GREAT database connection issues about cistopic

[cbravo93]

If you lower the request_interval it may be faster :)

[cbravo93]

Hi!

This error seems to come directly from the rGREAT package. Can it be related to the docker configuration? We have a singularity image with R and cisTopic (and dependencies) that we have tested and runs with no problems, if that can help.

[jk86754]

most likely related to docker configuration. Working with authors of rGREAT to try to figure this out.

[jk86754]

sorry, need to reopen this. Talking to the authors of rGREAT, it seems like I can get rGREAT to work outside of cisTopic (i.e. submitGreatJobs works). I specifically get this error with the implementation in cisTopic (i.e. GREAT command)

[cbravo93]

Which command have you used for running submitGreatJobs?

[jk86754]

I used

`greattest <- submitGreatJob([email protected], bg = NULL,
species = "hg19",
includeCuratedRegDoms = TRUE,
rule = c("basalPlusExt", "twoClosest", "oneClosest"),
adv_upstream = 5.0,
adv_downstream = 1.0,
adv_span = 1000.0,
adv_twoDistance = 1000.0,
adv_oneDistance = 1000.0,
request_interval = 300,
max_tries = 10,
version = "default",
base_url = "http://great.stanford.edu/public/cgi-bin")'

This seems to work fine.

[cbravo93]

Can you try using the cisTopic function with the same options?:

try <- GREAT(cisTopicObject, genome='hg19', fold_enrichment=2, geneHits=1, sign=0.05, bg = NULL,
includeCuratedRegDoms = TRUE,
rule = c("basalPlusExt", "twoClosest", "oneClosest"),
adv_upstream = 5.0,
adv_downstream = 1.0,
adv_span = 1000.0,
adv_twoDistance = 1000.0,
adv_oneDistance = 1000.0,
request_interval = 300,
max_tries = 10,
version = "default",
base_url = "http://great.stanford.edu/public/cgi-bin")

Cheers,

C

[jk86754]

is this the expected behavior? it has been going on for a couple of hours...
`> cisTopicObject <- GREAT(cisTopicObject, genome='hg19', fold_enrichment=2, geneHits=1, sign=0.05, bg = NULL,

•          includeCuratedRegDoms = TRUE,
  

•          rule = c("basalPlusExt", "twoClosest", "oneClosest"),
  

•          adv_upstream = 5.0,
  

•          adv_downstream = 1.0,
  

•          adv_span = 1000.0,
  

•          adv_twoDistance = 1000.0,
  

•          adv_oneDistance = 1000.0,
  

•          request_interval = 300,
  

•          max_tries = 10,
  

•          version = "default",
  

•          base_url = "http://great.stanford.edu/public/cgi-bin")`
  

Don't make too frequent requests. The time break is 300s.
Please wait for 240s for the next request.
The time break can be set by request_interval argument.

|===========================================================================| 100%
Don't make too frequent requests. The time break is 300s.
Please wait for 242s for the next request.
The time break can be set by request_interval argument.

|===========================================================================| 100%

No error message yet.

Thanks for your continued help!

[jk86754]

it seems like this indeed worked. are there any parameters in the command above you would recommend changing/tuning?

[jk86754]

Thanks for your help! Both the paper and R package are really nice work.