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stevekm / reportIT

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
GNU General Public License v3.0
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sometimes the IGV reporting script gets hung up #22

Open stevekm opened 7 years ago

stevekm commented 7 years ago

Occasionally, when the IGV snapshot script gets run under a qsub cluster job, the script hangs indefinitely, seemingly just before IGV gets loaded. This has not been observed when running the scripts in the current session (non-qsub), may be caused by the cluster environment. Currently the only known solution is to simply kill the qsub job and re-run until it goes to completion, or forgo the qsub job submission.

stevekm commented 7 years ago

looks like this might be happening when run interactively as well, might need to increase the memory allocation to the process?

stevekm commented 7 years ago

Have also noticed that on at least one occasion, the scripts have continued to run but the SGE log has stopped getting updates. This was apparent since files were being created and updated but output to the SGE std out log stopped in the middle of running one of the IGV scripts.