[HELP]

[kpawlowski13]

Hi,

I would like to download a fasta file with all the proteins from all the known defense systems.
The Web wiki at
https://defensefinder.mdmlab.fr/wiki/refseq
is crashing:
"MeiliSearchCommunicationError: Load failed"

However, I found this fasta file in this GitHub repo:
tests/data/prot/df_test_prot.faa

Could you confirm that it contains what I need?
It seems the file has some 2.6 k proteins vs 561 expected?

Thanks!

[jeanrjc]

Hello, you cannot download a fasta file with all hit from the refseq DB on the wiki. What you can do, is to download the table with all the hits' refseq ID. With those ID, you can then download the protein files from refseq, using ncbi download tools.

[kpawlowski13]

Hi, ok, I get it, But, the problem the refseq DB on the wiki keeps crashing.
Is there another way to fetch the list of refs IDs?

[jeanrjc]

It does not crash on my side. When does it crash for you, at which step ?

[kpawlowski13]

When I go to
https://defensefinder.mdmlab.fr
and hit the "REFSEQ DB " link on top,
after few seconds I get this message:

[rplanel]

Hi, I don't experience this issue on my side. Could you tell me which browser you use and it's version please ?

[kpawlowski13]

Hi, I am having this issue on a Mac using: Safari Version 18.1 (19619.2.8.111.5, 19619) or Firefox 128.5.1esr (64-bit) or Chrome Version 131.0.6778.109 (Official Build) (arm64) This happens on university network, and also on home network. I am in the USA, perhaps this has something to do with the problem? Krzysztof From: rplanel ***@***.***> Date: Friday, December 6, 2024 at 7:10 AM To: mdmparis/defense-finder ***@***.***> Cc: Krzysztof Pawlowski ***@***.***>, Author ***@***.***> Subject: Re: [mdmparis/defense-finder] [HELP] (Issue #70) EXTERNAL MAIL Hi, I don't experience this issue on my side. Could you tell me which browser you use and it's version please ? — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/mdmparis/defense-finder/issues/70*issuecomment-2523224012__;Iw!!MznTZTSvDXGV0Co!DWxGvm23emtJM9vXvlUPLTRs6Fhj5ahr2yL-jkiBQYedEn2h1RqDpCfBPwuH0RRim3V3LJ9DW-6flJBPv4mKQj7mxtrO25NukvzFkicAFLp5$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/BNDJSDXU3ANRQ72ISCBQWSD2EGOZFAVCNFSM6AAAAABTABXN5WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMRTGIZDIMBRGI__;!!MznTZTSvDXGV0Co!DWxGvm23emtJM9vXvlUPLTRs6Fhj5ahr2yL-jkiBQYedEn2h1RqDpCfBPwuH0RRim3V3LJ9DW-6flJBPv4mKQj7mxtrO25NukvzFkvnGX5xs$>. You are receiving this because you authored the thread.Message ID: ***@***.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

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