Comments (7)
The new ghcr based images were still set to private by accident, I just made them public.
I would be very happy for feedback, I have cleaned-up quite a bit with the move to the github container registry and there might be still rough edges.
from mmseqs2-app.
Dear milot-mirdita,
Thank you for quick reply!
I could pass the authorization :-)
However, I got another error message after that. I would like to share it for debugging.
(base) user@user:~/software/mmseqs2/2/mmseqs2-app/docker-compose$ docker-compose up
Starting docker-compose_mmseqs-web-redis_1 ... done
Starting docker-compose_mmseqs-web-api_1 ... done
Starting docker-compose_mmseqs-web-worker_1 ... done
Starting docker-compose_mmseqs-web-webserver_1 ... done
Attaching to docker-compose_mmseqs-web-redis_1, docker-compose_mmseqs-web-api_1, docker-compose_mmseqs-web-webserver_1, docker-compose_mmseqs-web-worker_1
mmseqs-web-webserver_1 | /docker-entrypoint.sh: /docker-entrypoint.d/ is not empty, will attempt to perform configuration
mmseqs-web-webserver_1 | /docker-entrypoint.sh: Looking for shell scripts in /docker-entrypoint.d/
mmseqs-web-webserver_1 | /docker-entrypoint.sh: Launching /docker-entrypoint.d/10-listen-on-ipv6-by-default.sh
mmseqs-web-webserver_1 | 10-listen-on-ipv6-by-default.sh: info: can not modify /etc/nginx/conf.d/default.conf (read-only file system?)
mmseqs-web-redis_1 | 1:C 07 Jul 2022 00:32:21.043 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
mmseqs-web-redis_1 | 1:C 07 Jul 2022 00:32:21.043 # Redis version=7.0.2, bits=64, commit=00000000, modified=0, pid=1, just started
mmseqs-web-redis_1 | 1:C 07 Jul 2022 00:32:21.043 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
mmseqs-web-webserver_1 | /docker-entrypoint.sh: Launching /docker-entrypoint.d/20-envsubst-on-templates.sh
mmseqs-web-webserver_1 | /docker-entrypoint.sh: Launching /docker-entrypoint.d/30-tune-worker-processes.sh
mmseqs-web-webserver_1 | /docker-entrypoint.sh: Configuration complete; ready for start up
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.044 * monotonic clock: POSIX clock_gettime
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.044 * Running mode=standalone, port=6379.
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.044 # Server initialized
mmseqs-web-worker_1 | 2022/07/07 00:32:21 MMseqs2 worker
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * Loading RDB produced by version 7.0.2
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * RDB age 5 seconds
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * RDB memory usage when created 0.92 Mb
mmseqs-web-api_1 | 2022/07/07 00:32:21 MMseqs2 Webserver
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * Done loading RDB, keys loaded: 1, keys expired: 0.
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * DB loaded from disk: 0.000 seconds
mmseqs-web-redis_1 | 1:M 07 Jul 2022 00:32:21.045 * Ready to accept connections
mmseqs-web-api_1 | panic: Key: 'ParamsDisplayV1.Status' Error:Field validation for 'Status' failed on the 'required' tag
mmseqs-web-api_1 | Key: 'ParamsDisplayV1.Display.Name' Error:Field validation for 'Name' failed on the 'required' tag
mmseqs-web-api_1 | Key: 'ParamsDisplayV1.Display.Path' Error:Field validation for 'Path' failed on the 'required' tag
mmseqs-web-api_1 |
mmseqs-web-api_1 | goroutine 7 [running]:
mmseqs-web-api_1 | main.server.func1()
mmseqs-web-api_1 | /opt/build/server.go:33 +0x245
mmseqs-web-api_1 | created by main.server
mmseqs-web-api_1 | /opt/build/server.go:30 +0x110
docker-compose_mmseqs-web-api_1 exited with code 2
mmseqs-web-webserver_1 | 2022/07/07 00:32:21 [emerg] 1#1: host not found in upstream "mmseqs-web-api" in /etc/nginx/conf.d/default.conf:13
mmseqs-web-webserver_1 | nginx: [emerg] host not found in upstream "mmseqs-web-api" in /etc/nginx/conf.d/default.conf:13
docker-compose_mmseqs-web-webserver_1 exited with code 1
My computer environment
- Ubuntu18.04 LTE (all packages are updated)
- Docker version 20.10.17, build 100c701
- docker-compose version 1.27.4, build 40524192
- Main memory: 64GB
Thanks,
from mmseqs2-app.
Can you please execute and share the output here:
ls databases
head databases/*.params
from mmseqs2-app.
Dear Milot-mirdita,
thank you very much for reply.
it is here.
(base) user@user:~/software/mmseqs2/2/mmseqs2-app/docker-compose$ ls databases/
pdb70_latest_msa pdb70_latest_msa.dbtype pdb70_latest_msa.index pdb70_latest.params
(base) user@user:~/software/mmseqs2/2/mmseqs2-app/docker-compose$ head databases/*.params
{
"name": "PDB70",
"version": "latest",
"default": true,
"order": 0,
"index": "-s 6",
"search": "-s 6"
}
I prepared for PDB70 database with "MMseqs2-App/docker-compose/examples/pdb70/setup.sh".
Please feel free to contact me if you need further information.
Thanks,
from mmseqs2-app.
Try replacing the content of the pdb70_latest.params
with and then starting the server:
{"name":"PDB70","version":"latest","path":"pdb70_latest","default":true,"order":1,"taxonomy":false,"index":"-s 6","search":"-s 6","status":"PENDING"}
Seems like i need to update the scripts in examples
, I think they are currently outdated.
from mmseqs2-app.
Dear milot-mirdita,
Thank you for your great support!
I could run the MMSeqs2 server with PDB70 database !
it works very well :-)
from mmseqs2-app.
For the future, I added a new feature to make DB installation easier.
You can run:
docker-compose run db-setup
to list available databases
and then
docker-compose run db-setup PDB70
to download and setup the database.
This should support all databases that are available in mmseqs databases
from mmseqs2-app.
Related Issues (20)
- local colabfold_batch cannot communicate with local mmseq2 web api HOT 19
- Full target/query alignment being truncated in web UI HOT 3
- pairaln mode does not support the binary version of the taxonomy files HOT 5
- mmseqs-server: errors when called from colabfold_batch HOT 2
- App does not work with latest mmseqs version HOT 2
- Pass --max-seqs through GUI or server API?
- Implement three diferent states for visualizing query structure in Structure Viewer
- Possible to add single or multiple sequences to existing database
- Temporary redirect issue HOT 6
- Foldseek all database view rework
- Running it in kubernetes HOT 4
- Historical jobs not loaded: "Job failed. Please try again later."
- jobs stuck in PENDING status with local mmseqs-web API HOT 2
- "docker-compose run db-setup PDB" not working HOT 2
- host not found in upstream "mmseqs-web-api HOT 7
- "405 Not Allowed" returned for the queries HOT 4
- Foldseek jobs are not persistent from GUI HOT 5
- Local Foldseek searches are no longer working HOT 6
- docker-compose run db-setup XXX fails due to no space left on device
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