{"action":"created","issue":{"url":"https://api.github.com/repos/kakitone/finishingTool/issues/19","repository_url":"https://api.github.com/repos/kakitone/finishingTool","labels_url":"https://api.github.com/repos/kakitone/finishingTool/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/kakitone/finishingTool/issues/19/comments","events_url":"https://api.github.com/repos/kakitone/finishingTool/issues/19/events","html_url":"https://github.com/kakitone/finishingTool/issues/19","id":365186559,"node_id":"MDU6SXNzdWUzNjUxODY1NTk=","number":19,"title":"finisherSC.py fails to run because it wants /Users/kakitlam/Downloads/MUMmer3.23","user":{"login":"SchwarzEM","id":1641641,"node_id":"MDQ6VXNlcjE2NDE2NDE=","avatar_url":"https://avatars2.githubusercontent.com/u/1641641?v=4","gravatar_id":"","url":"https://api.github.com/users/SchwarzEM","html_url":"https://github.com/SchwarzEM","followers_url":"https://api.github.com/users/SchwarzEM/followers","following_url":"https://api.github.com/users/SchwarzEM/following{/other_user}","gists_url":"https://api.github.com/users/SchwarzEM/gists{/gist_id}","starred_url":"https://api.github.com/users/SchwarzEM/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SchwarzEM/subscriptions","organizations_url":"https://api.github.com/users/SchwarzEM/orgs","repos_url":"https://api.github.com/users/SchwarzEM/repos","events_url":"https://api.github.com/users/SchwarzEM/events{/privacy}","received_events_url":"https://api.github.com/users/SchwarzEM/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-09-30T03:02:49Z","updated_at":"2018-09-30T22:45:22Z","closed_at":null,"author_association":"NONE","body":"When running the command:\r\n\r\n    python finisherSC.py -par 16 analysis_2018.09.29.01 MUMmer3.23 ;\r\n\r\n... I got the following error messages:\r\n\r\nERROR: The following critical files could not be used\r\n/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/postnuc\r\n/Users/kakitlam/Downloads/MUMmer3.23/aux_bin/prenuc\r\n/Users/kakitlam/Downloads/MUMmer3.23/mgaps\r\n/Users/kakitlam/Downloads/MUMmer3.23/mummer\r\nCheck your paths and file permissions and try again\r\nsh: MUMmer3.23/show-coords: cannot execute binary file\r\n\r\n...and, not surprisingly, failed to get any scaffolding to occur.\r\n\r\nThe binary file MUMmer3.23/show-coords has no obvious reason why it should not work:\r\n\r\n    ls -l MUMmer3.23/show-coords ;\r\n\r\n-rwxr-xr-x 1 schwarze mc5fpnp 155536 Nov 22  2016 MUMmer3.23/show-coords\r\n\r\nCan you please tell me why the program finisherSC.py expects me to supply it with anything, at all, in the directory \"/Users/kakitlam/Downloads/MUMmer3.23\"?  And can you tell me how to make it stop this inane demand, as well as how to tell it to work with a perfectly functional copy of MUMmer3.23/show-coords?\r\n\r\nThank you for any information that you have!"},"comment":{"url":"https://api.github.com/repos/kakitone/finishingTool/issues/comments/425758133","html_url":"https://github.com/kakitone/finishingTool/issues/19#issuecomment-425758133","issue_url":"https://api.github.com/repos/kakitone/finishingTool/issues/19","id":425758133,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNTc1ODEzMw==","user":{"login":"SchwarzEM","id":1641641,"node_id":"MDQ6VXNlcjE2NDE2NDE=","avatar_url":"https://avatars2.githubusercontent.com/u/1641641?v=4","gravatar_id":"","url":"https://api.github.com/users/SchwarzEM","html_url":"https://github.com/SchwarzEM","followers_url":"https://api.github.com/users/SchwarzEM/followers","following_url":"https://api.github.com/users/SchwarzEM/following{/other_user}","gists_url":"https://api.github.com/users/SchwarzEM/gists{/gist_id}","starred_url":"https://api.github.com/users/SchwarzEM/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SchwarzEM/subscriptions","organizations_url":"https://api.github.com/users/SchwarzEM/orgs","repos_url":"https://api.github.com/users/SchwarzEM/repos","events_url":"https://api.github.com/users/SchwarzEM/events{/privacy}","received_events_url":"https://api.github.com/users/SchwarzEM/received_events","type":"User","site_admin":false},"created_at":"2018-09-30T22:45:22Z","updated_at":"2018-09-30T22:45:22Z","author_association":"NONE","body":"But, why am I getting error messages from finisherSC.py asking me to supply it files in *this* directory:\r\n\r\n    /Users/kakitlam/Downloads/MUMmer3.23\r\n\r\n???\r\n\r\nThat's a pathname which assumes that I am running this program from the user account 'kakitlam' on a Mac computer.  Why is finisherSC hard-coded to expect me to have that directory at all?"}}
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