Open WaxRain opened 3 years ago
Hey @WaxRain
The current version is compatible with Guppy 4.0.X - I'm just working on an update to move to 4.4.X.
Exception: Bad request
I tried Guppy v4.0.15 and pyguppyclient v0.0.7a1, then I got Bad request exception.
(venv3)[software/pyguppyclient$ make test
nosetests -v --with-doctest --with-coverage --cover-package pyguppyclient
Doctest: pyguppyclient.utils.bases_fmt ... ok
Doctest: pyguppyclient.utils.batches ... ok
Doctest: pyguppyclient.utils.distribute ... ok
Doctest: pyguppyclient.utils.parse_config ... ok
test the caller ... ok
test loaded configs ... ok
try and load in invalid config ... ok
test a read with state ... ok
test a read without state ... ok
test the client api without sending a read ... ok
Name Stmts Miss Cover Missing
------------------------------------------------------------------------------------
pyguppyclient/__init__.py 7 0 100%
pyguppyclient/caller.py 47 17 64% 70-94
pyguppyclient/client.py 147 61 59% 43-44, 47, 53, 69, 77, 88, 124-133, 148-149, 158-167, 170-171, 174, 177-189, 192-197, 204, 207-208, 211-212, 215-222, 228-236, 245
pyguppyclient/decode.py 107 26 76% 107-109, 112-120, 146, 148, 161-163, 167-199
pyguppyclient/guppy_ipc/AlignmentIndex.py 29 14 52% 14-17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/AlignmentResults.py 125 78 38% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88, 92-95, 99-102, 106-109, 113-116, 120-123, 127-130, 134-137, 141-144, 148-151
pyguppyclient/guppy_ipc/BarcodeArrangementResults.py 123 82 33% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-85, 89-96, 100-107, 111-118, 122-125, 129-132, 136-139, 143-146
pyguppyclient/guppy_ipc/BarcodeKitDefinition.py 71 42 41% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88
pyguppyclient/guppy_ipc/BarcodeMidDetectResults.py 35 18 49% 14-17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/BarcodeResults.py 47 26 45% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60
pyguppyclient/guppy_ipc/BaseModData.py 50 29 42% 14-17, 21, 25, 29-32, 36-39, 43-47, 51-54, 58-61, 65-66
pyguppyclient/guppy_ipc/CalledBlockData.py 206 140 32% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-88, 92-95, 99-102, 106-109, 113-116, 120-123, 127-130, 134-137, 141-144, 148-155, 159-162, 166-172, 176-183, 187-191, 195-198, 202-205, 209-210, 214-221, 225-234, 238-241, 245-246
pyguppyclient/guppy_ipc/ClientStats.py 29 14 52% 14-17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/ConfigData.py 96 52 46% 14-17, 21, 38, 45, 49-50, 54-63, 67-70, 74-75, 79-83, 87-90, 94-95, 99-108, 112-115, 119-120
pyguppyclient/guppy_ipc/Configuration.py 65 25 62% 14-17, 21, 29-32, 36-39, 43-46, 50-53, 60, 67, 74, 81
pyguppyclient/guppy_ipc/Content.py 7 0 100%
pyguppyclient/guppy_ipc/FlipflopTraceData.py 59 36 39% 14-17, 21, 25, 29-33, 37-40, 44-47, 51-52, 56-60, 64-67, 71-74, 78-79
pyguppyclient/guppy_ipc/MessageData.py 48 8 83% 21, 36, 40-43, 50, 60
pyguppyclient/guppy_ipc/ProtocolVersion.py 16 0 100%
pyguppyclient/guppy_ipc/ReadBlockData.py 106 69 35% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67, 71-74, 78-81, 85-89, 93-96, 100-103, 107-108, 112-119, 123-130
pyguppyclient/guppy_ipc/ReadBlockType.py 5 0 100%
pyguppyclient/guppy_ipc/RunlengthTraceData.py 149 100 33% 14-17, 21, 25, 29-32, 36-40, 44-47, 51-54, 58-59, 63-67, 71-74, 78-81, 85-86, 90-94, 98-101, 105-108, 112-113, 117-121, 125-128, 132-135, 139-140, 144-148, 152-155, 159-162, 166-167, 171-175, 179-182, 186-189, 193-194
pyguppyclient/guppy_ipc/ScalingData.py 53 30 43% 14-17, 21, 25, 29-32, 36-39, 43-46, 50-53, 57-60, 64-67
pyguppyclient/guppy_ipc/ScalingOverrideData.py 29 14 52% 14-17, 21, 25, 29-32, 36-39
pyguppyclient/guppy_ipc/ServerStats.py 62 37 40% 14-17, 21, 29-32, 36-39, 43-46, 50-53, 57-66, 70-73, 77-78
pyguppyclient/guppy_ipc/SimpleReplyData.py 35 18 49% 14-17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/SimpleReplyType.py 17 0 100%
pyguppyclient/guppy_ipc/SimpleRequestData.py 35 18 49% 14-17, 21, 25, 29-32, 36-39, 43-46
pyguppyclient/guppy_ipc/SimpleRequestType.py 14 0 100%
pyguppyclient/guppy_ipc/TraceData.py 4 0 100%
pyguppyclient/guppy_ipc/__init__.py 0 0 100%
pyguppyclient/io.py 24 7 71% 32, 39-40, 47-50
pyguppyclient/ipc.py 69 22 68% 34, 44, 50, 93, 99-112, 115-117, 135-141
pyguppyclient/utils.py 24 0 100%
------------------------------------------------------------------------------------
TOTAL 1940 983 49%
----------------------------------------------------------------------
Ran 10 tests in 4.824s
OK
python3 examples/pyguppyclient -t 5 dna_r9.4.1_450bps_fast tests/reads/testdata//multi > /dev/null
