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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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ERROR: Guppy server initialization failed. #278

Closed Flower9618 closed 2 years ago

Flower9618 commented 2 years ago

Hi, when I run Megalodon on server. There is an error: """ [03:37:24] Running Megalodon version 2.5.0 **** WARNING: "mods" output requested, so "per_read_mods" will be added to outputs. **** [03:37:24] Loading guppy basecalling backend DBG 03:37:24 : Guppy version: "4.2.2" --- MainProcess-MainThread backends.py:938 DBG 03:37:24 : Pyguppy version: "4.2.2" --- MainProcess-MainThread backends.py:939 DBG 03:37:24 : guppy server init command: "ont-guppy/bin/guppy_basecall_server -p auto -l maternal_plasma_3/M1> DBG 03:37:24 : Found guppy log file: guppy_log/guppy_basecall_server_log-2022-05-01_03-37-24.log --- MainProce>

    ERROR: Guppy server initialization failed. See guppy logs in [--output-directory] for more details.
            Try running the guppy server initialization command found in log.txt in order to pinpoint the source of this issue.

"""

And when I look at the guppy_log.txt, there is a message: """ 2022-05-01 03:37:24.611024 [guppy/message] ONT Guppy basecall server software version 4.2.2+effbaf8, client-server API version 3.2.0 config file: dna_r9.4.1_450bps_hac.cfg model file: template_r9.4.1_450bps_hac.jsn log path: guppy_log chunk size: 2000 chunks per runner: 512 max queued reads: 2000 num basecallers: 4 num socket threads: 2 max returned events: 50000 gpu device: cuda:0,1,2 kernel path:
runners per device: 4

2022-05-01 03:37:24.611460 [guppy/info] crashpad_handler not supported on this platform. 2022-05-01 03:37:24.613000 [guppy/info] Listening on port 44161. 2022-05-01 03:37:25.484891 [guppy/info] CUDA device 0 (compute 8.0) initialised, memory limit 42506321920B (42070114304B free)

2022-05-01 03:37:25.485144 [guppy/error] Loading fatbin file shared.fatbin failed with: CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:54: CUDA_ERROR_NO_BINARY_FOR_GPU """

I find someone has a similar guppy server initialization problem, but the message in detail is different, which is _CUDA_ERROR_NO_BINARY_FORGPU in my error. I do not know how to solve it.

marcus1487 commented 2 years ago

This error seems to indicate a GPU device that is not compatible with Guppy. Please see the community page for Guppy GPU requirements. I would also recommend upgrading to the most recent version of Guppy.