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Not too bothersome I guess…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":79,"like_count":3,"has_summary":false,"last_poster_username":"Claudio_Duran","category_id":8,"op_like_count":1,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":317,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster","user_id":322,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster","user_id":2,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":368,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"226 have a problem on the md5sum.txt","id":739,"title":"226 have a problem on the md5sum.txt","slug":"226-have-a-problem-on-the-md5sum-txt","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2025-05-29T11:55:23.451Z","last_posted_at":"2025-07-09T15:28:58.922Z","bumped":true,"bumped_at":"2025-07-09T15:28:58.922Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"HI I also find the error on the md5sum.txt of 226, which is similar to the latest version. It has caused some error when I used kraken2.","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":51,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":353,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Missing MD5SUM.txt on releases/latest/","id":733,"title":"Missing MD5SUM.txt on releases/latest/","slug":"missing-md5sum-txt-on-releases-latest","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2025-05-22T05:11:58.390Z","last_posted_at":"2025-07-04T02:22:36.732Z","bumped":true,"bumped_at":"2025-07-04T02:22:36.732Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"The file is available at GTDB Data - /releases/release226/226.0/, but not at GTDB Data - /releases/latest/. \nThis is causing the CAT_pack download to fail (and likely affects other tools that rely on the file’s availabil…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":37,"like_count":0,"has_summary":false,"last_poster_username":"aaronmussig","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":350,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":1,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"ValueError: ‘gtdb_taxonomy’ is not in list when metadata file lacks header","id":752,"title":"ValueError: 'gtdb_taxonomy' is not in list when metadata file lacks header","slug":"valueerror-gtdb-taxonomy-is-not-in-list-when-metadata-file-lacks-header","posts_count":3,"reply_count":0,"highest_post_number":3,"image_url":"https://forum.gtdb.ecogenomic.org/uploads/default/optimized/1X/da242873b0b1d787fe47c179e7e5220652901291_2_1024x399.png","created_at":"2025-07-02T02:22:59.739Z","last_posted_at":"2025-07-03T06:50:03.717Z","bumped":true,"bumped_at":"2025-07-03T06:50:03.717Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hi, GTDB team! \nI’m encountering an error while running the gtdb_to_ncbi_majority_vote.py script. \nEnvironment\nCentOS Linux 7 (Core) \ngtdbtk-2.4.1 \nDescription:\nWhen running \ngtdb_to_ncbi_majority_vote.py --gtdbtk_output…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":29,"like_count":1,"has_summary":false,"last_poster_username":"Rianjie_GMU","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":true,"can_have_answer":true,"can_vote":false,"posters":[{"extras":"latest","description":"Original Poster, Most Recent Poster","user_id":354,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster, Accepted Answer","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"g__CAIMXF01 - was assinged, but there are no info here","id":750,"title":"g__CAIMXF01 - was assinged, but there are no info here","slug":"g-caimxf01-was-assinged-but-there-are-no-info-here","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2025-06-16T15:23:56.612Z","last_posted_at":"2025-06-16T18:45:54.718Z","bumped":true,"bumped_at":"2025-06-16T18:45:54.718Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello dear GTDB team! \nI have a question, I had some mags, and one of them was assinged with gtdbtk as \nd__Bacteria; \np__Proteobacteria; \nc__Gammaproteobacteria; \no__Burkholderiales; \nf__Burkholderiaceae; \ng__CAIMXF01; \ns…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":33,"like_count":2,"has_summary":false,"last_poster_username":"m.chuvochina","category_id":8,"op_like_count":1,"pinned_globally":false,"featured_link":null,"has_accepted_answer":true,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":355,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster, Accepted Answer","user_id":5,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"LBA issue in GTDB","id":747,"title":"LBA issue in GTDB","slug":"lba-issue-in-gtdb","posts_count":4,"reply_count":2,"highest_post_number":4,"image_url":null,"created_at":"2025-06-10T13:44:45.812Z","last_posted_at":"2025-06-12T09:00:10.632Z","bumped":true,"bumped_at":"2025-06-12T09:00:10.632Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Dear GTDB team, \nI have recently noticed that some of the classifications in the GTDB seem to be occasionally skewed due to the long branch attraction. \nFor example, highly reduced endosymbiont Legionella polyplacis, sho…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":60,"like_count":2,"has_summary":false,"last_poster_username":"Phil_Hugenholtz","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":true,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":356,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster, Accepted