Comments (8)
Hi, @liamxg, it depends on what version you want to use.
Nextclade Web (the web version, on https://clades.nextstrain.org) can handle ~1000 sequences at a time, depending on your browser and computer resources (computation is done inside your browser, on your computer). If you need to use Nextclade Web, then we recommend to split your data into smaller batches and/or subsample it.
For large-scale analysis we recommend using Nextclade CLI (command line version; see docs here: https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli.html). You can see how we use it internally in:
- https://github.com/nextstrain/ncov-ingest (fetching from GISAID and Genbank databases, alignment and basic analysis)
- https://github.com/nextstrain/ncov (phylogenetic analysis)
Feel free to join our discussion forums, where you can discuss your case with other users and with Nextstrain team: https://discussion.nextstrain.org/
from nextclade.
Dear @ivan-aksamentov,
Thanks.
Could you help me out:
nextclade run
--input-dataset data/sars-cov-2
--output-all=output/
data/sars-cov-2/sequences.fasta
Error:
0: --input-dataset: path is invalid. Expected a directory path or a zip archive file path, but got: '"data/sars-cov-2"'
Location:
packages_rs/nextclade-cli/src/cli/nextclade_loop.rs:55
Backtrace omitted. Run with RUST_BACKTRACE=1 environment variable to display it.
Run with RUST_BACKTRACE=full to include source snippets.
from nextclade.
using more than 5 million sequences.
from nextclade.
What's inside data/sars-cov-2
?
from nextclade.
Dear @ivan-aksamentov,
from nextclade.
@liamxg If Nextclade cannot find dataset files, it means you probably confused your directories. This is not related to Nextclade, so you will have to figure this out yourself, sorry. I'd suggest to delete everything and start over paying attention to what paths you are giving to Nextclade and what these paths actually contain. Make sure you read nextclade --help
, nextclade dataset get --help
and nextclade run --help
.
Please open a new issue if you have questions or reports related to Nextclade.
from nextclade.
Dear @ivan-aksamentov,
Solved. Thanks.
from nextclade.
Dear @ivan-aksamentov,
Is is possible to run more than 5 million sequences at once using Nextclade CLI?
from nextclade.
Related Issues (20)
- web(minor): when customizing dataset files, it always says "pasted sequences" even if the field is for tree HOT 2
- I upload 1490 sequences to nextclade, and upload to auspice.us, why it shows me 4255 sequences?
- Allow suppression of ` |(reverse complement)` suffix in header of alignment output HOT 2
- how many genomes can nextclade handle? HOT 1
- PCR primer mutation functionality[v3] HOT 13
- 3.0.0 version not retrieving RSV datasets HOT 1
- Can support be extended for SC2 Datasets V2 for another month? HOT 4
- Feature Request: Dataset download all datasets within specified path HOT 4
- Beginners Help with Nextclade CLI HOT 6
- Empty input file causes uncaught error in v3 (it didn't in v2)
- Erroneous Clade Assignment or More Refined Tool? HOT 4
- Add a BA.1 reference for the web nextclade version HOT 4
- error when using `nextclade dataset get --verbosity` flag HOT 3
- 21L Tree Updates? HOT 2
- `--input-pcr-primers` listed in CLI help options despite being removed in v3 HOT 2
- When using `?input-fasta=` url query param without specifying dataset, web auto-starts analysis (prematurely) HOT 5
- Scrollbar shown for dataset names in dataset picker HOT 9
- how to generate the result table by the cli version auspice HOT 4
- output TSV column(s) for missing bases at beginning and end of sequence? HOT 1
- --input-dataset parameter HOT 5
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from nextclade.