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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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no response after I upload 1400 sequences. #361

Open liamxg opened 6 months ago

liamxg commented 6 months ago
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AngieHinrichs commented 6 months ago

Hi @liamxg, sorry but 1400 may be too many sequences for the web interface to handle all at the same time. If these sequences have already been in GISAID (or GenBank or GenBase) for a few days then hopefully most would have been added to the UShER tree already. If so, you can try uploading a file of sequence names or IDs instead of full sequences. You can upload a file in which each line has a full name|ID|date format (like France/ARA-HCL023182702301/2023|EPI_ISL_18568488|2023-11-21), or just a name (like France/ARA-HCL023182702301/2023) or just ID (like EPI_ISL_18568488).

liamxg commented 6 months ago

Dear @AngieHinrich, Thanks, I also just upload the ID of the 1400 sequences, but still do not work.

AngieHinrichs commented 6 months ago

Sorry to hear that. Is there any way to subdivide those sequences? Are they your own sequences, or are they from a repository like GISAID / GenBank / GenBase? (If so, which repository?)

liamxg commented 6 months ago

Dear @AngieHinrich,

they are all from GISAID.

liamxg commented 6 months ago

I upload the ID like this:

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liamxg commented 6 months ago

and then click upload button:

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liamxg commented 6 months ago

wait and is showed like this:

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liamxg commented 6 months ago

I try to upload 500 IDs, and still can not work.

AngieHinrichs commented 6 months ago

Sorry to hear that. Can you attach a file with the 500 IDs to this issue so I can try to reproduce the problem?

liamxg commented 6 months ago

Dear @AngieHinrich,

Could I send it to your email, please.

AngieHinrichs commented 6 months ago

Sure, it is angie at soe dot ucsc dot edu (replace with proper punctuation).

liamxg commented 6 months ago

Dear @AngieHinrichs,

Cool! Thank you again, sent!