Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)
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Medaka script failing due to GPU related Issue #10
Hello developers, I have followed the steps detailed as per the tutorial (https://github.com/Hydro3639/nanophase/blob/main/Usage_tutorial.md) on the provided text dataset. however, while running the script, I encountered the following error.
while checking the log file, I found the error was related to the Medaka polishing step, which utilizes GPU for the analysis. For some reason, the particular script is failing in the workflow (Pls check the log file).
I also tried to set up the environment variable TF_FORCE_GPU_ALLOW_GROWTH=true. in the nanophase environment. However, no luck. If I would want to disable GPU, where to set out the suggested command "--disable_cudnn" in the script.
Could you please suggest any other way to sort out the issue?
Hello developers, I have followed the steps detailed as per the tutorial (https://github.com/Hydro3639/nanophase/blob/main/Usage_tutorial.md) on the provided text dataset. however, while running the script, I encountered the following error.
while checking the log file, I found the error was related to the Medaka polishing step, which utilizes GPU for the analysis. For some reason, the particular script is failing in the workflow (Pls check the log file).
I also tried to set up the environment variable
TF_FORCE_GPU_ALLOW_GROWTH=true. in the nanophase environment. However, no luck. If I would want to disable GPU, where to set out the suggested command "--disable_cudnn" in the script.Could you please suggest any other way to sort out the issue?
medaka.polish (1).log nanophase.log
Thank you very much Venkat