Issue with CIBERSORTx Error 139

Question

[Hamdache]

Hi everyone,

I am facing an issue with running CIBERSORTx

Running CIBERSORTxFractions...

[Options] single_cell: TRUE
[Options] verbose: TRUE
[Options] username: *
[Options] token: *
[Options] mixture: mixture_file_for_cibersort.txt
[Options] sigmatrix: signature_matrix.txt
[Options] perm: 0
[Options] label: fbdd28e0-d4d9-11ef-b7f7-3380cca208ed
[Options] rmbatchBmode: FALSE
[Options] rmbatchSmode: FALSE
[Options] sourceGEPs: signature_matrix.txt [Options] QN: FALSE
[Options] absolute: FALSE
[Options] abs_method: sig.score

terminate called after throwing an instance of 'std::system_error'
what(): Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable
Something went wrong: Error code 139.
Please try again with 'verbose=TRUE'
Erreur : '/Bureau/CTF/user_projects/src/temp/output/CIBERSORTx_fbdd28e0-d4d9-11ef-b7f7-3380cca208ed_Results.txt' does not exist.

I suspect that the issue might be related to the Docker container during the creation of the container command. I've already verified file permissions and tried changing the output directory, but the issue persists.

Has anyone encountered a similar problem? Any advice or potential fixes would be greatly appreciated.

Thanks!

[i.sudbery]

Please provide the full command you used for execution. I looks to be to do with a failure to resolve an internet address.

[Hamdache]

Thank you for your response. The issue occurred while executing the following function in R:

computeCBSX = function(TPM_matrix, signature_file, name, password, name_signature){
  set_cibersortx_credentials(name, password)

cbsx = omnideconv::deconvolute_cibersortx(
    TPM_matrix, 
    signature_file,
    container = "docker",
  input_dir = "/Bureau/CTF/user_projects/src/temp/input", 
 output_dir="/Bureau/CTF/user_projects/src/temp/output",
    verbose = TRUE
  )
  return(cbsx)
}          

and when I am using the function without verbose = TRUE I have :

Something went wrong: Error code 139. Please try again with 'verbose=TRUE'
Erreur : '/tmp/RtmpyVIJ5s/CIBERSORTx_e6de9c6a-d4e0-11ef-b7f7-3380cca208ed_Results.txt' does not exist.

Thanks for your help

[GenoMax]

Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable

Does your docker container have access to internet/network?

[Hamdache]

Apparently yes I tried ping -c 4 google.com

 ping -c 4 google.com
PING google.com (142.251.37.174) 56(84) bytes of data.
64 bytes from mrs09s14-in-f14.1e100.net (142.251.37.174): icmp_seq=1 ttl=117 time=6.56 ms
64 bytes from mrs09s14-in-f14.1e100.net (142.251.37.174): icmp_seq=2 ttl=117 time=6.56 ms
64 bytes from mrs09s14-in-f14.1e100.net (142.251.37.174): icmp_seq=3 ttl=117 time=6.63 ms
64 bytes from mrs09s14-in-f14.1e100.net (142.251.37.174): icmp_seq=4 ttl=117 time=6.62 ms

--- google.com ping statistics ---
4 packets transmitted, 4 received, 0% packet loss, time 3004ms
rtt min/avg/max/mdev = 6.556/6.588/6.625/0.031 ms

[GenoMax]

If you are able to resolve the name of the resource by doing host cibersortx.stanford.edu then it is possible that the method/API you are trying to use to access CIBERSORTx is no longer available or is being blocked by your local firewall or by the cibersort site itself.

[Hamdache]

Thanks for your help I will keep you updated

[jared.andrews07]

I believe the site was down earlier today for a bit as well, so it may have been on their end. They have a banner saying user login is now back up.