Answer","user_id":5,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":138,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Single tree for both bacteria and archaea","id":748,"title":"Single tree for both bacteria and archaea","slug":"single-tree-for-both-bacteria-and-archaea","posts_count":5,"reply_count":3,"highest_post_number":5,"image_url":null,"created_at":"2025-06-10T18:49:13.571Z","last_posted_at":"2025-06-12T02:53:13.364Z","bumped":true,"bumped_at":"2025-06-12T02:53:13.364Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Dear GTDB team, \nI understand different marker genes were used for bacteria and archaea and 2 separate trees were provided. My question is how can I have just one single tree including both kingdom? It makes a lot of sen…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":92,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":98,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Question about GTDB release r226","id":740,"title":"Question about GTDB release r226","slug":"question-about-gtdb-release-r226","posts_count":4,"reply_count":2,"highest_post_number":4,"image_url":"https://forum.gtdb.ecogenomic.org/uploads/default/optimized/1X/9230302d7df5aa3fd6ed9924cccdf7bc41832bc8_2_1024x388.jpeg","created_at":"2025-05-30T03:12:10.497Z","last_posted_at":"2025-06-02T22:22:14.876Z","bumped":true,"bumped_at":"2025-06-02T22:22:14.876Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello, I found that GTDB released a new version named r226. Many old species have disappeared even some new species have been added. I checked the completeness and contamination of some discarded representive genomes, an…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":211,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":true,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":290,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster, Accepted Answer","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Different species shared ANI higher than 95% or even 97% threshold","id":720,"title":"Different species shared ANI higher than 95% or even 97% threshold","slug":"different-species-shared-ani-higher-than-95-or-even-97-threshold","posts_count":3,"reply_count":1,"highest_post_number":3,"image_url":"https://forum.gtdb.ecogenomic.org/uploads/default/original/1X/18f65eebd435d0dbbe5804b5446a3f3e5031650b.png","created_at":"2025-03-28T12:21:47.326Z","last_posted_at":"2025-05-26T21:51:10.196Z","bumped":true,"bumped_at":"2025-05-26T21:51:10.196Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Recently, I performed an metagenomic analysis using AOA genomes downloaded from GTDB. However, I found some species shared ANI higher than 97%. In the ‘Q&A’ (GTDB - FAQ), the threshold to distinguish different species is…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":164,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":290,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster","user_id":42,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Gtdb database update","id":723,"title":"Gtdb database update","slug":"gtdb-database-update","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2025-04-17T09:05:57.348Z","last_posted_at":"2025-05-26T21:45:17.127Z","bumped":true,"bumped_at":"2025-05-26T21:45:17.127Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Dear GTDB groups, Is there a script to update the GTDB database from RS220 to RS226 without having to download all the RS226 data?kind regards","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":82,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":345,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"How to obtain the isolate source of a large number of genomes?","id":712,"title":"How to obtain the isolate source of a large number of genomes?","slug":"how-to-obtain-the-isolate-source-of-a-large-number-of-genomes","posts_count":4,"reply_count":2,"highest_post_number":4,"image_url":null,"created_at":"2025-02-22T09:00:05.476Z","last_posted_at":"2025-03-28T22:43:39.073Z","bumped":true,"bumped_at":"2025-03-28T22:43:39.073Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello, everyone. Recently, I have been paying attention to the distribution of some species in different habitats around the world. Is there any simple way to obtain the isolated envrionments of several genomes? It is ha…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":113,"like_count":1,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":true,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":290,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster, Accepted Answer","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Request for scoring results in the metadata files","id":707,"title":"Request for scoring results in the metadata files","slug":"request-for-scoring-results-in-the-metadata-files","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2025-02-01T18:43:20.699Z","last_posted_at":"2025-02-06T17:15:41.324Z","bumped":true,"bumped_at":"2025-02-06T17:15:41.324Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"I was wondering if scoring information for all genomes could be incorporated into the metadata files for bacteria and archaea. Ideally, this