"Create database" fails for unknown reason
Closed this issue · 2 comments
Any ideas about where to start troubleshooting?
Creating a database of 32 phages consistently fails at about 27 seconds during step 1 of 2 of calculating phams. A database of 3 phages can be created, no problem.
My OS is Fedora 24, I'm running Docker version 1.10.3, build a612434/1.10.3
Here is what Docker vomits out while running (have run with and without sudo and experience same issue):
docker run --name pham --restart=always -p 8080:80 -v /home/fetz/ssd/docker/phamdb:/dockerdata:Z jglamine/phamdb:latest
[sudo] password for fetz:
2016-09-10 23:45:18,203 CRIT Supervisor running as root (no user in config file)
2016-09-10 23:45:18,203 WARN Included extra file "/etc/supervisor/conf.d/supervisor-app.conf" during parsing
2016-09-10 23:45:18,227 INFO RPC interface 'supervisor' initialized
2016-09-10 23:45:18,227 WARN cElementTree not installed, using slower XML parser for XML-RPC
2016-09-10 23:45:18,227 CRIT Server 'unix_http_server' running without any HTTP authentication checking
2016-09-10 23:45:18,227 INFO supervisord started with pid 1
2016-09-10 23:45:19,231 INFO spawned: 'celery-app' with pid 8
2016-09-10 23:45:19,232 INFO spawned: 'nginx-app' with pid 9
2016-09-10 23:45:19,235 INFO spawned: 'rabbitmq' with pid 10
2016-09-10 23:45:19,237 INFO spawned: 'set-secret-key' with pid 11
2016-09-10 23:45:19,239 INFO spawned: 'app-uwsgi' with pid 12
2016-09-10 23:45:19,241 INFO spawned: 'start-mysql' with pid 13
2016-09-10 23:45:19,272 INFO exited: set-secret-key (exit status 0; not expected)
2016-09-10 23:45:19,330 CRIT reaped unknown pid 72)
2016-09-10 23:45:19,408 CRIT reaped unknown pid 122)
2016-09-10 23:45:19,505 CRIT reaped unknown pid 231)
2016-09-10 23:45:19,513 CRIT reaped unknown pid 256)
2016-09-10 23:45:19,536 CRIT reaped unknown pid 306)
2016-09-10 23:45:19,537 CRIT reaped unknown pid 307)
2016-09-10 23:45:19,565 CRIT reaped unknown pid 333)
2016-09-10 23:45:19,566 CRIT reaped unknown pid 340)
2016-09-10 23:45:19,616 CRIT reaped unknown pid 354)
2016-09-10 23:45:19,647 CRIT reaped unknown pid 363)
2016-09-10 23:45:20,250 INFO success: celery-app entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2016-09-10 23:45:20,250 INFO success: nginx-app entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2016-09-10 23:45:20,251 INFO success: rabbitmq entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2016-09-10 23:45:20,251 INFO success: app-uwsgi entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2016-09-10 23:45:20,251 INFO success: start-mysql entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2016-09-10 23:45:20,293 INFO spawned: 'set-secret-key' with pid 515
2016-09-10 23:45:20,317 INFO exited: set-secret-key (exit status 0; not expected)
2016-09-10 23:45:20,524 CRIT reaped unknown pid 539)
2016-09-10 23:45:20,529 CRIT reaped unknown pid 545)
2016-09-10 23:45:20,587 CRIT reaped unknown pid 546)
2016-09-10 23:45:20,587 CRIT reaped unknown pid 586)
2016-09-10 23:45:22,351 INFO spawned: 'set-secret-key' with pid 653
2016-09-10 23:45:22,360 INFO exited: set-secret-key (exit status 0; not expected)
2016-09-10 23:45:25,365 INFO spawned: 'set-secret-key' with pid 682
2016-09-10 23:45:25,378 INFO exited: set-secret-key (exit status 0; not expected)
2016-09-10 23:45:26,364 INFO gave up: set-secret-key entered FATAL state, too many start retries too quickly
2016-09-10 23:45:27,799 CRIT reaped unknown pid 397)
2016-09-10 23:45:27,820 INFO exited: rabbitmq (exit status 0; expected)
2016-09-10 23:45:27,992 INFO exited: start-mysql (exit status 0; expected)
2016-09-10 23:45:28,151 CRIT reaped unknown pid 616)
I am closing this issue because I isolated the problem to a single, strangely formatted genbank file from one of the phages.
Awesome, I'm glad you figured it out! I'm sorry there weren't more detailed
error messages, ideally it should tell you when it can't read a genbank
file.
On Sep 11, 2016 6:14 AM, "Nathan Brown" notifications@github.com wrote:
I am closing this issue because I isolated the problem to a single,
strangely formatted genbank file from one of the phages.—
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