Waiting to start (tilesets)...

[decarlin]

Hi there~

Following your tutorial, I tried:

sudo higlass-manage view /tmp/sample.mcool

(sudo since otherwise the connection timesout)

Instead, I just get:

Waiting to start (tilesets)...
sending request 179
Waiting to start (tilesets)...
sending request 180
Waiting to start (tilesets)...
sending request 181
Waiting to start (tilesets)...
sending request 182
Waiting to start (tilesets)...
sending request 183
Waiting to start (tilesets)...
sending request 184

etc. forever. Nothing is served at http://localhost:8989/

Any idea what's up? I'm on macOS 11.6.4, chrome is the browser

Thanks

[pkerpedjiev]

Hi, sorry for the delayed response. Can you post the contents of ~/hg-tmp/nginx-stderr---supervisor* and of ~/hg-data/log/hgs.log?

[decarlin]

hmm, I see neither of these files. Could be related to the problem? I noticed in you test.sh script that you use mktemp, which works differently in macOS than most unix...

[decarlin]

p.s. the docker logs from the desktop app look like:

/usr/lib/python2.7/dist-packages/supervisor/options.py:298: UserWarning: Supervisord is running as root and it is searching for its configuration file in default locations (including its current working directory); you probably want to specify a "-c" argument specifying an absolute path to a configuration file for improved security.

'Supervisord is running as root and it is searching '

2022-03-22 22:46:17,578 CRIT Supervisor running as root (no user in config file)

2022-03-22 22:46:17,583 INFO supervisord started with pid 8

2022-03-22 22:46:18,588 INFO spawned: 'nginx' with pid 11

2022-03-22 22:46:18,590 INFO spawned: 'uwsgi' with pid 12

2022-03-22 22:46:18,623 INFO exited: nginx (exit status 1; not expected)

2022-03-22 22:46:19,940 INFO spawned: 'nginx' with pid 20

2022-03-22 22:46:19,941 INFO success: uwsgi entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)

2022-03-22 22:46:19,951 INFO exited: nginx (exit status 1; not expected)

2022-03-22 22:46:21,959 INFO spawned: 'nginx' with pid 21

2022-03-22 22:46:21,973 INFO exited: nginx (exit status 1; not expected)

2022-03-22 22:46:24,981 INFO spawned: 'nginx' with pid 22

2022-03-22 22:46:24,993 INFO exited: nginx (exit status 1; not expected)

2022-03-22 22:46:25,995 INFO gave up: nginx entered FATAL state, too many start retries too quickly

[pkerpedjiev]

Sorry, unacceptably long response time. On the off-chance that you're still interested in fixing this, could you check in /tmp/higlass-docker or start higlass-manage with the -t option and specify a temp directory. The logs from supervisord get dumped there and they usually provide some clue as to why nginx isn't starting.

Alternatively ~/hg-data/log/error.log may provide some information as well.

[adamnovak]

It seems like you can get into this situation if ~/hg-data is not actually writable by root inside the container, which can happen if e.g. your home directory is an NFS share and the NFS server doesn't let random hosts start demanding to create files as root in violation of normal permissions checks.

nginx can't make /data/log or /data/log/access.log, and just complains about missing directories and/or denied permissions in /var/log/nginx/error.log inside the container while refusing to start. docker logs on the container shows supervisord trying to start nginx a few times and then giving up.