{"action":"closed","issue":{"url":"https://api.github.com/repos/merenlab/anvio/issues/945","repository_url":"https://api.github.com/repos/merenlab/anvio","labels_url":"https://api.github.com/repos/merenlab/anvio/issues/945/labels{/name}","comments_url":"https://api.github.com/repos/merenlab/anvio/issues/945/comments","events_url":"https://api.github.com/repos/merenlab/anvio/issues/945/events","html_url":"https://github.com/merenlab/anvio/issues/945","id":354068897,"node_id":"MDU6SXNzdWUzNTQwNjg4OTc=","number":945,"title":"anvi-import-collection error (entries are not unique in some tables)","user":{"login":"nick-youngblut","id":2468572,"node_id":"MDQ6VXNlcjI0Njg1NzI=","avatar_url":"https://avatars0.githubusercontent.com/u/2468572?v=4","gravatar_id":"","url":"https://api.github.com/users/nick-youngblut","html_url":"https://github.com/nick-youngblut","followers_url":"https://api.github.com/users/nick-youngblut/followers","following_url":"https://api.github.com/users/nick-youngblut/following{/other_user}","gists_url":"https://api.github.com/users/nick-youngblut/gists{/gist_id}","starred_url":"https://api.github.com/users/nick-youngblut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nick-youngblut/subscriptions","organizations_url":"https://api.github.com/users/nick-youngblut/orgs","repos_url":"https://api.github.com/users/nick-youngblut/repos","events_url":"https://api.github.com/users/nick-youngblut/events{/privacy}","received_events_url":"https://api.github.com/users/nick-youngblut/received_events","type":"User","site_admin":false},"labels":[{"id":82726073,"node_id":"MDU6TGFiZWw4MjcyNjA3Mw==","url":"https://api.github.com/repos/merenlab/anvio/labels/bug","name":"bug","color":"fc2929","default":true},{"id":905017678,"node_id":"MDU6TGFiZWw5MDUwMTc2Nzg=","url":"https://api.github.com/repos/merenlab/anvio/labels/priority","name":"priority","color":"b60205","default":false}],"state":"closed","locked":false,"assignee":{"login":"ozcan","id":940884,"node_id":"MDQ6VXNlcjk0MDg4NA==","avatar_url":"https://avatars3.githubusercontent.com/u/940884?v=4","gravatar_id":"","url":"https://api.github.com/users/ozcan","html_url":"https://github.com/ozcan","followers_url":"https://api.github.com/users/ozcan/followers","following_url":"https://api.github.com/users/ozcan/following{/other_user}","gists_url":"https://api.github.com/users/ozcan/gists{/gist_id}","starred_url":"https://api.github.com/users/ozcan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ozcan/subscriptions","organizations_url":"https://api.github.com/users/ozcan/orgs","repos_url":"https://api.github.com/users/ozcan/repos","events_url":"https://api.github.com/users/ozcan/events{/privacy}","received_events_url":"https://api.github.com/users/ozcan/received_events","type":"User","site_admin":false},"assignees":[{"login":"ozcan","id":940884,"node_id":"MDQ6VXNlcjk0MDg4NA==","avatar_url":"https://avatars3.githubusercontent.com/u/940884?v=4","gravatar_id":"","url":"https://api.github.com/users/ozcan","html_url":"https://github.com/ozcan","followers_url":"https://api.github.com/users/ozcan/followers","following_url":"https://api.github.com/users/ozcan/following{/other_user}","gists_url":"https://api.github.com/users/ozcan/gists{/gist_id}","starred_url":"https://api.github.com/users/ozcan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ozcan/subscriptions","organizations_url":"https://api.github.com/users/ozcan/orgs","repos_url":"https://api.github.com/users/ozcan/repos","events_url":"https://api.github.com/users/ozcan/events{/privacy}","received_events_url":"https://api.github.com/users/ozcan/received_events","type":"User","site_admin":false}],"milestone":null,"comments":6,"created_at":"2018-08-26T06:02:42Z","updated_at":"2018-09-20T01:09:05Z","closed_at":"2018-09-20T01:09:05Z","author_association":"NONE","body":"I'm running anvio version:\r\n\r\n```\r\nAnvi'o version ...............................: margaret (vunknown)\r\nProfile DB version ...........................: 29\r\nContigs DB version ...........................: 12\r\nPan DB version ...............................: 12\r\nGenome data storage version ..................: 6\r\nAuxiliary data storage version ...............: 2\r\nStructure DB version .........................: 1\r\n(/ebio/abt3_projects/software/dev/llmga/.snakemake/conda/3b8a2f3c)\r\n```\r\n\r\n...and I'm getting the following error when running `anvi-import-collection` on a set of bins generated with `maxbin2`:\r\n\r\n```\r\nContig/split name conversion .................: 56166 contig names converted into 56166 split names.\r\nItem names in input ..........................: 56,166\r\nNum bins in input ............................: 190\r\nItems in profile database ....................: 57,501\r\nItem names shared between input and db .......: 56,166\r\n\r\nWARNING\r\n===============================================\r\n1335 item(s) that were in the database, but were not in the input file, will not\r\nbe described by any bin in the collection MaxBin2_low_prob. That is totally\r\nfine, but anvi'o hopes that you are aware of that. This means you have more\r\nthings in your database than the number of things your input file describes.\r\nHere is an example of something that is in your database but not in any bin in\r\nyour input file: coassemble_26409_split_00001.\r\n\r\n\r\n\r\nConfig Error: This is one of the core functions of anvi'o you never want to hear from, but\r\n              there seems to be something wrong with the table 'collections_bins_info' that\r\n              you are trying to read from. While there are 516 items in this table, there are\r\n              only 326 unique keys, which means some of them are going to be overwritten when\r\n              this function creates a final dictionary of data to return. This may be a\r\n              programmer error when the data was being inserted into the database, but needs\r\n              fixin' before we can continue. If you are a user, please get in touch with\r\n              anvi'o developers about this error. If you are a programmer, you probably did\r\n              something wrong :(\r\n```\r\n\r\nFor generating the contig db, I used the `--skip-mindful-splitting` option, since I had already split my contigs prior to the import. The `maxbin2` binning was done on the split contigs, so all of the contig naming should be the same. As far as I can tell, none of my contigs are named with \"*_split_00001\" in my contigs database or in my maxbin2 bins. \r\n\r\nFor the `anvi-import-collection` command, I'm using `--contigs-mode`, which I thought prevented renaming of the contigs. However, the log for the import states: \r\n\r\n```\r\nContig/split name conversion .................: 56166 contig names converted into 56166 split names.\r\n```\r\n\r\n...so it appears that `anvi-import-collection` is renaming contigs labeled such as `coassemble_26409` to `coassemble_26409_split_00001`, which results in a key mismatch between the collection contig names and the database contigs names. Is this a bug with `anvi-import-collection --contigs-mode` or am I just doing something wrong? \r\n\r\nI can't find a lot of documentation on `--contigs-mode`, so it's hard to tell if I'm using it wrong. The docs on `anvi-import-collection` state:\r\n\r\n```\r\n  --contigs-mode        Use this flag if your binning was done on contigs\r\n                        instead of splits. Please refer to the documentation\r\n                        for help.\r\n```\r\n\r\n...but where in the `documentation` should I be looking? There's a ton of documentation on the anvio website, and I don't see any search bar for finding all docs relating to `--contigs-mode`. I could only find this info at http://merenlab.org/2016/06/22/anvio-tutorial-v2/:\r\n\r\n> But if you have contig names, you can import them using anvi-import-collection with the flag --contigs-mode.\r\n"}}
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