# Latest **URL:** https://nextstrain.discourse.group/latest.md?page=3 [Latest](https://nextstrain.discourse.group/latest.md) · [Categories](https://nextstrain.discourse.group/categories.md) **Page:** 4 --- ## [Load json fails when change dataset on nextstrain](https://nextstrain.discourse.group/t/load-json-fails-when-change-dataset-on-nextstrain/1778)
**Author:** [@duxx](https://nextstrain.discourse.group/u/duxx)\ **Replies:** 1\ **Last updated:** [November 20, 2024, 3:30am UTC](https://nextstrain.discourse.group/t/load-json-fails-when-change-dataset-on-nextstrain/1778 "2024-11-20T03:30:18Z")
Hello nextstrain team. It’s hard to explain so I give you example. if you access “auspice” page and change A to B then fails. Obviously, I need to set one of F/G/WGS below /rsv/B/. but you can see below works. i… --- ## [\`nextclade sort\` Using a serverless local dataset for sorting](https://nextstrain.discourse.group/t/nextclade-sort-using-a-serverless-local-dataset-for-sorting/1777)
**Author:** [@eakin](https://nextstrain.discourse.group/u/eakin)\ **Replies:** 2\ **Last updated:** [November 20, 2024, 2:10am UTC](https://nextstrain.discourse.group/t/nextclade-sort-using-a-serverless-local-dataset-for-sorting/1777 "2024-11-20T02:10:42Z")
Greetings everyone! I see that nextclade sort accepts a --server flag for querying a hosted dataset collection to sort input sequences. However, this would be a bit awkward for my use case on a local machine. Is it cur… --- ## [Error: Alignment must have at least 3 sequences](https://nextstrain.discourse.group/t/error-alignment-must-have-at-least-3-sequences/599)
**Author:** [@jbarnell](https://nextstrain.discourse.group/u/jbarnell)\ **Replies:** 9\ **Last updated:** [November 7, 2024, 6:06am UTC](https://nextstrain.discourse.group/t/error-alignment-must-have-at-least-3-sequences/599 "2024-11-07T06:06:09Z")
Hello, It’s been awhile since I’ve run the local build of nextstrain on my computer, so I went ahead and updated everything, first from github, then from the CLI using “conda update --all” Ever since the update, I have… --- ## [Iqtree error: Tree taxa and alignment sequence do not match](https://nextstrain.discourse.group/t/iqtree-error-tree-taxa-and-alignment-sequence-do-not-match/1761)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 10\ **Last updated:** [November 6, 2024, 7:36am UTC](https://nextstrain.discourse.group/t/iqtree-error-tree-taxa-and-alignment-sequence-do-not-match/1761 "2024-11-06T07:36:40Z")
Hi all, Suddenly I get an error with IQTree that I have not seen before when using Nextstrain: \[Fri Oct 25 10:57:05 2024\] Job 3: Building tree Reason: Missing output files: nextstrain\_results/tree\_raw.nwk; Input files … --- ## [Web App and Nextclade (Pango)](https://nextstrain.discourse.group/t/web-app-and-nextclade-pango/1768)
**Author:** [@ABissonn](https://nextstrain.discourse.group/u/ABissonn)\ **Replies:** 1\ **Last updated:** [November 1, 2024, 7:54pm UTC](https://nextstrain.discourse.group/t/web-app-and-nextclade-pango/1768 "2024-11-01T19:54:59Z")
Hello, I am a research specialist at the Marshfield Clinic Research Institute, and I have previously used the Nextclade web app for Flu and SARS-CoV-2 lineage reports. Recently, I noticed our SARS-CoV-2 bioinformatics a… --- ## [Fix\_tree.py error for mpox trees](https://nextstrain.discourse.group/t/fix-tree-py-error-for-mpox-trees/1762)
