# Uncategorized **URL:** https://nextstrain.discourse.group/c/uncategorized/1.md [Latest](https://nextstrain.discourse.group/latest.md) · [Categories](https://nextstrain.discourse.group/categories.md) --- ## [SARS-CoV-2 workflow: nextclade.tsv.zst description](https://nextstrain.discourse.group/t/sars-cov-2-workflow-nextclade-tsv-zst-description/2255)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 3\ **Last updated:** [July 19, 2026, 7:03am UTC](https://nextstrain.discourse.group/t/sars-cov-2-workflow-nextclade-tsv-zst-description/2255 "2026-07-19T07:03:58Z")
The documentation page SARS-CoV-2 workflow \> Remote inputs mentions a file nextclade.tsv.zst which sounds intriguing. In my imagination, it is the output from processing all the sequences.fasta.zst output through the ne… --- ## [SARS-CoV-2 - no entry in nightly build for RW.1.1.2?](https://nextstrain.discourse.group/t/sars-cov-2-no-entry-in-nightly-build-for-rw-1-1-2/2232)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 1\ **Last updated:** [July 4, 2026, 6:07am UTC](https://nextstrain.discourse.group/t/sars-cov-2-no-entry-in-nightly-build-for-rw-1-1-2/2232 "2026-07-04T06:07:14Z")
In the SARS-CoV-2 nightly build, I can see the new entries for RW.1.1.1 and RW.1.1.3, but RW.1.1.2 appears to be missing? I’m downloading from: https://nextstrain.org/charon/getDataset?prefix=staging/nextclade/sars-cov… --- ## [Treetime dating - Negative branch lengths](https://nextstrain.discourse.group/t/treetime-dating-negative-branch-lengths/2045)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [May 25, 2026, 3:26pm UTC](https://nextstrain.discourse.group/t/treetime-dating-negative-branch-lengths/2045 "2026-05-25T15:26:45Z")
Hello everyone, I am trying to build a dated phylogenetic tree using TreeTime (version 0.12.1). I used the following command: treetime --tree tree.treefile --aln aln.fasta --dates dates.csv \\ --reconstruct-tip-stat… --- ## [SARS-CoV-2 - no PQ.16.1.1 calls?](https://nextstrain.discourse.group/t/sars-cov-2-no-pq-16-1-1-calls/2031)
**Author:** [@mike\_honey](https://nextstrain.discourse.group/u/mike_honey)\ **Replies:** 2\ **Last updated:** [May 25, 2026, 12:34am UTC](https://nextstrain.discourse.group/t/sars-cov-2-no-pq-16-1-1-calls/2031 "2026-05-25T00:34:54Z")
Yesterday I pushed the last few months of samples from GISAID through the latest Nextclade nightly build. I got 16 samples of PQ.16.1, but none at all of PQ.16.1.1. Is there some issue with it at your end? --- ## [Include external tools in the Nextstrain Snakemake workflow](https://nextstrain.discourse.group/t/include-external-tools-in-the-nextstrain-snakemake-workflow/2021)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 3\ **Last updated:** [February 6, 2026, 5:58pm UTC](https://nextstrain.discourse.group/t/include-external-tools-in-the-nextstrain-snakemake-workflow/2021 "2026-02-06T17:58:03Z")
Hi, I’m using the nextstrain build Docker-based workflow. And I want to include the tool “Treemmer” to reduce a phylogenetic tree afte the initial “augur tree”. Treemmer can be installed locally, but is also available a… --- ## [How to get the correct time axis when using augur refine and timetree?](https://nextstrain.discourse.group/t/how-to-get-the-correct-time-axis-when-using-augur-refine-and-timetree/2020)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 4\ **Last updated:** [February 4, 2026, 9:18pm UTC](https://nextstrain.discourse.group/t/how-to-get-the-correct-time-axis-when-using-augur-refine-and-timetree/2020 "2026-02-04T21:18:11Z")
