Comments (2)
There is no hard limit, but Nextclade Web is running all computations on your local computer and uses 32-bit WebAssembly underneath, which is limited to ~3.5 GBytes of memory (RAM). 64-bit WebAssembly exists, but is not yet supported in any browsers yet, so it is not currently feasible to use it.
Another soft limit is that Auspice cannot render this many nodes on the tree anyways, and the tree JSON representation becomes too huge to be manageable.
In the end, it depends on what sequences you analyze - larger genomes and lower quality sequences require more memory. As well as how much memory you have available on your computer. Closing unused browser tabs (especially other Nextclade tabs) and other programs might help to free up the memory (up to the maximum of 3.5 GBytes). In Nextclade's settings you can reduce number of parallel threads and turn off extra markers in sequence views to reduce memory consumption. You can use Chrome's task manager (Menu -> More tools -> Task manager) as well as system memory monitoring tools to keep track of memory and CPU usage.
Additionally, you can split your inputs into chunks and analyze them separately.
If you need large-scale analysis, our recommended solution is to run Nextclade CLI, which can analyze virtually unlimited number of sequences (especially if the Auspice tree JSON is not requested in the outputs). It uses less memory and is much faster. It is not as convenient though, does not have any visualization (but you can use Excel on the TSV output file) and requires some command-line skills.
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Thanks. I always have a million tabs open, so maybe I need to change that. Despite reading about 200 pages on the topic, I have zero command-line skills, so using the CLI isn't really an option.
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Related Issues (20)
- How to decide if the reversionSubstitutions are valid variants or not and whether to keep them? HOT 2
- Direct Auspice SVG Download
- ENH: enlarge Visualization when more nucleotides/Codons even if mutations not fall in striclty adjacent codons but close enough to need a whole view. HOT 2
- Updating certain parts of the JSON file output from Map to Array HOT 2
- linux-musl artefact gets slower rather than faster when parallelizing in contrast to gnu HOT 5
- Parsing PCR primers HOT 1
- how many SARS-COV-2 sequences can nextclade handle in a MSA file? HOT 8
- Is there any example for handling HIV data? HOT 2
- Web crash: The target <seqName> could not be identified in the dom HOT 2
- Show "browser not supported HOT 1
- Show "browser not supported" modal only once per session HOT 3
- if the qc.overallStatus of my sequences are mediocre, can we keep them for next step analysis? HOT 5
- web-based nextclade issue when using another reference HOT 8
- 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
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