**Author:** [@dlu](https://nextstrain.discourse.group/u/dlu)\ **Replies:** 3\ **Last updated:** [October 28, 2024, 6:04pm UTC](https://nextstrain.discourse.group/t/fix-tree-py-error-for-mpox-trees/1762 "2024-10-28T18:04:44Z")
In the step python3 scripts/fix\_tree.py --alignment results/aspen/masked.fasta --input-tree results/aspen/tree\_raw.nwk --output results/aspen/tree\_fixed.nwk For some … --- ## [RSV-A lineage reference sequences have discordant clade assignments](https://nextstrain.discourse.group/t/rsv-a-lineage-reference-sequences-have-discordant-clade-assignments/1760)
**Author:** [@davidbacsik](https://nextstrain.discourse.group/u/davidbacsik)\ **Replies:** 3\ **Last updated:** [October 27, 2024, 2:05am UTC](https://nextstrain.discourse.group/t/rsv-a-lineage-reference-sequences-have-discordant-clade-assignments/1760 "2024-10-27T02:05:00Z")
I am working on building a high quality reference tree with sequences from all of the RSV-A lineages defined using the 2024 Consortium criteria. My goal is to use this tree as a reference to infer the clade of novel sequ… --- ## [Nextstrain Installation](https://nextstrain.discourse.group/t/nextstrain-installation/1757)
**Author:** [@NikitaSitharam](https://nextstrain.discourse.group/u/NikitaSitharam)\ **Replies:** 8\ **Last updated:** [October 22, 2024, 5:07pm UTC](https://nextstrain.discourse.group/t/nextstrain-installation/1757 "2024-10-22T17:07:08Z")
Hi Nextstrain Team, I have been running workflows using the Nextstrain CLI for the last 3 months. However, today I tried to run a workflow but keep getting this error: Traceback (most recent call last): File "/Users… --- ## [Question about frequency values in builds files](https://nextstrain.discourse.group/t/question-about-frequency-values-in-builds-files/1748)
**Author:** [@adalisan](https://nextstrain.discourse.group/u/adalisan)\ **Replies:** 3\ **Last updated:** [October 15, 2024, 4:33pm UTC](https://nextstrain.discourse.group/t/question-about-frequency-values-in-builds-files/1748 "2024-10-15T16:33:48Z")
I have a question about the seasonal-flu builds of nextflu. I thought the “frequency” column in the output file builds/\//forecast\_.tsv is actually the frequency estimate of a tip/strain at the current timep… --- ## [How to type RSV clades](https://nextstrain.discourse.group/t/how-to-type-rsv-clades/1750)
**Author:** [@martahp](https://nextstrain.discourse.group/u/martahp)\ **Replies:** 3\ **Last updated:** [October 9, 2024, 4:02pm UTC](https://nextstrain.discourse.group/t/how-to-type-rsv-clades/1750 "2024-10-09T16:02:45Z")
Please, when you upload more than one RSV genome.fasta and it chooses a reference for each one, how do you know which ones are RSV-A and which ones are RSV-B? How to type the sequence because if you choose one reference… --- ## [Nextclade set of possible lineages or distance metric](https://nextstrain.discourse.group/t/nextclade-set-of-possible-lineages-or-distance-metric/1729)
**Author:** [@Thomas](https://nextstrain.discourse.group/u/Thomas)\ **Replies:** 2\ **Last updated:** [October 6, 2024, 6:03pm UTC](https://nextstrain.discourse.group/t/nextclade-set-of-possible-lineages-or-distance-metric/1729 "2024-10-06T18:03:03Z")
Hi, We are trying to assign RSV lineages based on partial sequences of L as only some of the amplicons succeeded. We tested, how well the available regions is suited to obtain the lineage and realized that in about 8% o… --- ## [Next Strain Q/A](https://nextstrain.discourse.group/t/next-strain-q-a/1705)
**Author:** [@yogesh.harsha](https://nextstrain.discourse.group/u/yogesh.harsha)\ **Replies:** 0\ **Last updated:** [July 31, 2024, 3:00pm UTC](https://nextstrain.discourse.group/t/next-strain-q-a/1705 "2024-07-31T15:00:37Z")
Hello I have some questions asked by our cloud governance team before implementing the use of Next Strain in our ecosystem. Can SSO be configured in next Strain? Can you please provide the data center cloud location f… --- ## [Are gaps due to true insertions ok to leave in the alignment?](https://nextstrain.discourse.group/t/are-gaps-due-to-true-insertions-ok-to-leave-in-the-alignment/1713)
