https://api.github.com/users/xingma/repos","events_url":"https://api.github.com/users/xingma/events{/privacy}","received_events_url":"https://api.github.com/users/xingma/received_events","type":"User","site_admin":false},"created_at":"2016-12-28T02:50:46Z","updated_at":"2016-12-28T02:50:46Z","body":"I think the problem is double \"-g\" in your command before."}}
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