tabix file error: http://egg.wustl.edu/d/hg19/refGene.gz

[jgrundstad]

I'm running into an issue when trying to load the RefSeq genes annotation track. When looking at the /var/log/apache2/error.log I see the following:

subtleKnife starting... >>>>>
cgi param parsed
Hooked to hg19
reviveScaffold() done
normal dsp...
runmode: 0, jux tk: not available
not jumping...
not moving...
    entire length computed: 961104...
showRegionSl:
usedSummaryNumber: 4260
entireLength: 961104
(0) chr7 [0,26733030 >> 27694134,159138663] len: 961104 sp:4260
tabix file error: http://egg.wustl.edu/d/hg19/refGene.gz
track sl made
done

I'm able to wget the file in the URL, and successfully run tabix to generate an index on the command line:

root@6ab2509a73ea:~# wget http://egg.wustl.edu/d/hg19/refGene.gz
--2018-06-12 19:27:22--  http://egg.wustl.edu/d/hg19/refGene.gz
Resolving egg.wustl.edu (egg.wustl.edu)... 128.252.187.84
Connecting to egg.wustl.edu (egg.wustl.edu)|128.252.187.84|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://egg.wustl.edu/d/hg19/refGene.gz [following]
--2018-06-12 19:27:23--  https://egg.wustl.edu/d/hg19/refGene.gz
Connecting to egg.wustl.edu (egg.wustl.edu)|128.252.187.84|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 4049514 (3.9M) [application/x-gzip]
Saving to: ‘refGene.gz’

refGene.gz    100

[==================================================================================================================================>]   3.86M 
 5.69MB/s    in 0.7s    

2018-06-12 19:27:23 (5.69 MB/s) - ‘refGene.gz’ saved [4049514/4049514]

root@6ab2509a73ea:~# ls
eg  load  mysql.sh  refGene.gz  run.sh  setup.sh
root@6ab2509a73ea:~# tabix -p bed refGene.gz 
root@6ab2509a73ea:~# ls
eg  load  mysql.sh  refGene.gz  refGene.gz.tbi  run.sh  setup.sh
root@6ab2509a73ea:~# 

[lidaof]

Please use https:// instead http:// in the URL, I am also updating our datahub and config files. Thanks!

[jgrundstad]

Hi, and thanks for the fast response!

I'm using the Tracks -> Genes -> "RefSeq genes" button to load the track. Is there a config file I can edit to make that change available to our users?

[lidaof]

hi @jgrundstad, the file by default is located at /srv/epgg/data/data/subtleKnife/hg19/config/tracks.json.

[jgrundstad]

Great, thank you. It seems I needed to re-run the setup.sh script after making the edit for it to take. The track is displaying properly. Thanks again!

[lidaof]

You are very welcome!