**Author:** [@vzubach](https://nextstrain.discourse.group/u/vzubach)\ **Replies:** 1\ **Last updated:** [August 20, 2024, 8:54pm UTC](https://nextstrain.discourse.group/t/are-gaps-due-to-true-insertions-ok-to-leave-in-the-alignment/1713 "2024-08-20T20:54:14Z")
Hello I am new to Nextstrain and still have a lot to learn. I am working with measles sequences. Most of my samples are 15678nt long. But I have samples that have 6nt long insertions, and some indels which are all true.… --- ## [View in NextClade Feature](https://nextstrain.discourse.group/t/view-in-nextclade-feature/1740)
**Author:** [@whottel](https://nextstrain.discourse.group/u/whottel)\ **Replies:** 0\ **Last updated:** [September 20, 2024, 8:25pm UTC](https://nextstrain.discourse.group/t/view-in-nextclade-feature/1740 "2024-09-20T20:25:31Z")
Hello, I was trying out the “View in Other Platforms” option for Nextclade with Mpox data. I tried the mpox clade IIb tree (updated 2024-09-20), and when I dropped in data I wanted to add in NextClade I saw a mismatch … --- ## [Comparable mutation metrics?](https://nextstrain.discourse.group/t/comparable-mutation-metrics/1716)
**Author:** [@D600](https://nextstrain.discourse.group/u/D600)\ **Replies:** 1\ **Last updated:** [September 18, 2024, 1:43pm UTC](https://nextstrain.discourse.group/t/comparable-mutation-metrics/1716 "2024-09-18T13:43:15Z")
Greetings, To the experts this should be a simple question. When I see the mutation rate estimate for influenza A stated as 4.56e-3 subs per site per year, while for SARS CoV-2 stated as 35.145 subs per year, are thes… --- ## [Tree shows an X at the end of branches... what do they mean?](https://nextstrain.discourse.group/t/tree-shows-an-x-at-the-end-of-branches-what-do-they-mean/1695)
**Author:** [@ggreaves](https://nextstrain.discourse.group/u/ggreaves)\ **Replies:** 2\ **Last updated:** [July 22, 2024, 9:56pm UTC](https://nextstrain.discourse.group/t/tree-shows-an-x-at-the-end-of-branches-what-do-they-mean/1695 "2024-07-22T21:56:34Z")
Hi there, this may be a silly question, but what do the black X at the end of tree branches mean? --- ## [Difference between sequence samples based on Dataset](https://nextstrain.discourse.group/t/difference-between-sequence-samples-based-on-dataset/1734)
**Author:** [@neto](https://nextstrain.discourse.group/u/neto)\ **Replies:** 1\ **Last updated:** [September 16, 2024, 5:42pm UTC](https://nextstrain.discourse.group/t/difference-between-sequence-samples-based-on-dataset/1734 "2024-09-16T17:42:38Z")
Dear, I’m new here and I want to ask you a very beginner question. I need to get some information about SARS-CoV-2 in the South America countries, including the number of samples deposited in the GISAID in the last 3 m… --- ## [Reduce number of references in RSV phylogenetic tree - Nextclade CLI](https://nextstrain.discourse.group/t/reduce-number-of-references-in-rsv-phylogenetic-tree-nextclade-cli/1728)
**Author:** [@jojo](https://nextstrain.discourse.group/u/jojo)\ **Replies:** 1\ **Last updated:** [September 9, 2024, 6:24am UTC](https://nextstrain.discourse.group/t/reduce-number-of-references-in-rsv-phylogenetic-tree-nextclade-cli/1728 "2024-09-09T06:24:44Z")
Hello, I’m running Nextclade CLI on some RSV samples using the RSV Nextstrain datasets and I notice the phylogenetic tree that is produced is very large. How would you suggest to subsample the dataset to reduce the numb… --- ## [Mpox Sequence Changes from Root](https://nextstrain.discourse.group/t/mpox-sequence-changes-from-root/1726)
