{"action":"created","issue":{"url":"https://api.github.com/repos/benjjneb/dada2/issues/631","repository_url":"https://api.github.com/repos/benjjneb/dada2","labels_url":"https://api.github.com/repos/benjjneb/dada2/issues/631/labels{/name}","comments_url":"https://api.github.com/repos/benjjneb/dada2/issues/631/comments","events_url":"https://api.github.com/repos/benjjneb/dada2/issues/631/events","html_url":"https://github.com/benjjneb/dada2/issues/631","id":387268706,"node_id":"MDU6SXNzdWUzODcyNjg3MDY=","number":631,"title":"Assigning taxonomy with new database","user":{"login":"carolina671","id":45498890,"node_id":"MDQ6VXNlcjQ1NDk4ODkw","avatar_url":"https://avatars2.githubusercontent.com/u/45498890?v=4","gravatar_id":"","url":"https://api.github.com/users/carolina671","html_url":"https://github.com/carolina671","followers_url":"https://api.github.com/users/carolina671/followers","following_url":"https://api.github.com/users/carolina671/following{/other_user}","gists_url":"https://api.github.com/users/carolina671/gists{/gist_id}","starred_url":"https://api.github.com/users/carolina671/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carolina671/subscriptions","organizations_url":"https://api.github.com/users/carolina671/orgs","repos_url":"https://api.github.com/users/carolina671/repos","events_url":"https://api.github.com/users/carolina671/events{/privacy}","received_events_url":"https://api.github.com/users/carolina671/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-12-04T12:44:48Z","updated_at":"2018-12-11T08:00:48Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI would like to run the dada2 pipeline with a different database, as ai am working with a gene different to 16S, specifically i work with the nifH gene which has its own database. This database can be found in .arb format (https://wwwzehr.pmc.ucsc.edu/nifH_Database_Public/) or in a fasta format ( http://www.css.cornell.edu/faculty/buckley/nifH_database_2012.fasta). \r\n\r\nSince the silva file for assigning the 16S taxonomy is in a fasta file .arb format is an updated version, i  tried unsuccesfully to convert the .arb file to a fasta file using qiime.  Maybe do you have any other ideas on how to make it readable for the pipeline?\r\n\r\nAlso I tried to assign the taxonomy directly with the fasta file but i am getting the following errors:\r\n\r\n> NIFHdatabase<- \"~/DATA/NIFH/nifH_database_2012.fasta\"\r\n> taxaNIFH <- assignTaxonomy(seqtab.nochimNIFH, NIFHdatabase, multithread=TRUE)\r\nError in assignTaxonomy(seqtab.nochimNIFH, NIFHdatabase, multithread = TRUE) : \r\n  Incorrect reference file format for assignTaxonomy.\r\nIn addition: Warning message:\r\nIn .Call2(\"fasta_index\", filexp_list, nrec, skip, seek.first.rec,  :\r\n  reading FASTA file /frontiers-shared/home/b6001443/DATA/NIFH/nifH_database_2012.fasta: ignored 4679468 invalid one-letter sequence codes\r\n\r\nSince the fasta files are aligned and therefore contain some gaps the i tried to remove the gaps on the sequences and the I got the following errors:\r\n\r\n> NIFHdatabase<- \"~/DATA/NIFH/nifH_database_2012.fasta.txt\"\r\nWarning messages:\r\n1: replacing previous import ‘BiocGenerics::path’ by ‘Rsamtools::path’ when loading ‘GenomicAlignments’ \r\n2: multiple methods tables found for ‘rglist’ \r\n3: replacing previous import ‘BiocGenerics::path’ by ‘Rsamtools::path’ when loading ‘ShortRead’ \r\n> taxaNIFH <- assignTaxonomy(seqtab.nochimNIFH, NIFHdatabase, multithread=TRUE)\r\nError in (function (classes, fdef, mtable)  : \r\n  unable to find an inherited method for function ‘windows’ for signature ‘\"DNAString\"’\r\n\r\nThanks!\r\n"},"comment":{"url":"https://api.github.com/repos/benjjneb/dada2/issues/comments/446107036","html_url":"https://github.com/benjjneb/dada2/issues/631#issuecomment-446107036","issue_url":"https://api.github.com/repos/benjjneb/dada2/issues/631","id":446107036,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NjEwNzAzNg==","user":{"login":"carolina671","id":45498890,"node_id":"MDQ6VXNlcjQ1NDk4ODkw","avatar_url":"https://avatars2.githubusercontent.com/u/45498890?v=4","gravatar_id":"","url":"https://api.github.com/users/carolina671","html_url":"https://github.com/carolina671","followers_url":"https://api.github.com/users/carolina671/followers","following_url":"https://api.github.com/users/carolina671/following{/other_user}","gists_url":"https://api.github.com/users/carolina671/gists{/gist_id}","starred_url":"https://api.github.com/users/carolina671/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carolina671/subscriptions","organizations_url":"https://api.github.com/users/carolina671/orgs","repos_url":"https://api.github.com/users/carolina671/repos","events_url":"https://api.github.com/users/carolina671/events{/privacy}","received_events_url":"https://api.github.com/users/carolina671/received_events","type":"User","site_admin":false},"created_at":"2018-12-11T08:00:48Z","updated_at":"2018-12-11T08:00:48Z","author_association":"NONE","body":"Hi,\r\n\r\nThanks so much for the information. \r\n\r\nDo you know if there is any way of converting a .arb file to  a fasta file using R?\r\n\r\nThanks,\r\n"}}
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