Error when searching nucleotide DB #3
Comments
|
Thanks for trying the MMseqs2 webserver! I've triggered rebuilding the docker images based on the latest MMseqs2 image. The issue should be fixed there. I can do more detailed testing in a couple days though. |
|
Thank you for the quick fix, I'll test it on my instance and will let you know if the problem persists. |
|
I tried the latest mmseqs-app-* docker images (running It is triggered by the |
|
I will look at the problem in detail in the evening. I know whats wrong, but its a little bit of a larger fix. |
|
Update: The docker images should work again. I split There is one more minor issue that I'll resolve soon, that MMseqs2 is currently not cleaning up correctly after itself and will leave an unnecessary number of files for each job. I'll fix that as soon as I can. |
|
I keep getting errors with the updated image: Adding UPDATE: using |
|
I tried to use the latest |
|
Yes, please to that. Sorry for the slow support. We have a deadline approaching soon :/ |
|
No problem, it's done. Thank you again! |
|
Hi, Thank you! |
|
I tested the mmseqs executables from the latest mmseqs2 docker image with the web app (by copying them manually into the web app docker image using EDIT: it works only after setting the |
|
Sorry for not rebuilding the containers sooner, once Docker Hub finishes you should have MMseqs2 r9 in them. Also a caveat: The nucleotide-nucleotide search is still in development by @martin-steinegger There is no manuscript or exhaustive benchmarks yet. |
|
No problem, that's great. I will keep an eye on the nt-nt search development :) I guess this issue can be closed, if you agree |
|
Okay :) we’d be happy for feedback if you run into any issues with the nt-nt search. |
|
Sure! I haven't yet, but I must say I only use it occasionally. Thanks again. |
|
I've found this thread very useful in debugging problems with nucleotide searches. Thanks @simone-pignotti and @milot-mirdita Now I have managed to have DNA and RNA databases up and running in mmseqs-app. However the search doesn't work and it looks purely like an API problem. The server logs seem to have quite happily run mmseqs. This is my DNA and RNA databases config: {
"databases": [
{
"name": "PDB DNA sequence (seqres)",
"version": "2020-02-18",
"path": "pdb_dna_sequence",
"default": false,
"order": 1,
"index": "--search-type 3",
"search": "--max-seqs 2000 --search-type 3"
},
{
"name": "PDB RNA sequence (seqres)",
"version": "2020-02-18",
"path": "pdb_rna_sequence",
"default": false,
"order": 2,
"index": "--search-type 3",
"search": "--max-seqs 2000 --search-type 3"
}
]
}And what I get from API ticket endpoint (e.g. So all looks ok there. However from result endpoint (e.g. Any ideas what can be wrong? |
|
Please execute the following command from within the Can you please answer in a new issue so we don't spam simone's email with notifications? |
I am using the docker version of the webserver, and I have successfully built and searched the example uniclust DB and another custom protein DB.
I have also built a DNA DB, but searching it produces an error. Both the building and the searching logs are attached, and the issue seems to be a wrong path:
I believe the splitsequence command is supposed to take
mydb_ntand notmydb_nt.idxas argument, therefore it should be an easy fix.I hope this is useful, let me know if you can't reproduce the issue.
Simone
createdb.log
search.log
The text was updated successfully, but these errors were encountered: