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ghm17 / LOGODetect

LOGODetect is a powerful tool to identify small segments that harbor local genetic correlation between two traits/diseases.
GNU General Public License v3.0
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Error in unserialize(node$con) : error reading from connection #25

Open Haoxiang-Qi opened 1 year ago

Haoxiang-Qi commented 1 year ago

I'm sorry to bother you. When I used the LOGO to analysis the same population GWAS summary data, I met a error:

Warning message: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, : Unknown option on commandline: --file Library snowfall loaded. Library snowfall loaded in cluster.

Error in unserialize(node$con) : error reading from connection Calls: sfLapply ... FUN -> recvData -> recvData.SOCKnode -> unserialize Execution halted

the LDSC has been calculated. Can you tell me how to solve this problem? Thanks a lot

kruthikaiyer0990 commented 5 months ago

Hi! Were you able to solve this? I'm getting the same error..

snowfall 1.84-6.3 initialized (using snow 0.4-4): parallel execution on 25 CPUs.

Warning message:
In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts,  :
  Unknown option on commandline: --file
Library snowfall loaded.
Library snowfall loaded in cluster.

Error in unserialize(node$con) : error reading from connection
Calls: sfLapply ... FUN -> recvData -> recvData.SOCKnode -> unserialize
Execution halted
ghm17 commented 5 months ago

Thanks for using our tool! Can you try running with fewer cores, like 5, with argument --n_cores 5 ?

kruthikaiyer0990 commented 5 months ago

Hi ! yes it worked with --n_cores 5 but sometimes it works with --n_cores 25 too. Any idea why this discrepancy ?

ghm17 commented 5 months ago

It may happen if memory is out and some parallel jobs have died. You can also try running 25 cores with larger memory. Hope it helps!