Failed to connect to cibersortx.stanford.edu:80: Connection timed out

Question

[abbas89]

I am running EcoTyper which is using cibersortx docker images. On the network of my institute I get this error, I tried many options for proxy settings with no luck. Any help would be appreciated.

Rscript EcoTyper_discovery_bulk.R -c config_discovery_bulk.yml

Step 1 (cell type fraction estimation): Running CIBERSORTxFractions on the discovery dataset...
Running CIBERSORTx fractions with no batch correction, using the 'TR4' signature matrix and 'MyDiscovery' dataset.
Running on docker...
>Running CIBERSORTxFractions...
>[Options] username: ****
>[Options] token: ****
>[Options] mixture: /src/data/mixture.txt
>[Options] sigmatrix: /src/data/sigmatrix.txt
>[Options] sourceGEPs: /src/data/sourceGEPs.txt
>[Options] verbose: TRUE
terminate called after throwing an instance of 'std::system_error'
  what():  Failed to connect to cibersortx.stanford.edu:80: Connection timed out
Error: 
Execution halted
Error: 
Execution halted
Error in RunJobQueue() : 
  EcoTyper failed. Please check the error message above!
Execution halted

Answer 1

[GenoMax]

If you go to the web address in the title you will see this announcement :

The CIBERSORTx website is undergoing emergency maintenance. We anticipate returning to partial operation on August 1, 2022 at 6:00 PM Pacific Daylight Time (GMT -7). (last updated July 28, 2022)

So try next week after Tuesday.

[abbas89]

Good catch, although I was having this error since a few days now. Also, someone from their team answered me but didn't mention this maintenance issue. But I hope you are right and it's just a problem with the website. Thanks

[Researcher]

Hi abbas89 Were you able to fix this issue, since the website is back to function? I am also getting the similar error while running CIBERSORTx by using singularity containers on the hpc.

Thanks

[GenoMax]

See https://cibersortx.stanford.edu/ for an update. Not fully operational as yet.

[Researcher]

Hi GenoMax Yes, I checked and read that "At this time, if you wish to run CIBERSORTx jobs using data not uploaded to this website, you can still do so using the Docker version of CIBERSORTx with access tokens." and I tried the same but with singularity container.

Thanks for your reply.