{"action":"opened","issue":{"url":"https://api.github.com/repos/mothur/mothur/issues/288","repository_url":"https://api.github.com/repos/mothur/mothur","labels_url":"https://api.github.com/repos/mothur/mothur/issues/288/labels{/name}","comments_url":"https://api.github.com/repos/mothur/mothur/issues/288/comments","events_url":"https://api.github.com/repos/mothur/mothur/issues/288/events","html_url":"https://github.com/mothur/mothur/issues/288","id":192655517,"number":288,"title":"screen.seqs errors with optimize option","user":{"login":"khyox","id":4109713,"avatar_url":"https://avatars.githubusercontent.com/u/4109713?v=3","gravatar_id":"","url":"https://api.github.com/users/khyox","html_url":"https://github.com/khyox","followers_url":"https://api.github.com/users/khyox/followers","following_url":"https://api.github.com/users/khyox/following{/other_user}","gists_url":"https://api.github.com/users/khyox/gists{/gist_id}","starred_url":"https://api.github.com/users/khyox/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/khyox/subscriptions","organizations_url":"https://api.github.com/users/khyox/orgs","repos_url":"https://api.github.com/users/khyox/repos","events_url":"https://api.github.com/users/khyox/events{/privacy}","received_events_url":"https://api.github.com/users/khyox/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-11-30T19:24:25Z","updated_at":"2016-11-30T19:24:25Z","closed_at":null,"body":"Mothur v.1.38.1 running on a GNU/Linux box. When using `screen.seqs` in a batch file, the combination of the options _count_, _alignreport_ and _minscore_ works properly filtering the sequences:\r\n\r\n```\r\n(...)\r\nalign.seqs(reference=/software/mothur/silva.v123.V4.fasta, flip=t)\r\n(...)\r\nOutput File Names:\r\nmyproject.trim.contigs.good.good.unique.align\r\nmyproject.trim.contigs.good.good.unique.align.report\r\n(...)\r\nsummary.seqs(fasta=current, count=current)\r\n(...)\r\nscreen.seqs(fasta=current, count=current, alignreport=myproject.trim.contigs.good.good.unique.align.report, minscore=50)\r\nUsing myproject.trim.contigs.good.good.count_table as input file for the count parameter.\r\nUsing myproject.trim.contigs.good.good.unique.align as input file for the fasta parameter.\r\n\r\nUsing 64 processors.\r\nProcessing sequence: 100\r\n(...)\r\nProcessing sequence: 384\r\n\r\nOutput File Names:\r\nmyproject.trim.contigs.good.good.unique.align.good.align.report\r\nmyproject.trim.contigs.good.good.unique.good.align\r\nmyproject.trim.contigs.good.good.unique.bad.accnos\r\nmyproject.trim.contigs.good.good.good.count_table\r\n\r\nIt took 1 secs to screen 24569 sequences.\r\n```\r\n\r\nHowever, when I try to use the _optimize_ option (with _count_ and _alignreport_), the code fails with errors about the _namefile_, which is not an input:\r\n\r\n```\r\n(...)\r\nscreen.seqs(fasta=current, count=current, alignreport=myproject.trim.contigs.good.good.unique.align.report, optimize=minscore, criteria=99)\r\nUsing myproject.trim.contigs.good.good.count_table as input file for the count parameter.\r\nUsing myproject.trim.contigs.good.good.unique.align as input file for the fasta parameter.\r\n\r\nUsing 64 processors.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_27033_7405 is not in your namefile, please correct.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_16105_10387 is not in your namefile, please correct.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_2853_13443 is not in your namefile, please correct.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_16835_17019 is not in your namefile, please correct.\r\n(...)\r\n```\r\n\r\nOn the other hand, the labels seem to exist in the current namefile (got with `get.current()` just before `screen.seqs`):\r\n```\r\n> egrep M01167_151_000000000-AV07A_1_1101_27033_7405 myproject.trim.contigs.good.good.names\r\nM01167_151_000000000-AV07A_1_1101_27033_7405\tM01167_151_000000000-AV07A_1_1101_27033_7405,...\r\n > egrep M01167_151_000000000-AV07A_1_1101_16105_10387 myproject.trim.contigs.good.good.names\r\nM01167_151_000000000-AV07A_1_1101_16105_10387\tM01167_151_000000000-AV07A_1_1101_16105_10387,...\r\n```\r\n\r\nFinally, I unsuccessfully try to circumvent the problem generating an updated namefile and using it in `screen.seqs`:\r\n\r\n```\r\nalign.seqs(reference=/software/mothur/silva.v123.V4.fasta, flip=t)\r\n(...)\r\nOutput File Names:\r\nmyproject.trim.contigs.good.good.unique.align\r\nmyproject.trim.contigs.good.good.unique.align.report\r\n(...)\r\nsummary.seqs(fasta=current, count=current)\r\n(...)\r\nunique.seqs(fasta=current, count=current, format=name)\r\nUsing myproject.trim.contigs.good.good.count_table as input file for the count parameter.\r\nUsing myproject.trim.contigs.good.good.unique.align as input file for the fasta parameter.\r\n(...)\r\nOutput File Names:\r\nmyproject.trim.contigs.good.good.unique.names\r\nmyproject.trim.contigs.good.good.unique.unique.align\r\n\r\nscreen.seqs(fasta=current, name=current, alignreport=gollum.trim.contigs.good.good.unique.align.report, optimize=minscore, criteria=99)\r\nUsing gollum.trim.contigs.good.good.unique.unique.align as input file for the fasta parameter.\r\nUsing gollum.trim.contigs.good.good.unique.names as input file for the name parameter.\r\n\r\nUsing 64 processors.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_27033_7405 is not in your namefile, please correct.\r\n[ERROR]: M01167_151_000000000-AV07A_1_1101_16105_10387 is not in your namefile, please correct.\r\n(...)\r\n```\r\nUnlucky again. \r\nThanks!"}}
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