Closed noguhiro2002 closed 2 years ago
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.
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
Thanks,
Can you please execute and share the output here:
ls databases
head databases/*.params
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,
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.
Dear milot-mirdita,
Thank you for your great support! I could run the MMSeqs2 server with PDB70 database ! it works very well :-)
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
Dear developer and community,
First of all, thank you for your great scientific work.
When I wanted to install the docker version of the current version (the latest version on 2022/Jul/7), the following error message confused me after typing "docker-compose up" command.
so if you have a solution to solve this issue, please help your power.
Thanks,