{"action":"created","issue":{"url":"https://api.github.com/repos/chadlaing/Panseq/issues/24","repository_url":"https://api.github.com/repos/chadlaing/Panseq","labels_url":"https://api.github.com/repos/chadlaing/Panseq/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/chadlaing/Panseq/issues/24/comments","events_url":"https://api.github.com/repos/chadlaing/Panseq/issues/24/events","html_url":"https://github.com/chadlaing/Panseq/issues/24","id":382712518,"node_id":"MDU6SXNzdWUzODI3MTI1MTg=","number":24,"title":"Cannot open settings.txt","user":{"login":"rupesh-sinha","id":38905384,"node_id":"MDQ6VXNlcjM4OTA1Mzg0","avatar_url":"https://avatars3.githubusercontent.com/u/38905384?v=4","gravatar_id":"","url":"https://api.github.com/users/rupesh-sinha","html_url":"https://github.com/rupesh-sinha","followers_url":"https://api.github.com/users/rupesh-sinha/followers","following_url":"https://api.github.com/users/rupesh-sinha/following{/other_user}","gists_url":"https://api.github.com/users/rupesh-sinha/gists{/gist_id}","starred_url":"https://api.github.com/users/rupesh-sinha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rupesh-sinha/subscriptions","organizations_url":"https://api.github.com/users/rupesh-sinha/orgs","repos_url":"https://api.github.com/users/rupesh-sinha/repos","events_url":"https://api.github.com/users/rupesh-sinha/events{/privacy}","received_events_url":"https://api.github.com/users/rupesh-sinha/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-20T15:20:57Z","updated_at":"2018-11-20T16:00:41Z","closed_at":null,"author_association":"NONE","body":"I have created a tab-delimited configuration file and named it as settings.txt and placed it in 'lib' directory. When I am giving the command perl lib/panseq.pl settings.txt the following result is returned:\r\n No such file or directory at /home/rks/Downloads/Panseq-master/lib/Modules/Setup/Settings.pm line 284.\r\nWhats the issue?\r\n\r\nMy configuration file \"settings.txt\" has the following contents:\r\n\tqueryDirectory\t/home/rks/Downloads/Panseq-master/16_genome_panseq/\r\n\tbaseDirectory\t/home/rks/Downloads/Panseq-master/output_panseq_P_pel/\r\n\tnumberOfCores\t4\r\n\tminimumNovelRegionSize\t500\r\n\tnovelRegionFinderMode\tno_duplicates\r\n\tfragmentationSize\t500\r\n\tpercentIdentityCutoff\t85\r\n\tcoreGenomeThreshold\t3\r\n\trunMode \tpan\r\n\tcdhitDirectory  /home/rks/Downloads/cdhit-master/\r\n\tstoreAlleles\t1\r\n\tallelesToKeep\t2\r\n\tnameOrId\tname\r\n\tframeshift\t1\r\n\toverwrite\t1\r\n\tmaxNumberResultsInMemory \t500\r\n\tblastWordSize\t11\r\n\tnucB    200\r\n\tnucC    65\r\n\tnucD    0.12\r\n\tnucG    90\r\n\tnucL    20\r\n\tcdhit   1\r\n\tsha1    1\r\n\r\n\r\nPlease let me know the solution for this issue"},"comment":{"url":"https://api.github.com/repos/chadlaing/Panseq/issues/comments/440325886","html_url":"https://github.com/chadlaing/Panseq/issues/24#issuecomment-440325886","issue_url":"https://api.github.com/repos/chadlaing/Panseq/issues/24","id":440325886,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MDMyNTg4Ng==","user":{"login":"chadlaing","id":852715,"node_id":"MDQ6VXNlcjg1MjcxNQ==","avatar_url":"https://avatars2.githubusercontent.com/u/852715?v=4","gravatar_id":"","url":"https://api.github.com/users/chadlaing","html_url":"https://github.com/chadlaing","followers_url":"https://api.github.com/users/chadlaing/followers","following_url":"https://api.github.com/users/chadlaing/following{/other_user}","gists_url":"https://api.github.com/users/chadlaing/gists{/gist_id}","starred_url":"https://api.github.com/users/chadlaing/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chadlaing/subscriptions","organizations_url":"https://api.github.com/users/chadlaing/orgs","repos_url":"https://api.github.com/users/chadlaing/repos","events_url":"https://api.github.com/users/chadlaing/events{/privacy}","received_events_url":"https://api.github.com/users/chadlaing/received_events","type":"User","site_admin":false},"created_at":"2018-11-20T16:00:41Z","updated_at":"2018-11-20T16:00:41Z","author_association":"OWNER","body":"Do the tests work when you run `perl t/output.t`?"}}
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