Hi, I’m running this command: Shell command: augur refine --tree nextstrain\_results/tree\_raw.nwk --alignment nextstrain\_results/aligned.fasta --metadata phylogeny/genotypes\_combined… --- ## [Nextclade short clade annotation H1N1](https://nextstrain.discourse.group/t/nextclade-short-clade-annotation-h1n1/2016)
**Author:** [@georges.hanna](https://nextstrain.discourse.group/u/georges.hanna)\ **Replies:** 1\ **Last updated:** [January 15, 2026, 9:15pm UTC](https://nextstrain.discourse.group/t/nextclade-short-clade-annotation-h1n1/2016 "2026-01-15T21:15:29Z")
Hello, I am trying to annotate H1N1 sequences uysing nextclade web version and the ref dataset of 2019, but when I download the tsv output annotation file, I cannot find columns for short clade and legacy-clade. The onl… --- ## [How to set up next strain](https://nextstrain.discourse.group/t/how-to-set-up-next-strain/2011)
**Author:** [@N\_MBERS](https://nextstrain.discourse.group/u/N_MBERS)\ **Replies:** 2\ **Last updated:** [January 8, 2026, 7:17pm UTC](https://nextstrain.discourse.group/t/how-to-set-up-next-strain/2011 "2026-01-08T19:17:37Z")
Hii this is Kelvin from the last meeting just wanted to know how to set up nextstrain tool --- ## [How can one identify host-adaptive/associated mutations from a tree?](https://nextstrain.discourse.group/t/how-can-one-identify-host-adaptive-associated-mutations-from-a-tree/1899)
**Author:** [@ankeetkumar](https://nextstrain.discourse.group/u/ankeetkumar)\ **Replies:** 0\ **Last updated:** [May 25, 2025, 10:53am UTC](https://nextstrain.discourse.group/t/how-can-one-identify-host-adaptive-associated-mutations-from-a-tree/1899 "2025-05-25T10:53:02Z")
Dear all, I want to identify host-adaptive/associated mutations from sequence data. Can I get guidance on this? Thanks --- ## [How to map SARS-COV-2 Clades to WHO name?](https://nextstrain.discourse.group/t/how-to-map-sars-cov-2-clades-to-who-name/1859)
**Author:** [@jwang58](https://nextstrain.discourse.group/u/jwang58)\ **Replies:** 1\ **Last updated:** [March 15, 2025, 7:33am UTC](https://nextstrain.discourse.group/t/how-to-map-sars-cov-2-clades-to-who-name/1859 "2025-03-15T07:33:34Z")
Can someone help on the SARS-COV-2 Clades to WHO name ? --- ## [Annotation error for aa translation](https://nextstrain.discourse.group/t/annotation-error-for-aa-translation/1824)
**Author:** [@NyxMoiren](https://nextstrain.discourse.group/u/NyxMoiren)\ **Replies:** 2\ **Last updated:** [February 3, 2025, 7:27pm UTC](https://nextstrain.discourse.group/t/annotation-error-for-aa-translation/1824 "2025-02-03T19:27:15Z")
Hi all, we already successfully loaded other annotation files into our nextstrain build (for chromosome and also one plasmid). While trying to get another plasmid annotated, we ran into the error given below. Also googl… --- ## [Aligned nucleotide sequence does not match the CDS translation](https://nextstrain.discourse.group/t/aligned-nucleotide-sequence-does-not-match-the-cds-translation/1810)
**Author:** [@Dylan\_Lebatteux](https://nextstrain.discourse.group/u/Dylan_Lebatteux)\ **Replies:** 1\ **Last updated:** [January 9, 2025, 9:27pm UTC](https://nextstrain.discourse.group/t/aligned-nucleotide-sequence-does-not-match-the-cds-translation/1810 "2025-01-09T21:27:56Z")
Hello everyone, First of all, I would like to thank your team for your work and contributions to the scientific community. I am currently facing the following issue: I have aligned sequences of a gene (UL73) from the H… --- ## [Frequency map problem](https://nextstrain.discourse.group/t/frequency-map-problem/1796)
