{"action":"created","issue":{"url":"https://api.github.com/repos/mothur/mothur/issues/493","repository_url":"https://api.github.com/repos/mothur/mothur","labels_url":"https://api.github.com/repos/mothur/mothur/issues/493/labels{/name}","comments_url":"https://api.github.com/repos/mothur/mothur/issues/493/comments","events_url":"https://api.github.com/repos/mothur/mothur/issues/493/events","html_url":"https://github.com/mothur/mothur/issues/493","id":341341014,"node_id":"MDU6SXNzdWUzNDEzNDEwMTQ=","number":493,"title":"mothur \"unable to open\" files in make.contigs","user":{"login":"rlh13","id":30531444,"node_id":"MDQ6VXNlcjMwNTMxNDQ0","avatar_url":"https://avatars2.githubusercontent.com/u/30531444?v=4","gravatar_id":"","url":"https://api.github.com/users/rlh13","html_url":"https://github.com/rlh13","followers_url":"https://api.github.com/users/rlh13/followers","following_url":"https://api.github.com/users/rlh13/following{/other_user}","gists_url":"https://api.github.com/users/rlh13/gists{/gist_id}","starred_url":"https://api.github.com/users/rlh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rlh13/subscriptions","organizations_url":"https://api.github.com/users/rlh13/orgs","repos_url":"https://api.github.com/users/rlh13/repos","events_url":"https://api.github.com/users/rlh13/events{/privacy}","received_events_url":"https://api.github.com/users/rlh13/received_events","type":"User","site_admin":false},"labels":[{"id":327659311,"node_id":"MDU6TGFiZWwzMjc2NTkzMTE=","url":"https://api.github.com/repos/mothur/mothur/labels/Command:Make.contigs","name":"Command:Make.contigs","color":"fbca04","default":false},{"id":303524696,"node_id":"MDU6TGFiZWwzMDM1MjQ2OTY=","url":"https://api.github.com/repos/mothur/mothur/labels/Support","name":"Support","color":"bfe5bf","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/mothur/mothur/milestones/7","html_url":"https://github.com/mothur/mothur/milestone/7","labels_url":"https://api.github.com/repos/mothur/mothur/milestones/7/labels","id":1473828,"node_id":"MDk6TWlsZXN0b25lMTQ3MzgyOA==","number":7,"title":"Bug / Support Tracking","description":"Goals\r\n\r\n* Help find problem areas in the code through better bug tracking.\r\n* Improve documentation by identifying areas where additional support is requested.\r\n","creator":{"login":"mothur-westcott","id":1379958,"node_id":"MDQ6VXNlcjEzNzk5NTg=","avatar_url":"https://avatars3.githubusercontent.com/u/1379958?v=4","gravatar_id":"","url":"https://api.github.com/users/mothur-westcott","html_url":"https://github.com/mothur-westcott","followers_url":"https://api.github.com/users/mothur-westcott/followers","following_url":"https://api.github.com/users/mothur-westcott/following{/other_user}","gists_url":"https://api.github.com/users/mothur-westcott/gists{/gist_id}","starred_url":"https://api.github.com/users/mothur-westcott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mothur-westcott/subscriptions","organizations_url":"https://api.github.com/users/mothur-westcott/orgs","repos_url":"https://api.github.com/users/mothur-westcott/repos","events_url":"https://api.github.com/users/mothur-westcott/events{/privacy}","received_events_url":"https://api.github.com/users/mothur-westcott/received_events","type":"User","site_admin":false},"open_issues":22,"closed_issues":12,"state":"open","created_at":"2015-12-24T17:40:44Z","updated_at":"2018-07-16T15:21:27Z","due_on":null,"closed_at":null},"comments":1,"created_at":"2018-07-15T18:24:52Z","updated_at":"2018-07-16T15:23:05Z","closed_at":null,"author_association":"NONE","body":"I am running the make.contigs command in Mothur but, while it recognizes all of the sample names from the stability file, it is for some reason unable to open them. They are in fastq format. I am posting the error only for one of the samples since it is the same for all of the sample files in the folder and have replaced the remainder of the file paths with \"..\" for privacy. What am I doing incorrectly?\r\n\r\nmake.contigs(file=stability.file, processors=8, inputdir=../cutadapt/, outputdir=../mothur_data/)\r\n\r\nUnable to open ../cutadapt/MoNat1. Trying default ../mothur/MoNat1\r\nUnable to open ../mothur/MoNat1. Trying output directory ../mothur_data/MoNat1\r\nUnable to open ../mothur_data/MoNat1. Trying mothur's executable directory ../mothur/MoNat1\r\n[WARNING]: can't find ../mothur/MoNat1, ignoring pair.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/mothur/mothur/issues/comments/405284588","html_url":"https://github.com/mothur/mothur/issues/493#issuecomment-405284588","issue_url":"https://api.github.com/repos/mothur/mothur/issues/493","id":405284588,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNTI4NDU4OA==","user":{"login":"rlh13","id":30531444,"node_id":"MDQ6VXNlcjMwNTMxNDQ0","avatar_url":"https://avatars2.githubusercontent.com/u/30531444?v=4","gravatar_id":"","url":"https://api.github.com/users/rlh13","html_url":"https://github.com/rlh13","followers_url":"https://api.github.com/users/rlh13/followers","following_url":"https://api.github.com/users/rlh13/following{/other_user}","gists_url":"https://api.github.com/users/rlh13/gists{/gist_id}","starred_url":"https://api.github.com/users/rlh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rlh13/subscriptions","organizations_url":"https://api.github.com/users/rlh13/orgs","repos_url":"https://api.github.com/users/rlh13/repos","events_url":"https://api.github.com/users/rlh13/events{/privacy}","received_events_url":"https://api.github.com/users/rlh13/received_events","type":"User","site_admin":false},"created_at":"2018-07-16T15:23:05Z","updated_at":"2018-07-16T15:23:05Z","author_association":"NONE","body":"Here is the stability file. I concatenated the R1 and R2 files before using cutadapt to demultiplex and remove primers. That is why there is only 1 fastq file for each sample. I did this because previously I tried joining paired ends and it resulted in a large drop in quality.\r\n\r\n[stability.file.txt](https://github.com/mothur/mothur/files/2198179/stability.file.txt)\r\n"}}
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