uwsgi_response_write_body_do() TIMEOUT "downloading bam files"


Our Environment:
Galaxy: 19_09 ;
OS: Ubuntu 18.04.2 LTS
Database: Postgres <<<— one of the few deviations from default install
Galaxy is nearly a default install and not configured to run behind nginx.
nginx does not appear to be running nor can I find an nginx.conf file anywhere on the machine.

I am a newbie admin and my users are running into an issue when downloading larger files. They can download index files which are about 96bytes. However, the bam files (~15MB) fail. This is Galaxy 19_09 and it is not configured to run behind nginx; a nearly default installation. I’ve read several posts about “proxy_max_temp_file_size” setting in nginx but nginx is not setup or running on the server.

I found these posts but they are all related to nginx

Local galaxy nginx max file download size 1GB

I’m not sure where to go from here. Hoping someone has experience with this issue.

One of the errors from Galaxy.log:

[pid: 80680|app: 0|req: 2126/2264] () {40 vars in 832 bytes} [Wed Apr 15 12:01:28 2020] GET /api/histories/2fdbd5c5858e78fb/contents/datasets/2ea0c1fdff88d4e3 => generated 7749 bytes in 31 msecs (HTTP/1.1 200) 3 headers in 139 bytes (1 switches on core 0) - - [15/Apr/2020:12:01:32 -0400] "GET /datasets/2ea0c1fdff88d4e3/display?to_ext=bam HTTP/1.1" 200 148073827 "" "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:75.0) Gecko/20100101 Firefox/75.0"
uwsgi_response_write_body_do() TIMEOUT !!!
IOError: write error
[pid: 80680|app: 0|req: 2127/2265] () {40 vars in 813 bytes} [Wed Apr 15 12:01:32 2020] GET /datasets/2ea0c1fdff88d4e3/display?to_ext=bam => generated 6160384 bytes in 6199 msecs (HTTP/1.1 200) 5 headers in 263 bytes (97 switches on core 1)

Hello, Wanted to post an update. I just heard from the users that after I bounced that Galaxy server the issue has magically gone away.

For now assume this issue is resolved. Thank you.

1 Like

Ah, magic in system administration is always a relief! :upside_down_face:

Very glad you were able to sort out the problems, and thanks for posting back!