**Author:** [@Haya.Bader94](https://nextstrain.discourse.group/u/Haya.Bader94)\ **Replies:** 2\ **Last updated:** [December 20, 2024, 4:46pm UTC](https://nextstrain.discourse.group/t/frequency-map-problem/1796 "2024-12-20T16:46:16Z")
Hi everyone I have a problem in making the frequency tree of. SARS\_CoV-2 lineages If there is any one can help me plz :pray: --- ## [\`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… --- ## [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 … --- ## [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… --- ## [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… --- ## [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… --- ## [How to change the reference sequence?](https://nextstrain.discourse.group/t/how-to-change-the-reference-sequence/1686)
**Author:** [@XingguangLi](https://nextstrain.discourse.group/u/XingguangLi)\ **Replies:** 2\ **Last updated:** [July 18, 2024, 12:12am UTC](https://nextstrain.discourse.group/t/how-to-change-the-reference-sequence/1686 "2024-07-18T00:12:36Z")
How to I change Reference: HIV-1, strain HXB2 (NC\_001802) to another reference in nextclade? --- ## [Lost the tip names (labels)](https://nextstrain.discourse.group/t/lost-the-tip-names-labels/1676)
**Author:** [@Kritchy](https://nextstrain.discourse.group/u/Kritchy)\ **Replies:** 2\ **Last updated:** [July 11, 2024, 11:34pm UTC](https://nextstrain.discourse.group/t/lost-the-tip-names-labels/1676 "2024-07-11T23:34:25Z")
I lost the tip labels (derived from the FASTA file headers) on my phylogenetic tree, but they are still visible when I hover my mouse pointer over the tips. Could you please suggest how to fix this? --- ## [Reference tree for RSV used in NextClade webstie](https://nextstrain.discourse.group/t/reference-tree-for-rsv-used-in-nextclade-webstie/1657)
**Author:** [@Thomas](https://nextstrain.discourse.group/u/Thomas)\ **Replies:** 3\ **Last updated:** [June 19, 2024, 9:07pm UTC](https://nextstrain.discourse.group/t/reference-tree-for-rsv-used-in-nextclade-webstie/1657 "2024-06-19T21:07:17Z")
Hi, If I understand it correctly, then in the publication: ‘The unified proposal for classification of human respiratory syncytial virus below the subgroup level’., a set of 1480 RSV-A sequences and 1385 RSV-B sequences… --- ## [How can I know the Nextclade\_pango for each of SC2 sequences?](https://nextstrain.discourse.group/t/how-can-i-know-the-nextclade-pango-for-each-of-sc2-sequences/1604)
**Author:** [@XingguangLi](https://nextstrain.discourse.group/u/XingguangLi)\ **Replies:** 4\ **Last updated:** [June 15, 2024, 7:46am UTC](https://nextstrain.discourse.group/t/how-can-i-know-the-nextclade-pango-for-each-of-sc2-sequences/1604 "2024-06-15T07:46:13Z")
Hi, If I have 16 million of SC2 sequences, how can I know the Nextclade\_pango for each of SC2 sequences? --- ## [Question about mafft alignment using a reference sequence](https://nextstrain.discourse.group/t/question-about-mafft-alignment-using-a-reference-sequence/1614)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 2\ **Last updated:** [June 14, 2024, 6:14am UTC](https://nextstrain.discourse.group/t/question-about-mafft-alignment-using-a-reference-sequence/1614 "2024-06-14T06:14:29Z")
Hi, I add the following arguments to augur align: augur align \\ --sequences {input.sequences} \\ --reference-sequence {input.reference} \\ --nthreads 10 \\ --method … --- ## [Selection of RSV reference sequences](https://nextstrain.discourse.group/t/selection-of-rsv-reference-sequences/1655)
