Help and Getting Started


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About the Help and Getting Started category

Whether you’re just getting started or a seasoned expert, this is the place to troubleshoot problems, debug workflows, and puzzle over analyses. If you need or can offer help with Nextstrain, make a new topic in this cat…

2 376 June 19, 2020
Augur.io not found
0 6 January 21, 2022
Narrative making
4 65 January 21, 2022
Using existing alignment
3 27 January 20, 2022
Validation of results/default-build/ncov_with_accessions.json failed
1 34 January 20, 2022
Error in rule "align"
3 47 January 19, 2022
Changing default reference
1 20 January 19, 2022
Error when running sanitize_sequences.py on whole GISAID dump
0 22 January 19, 2022
Error in Rule Refine when run ncov
2 50 January 17, 2022
Subsampling sequences genetically related to a focal sample
0 23 January 14, 2022
Help with Build
2 66 December 24, 2021
Large, novel Spike deletions of unknown origin (not reproducible outside nextstrain framework)
3 165 December 23, 2021
How to pass an sequence index into a build?
2 44 December 21, 2021
Drop of Czech Republic samples & division reconstruction
1 68 December 20, 2021
Masking Question
1 55 December 20, 2021
SARS-CoV-2 tutorial Docker default issue
1 51 December 17, 2021
Followed data prep instructions, nextstrain fails
20 102 December 16, 2021
Example doesn't run
0 48 November 23, 2021
Error: augur clades\ KeyError: 'muts'
2 89 November 21, 2021
Augur refine error when call --timetree \
11 166 November 19, 2021
Error in rule proximity_score: Fasta file appears to have sequences of different lengths!
8 129 November 14, 2021
How to set the multiple divisions data
1 60 November 14, 2021
The most basic of build help
5 120 November 11, 2021
Auspice fails to fetch frequencies and frequencies cannot be normalized
5 217 November 8, 2021
Error in rule sanitize_metadata: ncov workflow
5 106 November 7, 2021
Using Genomic Epidemiology from GISAID
1 76 November 5, 2021
Sanitize_metadata.py error: ERROR: ' ' expected after '"'
6 135 November 5, 2021
Error while generating the nextstrain for only Israel Sequences
6 139 November 3, 2021
Problem with Setup
5 146 October 29, 2021
Regarding Build for USA- Missing Data
9 132 October 27, 2021