**Author:** [@whottel](https://nextstrain.discourse.group/u/whottel)\ **Replies:** 2\ **Last updated:** [September 5, 2024, 3:08pm UTC](https://nextstrain.discourse.group/t/mpox-sequence-changes-from-root/1726 "2024-09-05T15:08:29Z")
Hello, In looking at the mpox build and for B.1 samples I noticed that there are seveal OPG’s listed with multiple changes that I am unclear on interpretation. Using MPXV/AR-ANLIS037/2022 as an example, OPG153 lists a s… --- ## ["Could not determine delimiter" error with metadata files](https://nextstrain.discourse.group/t/could-not-determine-delimiter-error-with-metadata-files/1723)
**Author:** [@maryj](https://nextstrain.discourse.group/u/maryj)\ **Replies:** 5\ **Last updated:** [August 28, 2024, 9:16pm UTC](https://nextstrain.discourse.group/t/could-not-determine-delimiter-error-with-metadata-files/1723 "2024-08-28T21:16:15Z")
I am running in Docker on Windows and I’m fairly new to Nextstrain, but I have run through the Zika tutorial and a flu example build successfully. Now I’m trying to tweak and modify the example flu build and I’m running … --- ## [Methods to automate the list of pangos for augur filter?](https://nextstrain.discourse.group/t/methods-to-automate-the-list-of-pangos-for-augur-filter/1665)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 8\ **Last updated:** [August 27, 2024, 5:32pm UTC](https://nextstrain.discourse.group/t/methods-to-automate-the-list-of-pangos-for-augur-filter/1665 "2024-08-27T17:32:15Z")
Hi, I frequently SARS-CoV-2 builds, and every time I need to update the list of pangos to filter on. For example like this: builds: ba\_2\_86: pango\_lineage: "\['BA.2.86', 'BA.2.86.1', 'JN.1', 'JN.1.1', 'JN.1.… --- ## [Question about upload protocol for remote upload](https://nextstrain.discourse.group/t/question-about-upload-protocol-for-remote-upload/1719)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 1\ **Last updated:** [August 20, 2024, 6:38pm UTC](https://nextstrain.discourse.group/t/question-about-upload-protocol-for-remote-upload/1719 "2024-08-20T18:38:41Z")
Hi, Asking for my IT department here, so apologize if I use the wrong words… But what kind of upload protocol is used from nextstrain remote upload (e.g. ftp) and what port? We’re trying to set up our nextstrain build a… --- ## [Mpox lineage in metadata is different from what shows in the tree](https://nextstrain.discourse.group/t/mpox-lineage-in-metadata-is-different-from-what-shows-in-the-tree/1714)
**Author:** [@dlu](https://nextstrain.discourse.group/u/dlu)\ **Replies:** 2\ **Last updated:** [August 20, 2024, 4:58pm UTC](https://nextstrain.discourse.group/t/mpox-lineage-in-metadata-is-different-from-what-shows-in-the-tree/1714 "2024-08-20T16:58:12Z")
We’re using a fork from the mpox repo 2 years ago and I just wanted to check in case there is an obvious answer for this. We have some samples that have lineage B.1.20 in the metadata (downloaded from data.nextstrain.or… --- ## [Tree topology different than expected](https://nextstrain.discourse.group/t/tree-topology-different-than-expected/1712)
**Author:** [@vzubach](https://nextstrain.discourse.group/u/vzubach)\ **Replies:** 0\ **Last updated:** [August 16, 2024, 1:07pm UTC](https://nextstrain.discourse.group/t/tree-topology-different-than-expected/1712 "2024-08-16T13:07:25Z")
Hello I am working on some WGS (about 16kb) measles cases from 2018 to 2024. I have one epidemiologically confirmed cluster that is not showing the tree topology I expected. Sample A infected B, C, and D. Sample D infec… --- ## [Influenza vaccine selection dates](https://nextstrain.discourse.group/t/influenza-vaccine-selection-dates/1710)
