{"action":"closed","issue":{"url":"https://api.github.com/repos/geronimp/graftM/issues/178","repository_url":"https://api.github.com/repos/geronimp/graftM","labels_url":"https://api.github.com/repos/geronimp/graftM/issues/178/labels{/name}","comments_url":"https://api.github.com/repos/geronimp/graftM/issues/178/comments","events_url":"https://api.github.com/repos/geronimp/graftM/issues/178/events","html_url":"https://github.com/geronimp/graftM/issues/178","id":130119914,"number":178,"title":"graftm create --graftm_package is a bit picky","user":{"login":"wwood","id":15348,"avatar_url":"https://avatars.githubusercontent.com/u/15348?v=3","gravatar_id":"","url":"https://api.github.com/users/wwood","html_url":"https://github.com/wwood","followers_url":"https://api.github.com/users/wwood/followers","following_url":"https://api.github.com/users/wwood/following{/other_user}","gists_url":"https://api.github.com/users/wwood/gists{/gist_id}","starred_url":"https://api.github.com/users/wwood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wwood/subscriptions","organizations_url":"https://api.github.com/users/wwood/orgs","repos_url":"https://api.github.com/users/wwood/repos","events_url":"https://api.github.com/users/wwood/events{/privacy}","received_events_url":"https://api.github.com/users/wwood/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-01-31T12:04:15Z","updated_at":"2016-05-02T05:50:17Z","closed_at":"2016-05-02T05:50:17Z","body":"```\r\nuqbwoodc@curtin:20160131:/srv/projects/abisko/shotgun_abundance/103_contig_tree_relative_abundances/1_test$ ~/git/graftM/bin/graftM create --graftm_package another.gpkg/ --taxonomy /tmp/mytax2 --sequences another.gpkg/2.16.ribosomal_protein_S5_seqs_clus_97.faa\r\n                         \r\n                             GraftM 0.9.4\r\n01/31/2016 10:00:05 PM WARNING: Program found with multiple commands: taxit FastTreeMP seqmagick hmmalign mafft. Arbitrarily selecting FastTreeMP\r\n\r\n                            CREATE\r\n\r\n                   Joel Boyd, Ben Woodcroft\r\n\r\n                                                    /\r\n              >a                                   /\r\n              -------------                       /\r\n              >b                        |        |\r\n              --------          >>>     |  GPKG  |\r\n              >c                        |________|\r\n              ----------\r\n\r\n01/31/2016 10:00:05 PM INFO: GraftM package another.gpkg/ specified to update with sequences in another.gpkg/2.16.ribosomal_protein_S5_seqs_clus_97.faa\r\nTraceback (most recent call last):\r\n  File \"/srv/whitlam/home/users/uqbwoodc/git/graftM/bin/graftM\", line 346, in <module>\r\n    Run(args).main()\r\n  File \"/srv/home/uqbwoodc/git/graftM/bin/../graftm/run.py\", line 563, in main\r\n    raise UnrecognisedSuffixError(\"Unrecognised suffix on GraftM package %s. Please provide a graftM package with the correct suffix (.gpkg)\" % (self.args.graftm_package))\r\ngraftm.run.UnrecognisedSuffixError: Unrecognised suffix on GraftM package another.gpkg/. Please provide a graftM package with the correct suffix (.gpkg)\r\n```\r\nI think the root of this issue is that 'update' shouldn't be a thing, rather, it should be used as a convenience method to specify the things required to build a new package (taxtastic taxonomy/seqinfo, sequences, rooted tree, that all?), but defer to other command line parameters e.g. if rerooted_annotated_tree is given, get the tree and the taxonomy from that.\r\n\r\nAlso, the warning looks not right:\r\n```\r\n01/31/2016 10:00:05 PM WARNING: Program found with multiple commands: taxit FastTreeMP seqmagick hmmalign mafft. Arbitrarily selecting FastTreeMP\r\n```\r\n\r\nThanks."}}