"Create database" fails for unknown reason

[nmb85]

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)

[nmb85]

I am closing this issue because I isolated the problem to a single, strangely formatted genbank file from one of the phages.

[jglamine]

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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