**Author:** [@Thomas](https://nextstrain.discourse.group/u/Thomas)\ **Replies:** 2\ **Last updated:** [May 23, 2024, 6:09pm UTC](https://nextstrain.discourse.group/t/selection-of-rsv-reference-sequences/1655 "2024-05-23T18:09:23Z")
Hi all, I was wondering how the reference sequences for RSV-A and RSV-B in nextclade were selected. Were there any special considerations when picking EPI\_ISL\_412866 for RSV-A? I’m assuming a more recent sequence with h… --- ## [Problems for the SARS-CoV-2 Workflow](https://nextstrain.discourse.group/t/problems-for-the-sars-cov-2-workflow/1388)
**Author:** [@lfy](https://nextstrain.discourse.group/u/lfy)\ **Replies:** 1\ **Last updated:** [May 19, 2023, 11:50am UTC](https://nextstrain.discourse.group/t/problems-for-the-sars-cov-2-workflow/1388 "2023-05-19T11:50:39Z")
Dear nextstrain team, when we run the SARS-CoV-2 Workflow, why some variants (such as XBB.1.16, BA.2.75) not found in tree and they don’t show up in the auspice.us. We have uploaded our data under ncov/data/. This is o… --- ## [Inferring pathogen.json from a nextclade.tsv results](https://nextstrain.discourse.group/t/inferring-pathogen-json-from-a-nextclade-tsv-results/1611)
**Author:** [@quietjen](https://nextstrain.discourse.group/u/quietjen)\ **Replies:** 0\ **Last updated:** [April 16, 2024, 2:54pm UTC](https://nextstrain.discourse.group/t/inferring-pathogen-json-from-a-nextclade-tsv-results/1611 "2024-04-16T14:54:38Z")
Posting for discussion: While creating a Nextclade dataset, had wondered if there’s a method to fine-tune reasonable attribute cutoffs in the pathogen.json file based on the nextclade.tsv QC columns. Non-urgent question… --- ## [When Nextclade CLI calls clades but Nextclade Web does not](https://nextstrain.discourse.group/t/when-nextclade-cli-calls-clades-but-nextclade-web-does-not/1610)
**Author:** [@quietjen](https://nextstrain.discourse.group/u/quietjen)\ **Replies:** 0\ **Last updated:** [April 16, 2024, 2:49pm UTC](https://nextstrain.discourse.group/t/when-nextclade-cli-calls-clades-but-nextclade-web-does-not/1610 "2024-04-16T14:49:06Z")
Posting here in case others run into the same problem. I was building a Nextclade dataset. During testing the Nextclade CLI called clades while the Nextclade Web left the clades column blank. After chatting with Corneli… --- ## [IQTREE error: Some sequences (see above) are problematic, please check your alignment again](https://nextstrain.discourse.group/t/iqtree-error-some-sequences-see-above-are-problematic-please-check-your-alignment-again/1605)
**Author:** [@jonr](https://nextstrain.discourse.group/u/jonr)\ **Replies:** 3\ **Last updated:** [April 11, 2024, 10:08pm UTC](https://nextstrain.discourse.group/t/iqtree-error-some-sequences-see-above-are-problematic-please-check-your-alignment-again/1605 "2024-04-11T22:08:22Z")
Hi, My build stops at the iqtree stage with the message: “ERROR: Some sequences (see above) are problematic, please check your alignment again” Job 3: Building tree Reason: Missing output files: nextstrain\_results/tree… --- ## [Can't open this page!](https://nextstrain.discourse.group/t/cant-open-this-page/1579)
**Author:** [@XingguangLi](https://nextstrain.discourse.group/u/XingguangLi)\ **Replies:** 1\ **Last updated:** [March 12, 2024, 3:39pm UTC](https://nextstrain.discourse.group/t/cant-open-this-page/1579 "2024-03-12T15:39:46Z")
Dear Core Nextstrain team, When I upload my data, it tells me can’t open this page! [Next page](https://nextstrain.discourse.group/c/uncategorized/1.md?page=1)