would include both the ANI score and quality score used to calculate the balanc…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":71,"like_count":1,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":335,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Possible to provide a test database","id":699,"title":"Possible to provide a test database","slug":"possible-to-provide-a-test-database","posts_count":4,"reply_count":2,"highest_post_number":4,"image_url":null,"created_at":"2025-01-06T00:09:18.187Z","last_posted_at":"2025-01-09T15:38:03.984Z","bumped":true,"bumped_at":"2025-01-09T15:38:03.984Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello, \nCurrently, I work on a data manager for the Galaxy Project (https://usegalaxy.org), which has the purpose of saving the whole data on the server where each user can use it without the need to download it for each…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":104,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":329,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Contamination in Pseudomonas sp000955805","id":661,"title":"Contamination in Pseudomonas sp000955805","slug":"contamination-in-pseudomonas-sp000955805","posts_count":3,"reply_count":0,"highest_post_number":3,"image_url":null,"created_at":"2024-08-19T18:16:29.032Z","last_posted_at":"2024-10-11T15:30:48.708Z","bumped":true,"bumped_at":"2024-12-16T22:52:43.594Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hi, just want to report that there is a contamination in the genome GTDB - Loading.... The genomes has perfect matches to 16 different RNA sequences in the ERCC RNA spike-in mix. Considering the mix is artificially desig…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":60,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":314,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster","user_id":138,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Inquiry Regarding Matching 16S rRNA genes and MAGs","id":543,"title":"Inquiry Regarding Matching 16S rRNA genes and MAGs","slug":"inquiry-regarding-matching-16s-rrna-genes-and-mags","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":null,"created_at":"2023-12-12T06:58:39.891Z","last_posted_at":"2024-11-14T17:53:26.235Z","bumped":true,"bumped_at":"2024-11-14T17:53:26.235Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello, \nRecently in my research project, I extracted DNA from an environmental sample and conducted both metagenomic sequencing and amplicon sequencing. The MAGs were classified using GTDB-tk, while the taxonomy of the A…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":440,"like_count":1,"has_summary":false,"last_poster_username":"jcmcnch","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":257,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":325,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"Determining uncultured bacterial group/clade from GTDB data","id":673,"title":"Determining uncultured bacterial group/clade from GTDB data","slug":"determining-uncultured-bacterial-group-clade-from-gtdb-data","posts_count":3,"reply_count":0,"highest_post_number":3,"image_url":null,"created_at":"2024-10-07T03:46:32.238Z","last_posted_at":"2024-11-12T06:35:35.302Z","bumped":true,"bumped_at":"2024-11-12T06:35:35.302Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hello everyone, \nI’ve downloaded the metadata for a particular bacterial group from the latest GTDB release (R220). I’m now interested in confirming whether this group has any cultured representatives. Could you advise o…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":68,"like_count":0,"has_summary":false,"last_poster_username":"Raaj","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":"latest","description":"Original Poster, Most Recent Poster","user_id":255,"primary_group_id":null,"flair_group_id":null},{"extras":null,"description":"Frequent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]},{"fancy_title":"MAG or Isolate and ambiguous checkm scores","id":675,"title":"MAG or Isolate and ambiguous checkm scores","slug":"mag-or-isolate-and-ambiguous-checkm-scores","posts_count":2,"reply_count":0,"highest_post_number":2,"image_url":"https://forum.gtdb.ecogenomic.org/uploads/default/original/1X/9b0db0cad0529a12d7423a3746a621e03804db8d.png","created_at":"2024-10-14T10:54:54.198Z","last_posted_at":"2024-10-30T13:08:10.065Z","bumped":true,"bumped_at":"2024-10-30T13:08:10.065Z","archetype":"regular","unseen":false,"pinned":false,"unpinned":null,"excerpt":"Hey, \nFirst, would it be possible to reveal what combination of fields in the metadata file is used to determine whether a genome will be displayed as MAG or isolate in the online browser? This topic has been discussed i…","visible":true,"closed":false,"archived":false,"bookmarked":null,"liked":null,"tags_descriptions":{},"views":83,"like_count":0,"has_summary":false,"last_poster_username":"donovan.parks","category_id":8,"op_like_count":0,"pinned_globally":false,"featured_link":null,"has_accepted_answer":false,"can_have_answer":true,"can_vote":false,"posters":[{"extras":null,"description":"Original Poster","user_id":137,"primary_group_id":null,"flair_group_id":null},{"extras":"latest","description":"Most Recent Poster","user_id":4,"primary_group_id":null,"flair_group_id":null}]}]}}