buttery-eel
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Error with exit code
Not sure if this is something fixed in a newer version as I am still using an old version. The issue is around returning the correct exit status.
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Basecalling
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[guppy/error] basecall_core::CUDACaller::thread_main: Exception in CUDACaller worker thread: Could not allocate CUDA shared buffer for runner, size 5203847936
terminate called after throwing an instance of 'std::runtime_error'
what(): Could not allocate CUDA shared buffer for runner, size 5203847936
[guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG
Process basecall_worker_3:
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/data/install/buttery-eel-0.4.1+guppy6.5.7/venv3/lib/python3.8/site-packages/src/buttery_eel.py", line 495, in submit_read
result = client.pass_read(
File "/data/install/buttery-eel-0.4.1+guppy6.5.7/venv3/lib/python3.8/site-packages/pyguppy_client_lib/pyclient.py", line 245, in pass_read
raise ConnectionError(
ConnectionError: Not connected to server. status code: <status.loading_config: 2>. PyGuppyClient(address='localhost:5000', config='dna_r9.4.1_450bps_sup', align_ref=None, bed_file=None, barcodes=None, status.loading_config, )
[guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG
Basecalling complete!
The program exists with 0 status and thus in a script the error check does not get triggered. Also that Basecalling complete should perhaps print basecalling failed :( ?