**Author:** [@adalisan](https://nextstrain.discourse.group/u/adalisan)\ **Replies:** 1\ **Last updated:** [August 15, 2024, 5:31pm UTC](https://nextstrain.discourse.group/t/influenza-vaccine-selection-dates/1710 "2024-08-15T17:31:04Z")
in the seasonal-flu github repository, the vaccine.json file contains the selection dates , seasonal-flu/config/h3n2/vaccine.json at master · nextstrain/seasonal-flu · GitHub . For this egg-based vaccine variant , th… --- ## [Resource for representative nucleotide changes for Nextstrain clades](https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698)
**Author:** [@meadow](https://nextstrain.discourse.group/u/meadow)\ **Replies:** 1\ **Last updated:** [August 2, 2024, 11:17pm UTC](https://nextstrain.discourse.group/t/resource-for-representative-nucleotide-changes-for-nextstrain-clades/1698 "2024-08-02T23:17:33Z")
Hello all, Firstly, thanks for the contribution to the field with Nextstrain and all the associated resources! We would like to use Nextstrain resources in our project, and I have been digging into your resources for a… --- ## [Download and rename all builds from nextstrain.org/groups](https://nextstrain.discourse.group/t/download-and-rename-all-builds-from-nextstrain-org-groups/1688)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 5\ **Last updated:** [August 1, 2024, 4:10pm UTC](https://nextstrain.discourse.group/t/download-and-rename-all-builds-from-nextstrain-org-groups/1688 "2024-08-01T16:10:55Z")
Hi, I want to rename old nextstrain builds on nextstrain.org/groups/niph to make it easier to navigate between different agents and builds inside the auspice tree viewer menu. But over time we have used a mix of differ… --- ## [Titer measurement formats and conversion to csv for nextflu](https://nextstrain.discourse.group/t/titer-measurement-formats-and-conversion-to-csv-for-nextflu/1690)
**Author:** [@adalisan](https://nextstrain.discourse.group/u/adalisan)\ **Replies:** 3\ **Last updated:** [July 30, 2024, 5:54pm UTC](https://nextstrain.discourse.group/t/titer-measurement-formats-and-conversion-to-csv-for-nextflu/1690 "2024-07-30T17:54:48Z")
I have csv files that were parsed from the published WIC-Crick reports. I believe these are in table format (strain vs strain). How do I put these in the format that the nextflu pipeline uses? I was able to get a rethink… --- ## [Confirming presence of amino acid that matches the reference sequence](https://nextstrain.discourse.group/t/confirming-presence-of-amino-acid-that-matches-the-reference-sequence/1701)
**Author:** [@T4R4](https://nextstrain.discourse.group/u/T4R4)\ **Replies:** 0\ **Last updated:** [July 30, 2024, 12:15am UTC](https://nextstrain.discourse.group/t/confirming-presence-of-amino-acid-that-matches-the-reference-sequence/1701 "2024-07-30T00:15:01Z")
Hello, I’m interested in using the nextclade output to detect the presence of specific amino acids associated with ab resistance in the F gene of RSV. Some of the amino acids I’m trying to confirm the presence of are i… --- ## [Mpox: nextstrain issue](https://nextstrain.discourse.group/t/mpox-nextstrain-issue/1683)
**Author:** [@Kritchy](https://nextstrain.discourse.group/u/Kritchy)\ **Replies:** 2\ **Last updated:** [July 20, 2024, 9:48am UTC](https://nextstrain.discourse.group/t/mpox-nextstrain-issue/1683 "2024-07-20T09:48:58Z")
Hello, I am working on mpox surveillance in Thailand.I initially attempted to run the mpox Nextstrain analysis on my local notebook using the default settings because I don’t yet have access to AWS S3. However, I encoun… [Previous page](https://nextstrain.discourse.group/latest.md?page=2) [Next page](https://nextstrain.discourse.group/latest.md?page=4)