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 198, in _process_chunk
return [fn(*args) for args in chunk]
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 198, in <listcomp>
return [fn(*args) for args in chunk]
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/caller.py", line 74, in basecall_batch
with GuppyBasecallerClient(config_name=self.config, host=self.host, port=self.port) as client:
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/client.py", line 39, in __enter__
self.connect()
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/client.py", line 73, in connect
config = self._load_config(self.config_name)
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/client.py", line 95, in _load_config
loaded_configs = {Config(c).name: Config(c) for c in self.get_configs()}
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/client.py", line 91, in get_configs
res = self.send(SimpleRequestType.GET_CONFIGS)
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/client.py", line 55, in send
return simple_response(self.recv())
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/ipc.py", line 103, in simple_response
raise Exception("Bad request")
Exception: Bad request
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "examples/pyguppyclient", line 49, in <module>
main(parser.parse_args())
File "examples/pyguppyclient", line 32, in main
samples = caller.basecall(files)
File "/media/mdb2/disk3/haoy/software/pyguppyclient/venv3/lib/python3.7/site-packages/pyguppyclient/caller.py", line 61, in basecall
return sum(pool.map(self.basecall_batch, work))
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 483, in _chain_from_iterable_of_lists
for element in iterable:
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
yield fs.pop().result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 435, in result
return self.__get_result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
Exception: Bad request
make: *** [Makefile:22: test] Error 1
what caused this error?
@WaxRain I've published v0.0.9 which supports Guppy 4.4.X and I see all tests passing - please give that a go.
Thanks for telling me that. I've tried the v0.09, and it worked well with Guppy 4.4.1.
I encountered another problem. I want to use Guppy with GPU mode, so I install cuda 11. When I run _guppy_basecallserver** by myself, it work well, while I run sudo service minknow start**, the guppy can't be waked up.
when I use _ont-guppy_4.2.2_linux64cuda11.tar.gz****, Guppy and Minknow worked well . But pyguppyclient raise an Error
Traceback (most recent call last):
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 198, in _process_chunk
return [fn(*args) for args in chunk]
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 198, in <listcomp>
return [fn(*args) for args in chunk]
File "/media/mdb2/disk4/anaconda3/lib/python3.7/site-packages/pyguppyclient/caller.py", line 74, in basecall_batch
with GuppyBasecallerClient(config_name=self.config, host=self.host, port=self.port) as client:
File "/media/mdb2/disk4/anaconda3/lib/python3.7/site-packages/pyguppyclient/client.py", line 45, in __enter__
self.connect()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/site-packages/pyguppyclient/client.py", line 83, in connect
self.config_name, self.pcl_client.get_error_message()
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: [timed_out] Timeout waiting for reply to request: LOAD_CONFIG
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "./examples/pyguppyclient", line 49, in <module>
main(parser.parse_args())
File "./examples/pyguppyclient", line 32, in main
samples = caller.basecall(files)
File "/media/mdb2/disk4/anaconda3/lib/python3.7/site-packages/pyguppyclient/caller.py", line 61, in basecall
return sum(pool.map(self.basecall_batch, work))
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/process.py", line 483, in _chain_from_iterable_of_lists
for element in iterable:
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 598, in result_iterator
yield fs.pop().result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 435, in result
return self.__get_result()
File "/media/mdb2/disk4/anaconda3/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
ConnectionError: Connect with 'dna_r9.4.1_450bps_fast' failed: [timed_out] Timeout waiting for reply to request: LOAD_CONFIG
So can you give me any advice on the _version_ selection of pyguppyclent, guppy, and minion? Thank you!
When I install pyguppyclient to connect Guppy, Errors occurred.
system: Ubuntu16.04 python: 3.7.4. Guppy: v4.2.2 or v4.4.1, I've tried 2 versions pyguppyclent: v0.0.6 or v0.07a
any advice to solve the problem? Thanks